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Archive for the ‘Infectious Disease & New Antibiotic Targets’ Category

newly developed oxazolidinone antibiotics

Larry H. Bernstein, MD, FCAP, Curator

LPBI

 

 

New Antibacterial oxazolidinones in pipeline by Wockhardt

by DR ANTHONY MELVIN CRASTO Ph.D

 

WCK ?

(5S)-N-{3-[3,5-difluoro-4-(4-hydroxy-4-methoxymethyl-piperidin-1-yl)-phenyl]-2-oxo-oxazolidin-5-ylmethyl}-acetamide

MF C19 H25 F2 N3 O5, MW 413.42

Acetamide, N-​[[(5S)​-​3-​[3,​5-​difluoro-​4-​[4-​hydroxy-​4-​(methoxymethyl)​-​1-​piperidinyl]​phenyl]​-​2-​oxo-​5-​oxazolidinyl]​methyl]​-

CAS 957796-51-9

Antibacterial oxazolidinones

THIS MAY BE WCK 4086?????

PATENT

WO 2015173664, US8217058, WO 2012059823, 

 

Oxazolidinone represent a novel chemical class of synthetic antimicrobial agents.Linezolid represents the first member of this class to be used clinically. Oxazolidinones display activity against important Gram-positive human and veterinary pathogens including Methicillin-Resistant Staphylococcus aureus (MRSA), Vancomycin Resistant Enterococci (VRE) and β-lactam Resistant Streptococcus pneumoniae (PRSP). The oxazolidinones also show activity against Gram-negative aerobic bacteria, Gram-positive and Gram-negative anaerobes. (Diekema D J et al., Lancet 2001 ; 358: 1975-82).

Various oxazolidinones and their methods of preparation are disclosed in the literature. International Publication No. WO 1995/25106 discloses substituted piperidino phenyloxazolidinones and International Publication No. WO 1996/13502 discloses phenyloxazolidinones having a multisubstituted azetidinyl or pyrrolidinyl moiety. US Patent Publication No. 2004/0063954, International Publication Nos. WO 2004/007489 and WO 2004/007488 disclose piperidinyl phenyl oxazolidinones for antimicrobial use.

Pyrrolidinyl/piperidinyl phenyl oxazohdinone antibacterial agents are also described in Kim H Y et al., Bioorg. & Med. Chem. Lett., (2003), 13:2227-2230. International Publication No. WO 1996/35691 discloses spirocyclic and bicyclic diazinyl and carbazinyl oxazolidinone derivatives. Diazepeno phenyloxazolidinone derivatives are disclosed in the International Publication No. WO 1999/24428. International Publication No. WO 2002/06278 discloses substituted aminopiperidino phenyloxazolidinone derivatives.

Various other methods of preparation of oxazolidinones are reported in US Patent No. 7087784, US Patent No. 6740754, US Patent No. 4948801 , US Patent No. 3654298, US Patent No. 5837870, Canadian Patent No. 681830, J. Med. Chem., 32, 1673 (1989), Tetrahedron, 45, 1323 (1989), J. Med. Chem., 33, 2569 (1990), Tetrahedron Letters, 37, 7937-40 (1996) and Organic Process Research and Development, 11 , 739-741(2007).

Indian Patent Application No. 2534/MUM/2007 discloses a process for the preparation of substituted piperidino phenyloxazolidinones. International Publication No. WO2012/059823 further discloses the process for the preparation of phosphoric acid mono-(L-{4-[(5)-5-(acetylaminomethyl)-2-oxo-oxazolidin-3-yl]-2,6-difluorophenyl}4-methoxymethyl piperidine-4-yl)ester.

US Patent No. 8217058 discloses (5S)-N-{3-[3,5-difluoro-4-(4-hydroxy-4-methoxymethyl-piperidin-l-yl)-phenyl]-2-oxo-oxazolidin-5-ylmethyl}-acetamide as an antibacterial agent and its process for preparation.

PATENT

WO2015173664

https://patentscope.wipo.int/search/en/detail.jsf?docId=WO2015173664&recNum=1&maxRec=&office=&prevFilter=&sortOption=&queryString=&tab=PCTDescription

 

 

PATENT

http://www.google.st/patents/WO2007132314A2?cl=en

 

Figure imgf000004_0001

Wockhardt Ltd,

Figure imgf000006_0001
Figure imgf000006_0002

(3) (4)

 

PATENT

WO 2012059823

http://www.google.co.in/patents/WO2012059823A1?cl=en

Phosphoric acid mono-(l-{4-[(S)-5-(acetylamino- methyl)-2-oxo-oxazolidin-3-yl]-2,6-difluorophenyl}-4-methoxymethyl-piperidin-4-yl) ester of Formula (A),
Figure imgf000022_0001
the process comprising the steps of:
a) Converting intermediate of Formula (1) into intermediate of Formula (3)
Figure imgf000022_0002
b) Converting intermediate of Formula (3) into intermediate of Formula (5)
Figure imgf000022_0003

c) Converting intermediate of Formula (5) into intermediate of structure (6)

Figure imgf000022_0004
(5) <6> d) Converting intermediate of Formula (6) into intermediate of Formula (10)
Figure imgf000023_0001
e) Converting intermediate of Formula (10) into intermediate of Formula (11),
Figure imgf000023_0002

f) Converting intermediate of Formula (11) into compound of Formula (A) or Pharmaceutically acceptable salts thereof

Figure imgf000023_0003

 

 

Figure imgf000006_0001
Figure imgf000006_0002
Figure imgf000006_0003

 

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Flu Virus Transmission

Larry H. Bernstein, MD, FCAP, Curator

LPBI

 

Mystery behind flu virus transmission solved

lu virus, influenza virus, soft palate

The epidemiological success of flu viruses relies on successful airborne transmission from person to person. But the viral properties governing the airborne transmission of flu viruses are complex. A new study reveals that the soft palate at the back of the roof of the mouth plays a key role in the flu viruses’ ability to transmit through air. Previous research had shown that airborne transmissibility is dependent on the viral surface hemagluttinin (HA) glycoprotein’s ability to bind to receptors on human respiratory cells. Some viral strains bind better to alfa 2-6 glycan receptors found primarily in humans and other mammals while others are better suited to bind alfa 2-3 glycan receptors found in birds.

In the current study, researchers made 4 mutations in the HA protein of the flu virus which made it better suited to bind the bird receptors than the human receptors. They then used this strain to infect ferrets that are often used as models of human influenza infection. In theory the mutated virus should not have spread but it traveled through the air just as well as the wild type virus strain. Upon sequencing the virus genome, the scientists found that it had undergone a genetic reversion that allowed its HA protein to bind to the bird as well as human receptors. This experiment validated that gain of binding to the human receptor is critical for aerosol transmission. On examining the different parts of the respiratory tract, scientists discovered that viruses that genetically reverted were most abundantly found in the soft palate. The researchers are next trying to figure out how this genetic reversion takes place and why particularly in the soft palate. They hypothesize that the viruses outcompete each other in the soft palate from which they can spread by packaging themselves into mucus droplets produced by cells in the soft palate.

From a pandemic point of view, this study enables the systematic evaluation of highly transmissible viruses. The findings published in Nature will enable scientists better understand how the flu virus develops airborne transmissibility while helping monitor strains that acquire the potential to cause Influenza outbreaks.

 

 

The soft palate is an important site of adaptation for transmissible influenza viruses (Sep 2015)

Lakdawala SS1, Jayaraman A2, Halpin RA3, Lamirande EW1, Shih AR1, Stockwell TB3, Lin X3, Simenauer A3, Hanson CT, et al.
Nature. 2015 Oct 1; 526(7571):122-5.    http://dx.doi.org:/10.1038/nature15379. Epub 2015 Sep 23.      http://www.ncbi.nlm.nih.gov/pubmed/26416728

Influenza A viruses pose a major public health threat by causing seasonal epidemics and sporadic pandemics. Their epidemiological success relies on airborne transmission from person to person; however, the viral properties governing airborne transmission of influenza A viruses are complex. Influenza A virus infection is mediated via binding of the viral haemagglutinin (HA) to terminally attached α2,3 or α2,6 sialic acids on cell surface glycoproteins. Human influenza A viruses preferentially bind α2,6-linked sialic acids whereas avian influenza A viruses bind α2,3-linked sialic acids on complex glycans on airway epithelial cells. Historically, influenza A viruses with preferential association with α2,3-linked sialic acids have not been transmitted efficiently by the airborne route in ferrets. Here we observe efficient airborne transmission of a 2009 pandemic H1N1 (H1N1pdm) virus (A/California/07/2009) engineered to preferentially bind α2,3-linked sialic acids. Airborne transmission was associated with rapid selection of virus with a change at a single HA site that conferred binding to long-chain α2,6-linked sialic acids, without loss of α2,3-linked sialic acid binding. The transmissible virus emerged in experimentally infected ferrets within 24 hours after infection and was remarkably enriched in the soft palate, where long-chain α2,6-linked sialic acids predominate on the nasopharyngeal surface. Notably, presence of long-chain α2,6-linked sialic acids is conserved in ferret, pig and human soft palate. Using a loss-of-function approach with this one virus, we demonstrate that the ferret soft palate, a tissue not normally sampled in animal models of influenza, rapidly selects for transmissible influenza A viruses with human receptor (α2,6-linked sialic acids) preference.

 

 

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Protein regulator of HIV replication

Larry H. Bernstein, MD, FCAP, Curator

LPBI

 

Updated 11/26/2015

 

Closing the loop on an HIV escape mechanism

University of Delaware

http://www.rdmag.com/news/2015/11/closing-loop-hiv-escape-mechanism

 

Tatyana Polenova, professor of chemistry and biochemistry at UD (background, left), with her UD research team involved in the HIV study. Next to her is Huilan Zhang. In the foreground, from left, are Guangjin Hou and Manman Lu.

http://www.rdmag.com/sites/rdmag.com/files/newsletter-ads/CHEM-Polenova_Research_Groups-111015-015.jpg

Tatyana Polenova, professor of chemistry and biochemistry at UD (background, left), with her UD research team involved in the HIV study. Next to her is Huilan Zhang. In the foreground, from left, are Guangjin Hou and Manman Lu.

 

Nearly 37 million people worldwide are living with HIV. When the virus destroys so many immune cells that the body can’t fight off infection, AIDS will develop. The disease took the lives of more than a million people last year.

For the past three and a half years, a team of researchers from six universities, led by the University of Delaware and funded by the National Institutes of Health and the National Science Foundation, has been working to uncover new information about a protein that regulates HIV’s capability to hijack a cell and start replicating. Their findings, reported recently in the Proceedings of the National Academy of Sciencespoint to a new avenue for developing potential strategies to thwart the virus.

The team included scientists from UD, the University of Pittsburgh School of Medicine, University of Illinois at Urbana-Champaign, Carnegie Mellon University, the National High Magnetic Field Laboratory at Florida State University and Vanderbilt University School of Medicine. They used a combination of high-tech tools and techniques, including magic-angle-spinning nuclear magnetic resonance (NMR) spectroscopy and computer simulations of molecules, to examine the interactions between HIV and the host-cell protein cyclophilin A (CypA), right down to the movement of individual atoms.

“In a nutshell, we found that the infectivity of HIV is regulated by the motions of these proteins,” says Tatyana Polenova, professor of chemistry and biochemistry at the University of Delaware, who led the study. “It’s a subtle regulation strategy that does not involve major structural changes in the virus.”

Sixty times smaller than a red blood cell, HIV contains a cone-shaped shell, or capsid, made of protein, which surrounds two strands of RNA and the enzymes the virus needs for replication. Like any virus, HIV can only produce copies of itself once it has invaded a host organism. Then it will begin directing certain host cells to begin producing the virus.

But how does HIV invade a cell? In humans, the protein CypA can either promote or inhibit viral infection through interactions with the HIV capsid, although the exact mechanism is not yet known. A portion of the HIV capsid protein, called the CypA loop, is responsible for binding to the CypA in the human host cell. Once this occurs, the virus typically becomes infectious.

However, a change of just one amino acid in the CypA loop can cause the virus to operate opposite from how it does normally, allowing the virus to become non-infectious when CypA is present, and to become infectious when there is no CypA present. Such changes are called “escape mutations,” Polenova says, because they allow the virus to “escape” from its dependence on CypA.

To home in on this escape mechanism, the research team examined assemblies of different variants of HIV capsid protein complexed with CypA. Using magic-angle-spinning NMR, they recorded the motions in these assemblies, atom by atom, on time scales ranging from nanoseconds to milliseconds, from a billionth of a second to a thousandth of a second.

The team found that a reduction in the naturally occurring motions in the binding region due to the mutations allowed the virus to escape from CypA dependence. Magic-angle-spinning NMR experiments provided a direct probe of these motions, recording the changes in the magnetic interactions between nuclei. Computer simulations allowed the team to visualize the motions.

Some portions of the capsid protein do not move at all or move only a little while other portions undergo large-amplitude motions distributed over a wide range of time scales, with the most dynamic region being the CypA loop. Polenova says it is rather surprising that such extensive motions are present in the assembled capsid, and that these dynamics could be detected by both NMR and computer simulations.

“It is the first time that quantitative agreement between experiment and computation was achieved in a dynamics study, and it’s particularly exciting that this was attained for such a complex system,” Polenova says. “We hope this work may guide the development of new therapeutic interventions, such as small molecules that would serve as interactors with the HIV capsid and inhibit these dynamics.”

Polenova says the diverse team of researchers, with expertise in HIV virology, structural biology, biophysics and biochemistry, was critical to the study’s success, along with access to national high-field NMR facilities through the National High Magnetic Field Laboratory. The team was assembled through the NIH-funded Pittsburgh Center for HIV Protein Interactions. Led by Prof. Angela Gronenborn, the center brings together high-caliber scientists and facilities to elucidate the interactions of HIV proteins with host cell factors.

 

Atomic-resolution structure of the CAP-Gly domain of dynactin on polymeric microtubules determined by magic angle spinning NMR spectroscopy

 

Significance

Microtubules and their associated proteins are central to most cellular functions. They have been extensively studied at multiple levels of resolution; however, significant knowledge gaps remain. Structures of microtubule-associated proteins bound to microtubules are not known at atomic resolution. We used magic angle spinning NMR to solve a structure of dynactin’s cytoskeleton-associated protein glycine-rich (CAP-Gly) domain bound to microtubules and to determine the intermolecular interface, the first example, to our knowledge, of the atomic-resolution structure of a microtubule-associated protein on polymeric microtubules. The results reveal remarkable structural plasticity of CAP-Gly, which enables CAP-Gly’s binding to microtubules and other binding partners. This approach offers atomic-resolution information of microtubule-binding proteins on microtubules and opens up the possibility to study critical parameters such as protonation states, strain, and dynamics on multiple time scales.

 

Microtubules and their associated proteins perform a broad array of essential physiological functions, including mitosis, polarization and differentiation, cell migration, and vesicle and organelle transport. As such, they have been extensively studied at multiple levels of resolution (e.g., from structural biology to cell biology). Despite these efforts, there remain significant gaps in our knowledge concerning how microtubule-binding proteins bind to microtubules, how dynamics connect different conformational states, and how these interactions and dynamics affect cellular processes. Structures of microtubule-associated proteins assembled on polymeric microtubules are not known at atomic resolution. Here, we report a structure of the cytoskeleton-associated protein glycine-rich (CAP-Gly) domain of dynactin motor on polymeric microtubules, solved by magic angle spinning NMR spectroscopy. We present the intermolecular interface of CAP-Gly with microtubules, derived by recording direct dipolar contacts between CAP-Gly and tubulin using double rotational echo double resonance (dREDOR)-filtered experiments. Our results indicate that the structure adopted by CAP-Gly varies, particularly around its loop regions, permitting its interaction with multiple binding partners and with the microtubules. To our knowledge, this study reports the first atomic-resolution structure of a microtubule-associated protein on polymeric microtubules. Our approach lays the foundation for atomic-resolution structural analysis of other microtubule-associated motors.

 

How Viruses Commandeer Human Proteins

http://www.technologynetworks.com/Proteomics/news.aspx?ID=185156

 

Researchers have produced the first image of an important human protein as it binds with ribonucleic acid (RNA), a discovery that could offer clues to how some viruses, including HIV, control expression of their genetic material.

 

RNA is one of three macromolecules — along with DNA and proteins — essential to all forms of life. By understanding how hnRNP A1 binds to RNA, the scientists may find ways to jam up components of the replication machinery when the protein is coopted by disease.

The team of scientists reveals the mechanism used by the protein, hnRNP A1 to link to the section of RNA, called the ‘hairpin loop.’

They found that hnRNP A1, a protein essential to cell function and virus replication, has a significantly different structure than its only previously known form: binding to DNA.

“We solved the three-dimensional structure of the protein bound to an RNA hairpin derived from the HIV virus,” said Blanton Tolbert, a chemistry professor at Case Western Reserve. “But because the hairpin loop is found in other viruses and throughout healthy cells, our findings may help explain how the protein connects to the other hairpin targets.”

Tolbert began this research six years ago, frustrated that the only information available was the structure of the protein bound to a synthetic DNA, which isn’t its natural target.

Proteins that bind hairpins sense both the structure and the sequence information presented in the loop. The structure of the DNA complex did not demonstrate the molecular recognition that must take place to bind RNA hairpins.

The process

To discover the structure bound to RNA, the researchers combined three techniques: X-ray crystallography, nuclear magnetic resonance spectroscopy and small angle x-ray scattering. Each technique yielded a piece of the puzzle.

To bind to RNA, hnRNP A1 has two domains, RRM1 and RRM2, which are akin to hands. Scientists already knew both hands are needed to connect to RNA.

But the researchers found that, instead of each domain grabbing a section of the loop, only RRM1 makes contact with the RNA. RRM2 acts as support, helping organize RRM1 into the structure needed to conform to a certain section of the loop.

To confirm that the structures are key to binding, the researchers inserted mutations by changing amino acids on the surface of the domains.

Surprisingly, mutations on the far side of RRM1 — the surface not in contact with the RNA but with the RRM2 — caused decoupling at that site and substantially weakened the affinity for RNA.

Without the normal connection between the two domains, RRM1 fails to adopt the geometric shape that conforms to the RNA hairpin loop.

The researchers are further investigating how the protein transmits the effects of RRM2 to RRM1 and bind. They are also exploring the development of antagonistic agents that would disrupt the interaction of the protein with viruses.

 

Natural defense protein against HIV discovered

HIV-1, ERManI, antiretroviral, defense protein

Earlier research had shown that it was possible to interfere with HIV spread but the exact molecular mechanisms had not been identified. For the first time, scientists have identified ERManI (Endoplasmic Reticulum Class I α-Mannosidase) as the essential host protein that slows the spread of HIV-1. Scientists investigated how the four ER-associated glycoside hydrolase family 47 (GH47) α-mannosidases, ERManI, and ER-degradation enhancing α-mannosidase-like (EDEM) proteins 1, 2, and 3, are involved in the HIV-1 envelope (Env) degradation process. Ectopic expression of these four α-mannosidases uncovered that only ERManI inhibited HIV-1 Env expression in a dose-dependent manner. Basically, ERManI is a host enzyme that adds sugars to proteins. The Env glycoprotein is targeted to the endoplasmic reticulum-associated protein degradation pathway for degradation after infecting cells. And ERManI was found to interact with the Env and initiate this degradation pathway.

With this discovery, ERManI has the potential as a new antiretroviral treatment option. Currently there is no cure for HIV-1 and once patients are infected, they have it for life. Current antiretroviral therapies can prolong life but cannot fully cure a patient. ERManI is different from current treatments in the sense that it can help the body protect itself.

 

ERManI (Endoplasmic Reticulum Class I α-Mannosidase) Is Required for HIV-1 Envelope Glycoprotein Degradation via Endoplasmic Reticulum-associated Protein Degradation Pathway (Sep 2015)

ERManI (Endoplasmic Reticulum Class I α-Mannosidase) Is Required for HIV-1 Envelope Glycoprotein Degradation via Endoplasmic Reticulum-associated Protein Degradation Pathway.

Previously, we reported that the mitochondrial translocator protein (TSPO) induces HIV-1 envelope (Env) degradation via the endoplasmic reticulum (ER)-associated protein degradation (ERAD) pathway, but the mechanism was not clear. Here we investigated how the four ER-associated glycoside hydrolase family 47 (GH47) α-mannosidases, ERManI, and ER-degradation enhancing α-mannosidase-like (EDEM) proteins 1, 2, and 3, are involved in the Env degradation process. Ectopic expression of these four α-mannosidases uncovers that only ERManI inhibits HIV-1 Env expression in a dose-dependent manner. In addition, genetic knock-out of the ERManI gene MAN1B1 using CRISPR/Cas9 technology disrupts the TSPO-mediated Env degradation. Biochemical studies show that HIV-1 Env interacts with ERManI, and between the ERManI cytoplasmic, transmembrane, lumenal stem, and lumenal catalytic domains, the catalytic domain plays a critical role in the Env-ERManI interaction. In addition, functional studies show that inactivation of the catalytic sites by site-directed mutagenesis disrupts the ERManI activity. These studies identify ERManI as a critical GH47 α-mannosidase in the ER-associated protein degradation pathway that initiates the Env degradation and suggests that its catalytic domain and enzymatic activity play an important role in this process.

 

T cell editing using CRISPR/Cas9 could revolutionize HIV therapeutics
September 15, 2015   

T cell therapy, HIV

Reinforcing the immune system by engineering lymphocytes to target and destroy viruses has the potential to be an effective therapy for many diseases. One potential approach to this strategy is to alter the genome of lymphocytes so that proteins that are typically hijacked by viruses are no longer present. While conceptually feasible, editing T cells has been challenging in practice; however, with the advent of mammalian cell editing using CRISPR/Cas9, T-cell editing is closer to becoming a reality.

How can CRISPR/Cas9 bring us closer to finding a cure for HIV?

In a study recently published in PNAS, scientists have optimized a protocol to introduce nucleotide replacements that would inhibit CXCR4 expression. The authors streamlined the CRISPR/Cas9 editing process by electroporating Cas9 ribonucleoproteins (RNPs) into CD4+ T cells. The RNPs, consisting of both a recombinant Cas9 enzyme and guide RNA, vastly improved editing efficiency, ultimately promoting knock-out of the CXCR4 cell-surface receptor. Taken together, these result suggest the potential of a new cell therapy approach for the fight against HIV.

Generation of knock-in primary human T cells using Cas9 ribonucleoproteins
Kathrin Schumann a , b , 1 Steven Lin c , 1 Eric Boyer a , b Dimitre R. Simeonov a , b , d Meena Subramaniam e , f Rachel E. Gate e , f , et al.  PNAS. 2015; 112(33): 10437-10442. http://dx.doi.org:/10.1073/pnas.1512503112

Significance

T-cell genome engineering holds great promise for cancer immunotherapies and cell-based therapies for HIV, primary immune deficiencies, and autoimmune diseases, but genetic manipulation of human T cells has been inefficient. We achieved efficient genome editing by delivering Cas9 protein pre-assembled with guide RNAs. These active Cas9 ribonucleoproteins (RNPs) enabled successful Cas9-mediated homology-directed repair in primary human T cells. Cas9 RNPs provide a programmable tool to replace specific nucleotide sequences in the genome of mature immune cells—a longstanding goal in the field. These studies establish Cas9 RNP technology for diverse experimental and therapeutic genome engineering applications in primary human T cells.

 

T-cell genome engineering holds great promise for cell-based therapies for cancer, HIV, primary immune deficiencies, and autoimmune diseases, but genetic manipulation of human T cells has been challenging. Improved tools are needed to efficiently “knock out” genes and “knock in” targeted genome modifications to modulate T-cell function and correct disease-associated mutations. CRISPR/Cas9 technology is facilitating genome engineering in many cell types, but in human T cells its efficiency has been limited and it has not yet proven useful for targeted nucleotide replacements. Here we report efficient genome engineering in human CD4+ T cells using Cas9:single-guide RNA ribonucleoproteins (Cas9 RNPs). Cas9 RNPs allowed ablation of CXCR4, a coreceptor for HIV entry. Cas9 RNP electroporation caused up to ∼40% of cells to lose high-level cell-surface expression of CXCR4, and edited cells could be enriched by sorting based on low CXCR4 expression. Importantly, Cas9 RNPs paired with homology-directed repair template oligonucleotides generated a high frequency of targeted genome modifications in primary T cells. Targeted nucleotide replacement was achieved in CXCR4 and PD-1 (PDCD1), a regulator of T-cell exhaustion that is a validated target for tumor immunotherapy. Deep sequencing of a target site confirmed that Cas9 RNPs generated knock-in genome modifications with up to ∼20% efficiency, which accounted for up to approximately one-third of total editing events. These results establish Cas9 RNP technology for diverse experimental and therapeutic genome engineering applications in primary human T cells.

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New antibiotics to address anti-microbial resistance

Larry H. Bernstein, MD, FCAP, Curator

LPBI

 

WCK 5107 in PHASE 1 FROM WOCKHARDT

Dr. Anthony Melvin Castro

 

Figure imgf000036_0001

WCK 5107

Wockhardt Limited

Useful for treating bacterial infections

CAS 1436861-97-0

disclosed in PCT International Patent Application No. PCT/IB2012/054290D

trans- sulphuric acid mono-[2-(N’-[(R)-piperidin-3-carbonyl]-hydrazinocarbonyl)-7-oxo-l,6-diaza-bicyclo[3.2.1]oct-6-yl] ester

(2S, 5R)-sulphuric acid mono-[2-(N’-[(R)-piperidin-3-carbonyl]-hydrazinocarbonyl)-7-oxo-l,6-diaza-bicyclo[3.2.1]oct-6-yl] ester

(lR,2S,5R)-l,6-Diazabicyclo [3.2.1] octane-2-carboxylic acid, 7-oxo-6-(sulfooxy)-, 2-[2-[(3R)-3-piperidinylcarbonyl]hydrazide]

trans- sulphuric acid mono-[2-(N’-[(R)-piperidin-3-carbonyl]-hydrazinocarbonyl)-7-oxo-l,6-diaza-bicyclo[3.2.1]oct-6-yl] ester

(2S, 5R)-sulphuric acid mono-[2-(N’-[(R)-piperidin-3-carbonyl]-hydrazinocarbonyl)-7-oxo-l,6-diaza-bicyclo[3.2.1]oct-6-yl] ester

(lR,2S,5R)-l,6-Diazabicyclo [3.2.1] octane-2-carboxylic acid, 7-oxo-6-(sulfooxy)-, 2-[2-[(3R)-3 -piperidinylcarbonyl] hydrazide]

 

In September 2015, the drug was reported to be in phase I clinical trial.One of the family members US09132133, claims a combination of sulbactam and WCK-5107.

Bacterial infections continue to remain one of the major causes contributing towards human diseases. One of the key challenges in treatment of bacterial infections is the ability of bacteria to develop resistance to one or more antibacterial agents over time. Examples of such bacteria that have developed resistance to typical antibacterial agents include: Penicillin-resistant Streptococcus pneumoniae, Vancomycin-resistant Enterococci, and Methicillin-resistant Staphylococcus aureus. The problem of emerging drug-resistance in bacteria is often tackled by switching to newer antibacterial agents, which can be more expensive and sometimes more toxic. Additionally, this may not be a permanent solution as the bacteria often develop resistance to the newer antibacterial agents as well in due course. In general, bacteria are particularly efficient in developing resistance, because of their ability to multiply very rapidly and pass on the resistance genes as they replicate.

Treatment of infections caused by resistant bacteria remains a key challenge for the clinician community. One example of such challenging pathogen is Acinetobacter baumannii (A. baumannii), which continues to be an increasingly important and demanding species in healthcare settings. The multidrug resistant nature of this pathogen and its unpredictable susceptibility patterns make empirical and therapeutic decisions more difficult. A. baumannii is associated with infections such as pneumonia, bacteremia, wound infections, urinary tract infections and meningitis.

Therefore, there is a need for development of newer ways to treat infections that are becoming resistant to known therapies and methods. Surprisingly, it has been found that a compositions comprising cefepime and certain nitrogen containing bicyclic compounds (disclosed in PCT/IB2012/054290) exhibit unexpectedly synergistic antibacterial activity, even against highly resistant bacterial strains.

PATENT

http://www.google.com/patents/WO2013030733A1?cl=en

 

 

……

REFERENCES

Study to Evaluate the Safety, Tolerability, and Pharmacokinetics of WCK-5107 Alone and in Combination With Cefepime (NCT02532140)  https://clinicaltrials.gov/show/NCT02532140
ClinicalTrials.gov Web Site 2015, September 01, To evaluate the safety,tolerability and pharmacokinetics of single intravenous doses of WCK 5107 alone and in combination with cefepime in healthy adult human subjects.

WO2013030733A1* Aug 24, 2012 Mar 7, 2013 Wockhardt Limited 1,6- diazabicyclo [3,2,1] octan-7-one derivatives and their use in the treatment of bacterial infections
WO2014135931A1* Oct 12, 2013 Sep 12, 2014 Wockhardt Limited A process for preparation of (2s, 5r)-7-oxo-6-sulphooxy-2-[((3r)-piperidine-3-carbonyl)-hydrazino carbonyl]-1,6-diaza-bicyclo [3.2.1]- octane
IB2012054290W Title not available

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Experience with Trauma Surgery

Author: Larry H. Bernstein, MD, FCAP

 

 

In 1987, I went on vacation to Bermuda with my wife and two children.  It was a beautiful place, and the weather and the ocean were wonderful to experience.  One could travel by bus, which was very safe, which I preferred. My older daughter wanted to use a moped, which we allowed on the condition that she first be trained.  On the last day, she went to return the moped, but the station was out for lunch.  I was a photograper and wanted to photograph the white bird of Burmuda. I put my camera in the rear, but as I left the station my moped was hit by an oncoming moped that I failed to see, unaccustomed to the British style driving.  An ambulance arrived within a few minutes as I lay on the ground. My wife sent the kids home and made arrangements for my secretary to look after them.  I was impressed with the surgeon when I arrived at the hospital. He wheeled me to the bed I was to stay in. I had two blood transfusions.  He took me to the operating room, but I don’t recall any details. He had a McGill University resident who later wrote a thesis about the experience.  I was pretty knocked out, but there was another patient in the room who had fallen down his steps. He was a WWII RAF veteran who had bombed the Germans. He told me the stories about his experience.  We contacted the burn surgeon, Walter Pleban, who arranged to have me flown to Bridgeport, CT, and he arranged for the best orthopedic surgeons to admit me on arrival.  In my flight there was another patient who was dying of endstage HIV AIDS.

Herbert Hermele observed how serious this was because there were three fractures of the right tibia. The good news was that there was no need to amputate because I had the nervous innervation, but I lost a popliteal artery.  I was admitted, and at first there was only a small room. The nurse was a very competent young woman of Portuguese descent. She was able to move me as needed. I was moved when a better room became available.  It was very good when the night shift nurse came in because I was able to talk to her with some attachment.  The Vice President had me provided with good meals, as I was the director of blood bank and chemistry.  I also had visits by my supervisors and other staff.

It was not an easy time, but I was privileged because of my standing with the medical and laboratory staff.  I had a longer stay than usual because I had an infection with two gram negative resistant strains of bacteria –serratia marcesans and Enterobacter. I was put on a gram negative penicillin and the next morning I felt dizzy. When Dr. Pleban came to see me I told him that I was having a penicillin reaction because I was aware that my twin sister was allergic to penicillin. As a result, the prescription was changed and it was an improved situation.  I underwent 10 operative procedures in some weeks. Dr. Hermeles partner put an antibiotic plug into the wound and it healed.  It was only after the infection cleared that a superb reconstructive surgeon was called in and he made skin grafts to close the wound after he disconnected a tendon and pulled muscle over the wound.  I also had a call from IJ Good, University Professor of Statistics at Virginia Polytech, who had completed writing a program to analyze data that I had provided him 2 years earlier – of MB isoenzyme CK at 6 hours and 12 hours later for diagnosis of heart attack.  We published the work in the prestigious journal, Clinical Chemistry and the President of the College of American Pathologists took note of the paper. I was finally sent home, without needing excess stay to the hospital environment.  I had physical therapy at home, and my bed was made on the first floor.  When I returned to work my infection site oozed, so I went to the Chief of Infectious Disease.  He prescribed a new quinolone antibiotic that could be taken orally. The infection subsided and it has never returned.

My sister came from San Diego, California and she brought me a recording she made for imaging to heal.  It went on that I was climbing a step to the heavens and getting better and better.  She also emphases laughing.

I can only look back and recall how fortunate I was to have the attention and kindness at that time. It was in excess of what many patients experience.  I do recall that the Hungarian-Cuban music teacher my daughter had had thousands of musical pieces and thousands of stories so that she was one of the most entertaining patients ever admitted to Bridgeport Hospital.

 

 

 

 

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Ebola therapy breakthrough

Larry H. Bernstein, MD, FCAP, Curator

LPBI

 

Updated 11/23/2015

Giant Molecules Inhibit Ebola Infection

Nov 11, 2015   http://www.technologynetworks.com/medchem/news.aspx?ID=185080

European researchers have designed a “giant” molecule formed by thirteen fullerenes covered by carbohydrates which, by blocking this receptor, are able to inhibit the cell infection by an artificial ebola virus model.

 

Different studies have demonstrated that the ebola virus infection process starts when the virus reaches the cellular DC-SIGN receptor to infect the dendritic cells (of the immune system).

In this study researchers from the Universidad Complutense de Madrid/IMDEA-Nanociencia, the Instituto de Investigación Sanitaria Hospital 12 de Octubre (Madrid), and the Instituto de Investigaciones Químicas del CSIC-Universidad de Sevilla have collaborated, together with three european research groups (CNRS/Université de Strasbourg, France and Université de Namur, Belgium).

“Fullerenes are hollow cages exclusively formed by carbon atoms”, explains Nazario Martín, Professor of Organic Chemistry in the UCM and main author of the study. In this work, scientists have employed C60 fullerene, which is formed by 60 carbon atoms and has the shape of a truncated icosahedron, which resembles a football ball.

102815_web.jpg

These molecules decorated with specific carbohydrates (sugars) present affinity by the receptor used as an entry point to infect the cell and act blocking it, thus inhibiting the infection.

Researchers employed an artificial ebola virus by expressing one of its proteins, envelope protein GP1, responsible of its entry in the cells. In a model in vitro, this protein is covering a false virus, which is able of cell infection but not of replication.

“We have employed a cell model previously described in our lab which consists in a cell line of human lymphocytes expressing DC-SIGN receptor, which facilitates the entry of the virus in Dendritic Cells”, points out Rafael Delgado, researcher of the Hospital 12 de Octubre, and other of the authors of the study.

By blocking this receptor and inhibiting the virus infection, the authors think that the dissemination of the virus would decrease and the immune response increase, but this idea has still to be developed with in vivo studies.

The biggest fullerene system in the lab

The system designed by the chemists, based on carbon nanostructures developed in the UCM, mimic the presentation of carbohydrates surrounding virus like ebola or VIH.

The team has achieved an unprecedented success in fullerene chemistry and dendritic growth: connecting in one synthetic step twelve fullerene units, each with ten sugars, to other central fullerene, creating a globular superstructure with 120 sugar moieties on its surface, “this is the fastest dendrimeric growth developed in a laboratory up to now” says Beatriz Illescas, Professor in the UCM and coauthor of the work.

According to scientists, the results highlight the potential of these giant molecules as antiviral agents. “This work open the door to the design and preparation of new systems to inhibit the pathogens infection in cases where the current therapies are not effective or are inexistent, as occurs with the ebola virus”, clarifies Martín.

After these experiments on the cellular level, researchers will study the behavior of these systems in animal models, starting with mice. “We will study, on the one hand, the pharmacokinetics and, on the other, the antiviral activity in vivo” explains Javier Rojo, researcher of the Instituto de Investigaciones Químicas del CSIC and other of the authors of the study. Once the most effective compound has been identified, studies using the true ebola virus could be carried out.

 

 

http://www.sciencedirect.com/science/article/pii/S0092867400806935

DCSIGN, which is abundantly expressed by DC both in vitro and in vivo, … Whereas ICAM-3 binding by monocytes is for the greater part LFA-1 … The specificity of this adhesion receptor on DC for ICAM-3 is demonstrated by the ….

 

http://www.bloodjournal.org/content/100/5/1780.full.pdf

This subset coexpresses CD14, CD16, and CD33 and is thus of myeloid origin. In contrast to. CD14 monocytes, DCSIGN blood cells.

 

http://www.jimmunol.org/content/168/5/2118.full

Mar 1, 2002 Several receptors expressed by immature DCs belong to the C-type lectin superfamily, … Here, DCSIGN efficiently transmits the virus to T lymphocytes

 

http://journals.plos.org/plospathogens/article%3Fid%3D10.1371/journal.ppat.0020070

Jul 14, 2006 Although B cells that express DCSIGN do not replicate HIV-1, they serve as … receptors [12–15], with conflicting reports on expression of DCSIGN[16,17]. …..
human herpesvirus 8 infects DC and macrophages via DCSIGN …

 

http://www.jci.org/articles/view/25105/files/pdf

Results. The effect of human milk on direct HIV-1 infection of CD4+ T lymphocytesexpressing the DCSIGN receptor (Raji-DCSIGN) (8).

 

 

An indictment of Ebola response  

Panel calls for reform of global public health system in wake of epidemic

By B. D. Colen, Harvard Staff Writer

http://news.harvard.edu/gazette/story/2015/11/an-indictment-of-ebola-response/

 

http://media.news.harvard.edu/gazette/wp-content/uploads/2015/11/110515_Ebola_020_605.jpg

“The most egregious failure was by WHO in the delay in sounding the alarm,” said Harvard’s Ashish Jha.

An independent group of 19 international experts, convened by theHarvard Global Health Institute and the London School of Hygiene and Tropical Medicine (LSHTM), today issued a scathing analysis of the global response to the 2014-15 Ebola outbreak in West Africa.

The members of the Harvard-LSHTM Independent Panel on the Global Response to Ebola said that while the 2014-15 Ebola outbreak “engendered acts of understanding, courage, and solidarity,” it also caused “immense human suffering, fear and chaos, largely unchecked by high-level political leadership or reliable and rapid institutional responses.”

The report, published in the prestigious British medical journal The Lancet, is especially hard on the World Health Organization (WHO), which the panel contends failed to provide the leadership and support needed to deal properly with the outbreak of hemorrhagic fever that infected more than 28,000 people and claimed more than 11,000 lives.

The authors of the report, who were affiliated with, but functioned independently from, such disparate organizations as the Council on Foreign Relations, Médecins Sans Frontières, Indiana University law school, and theAIDS Health Care Foundation, reminded readers that the Ebola epidemic “brought national health systems to their knees, rolled back hard-won social and economic gains in a region recovering from civil wars, sparked worldwide panic, and cost at least several billion dollars in short-term control efforts and economic losses.”

“The most egregious failure was by WHO in the delay in sounding the alarm,” said Ashish Jha, director of the Harvard Global Health Institute, K.T. Li Professor of International Health at the Harvard T.H. Chan School of Public Health, and a professor of medicine at Harvard Medical School. “People at WHO were aware that there was an Ebola outbreak that was getting out of control by spring … and it took until August to declare a public health emergency … Those were precious months,” said Jha.

The panel was co-chaired by Professor Peter Piot, director of the LSHTM and co-discoverer of the Ebola virus. Piot said, “We need to strengthen core capacities in all countries to detect, report, and respond rapidly to small outbreaks, in order to prevent them from becoming large-scale emergencies. Major reform of national and global systems to respond to epidemics are not only feasible, but also essential so that we do not witness such depths of suffering, death, and social and economic havoc in future epidemics. The AIDS pandemic put global health on the world’s agenda. The Ebola crisis in West Africa should now be an equal game-changer for how the world prevents and responds to epidemics.”

Liberian Mosoka Fallah of Action Contre la Faim International and a member of the panel said, “The human misery and deaths from the Ebola epidemic in West Africa demand a team of independent thinkers to serve as a mirror of reflection on how and why the global response to the greatest Ebola calamity in human history was late, feeble, and uncoordinated. The threat of infectious disease anywhere is the threat of infectious disease everywhere. The world has become one big village.”

The global response to Ebola is being examined by a number of different panels, Jha said, including a group at WHO and another at the United Nations. During the height of the epidemic in fall, 2014, Jha met with Julio Frenk, then the dean of the Harvard Chan School, and Suerie Moon, research director and co-chair of the Harvard Kennedy School’s Forum on Global Governance for Health, and a Harvard Chan faculty member. Together, they “decided this deserves independent examination; we can’t let this happen again,” Jha said.

“The Ebola outbreak is a stark reminder of the fragility of health security in an interdependent word,” the report reads, “and of the importance of building a more robust global system to protect all people from such risks.

“A more humane, competent, and timely response to future outbreaks requires greater willingness to assist affected populations, and systematic investments to enable the global community to perform four key functions: strengthen core capacities within and among countries to prevent, detect, and respond to outbreaks when and where they occur; mobilize faster and more effective external assistance when countries are unable to prevent an outbreak from turning into a crisis alone; rapidly produce and widely share relevant knowledge, from community mobilization strategies to protective measures for health workers, from rapid diagnostic tools to vaccines; [and] provide stewardship over the whole system, entailing strong leadership, coordination, priority setting, and robust accountability from all involved actors.”

Though it pulls no punches in its criticism of the ways institutions and nations responded to the Ebola crisis, the Harvard-LSHTM report is also a positive document, offering 10 concrete recommendations to strengthen public health systems and future responses.

Those recommendations fall into four areas: preventing major disease outbreaks; responding to outbreaks; producing and sharing data, knowledge, and technologies; and improving the governance of the global health system, “with a focus on the World Health Organization.”

One recommendation is that WHO create a dedicated center “for outbreak response, with strong technical capacity, protected budget, and clear lines of accountability,” and that that center be governed by a separate board independent of the WHO bureaucracy.

“Our primary goal is to convince the high-level political leaders, north and south, to seize the moment to make necessary and enduring changes to better prepare for future outbreaks, while memories of the human health costs of inaction remain vivid and fresh,” the report said.

“There is a high risk here of not learning our lessons,” said Jha. “We’ve had outbreaks like this before, and often you get thoughtful reviews, and august bodies that look at it, and people say, ‘We will get to this right away,’ and then other things draw our attention. I think we owe it to the more than 11,000 people who died in West Africa to see that that doesn’t happen this time.”

 

The Lancet 2015

http://www.thelancet.com/campaigns/ebola

Ebola—lessons learned: Authors from Harvard’s Global Health Institute and the London School of Hygiene and Tropical Medicine outline 10 proposals to help prevent future health catastrophes, based on experiences from the 2014-15 Ebola outbreak in west Africa.

Timeline infographic

Illustration demonstrating pathogenesis of vascular leak in Ebola virus disease - Copyright: Elsevier
http://www.thelancet.com/pb/assets/raw/pb/assets/raw/lancet/campaigns/ebola/ebola-main-281114.jpg

The current outbreak of Ebola in west Africa is both a public health emergency of international concern and a human tragedy.

The Lancet Ebola Resource Centre contains all related resources from The Lancet family of journals offered with free access to assist health workers and researchers in their important work to bring this outbreak to a close a quickly as possible.

Find out more about Ebola in The Lancet’s Seminar.

 

WORLD REPORT
Expert panel slams WHO’s poor showing against Ebola
John Maurice
The Lancet, July 13, 2015;Vol. 386, No. 9990, e1

Criticism of WHO’s response to the west African Ebola crisis spawned an expert review that this week proposed several solutions to restore the agency’s performance. John Maurice reports.

WHO suffers from an incapacity “to deliver a full emergency public health response” against a severe epidemic. So concluded a panel of six international health experts in a damning report released on July 7. They prescribed 21 actions aimed at restoring WHO’s “pre-eminence as the guardian of global public health”.

The panel was commissioned by WHO Director-General Margaret Chan in response to widespread criticism that WHO had mishandled its response to the west African Ebola epidemic. The panel corroborated many of the criticisms. Chief among them was the “unjustifiable” time it took WHO to declare the outbreak a “public health emergency of international concern”. Chan made this declaration 5 months after the escalating spread of Ebola had become evident. WHO officials claim that the delay in making the official declaration did not affect its operations involving some 100 staff in the field in the early months of the epidemic.

WHO’s Member States also drew sharp criticism from the panel. Many applied travel bans during the epidemic without WHO authorisation, thereby contravening the International Health Regulations (IHR) and “causing negative political, economic and social consequences for the affected countries”. Perhaps the most damning criticism of WHO came from Médecins sans Frontières (MSF), whose teams were among the first to arrive at the scene of the outbreak in March, 2014. An MSF reportpublished in March, 2015, describes how MSF was unable to convince WHO that the epidemic was out of control. “WHO officials”, the report notes, “called us alarmists”.

Four of the panel’s recommendations stand out: countries should be given incentives to comply with the IHR and disincentives, such as sanctions, when they flout them; a brand-new WHO Centre for Emergency Preparedness and Response should be created; a contingency fund of US$100 million to be used solely to finance outbreak responses should be established; and an intermediate trigger should be set up to alert the health community to a health crisis before it becomes an emergency.

Asked whether the panel’s report meets her concerns, MSF president Joanne Liu tells The Lancet: “It has many strong points for us. But how they will translate into real action on the ground” is unclear. Liu is particularly pleased with the panel’s call for greater community engagement in epidemic response efforts. “As regards an intermediate alert”, she says, “it should be based on the needs of the affected communities, not just on a perceived security risk for other countries. MSF didn’t wait for an official declaration before going into the field.”

David Heymann, head and senior fellow at the Centre on Global Health Security in Chatham House, London, wonders whether the panel’s recommendations for fundamental changes in the decision-making processes can be implemented. “WHO has a flawed structure and I’m not sure its Member States have the will to change that.” He commends the panel’s call for strengthening existing emergency response mechanisms, such as the Global Outbreak Alert and Response Network (GOARN). “This is an agile, sustainable network of epidemiologists, logisticians, and other field-support experts from WHO Member States. It goes immediately into action to prevent outbreaks from becoming emergencies of international concern and has worked extremely well in previous Ebola outbreaks and in the 2003 SARS epidemic.” He believes that the existence of GOARN, with an added external advisory group, obviates the need for the new WHO emergency response centre proposed by the panel.

Will WHO implement the recommendations? “If it doesn’t implement them now”, says Jeremy Farrar, director of the Wellcome Trust, “it will never do so, because the Ebola epidemic has really shocked people and has exposed the structural weaknesses in WHO. Reforming its emergency response capabilities means reducing the bureaucracy and speeding up its capacity to respond. And that means appointing the very best people.” Farrar is enthusiastic about the proposed creation of a new WHO emergency response body. “It should be overseen by an independent board and needs to be outside the influence of politics and truly independent. It also needs to be given the right authority, the right budget, and the right mandate in order to attract the right leadership.”

Rick Brennan, director of WHO’s emergency operations, found the panel’s report constructive. “Work has already begun on several of the recommendations, such as increasing staff and funds for emergency operations and integrating our health security and humanitarian work. I’m convinced that we will implement the rest of the recommendations, including the creation of a new WHO health emergency centre.”

Experts were unanimous on one point made in the report. With 20–30 cases occurring every week, Ebola in west Africa is not over and many eyes are now on WHO’s role in ending it.

EDITORIAL
A plan to protect the world—and save WHO
The Lancet July 11, 2015
The Lancet, Vol. 386, No. 9989, p103

“WHO must reestablish its pre-eminence as the guardian of global public health.” These words resonate throughout the final report of the Ebola Interim Assessment Panel, requested by WHO’s Executive Board, chaired by Dame Barbara Stocking, and published this week. The findings of the panel present a devastating critique of WHO and the chronic inaction of its member states, which together created the conditions for an Ebola virus disease outbreak of unprecedented ferocity and human tragedy. The Stocking Report, as it will come to be known, sets out in agonising detail how the entire global health system fatally let down the people of west Africa.

Stocking reserves her harshest criticism for WHO. The delays in announcing a Public Health Emergency of International Concern (it took 5 months from announcing an “unprecedented outbreak” in April, 2014, to declaring a public health emergency on August 8) was “unjustifiable”. The agency’s culture is unfit to manage an emergency response. Independent and courageous decision-making by the Director-General of WHO and her team “was absent in the early months of the Ebola crisis”. The agency was slow and reactive to events. WHO has lost its position as the authoritative body on health emergencies. It thought it could manage Ebola through polite behind-the-scenes international diplomacy. It failed to recognise that Ebola was a health emergency, not a diplomatic puzzle. And WHO’s communication strategy for Ebola simply “failed”. The agency failed to communicate proactively and it failed to establish itself as the authoritative voice on the Ebola outbreak. Member States of WHO are not spared. They have persistently failed to take the International Health Regulations (IHR, 2005) seriously—a position that is “irresponsible” and “untenable” for global health security. They should adopt the notion of “shared sovereignty”. They need to invest in WHO (the Panel proposes a modest 5% increase in assessed contributions in 2016).

The Panel’s recommendations are clear and forthright. Although WHO was severely criticised, Stocking argues that the agency should still take the lead for emergency health responses. But to do so, WHO must undergo “significant transformation”—not least, adequate funding and a change in culture. It must provide costed plans for establishing core public health capacities as set out in the IHR (2005). It should establish a new WHO Centre for Emergency Preparedness and Response, with an independent board that publishes a report on Global Health Security annually. WHO country and regional offices should be strengthened. The agency should take its role in accelerating the research and development of diagnostics, vaccines, and medicines more seriously. And WHO should do more to coordinate its activities with other parts of the humanitarian community. The IHR Review Committee should examine the value of an intermediate alert for a public health emergency, lowering the threshold at which the world can be warned of a new health risk. And sanctions against countries that violate the IHR should be considered.

The Panel makes clear that global health must be put at the centre of the global security agenda. But while its recommendations are cogent, there are three important omissions that deserve attention. First, the Panel does not address the vicious cycle within which WHO is caught. The reason why WHO is so poorly resourced is that it lacks the confidence of donors. As the agency continues to underperform because of chronic underinvestment, so that lack of confidence (and the resultant unwillingness to invest) only worsens. The Panel presents no way out of this endless circle of failure. Second, one of the most important responsibilities for governments is the preservation of public order and national security. In the context of Ebola (indeed, any health crisis), this means creating resilient health systems to protect populations from unexpected shocks, as explained by Mosoka Fallah and colleagues in a letter from Liberia’s Ministry of Health this week. Universal health coverage should have been emphasised as a crucial instrument in building global health security. Finally, the Panel rightly notes that, “While WHO has already accepted the need for transformation of its organisational culture and delivery, it will need to be held accountable to ensure that this transformation is achieved”. However, nowhere does the Panel recommend the accountability mechanism to monitor and review the implementation of its recommendations. Our fear is that the unique opportunity presented by the Stocking Report will be squandered. We have little confidence that the governing bodies of WHO will deliver on the expectations of Stocking and her team. The responsibility for action therefore falls to WHO’s Director-General. Dr Margaret Chan has 20 months to save her agency from further and possibly irreversible reputational damage.

ReEBOV Antigen Rapid Test kit for point-of-care and laboratory-based testing for Ebola virus disease: a field validation study
Mara Jana Broadhurst, John Daniel Kelly, Ann Miller, Amanda Semper, Daniel Bailey, et al.

The Lancet, June 25, 2015; Vol. 386, No. 9996, p867–874    http://dx.doi.org/10.1016/S0140-6736(15)61042-X    
Background  At present, diagnosis of Ebola virus disease requires transport of venepuncture blood to field biocontainment laboratories for testing by real-time RT-PCR, resulting in delays that complicate patient care and infection control efforts. Therefore, an urgent need exists for a point-of-care rapid diagnostic test for this disease. In this Article, we report the results of a field validation of the Corgenix ReEBOV Antigen Rapid Test kit.
Methods   We performed the rapid diagnostic test on fingerstick blood samples from 106 individuals with suspected Ebola virus disease presenting at two clinical centres in Sierra Leone. Adults and children who were able to provide verbal consent or assent were included; we excluded patients with haemodynamic instability and those who were unable to cooperate with fingerstick or venous blood draw. Two independent readers scored each rapid diagnostic test, with any disagreements resolved by a third. We compared point-of-care rapid diagnostic test results with clinical real-time RT-PCR results (RealStar Filovirus Screen RT-PCR kit 1·0; altona Diagnostics GmbH, Hamburg, Germany) for venepuncture plasma samples tested in a Public Health England field reference laboratory (Port Loko, Sierra Leone). Separately, we performed the rapid diagnostic test (on whole blood) and real-time RT-PCR (on plasma) on 284 specimens in the reference laboratory, which were submitted to the laboratory for testing from many clinical sites in Sierra Leone, including our two clinical centres.
Findings   In point-of-care testing, all 28 patients who tested positive for Ebola virus disease by RT-PCR were also positive by fingerstick rapid diagnostic test (sensitivity 100% [95% CI 87·7–100]), and 71 of 77 patients who tested negative by RT-PCR were also negative by the rapid diagnostic test (specificity 92·2% [95% CI 83·8–97·1]). In laboratory testing, all 45 specimens that tested positive by RT-PCR were also positive by the rapid diagnostic test (sensitivity 100% [95% CI 92·1–100]), and 214 of 232 specimens that tested negative by RT-PCR were also negative by the rapid diagnostic test (specificity 92·2% [88·0–95·3]). The two independent readers agreed about 95·2% of point-of-care and 98·6% of reference laboratory rapid diagnostic test results. Cycle threshold values ranged from 15·9 to 26·3 (mean 22·6 [SD 2·6]) for the PCR-positive point-of-care cohort and from 17·5 to 26·3 (mean 21·5 [2·7]) for the reference laboratory cohort. Six of 16 banked plasma samples from rapid diagnostic test-positive and altona-negative patients were positive by an alternative real-time RT-PCR assay (the Trombley assay); three (17%) of 18 samples from individuals who were negative by both the rapid diagnostic test and altona test were also positive by Trombley.
Interpretation   The ReEBOV rapid diagnostic test had 100% sensitivity and 92% specificity in both point-of-care and reference laboratory testing in this population (maximum cycle threshold 26·3). With two independent readers, the test detected all patients who were positive for Ebola virus by altona real-time RT-PCR; however, this benchmark itself had imperfect sensitivity.
Malaria morbidity and mortality in Ebola-affected countries caused by decreased health-care capacity, and the potential effect of mitigation strategies: a modelling analysis
Patrick G T Walker, Michael T White, Jamie T Griffin, Alison Reynolds, Neil M Ferguson, Azra C Ghani
The Lancet Infectious Diseases, April 23, 2015; Vol. 15, No. 7, p825–832  http://dx.doi.org/10.1016/S1473-3099(15)70124-6    
Background  The ongoing Ebola epidemic in parts of west Africa largely overwhelmed health-care systems in 2014, making adequate care for malaria impossible and threatening the gains in malaria control achieved over the past decade. We quantified this additional indirect burden of Ebola virus disease.
Methods  We estimated the number of cases and deaths from malaria in Guinea, Liberia, and Sierra Leone from Demographic and Health Surveys data for malaria prevalence and coverage of malaria interventions before the Ebola outbreak. We then removed the effect of treatment and hospital care to estimate additional cases and deaths from malaria caused by reduced health-care capacity and potential disruption of delivery of insecticide-treated bednets. We modelled the potential effect of emergency mass drug administration in affected areas on malaria cases and health-care demand.
Findings  If malaria care ceased as a result of the Ebola epidemic, untreated cases of malaria would have increased by 45% (95% credible interval 43–49) in Guinea, 88% (83–93) in Sierra Leone, and 140% (135–147) in Liberia in 2014. This increase is equivalent to 3·5 million (95% credible interval 2·6 million to 4·9 million) additional untreated cases, with 10 900 (5700–21 400) additional malaria-attributable deaths. Mass drug administration and distribution of insecticide-treated bednets timed to coincide with the 2015 malaria transmission season could largely mitigate the effect of Ebola virus disease on malaria.
Interpretation  These findings suggest that untreated malaria cases as a result of reduced health-care capacity probably contributed substantially to the morbidity caused by the Ebola crisis. Mass drug administration can be an effective means to mitigate this burden and reduce the number of non-Ebola fever cases within health systems.

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Kurzweill Reports in Medical Science I

Curator: Larry H. Bernstein, MD, FCAP

 

 

 

E-coli bacteria found in some China farms and patients cannot be killed with antiobiotic drug of last resort

“One of the most serious global threats to human health in the 21st century” — could spread around the world, requiring “urgent coordinated global action”
November 20, 2015

http://www.kurzweilai.net/e-coli-bacteria-found-in-some-china-farms-and-patients-cannot-be-killed-with-antiobiotic-drug-of-last-resort

Colistin antibiotic overused in farm animals in China apparently caused E-coli bacteria to become completely resistant to treatment; E-coli strain has already spread to Laos and Malaysia (credit: Yi-Yun Liu et al./Lancet Infect Dis)

Widespread E-coli bacteria that cannot be killed with the antiobiotic drug of last resort — colistin — have been found in samples taken from farm pigs, meat products, and a small number of patients in south China, including bacterial strains with epidemic potential, an international team of scientists revealed in a paper published Thursday Nov. 19 in the journal The Lancet Infectious Diseases.

The scientists in China, England, and the U.S. found a new gene, MCR-1, carried in E-coli bacteria strain SHP45. MCR-1 enables bacteria to be highly resistant to colistin and other polymyxins drugs.

“The emergence of the MCR-1 gene in China heralds a disturbing breach of the last group of antibiotics — polymixins — and an end to our last line of defense against infection,” said Professor Timothy Walsh, from the Cardiff University School of Medicine, who collaborated on this research with scientists from South China Agricultural University.

Walsh, an expert in antibiotic resistance, is best known for his discovery in 2011 of the NDM-1 disease-causing antibiotic-resistant superbug in New Delhi’s drinking water supply. “The rapid spread of similar antibiotic-resistant genes such as NDM-1 suggests that all antibiotics will soon be futile in the face of previously treatable gram-negative bacterial infections such as E.coli and salmonella,” he said.

Likely to spread worldwide; already found in Laos and Malaysia

The MCR-1 gene was found on plasmids — mobile DNA that can be easily copied and transferred between different bacteria, suggesting an alarming potential to spread and diversify between different bacterial populations.

Structure of plasmid pHNSHP45 carrying MCR-1 from Escherichia coli strain SHP45 (credit: Yi-Yun Liu et al./Lancet Infect Dis)

“We now have evidence to suggest that MCR-1-positive E.coli has spread beyond China, to Laos and Malaysia, which is deeply concerning,” said Walsh.  “The potential for MCR-1 to become a global issue will depend on the continued use of polymixin antibiotics, such as colistin, on animals, both in and outside China; the ability of MCR-1 to spread through human strains of E.coli; and the movement of people across China’s borders.”

“MCR-1 is likely to spread to the rest of the world at an alarming rate unless we take a globally coordinated approach to combat it. In the absence of new antibiotics against resistant gram-negative pathogens, the effect on human health posed by this new gene cannot be underestimated.”

“Of the top ten largest producers of colistin for veterinary use, one is Indian, one is Danish, and eight are Chinese,” The Lancet Infectious Diseases notes. “Asia (including China) makes up 73·1% of colistin production with 28·7% for export including to Europe.29 In 2015, the European Union and North America imported 480 tonnes and 700 tonnes, respectively, of colistin from China.”

Urgent need for coordinated global action

“Our findings highlight the urgent need for coordinated global action in the fight against extensively resistant and pan-resistant gram-negative bacteria,” the journal paper concludes.

“The implications of this finding are enormous,” an associated editorial comment to the The Lancet Infectious Diseases paper stated. “We must all reiterate these appeals and take them to the highest levels of government or face increasing numbers of patients for whom we will need to say, ‘Sorry, there is nothing I can do to cure your infection.’”

Margaret Chan, MD, Director-General of the World Health Organization, warned in 2011 that “the world is heading towards a post-antibiotic era, in which many common infections will no longer have a cure and, once again, kill unabated.”

“Although in its 2012 World Health Organization Advisory Group on Integrated Surveillance of Antimicrobial Resistance (AGISAR) report the WHO concluded that colistin should be listed under those antibiotics of critical importance, it is regrettable that in the 2014 Global Report on Surveillance, the WHO did not to list any colistin-resistant bacteria as part of their ‘selected bacteria of international concern,’” The Lancet Infectious Diseases paper says, reflecting WHO’s inaction in Ebola-stricken African countries, as noted last September by the international medical humanitarian organization Médecins Sans Frontières.

Funding for the E-coli bacteria study was provided by the Ministry of Science and Technology of China and National Natural Science Foundation of China.


Abstract of Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study

Until now, polymyxin resistance has involved chromosomal mutations but has never been reported via
horizontal gene transfer. During a routine surveillance project on antimicrobial resistance in commensal Escherichia coli from food animals in China, a major increase of colistin resistance was observed. When an E coli strain, SHP45, possessing colistin resistance that could be transferred to another strain, was isolated from a pig, we conducted further analysis of possible plasmid-mediated polymyxin resistance. Herein, we report the emergence of the first plasmid-mediated polymyxin resistance mechanism, MCR-1, in Enterobacteriaceae.

The mcr-1 gene in E coli strain SHP45 was identified by whole plasmid sequencing and subcloning. MCR-1 mechanistic studies were done with sequence comparisons, homology modelling, and electrospray ionisation mass spectrometry. The prevalence of mcr-1 was investigated in E coli and Klebsiella pneumoniae strains collected from five provinces between April, 2011, and November, 2014. The ability of MCR-1 to confer polymyxin resistance in vivo was examined in a murine thigh model.

Polymyxin resistance was shown to be singularly due to the plasmid-mediated mcr-1 gene. The plasmid carrying mcr-1 was mobilised to an E coli recipient at a frequency of 10−1 to 10−3 cells per recipient cell by conjugation, and maintained in K pneumoniae and Pseudomonas aeruginosa. In an in-vivo model, production of MCR-1 negated the efficacy of colistin. MCR-1 is a member of the phosphoethanolamine transferase enzyme family, with expression in E coli resulting in the addition of phosphoethanolamine to lipid A. We observed mcr-1 carriage in E coli isolates collected from 78 (15%) of 523 samples of raw meat and 166 (21%) of 804 animals during 2011–14, and 16 (1%) of 1322 samples from inpatients with infection.

The emergence of MCR-1 heralds the breach of the last group of antibiotics, polymyxins, by plasmid-mediated resistance. Although currently confined to China, MCR-1 is likely to emulate other global resistance mechanisms such as NDM-1. Our findings emphasise the urgent need for coordinated global action in the fight against pan-drug-resistant Gram-negative bacteria.

 

Researchers discover signaling molecule that helps neurons find their way in the developing brain

November 20, 2015

http://www.kurzweilai.net/researchers-discover-signaling-molecule-that-helps-neurons-find-their-way-in-the-developing-brain

This image shows a section of the spinal cord of a mouse embryo. Neurons appear green. Commissural axons (which connect the two sides of the brain) appear as long, u-shaped threads, and the bottom, yellow segment of the structure represents the midline (between brain hemispheres). (credit: Laboratory of Brain Development and Repair/ The Rockefeller University)

Rockefeller University researchers have discovered a molecule secreted by cells in the spinal cord that helps guide axons (neuron extensions) during a critical stage of central nervous system development in the embryo. The finding helps solve the mystery: how do the billions of neurons in the embryo nimbly reposition themselves within the brain and spinal cord, and connect branches to form neural circuits?

Working in mice, the researchers identified an axon guidance factor, NELL2, and explained how it makes commissural axons (which connect the two sides of the brain).

The findings could help scientists understand what goes wrong in a rare disease called horizontal gaze palsy with progressive scoliosis. People affected by the condition often suffer from abnormal spine curvature, and are unable to move their eyes horizontally from side to side. The study was published Thursday Nov. 19 in the journal Science.


Abstract of Operational redundancy in axon guidance through the multifunctional receptor Robo3 and its ligand NELL2

Axon pathfinding is orchestrated by numerous guidance cues, including Slits and their Robo receptors, but it remains unclear how information from multiple cues is integrated or filtered. Robo3, a Robo family member, allows commissural axons to reach and cross the spinal cord midline by antagonizing Robo1/2–mediated repulsion from midline-expressed Slits and potentiating deleted in colorectal cancer (DCC)–mediated midline attraction to Netrin-1, but without binding either Slits or Netrins. We identified a secreted Robo3 ligand, neural epidermal growth factor-like-like 2 (NELL2), which repels mouse commissural axons through Robo3 and helps steer them to the midline. These findings identify NELL2 as an axon guidance cue and establish Robo3 as a multifunctional regulator of pathfinding that simultaneously mediates NELL2 repulsion, inhibits Slit repulsion, and facilitates Netrin attraction to achieve a common guidance purpose.

A sensory illusion that makes yeast cells self-destruct

A possible tactic for cancer therapeutics
November 20, 2015

http://www.kurzweilai.net/a-sensory-illusion-that-makes-yeast-cells-self-destruct

 

Effects of osmotic changes on yeast cell growth. (A) Schematic of the flow chamber used to create osmotic level oscillations for different periods of time. (B) Cell growth for these periods. The graphs show the average number of progeny cells (blue) before and after applying stress for different periods (gray shows orginal “no stress” line). The inset shows representative images of cells for two periods. (credit: Amir Mitchell et al./Science)

UC San Francisco researchers have discovered that even brainless single-celled yeast have “sensory biases” that can be hacked by a carefully engineered illusion — a finding that could be used to develop new approaches to fighting diseases such as cancer.

In the new study, published online Thursday November 19 in Science Express, Wendell Lim, PhD, the study’s senior author*, and his team discovered that yeast cells falsely perceive a pattern of osmotic levels (by applying potassium chloride) that alternate in eight minute intervals as massive, continuously increasing stress. In response, the microbes over-respond and kill themselves. (In their natural environment, salt stress normally gradually increases.)

The results, Lim says, suggest a whole new way of looking at the perceptual abilities of simple cells and this power of illusion could even be used to develop new approaches to fighting cancer and other diseases.

“Our results may also be relevant for cellular signaling in disease, as mutations affecting cellular signaling are common in cancer, autoimmune disease, and diabetes,” the researchers conclude in the paper. “These mutations may rewire the native network, and thus could modify its activation and adaptation dynamics. Such network rewiring in disease may lead to changes that can be most clearly revealed by simulation with oscillatory inputs or other ‘non-natural’ patterns.

“The changes in network response behaviors could be exploited for diagnosis and functional profiling of disease cells, or potentially taken advantage of as an Achilles’ heel to selectively target cells bearing the diseased network.”

https://youtu.be/CuDjZrM8xtA
UC San Francisco (UCSF) | Sensory Illusion Causes Cells to Self-Destruct

* Chair of the Department of Cellular and Molecular Pharmacology at UCSF, director of the UCSF Center for Systems and Synthetic Biology, and a Howard Hughes Medical Institute (HHMI) investigator.

** Normally, sensor molecules in a yeast cell detect changes in salt concentration and instruct the cell to respond by producing a protective chemical. The researchers found that the cells were perfectly capable of adapting when they flipped the salt stress on and off every minute or every 32 minutes. But to their surprise, when they tried an eight-minute oscillation of precisely the same salt level the cells quickly stopped growing and began to die off.


Abstract of Oscillatory stress stimulation uncovers an Achilles’ heel of the yeast MAPK signaling network

Cells must interpret environmental information that often changes over time. We systematically monitored growth of yeast cells under various frequencies of oscillating osmotic stress. Growth was severely inhibited at a particular resonance frequency, at which cells show hyperactivated transcriptional stress responses. This behavior represents a sensory misperception—the cells incorrectly interpret oscillations as a staircase of ever-increasing osmolarity. The misperception results from the capacity of the osmolarity-sensing kinase network to retrigger with sequential osmotic stresses. Although this feature is critical for coping with natural challenges—like continually increasing osmolarity—it results in a tradeoff of fragility to non-natural oscillatory inputs that match the retriggering time. These findings demonstrate the value of non-natural dynamic perturbations in exposing hidden sensitivities of cellular regulatory networks.

Google Glass helps cardiologists complete difficult coronary artery blockage surgery

November 20, 2015

http://www.kurzweilai.net/google-glass-helps-cardiologists-in-challenging-coronary-artery-blockage-surgery

 

Google Glass allowed the surgeons to clearly visualize the distal coronary vessel and verify the direction of the guide wire advancement relative to the course of the occluded vessel segment. (credit: Maksymilian P. Opolski et al./Canadian Journal of Cardiology

Cardiologists from the Institute of Cardiology, Warsaw, Poland have used Google Glass in a challenging surgical procedure, successfully clearing a blockage in the right coronary artery of a 49-year-old male patient and restoring blood flow, reports the Canadian Journal of Cardiology.

Chronic total occlusion, a complete blockage of the coronary artery, sometimes referred to as the “final frontier in interventional cardiology,” represents a major challenge for catheter-based percutaneous coronary intervention (PCI), according to the cardiologists.

That’s because of the difficulty of recanalizing (forming new blood vessels through an obstruction) combined with poor visualization of the occluded coronary arteries.

Coronary computed tomography angiography (CTA) is increasingly used to provide physicians with guidance when performing PCI for this procedure. The 3-D CTA data can be projected on monitors, but this technique is expensive and technically difficult, the cardiologists say.

So a team of physicists from the Interdisciplinary Centre for Mathematical and Computational Modelling of theUniversity of Warsaw developed a way to use Google Glass to clearly visualize the distal coronary vessel and verify the direction of the guide-wire advancement relative to the course of the blocked vessel segment.

Three-dimensional reconstructions displayed on Google Glass revealed the exact trajectory of the distal right coronary artery (credit: Maksymilian P. Opolski et al./Canadian Journal of Cardiology)

The procedure was completed successfully, including implantation of two drug-eluting stents.

“This case demonstrates the novel application of wearable devices for display of CTA data sets in the catheterization laboratory that can be used for better planning and guidance of interventional procedures, and provides proof of concept that wearable devices can improve operator comfort and procedure efficiency in interventional cardiology,” said lead investigatorMaksymilian P. Opolski, MD, PhD, of the Department of Interventional Cardiology and Angiology at the Institute of Cardiology, Warsaw, Poland.

“We believe wearable computers have a great potential to optimize percutaneous revascularization, and thus favorably affect interventional cardiologists in their daily clinical activities,” he said. He also advised that “wearable devices might be potentially equipped with filter lenses that provide protection against X-radiation.


Abstract of First-in-Man Computed Tomography-Guided Percutaneous Revascularization of Coronary Chronic Total Occlusion Using a Wearable Computer: Proof of Concept

We report a case of successful computed tomography-guided percutaneous revascularization of a chronically occluded right coronary artery using a wearable, hands-free computer with a head-mounted display worn by interventional cardiologists in the catheterization laboratory. The projection of 3-dimensional computed tomographic reconstructions onto the screen of virtual reality glass allowed the operators to clearly visualize the distal coronary vessel, and verify the direction of the guide wire advancement relative to the course of the occluded vessel segment. This case provides proof of concept that wearable computers can improve operator comfort and procedure efficiency in interventional cardiology.

Modulating brain’s stress circuity might prevent Alzheimer’s disease

Drug significantly prevented onset of cognitive and cellular effects in mice
November 17, 2015

http://www.kurzweilai.net/modulating-brains-stress-circuity-might-prevent-alzheimers-disease

 

Effect of drug treatment on AD mice in control group (left) or drug (right) on Ab plaque load. (credit: Cheng Zhang et al./Alzheimer’s & Dementia: The Journal of the Alzheimer’s Association)

In a novel animal study design that mimicked human clinical trials, researchers at University of California, San Diego School of Medicine report that long-term treatment using a small-molecule drug that reduces activity of  the brain’s stress circuitry significantly reduces Alzheimer’s disease (AD) neuropathology and prevents onset of cognitive impairment in a mouse model of the neurodegenerative condition.

The findings are described in the current online issue of the journal Alzheimer’s & Dementia: The Journal of the Alzheimer’s Association.

Previous research has shown a link between the brain’s stress signaling pathways and AD. Specifically, the release of a stress-coping hormone called corticotropin-releasing factor (CRF), which is widely found in the brain and acts as a neurotransmitter/neuromodulator, is dysregulated in AD and is associated with impaired cognition and with detrimental changes in tau protein and increased production of amyloid-beta protein fragments that clump together and trigger the neurodegeneration characteristic of AD.

“Our work and that of our colleagues on stress and CRF have been mechanistically implicated in Alzheimer’s disease, but agents that impact CRF signaling have not been carefully tested for therapeutic efficacy or long-term safety in animal models,” said the study’s principal investigator and corresponding author Robert Rissman, PhD, assistant professor in the Department of Neurosciences and Biomarker Core Director for the Alzheimer’s Disease Cooperative Study (ADCS).

The researchers determined that modulating the mouse brain’s stress circuitry mitigated generation and accumulation of amyloid plaques widely attributed with causing neuronal damage and death. As a consequence, behavioral indicators of AD were prevented and cellular damage was reduced.  The mice began treatment at 30-days-old — before any pathological or cognitive signs of AD were present — and continued until six months of age.

One particular challenge, Rissman noted, is limiting exposure of the drug to the brain so that it does not impact the body’s ability to respond to stress. “This can be accomplished because one advantage of these types of small molecule drugs is that they readily cross the blood-brain barrier and actually prefer to act in the brain,” Rissman said.

“Rissman’s prior work demonstrated that CRF and its receptors are integrally involved in changes in another AD hallmark, tau phosphorylation,” said William Mobley, MD, PhD, chair of the Department of Neurosciences and interim co-director of the Alzheimer’s Disease Cooperative Study at UC San Diego. “This new study extends those original mechanistic findings to the amyloid pathway and preservation of cellular and synaptic connections.  Work like this is an excellent example of UC San Diego’s bench-to-bedside legacy, whereby we can quickly move our basic science findings into the clinic for testing,” said Mobley.

Rissman said R121919 was well-tolerated by AD mice (no significant adverse effects) and deemed safe, suggesting CRF-antagonism is a viable, disease-modifying therapy for AD. Drugs like R121919 were originally designed to treat generalized anxiety disorder, irritable bowel syndrome and other diseases, but failed to be effective in treating those disorders.

Rissman noted that repurposing R121919 for human use was likely not possible at this point. He and colleagues are collaborating with the Sanford Burnham Prebys Medical Discovery Institute to design new assays to discover the next generation of CRF receptor-1 antagonists for testing in early phase human safety trials.

“More work remains to be done, but this is the kind of basic research that is fundamental to ultimately finding a way to cure — or even prevent —Alzheimer’s disease,” said David Brenner, MD, vice chancellor, UC San Diego Health Sciences and dean of UC San Diego School of Medicine. “These findings by Dr. Rissman and his colleagues at UC San Diego and at collaborating institutions on the Mesa suggest we are on the cusp of creating truly effective therapies.”


Abstract of Corticotropin-releasing factor receptor-1 antagonism mitigates beta amyloid pathology and cognitive and synaptic deficits in a mouse model of Alzheimer’s disease

Introduction: Stress and corticotropin-releasing factor (CRF) have been implicated as mechanistically involved in Alzheimer’s disease (AD), but agents that impact CRF signaling have not been carefully tested for therapeutic efficacy or long-term safety in animal models.

Methods: To test whether antagonism of the type-1 corticotropin-releasing factor receptor (CRFR1) could be used as a disease-modifying treatment for AD, we used a preclinical prevention paradigm and treated 30-day-old AD transgenic mice with the small-molecule, CRFR1-selective antagonist, R121919, for 5 months, and examined AD pathologic and behavioral end points.

Results: R121919 significantly prevented the onset of cognitive impairment in female mice and reduced cellular and synaptic deficits and beta amyloid and C-terminal fragment-β levels in both genders. We observed no tolerability or toxicity issues in mice treated with R121919.

Discussion: CRFR1 antagonism presents a viable disease-modifying therapy for AD, recommending its advancement to early-phase human safety trials.

Allen Institute researchers decode patterns that make our brains human
Conserved gene patterning across human brains provide insights into health and disease
November 17, 2015

http://www.kurzweilai.net/allen-institute-researchers-decode-patterns-that-make-our-brains-human

 

Percentage of known neuron-, astrocyte- and oligodendrocyte-enriched genes in 32 modules, ordered by proportion of neuron-enriched gene membership. (credit: Michael Hawrylycz et al./Nature Neuroscience)

Allen Institute researchers have identified a surprisingly small set of just 32 gene-expression patterns for all 20,000 genes across 132 functionally distinct human brain regions, and these patterns appear to be common to all individuals.

In research published this month in Nature Neuroscience, the researchers used data for six brains from the publicly available Allen Human Brain Atlas. They believe the study is important because it could provide a baseline from which deviations in individuals may be measured and associated with diseases, and could also provide key insights into the core of the genetic code that makes our brains distinctly human.

While many of these patterns were similar in human and mouse, many genes showed different patterns in human. Surprisingly, genes associated with neurons were most conserved (consistent) across species, while those for the supporting glial cells showed larger differences. The most highly stable genes (the genes that were most consistent across all brains) include those associated with diseases and disorders like autism and Alzheimer’s, and these genes include many existing drug targets.

These patterns provide insights into what makes the human brain distinct and raise new opportunities to target therapeutics for treating disease.

The researchers also found that the pattern of gene expression in cerebral cortex is correlated with “functional connectivity” as revealed by neuroimaging data from the Human Connectome Project.

“The human brain is phenomenally complex, so it is quite surprising that a small number of patterns can explain most of the gene variability across the brain,” says Christof Koch, Ph.D., President and Chief Scientific Officer at the Allen Institute for Brain Science. “There could easily have been thousands of patterns, or none at all. This gives us an exciting way to look further at the functional activity that underlies the uniquely human brain.”


Abstract of Canonical genetic signatures of the adult human brain

The structure and function of the human brain are highly stereotyped, implying a conserved molecular program responsible for its development, cellular structure and function. We applied a correlation-based metric called differential stability to assess reproducibility of gene expression patterning across 132 structures in six individual brains, revealing mesoscale genetic organization. The genes with the highest differential stability are highly biologically relevant, with enrichment for brain-related annotations, disease associations, drug targets and literature citations. Using genes with high differential stability, we identified 32 anatomically diverse and reproducible gene expression signatures, which represent distinct cell types, intracellular components and/or associations with neurodevelopmental and neurodegenerative disorders. Genes in neuron-associated compared to non-neuronal networks showed higher preservation between human and mouse; however, many diversely patterned genes displayed marked shifts in regulation between species. Finally, highly consistent transcriptional architecture in neocortex is correlated with resting state functional connectivity, suggesting a link between conserved gene expression and functionally relevant circuitry.

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Pharmacy International Conference

Larry H. Bernstein, MD, FCAP, Curator

LPBI

 

 

3rd Nirma Institute of Pharmacy International Conference
NIPiCON – 2016
January 21 – 23, 2016 ………….http://www.nipicon.org/.

Anthony Melvin Crasto   https://www.facebook.com/groups/worlddrugtracker/permalink/1170816792946389/

The pharmaceutical sciences is a dynamic and interdisciplinary field that combines a broad range of scientific disciplines that are critical to the discovery and development of new drugs and therapies. Over the years, pharmaceutical scientists have been instrumental in discovering and developing innovative drugs that save people’s lives and improve the quality of life.

NIPiCON was initiated in a year 2013 to offer a common platform for academicians, researchers, industrialists, clinical practitioners and young budding pharmacists to share their ideas and research work and finally emerge with new concepts, innovations and novel strategies for various challenges in the pharmaceutical field.

The 3 International Conference, NIPiCON 2016 aims to provide a knowledge sharing experience in the area of “Global Challenges in Drug Discovery, Development and Regulatory Affairs”.

Pharmaceutical innovation is a complex creative process that harnesses the application of knowledge and creativity for discovering, developing and bringing to clinical use, new medicinal products that extend or improve the lives of patients.A successful pharmaceutical R&D process is one that minimizes the time and cost needed to bring a compound from the scientific ‘idea’, through discovery and clinical development, to final regulatory approval and delivery to the patient. This conference will provide an open forum for the academicians, researchers, clinicians and professionals of pharmaceutical industry to enrich their knowledge in the area of drug discovery, development and its regulatory requirements.

The conference features plenary sessions which will be delivered by eminent national and international speakers from different disciplines of pharmaceutical field. In addition, there will be invited lectures and sessions delivered by distinguished and young researchers in their respective fields during parallel technical sessions. The conference willalso provide the opportunity to scientists and research scholars from various organizations to put forth their innovative ideas and research findings by means of deliberations, discussions and poster presentations.

 

NIPiCON was initiated in a year 2013 to offer a common platform for academicians, researchers, industrialists, clinical practitioners and young budding pharmacists to share their ideas and research work and finally emerge with new concepts, innovations and novel strategies for various challenges in the pharmaceutical field.

The 3 International Conference, NIPiCON 2016 aims to provide a knowledge sharing experience in the area of “Global Challenges in Drug Discovery, Development and Regulatory Affairs”.

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Rapid diagnosis of septicemia

Larry H. Bernstein, MD, FCAP, Curator

LPBI

 

Rapid Diagnosis of Infection in the Critically Ill, a Multicenter Study of Molecular Detection in Bloodstream Infections, Pneumonia, and Sterile Site Infections

Jean-Louis Vincent,  David Brealey, Nicolas Libert, Nour Elhouda Abidi, Michael O’Dwyer, Kai Zacharowski, Malgorzata Mikaszewska-Sokolewicz, et al.
Crit Care Med. 2015;43(11):2283-2291.     http://www.medscape.com/viewarticle/853105

Objective: Early identification of causative microorganism(s) in patients with severe infection is crucial to optimize antimicrobial use and patient survival. However, current culture-based pathogen identification is slow and unreliable such that broad-spectrum antibiotics are often used to insure coverage of all potential organisms, carrying risks of overtreatment, toxicity, and selection of multidrug-resistant bacteria. We compared the results obtained using a novel, culture-independent polymerase chain reaction/electrospray ionization-mass spectrometry technology with those obtained by standard microbiological testing and evaluated the potential clinical implications of this technique.

Design: Observational study.

Setting: Nine ICUs in six European countries.

Patients: Patients admitted between October 2013 and June 2014 with suspected or proven bloodstream infection, pneumonia, or sterile fluid and tissue infection were considered for inclusion.

Interventions: None.

Measurements and Main Results: We tested 616 bloodstream infection, 185 pneumonia, and 110 sterile fluid and tissue specimens from 529 patients. From the 616 bloodstream infection samples, polymerase chain reaction/electrospray ionization-mass spectrometry identified a pathogen in 228 cases (37%) and culture in just 68 (11%). Culture was positive and polymerase chain reaction/electrospray ionization-mass spectrometry negative in 13 cases, and both were negative in 384 cases, giving polymerase chain reaction/electrospray ionization-mass spectrometry a sensitivity of 81%, specificity of 69%, and negative predictive value of 97% at 6 hours from sample acquisition. The distribution of organisms was similar with both techniques. Similar observations were made for pneumonia and sterile fluid and tissue specimens. Independent clinical analysis of results suggested that polymerase chain reaction/electrospray ionization-mass spectrometry technology could potentially have resulted in altered treatment in up to 57% of patients.

Conclusions: Polymerase chain reaction/electrospray ionization-mass spectrometry provides rapid pathogen identification in critically ill patients. The ability to rule out infection within 6 hours has potential clinical and economic benefits.

Introduction

The availability of rapid and reliable infectious disease diagnostics that can provide results directly from patient specimens represents a major unmet need in managing critically ill patients. Current sepsis guidelines recommend initiation of IV antibiotic therapy as early as possible, ideally within the first hour,[1] as any delay in effective antimicrobial therapy may result in decreased survival.[2] Effective therapy requires that the identity of causative pathogens and their resistance patterns are known. However, the current standard-of-care, which depends on blood culture-based initial diagnosis, often takes at least 48–72 hours to provide a result. Furthermore, cultures often remain negative even when bacterial or fungal infections are strongly suspected,[3] in part, related to concurrent antibiotic treatment.[4]

Molecular diagnostic techniques that do not depend on growth of organisms in culture may offer a distinct advantage over current methods. Most of the recently described molecular methods, however, rely on culture amplification as a precursor to diagnosis.[5–8] Although these techniques may accelerate diagnosis for positive cultures, they do not address the significant proportion of false-negative cultures observed in patients with sepsis. In addition, many of these methods also use targeted pathogen detection with limited pathogen coverage such that negative results are often not highly predictive.

Polymerase chain reaction followed by electrospray ionization-mass spectrometry (PCR/ESI-MS) can detect more than 800 bloodstream infection (BSI)-relevant pathogens in a single assay and in approximately 6 hours.[9–13] It can also identify three classes of antibiotic resistance markers associated with resistance to methicillin (mecA), vancomycin (vanA/vanB), and carbapenems (KPC). Using this technique, we recently demonstrated 83% sensitivity and 94% specificity compared with culture for direct detection of pathogens in whole-blood specimens from patients with suspected BSIs.[13]

Here, we describe findings from the multicenter observational Rapid Diagnosis of Infections in the Critically Ill (RADICAL) study. The primary objective was to compare results obtained using the novel culture-independent PCR/ESI-MS technology with those obtained from standard microbiological testing as a measure of clinical performance. Secondarily, to broadly address the clinical value of PCR/ESI-MS detections, a panel of independent clinical adjudicators was used to identify changes in patient management that may have occurred had the results from the PCR/ESI-MS technology been available for clinical use and assumed to be correct.

Patient Inclusion and Exclusion Criteria

Patients were considered for inclusion if they had 1) suspected or proven severe infection or sepsis and or 2) suspected or proven healthcare-associated pneumonia (HAP/HCAP), ventilator-associated pneumonia (VAP), or severe community-acquired pneumonia (sCAP). Because pneumonia is the most common precipitating cause of sepsis, there may be an overlap between these two populations, but patients were included in one of the two groups, not both. Pneumonia (HAP/HCAP, VAP, and sCAP) was diagnosed in patients with an endotracheal tube in situ and a new infiltrate on chest radiograph plus temperature more than 38°C or less than 35°C, increased sputum production, increased or decreased WBC count (> 12 or < 4 cells/mL3), or a clinical suspicion of pneumonia, and the treating clinician expected the patient to still be intubated the next day.

The following exclusion criteria were used: the treating clinician expected the patient to be discharged from the ICU on the day of evaluation or the following day, the treatment intent was palliative, the clinician was not committed to aggressive treatment, or death was deemed imminent and inevitable. Patients who had previously been included, but were readmitted to the ICU during the same hospitalization, were not included a second time.

 

Data Analysis

Results obtained with the PCR/ESI-MS technology for each specimen were compared with those obtained using conventional microbiology methods for the same sample. If multiple specimens were taken from a patient per standard-of-care protocols, each was independently analyzed in this study. Agreement and concordance were assessed using a McNemar test[16] and Cohen κ.[17] All percentages and CIs for proportions were calculated using the exact method and are rounded to the nearest percentage. Direct comparison of positive and negative results was conducted with organism identification for each method (conventional microbiology vs PCR/ESI-MS) for each specimen type. Coagulase-negative staphylococcus and other common skin contaminants were annotated as “potential contaminants” for both methods and excluded from the overall analysis, as previously described.[13]

Discrepant results between the PCR/ESI-MS and culture cannot be directly confirmed by an independent method, as previously described.[13] Two approaches were used to resolve discrepancies. In a subset of patients, multiple samples were collected per standard-of-care. This included two independent fresh venipunctures (left arm vs right arm) or one venipuncture plus one sample collected from an indwelling line. Paired analysis of PCR/ESI-MS testing results between these independently collected samples was conducted to indicate the likelihood of true infection. In addition, independent clinical adjudication (described below) was performed using all the clinical data collected as part of the study, including standard-of-care microbiology results and PCR/ESI-MS results.

 

Results

Of 543 patients enrolled in the study, 14 did not have matching PCR/ESI-MS or standard-of-care microbiology results and were excluded from the final analysis. Table 1 shows the patient demographics, reflecting a typically heterogeneous ICU population: one third of the patients were admitted from the emergency department; 75% were exposed to one or more antibiotics prior to study enrolment. Overall mortality was 29%, with cardiac arrest, septic shock, multiple organ failure, and acute respiratory distress syndrome accounting for ~62% of deaths.

BSI Analysis

A total of 616 direct whole-blood specimens from the 529 patients were tested to assess the accuracy of organism identification. PCR/ESI-MS results from analysis of blood using the bacteria, antibiotic resistance, and Candida BSI assay were compared with results from standard clinical microbiology cultures. As shown in Table 2, there were 228 PCR/ESI-MS positive specimens (36.5%) for at least one pathogen compared with 68 positive specimens by culture (10.9%). The total number of positive tests for each method was statistically different (McNemar test statistic = 137.6; df = 1; p < 0.0001). There were 55 samples that were positive for the same organism with both techniques (Table 2), yielding an overall concordance of identification (calculated sensitivity) of 81% (95% CI, 70–89%) and a κ value of 0.25 (95% CI, 0.18–0.31). In 13 instances, culture identified an organism that was either negative by PCR/ESI-MS (6/13) or the identity of the organism reported by PCR/ESI-MS did not match the organism identified by microbiology testing (7/13) (Table S1, Supplemental Digital Content 1,http://links.lww.com/CCM/B418). In contrast, PCR/ESI-MS reported a BSI-relevant organism in 173 additional specimens that were culture negative, resulting in a calculated assay specificity of 69% (Table S2, Supplemental Digital Content 1, http://links.lww.com/CCM/B418). Finally, there were 384 concordant negative specimens, yielding a negative predictive value (NPV) of ~97% (95% CI, 94–98%).

The frequencies of organisms detected from BSI specimens are shown in Figure 1. The distributions of the top 10 species detected by microbiology and those detected by PCR/ESI-MS were similar. The largest single discrepancy between the two methods by sheer volume of detections was in the identification of Escherichia coli. Although culture and PCR/ESI-MS techniques both reported E. coli as the most abundant species, PCR/ESI-MS detection was 4-fold higher (89 vs 21). Other organisms in which blood culture performed less well included the enterococcus species, Enterococcus faecalis (1 vs 10) and Enterococcus faecium (2 vs 25), Candida albicans (2 vs 13), and Staphylococcus aureus (14 vs 31). In contrast, Pseudomonas aeruginosa detection was comparable between the two methods (6 vs 8). Additional analysis of the PCR/ESI-MS results showed that the levels (genome equivalent/mL) of organisms reported in the majority of these PCR/ESI-MS positive, but culture-negative, cases were similar to cases in which culture matched PCR/ESI-MS detections (data not shown).

Figure 1.

http://img.medscape.com/article/853/105/853105-fig1.jpg

Bacteria and Candida detected in the Rapid Diagnosis of Infections in the Critically Ill (RADICAL) study. Distribution of organisms reported by polymerase chain reaction/electrospray ionization-mass spectrometry (PCR/ESI-MS) (blue bar) and culture (red bar) observed in the RADICAL study are shown, sorted by decreasing order of PCR/ESI-MS reported organisms. Both methods showed similar distribution for the top eight reportable organisms that were seen >5 times by PCR/ESI-MS, with some minor reshuffling of the order. PCR/ESI-MS showed a longer tail of reportable organisms that were infrequent (≤5 times). Normal skin flora are shown below the line were not included in further analysis by either method.

 

Nonbloodstream Infections

Heterogeneous samples from patients with suspected pneumonia or sterile site infections were also obtained in several cases. Overall, there were 185 LRT samples (88 BAL, 96 ETA, and 1 other) and 110 SF&T samples (36 intraperitoneal fluid, 14 pleural fluid, 11 CSF, 13 tissue, and 36 other fluid types). Results from the analysis of these specimens are shown in Table 3. LRT and SF&T specimens often had multiple detections reported by both methods in several samples. Only the primary detections by either method were included in the analysis. The overall sensitivities for concordance between standard-of-care and PCR/ESI-MS were 84% (95% CI, 74–91%) and 85% (95% CI, 72–93%), respectively. As for the bloodstream infection data, the McNemar test for both the LRT and the SF&T sample data showed that the total number of samples considered positive was significantly different for culture versus PCR/ESI-MS (McNemar test statistic = 20.9 for LRT and 15.2 for SF&T; p < 0.0001 in both cases). Also similar to the bloodstream infection data, there was more agreement in the contingency table comparing culture to PCR/ESI-MS than would be expected by chance (LRT κ = 0.35; 95% confidence limits, 0.23, 0.47 and SF&T κ = 0.27; 95% confidence limits, 0.11, 0.43). For LRT specimens, there was no statistically significant difference in sensitivity (p = 0.677) or specificity (p = 0.444) when testing the hypothesis that the BAL proportion – the ETA proportion was equal to zero.

In 151 patients, two or more specimen types (BSI plus LRT and/or SF&T) were obtained and analyzed. In 86 of these 151 cases (57%), the same organisms were reported by PCR/ESI-MS in all samples tested from an individual patient (data not shown). In comparison, culture concordance between the sample types was seen in only 19 cases (12%), driven largely by no detection reported in the BSI culture results.

Resistance Markers

There were no identified cases of Klebsiella-associated carbapenemase. There was a single report of vancomycin-resistant Enterococci, which was matched across the two methods. There were 23 reports of mecA+ staphylococcus organisms (seven in BSI samples, 13 in LRT samples, and three in SF&T samples), with the following agreement between PCR/ESI-MS and culture: for BSI samples, results were concordant in four cases, and PCR/ESI-MS was positive and culture negative in three; for LRT samples, results were concordant in three cases, PCR/ESI-MS was positive with culture negative in nine, and PCR/ESI-MS was negative with culture positive in one; and the three cases in the SF&T samples were concordant across PCR/ESI-MS and culture.

 

 

Discussion

The important findings of the RADICAL study are that PCR/ESI-MS detected BSI pathogens with high overall sensitivity and NPV; PCR/ESI-MS was three times more likely to identify an organism than standard culture; and, if available, PCR/ESI-MS results may have altered the treatment regimen in as many as 57% of patients.

Sepsis affects a large proportion of the critically ill population. Despite improvements in recent years, morbidity and mortality rates remain high.[18] The importance of initiating treatment as soon as possible has been highlighted and shown to be associated with improved outcomes,[2] yet this finding needs to be balanced against the direct risks and stewardship issues arising from overzealous or inappropriate antibiotic use.

Rapid diagnosis of severe infection or sepsis is thus crucial not only to optimize a patient’s chances of survival but also to encourage responsible antibiotic use. However, diagnosing infection accurately in critically ill patients is challenging. Characteristic clinical and laboratory signs of severe infection, such as tachycardia, fever, and altered WBC count, are nonspecific and are often present in other acute conditions. Biomarkers, such as C-reactive protein and procalcitonin, are also nonspecific and are of more value in ruling out infection than in making a definite diagnosis.[19] Microbiological culture results are negative in many patients with sepsis, largely because prior antimicrobial therapy affects ex vivo growth in culture medium.[1] Certain microorganisms are also particularly difficult to culture, requiring specific growth media or a particular environment. As culture results often require several days to become available, patients with suspected severe infection are, therefore, often started on empiric broad-spectrum antibiotics to increase the likelihood that a pathogenic organism will be adequately covered. This approach, although valid in terms of preventing delays in starting treatment with currently available diagnostic techniques, has several negative aspects, including the potential for toxicity with multiple antibiotics, the high-associated costs, and the effects of antibiotic pressure on the development of antimicrobial resistance.[20]

Availability of a technique that could provide more rapid pathogen identification directly from patient samples could, therefore, represent a marked improvement in terms of enabling more rapid diagnosis and earlier initiation of appropriate antimicrobial therapy, with associated beneficial effects on outcomes, antimicrobial resistance, costs, and toxicity. Various methods have been suggested for this purpose, including single pathogen assays, which are of limited use in patients with suspected sepsis in whom multiple organisms may be involved; selected-pathogen assays, which use specific molecular targets to identify some 20–35 species;[21–23] and broad-range pathogen assays, which use universal or conserved targets to identify many hundreds of species, but for which earlier versions lacked sensitivity due to the small volumes of blood extracted for analysis.[24,25]

 

Importantly, in 41% of cases, the panel of independent experts would have recommended a change in management, including initiation of therapy, altered antimicrobial spectrum, and/or change in duration of therapy, based on the PCR/ESI-MS results. This percentage increased to 57 when PCR/ESI-MS tests were positive.

Second, the greater detection rate of E. coli, S. aureus, E. faecium, C. albicans, and Klebsiella pneumoniae by PCR/ESI-MS compared with routine culture was unanticipated, and the explanation is unclear. Prior to study inclusion, most patients were exposed to combinations of two or more antibiotics active against Gram-positive and Gram-negative organisms and were often receiving one or more antifungals in addition. As stated above, the bacterium/fungus may have been largely cleared with preexisting antibiotics, hence the negative culture results, but remaining DNA remnants in the circulation may have been sufficient to give a positive PCR/ESI-MS. The sensitivity of the technique increases the risk of identifying contaminants and commensals; however, the pathogens most frequently detected in the study are those associated with infection. Accepting the validity of these data, the PCR/ESI-MS test could be of importance to help target antimicrobial therapy in patients who have already started antimicrobials and have negative cultures (salvage microbiology).[29] Further, ideally interventional, studies are warranted to confirm and further explore these findings.

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Genomic Pathogen Typing, Volume 2 (Volume Two: Latest in Genomics Methodologies for Therapeutics: Gene Editing, NGS and BioInformatics, Simulations and the Genome Ontology), Part 1: Next Generation Sequencing (NGS)

Genomic Pathogen Typing

Larry H. Bernstein, MD, FCAP, Curator

LPBI

 

Genomic Pathogen Typing Using Solid-State Nanopores

Citation: Squires AH, Atas E, Meller A (2015) Genomic Pathogen Typing Using Solid-State Nanopores. PLoS ONE 10(11): e0142944.   http://dx.doi.org:/10.1371/journal.pone.0142944

Editor: Niyaz Ahmed, University of Hyderabad, INDIA

In clinical settings, rapid and accurate characterization of pathogens is essential for effective treatment of patients; however, subtle genetic changes in pathogens which elude traditional phenotypic typing may confer dangerous pathogenic properties such as toxicity, antibiotic resistance, or virulence. Existing options for molecular typing techniques characterize the critical genomic changes that distinguish harmful and benign strains, yet the well-established approaches, in particular those that rely on electrophoretic separation of nucleic acid fragments on a gel, have room for only incremental future improvements in speed, cost, and complexity. Solid-state nanopores are an emerging class of single-molecule sensors that can electrophoretically characterize charged biopolymers, and which offer significant advantages in terms of sample and reagent requirements, readout speed, parallelization, and automation. We present here the first application of nanopores for single-molecule molecular typing using length based “fingerprints” of critical sites in bacterial genomes. This technique is highly adaptable for detection of different types of genetic variation; as we illustrate using prototypical examples including Mycobacterium tuberculosis and methicillin-resistant Streptococcus aureus, the solid-state nanopore diagnostic platform may be used to detect large insertions or deletions, small insertions or deletions, and even single-nucleotide variations in bacterial DNA. We further show that Bayesian classification of test samples can provide highly confident pathogen typing results based on only a few tens of independent single-molecule events, making this method extremely sensitive and statistically robust.

 

Subtle genetic changes in bacteria can produce large variations in factors affecting pathogenicity, such as toxicity, antibiotic resistance, and virulence. These genetic variations are not only used to trace the epidemic and phylogenetic relationships among strains of bacteria, but are also critically important in clinical settings for proper patient diagnosis and treatment. Most existing approaches require sample incubation and growth over the course of multiple days prior to testing, and nearly all require expert handling of samples and interpretation of results. Traditional phenotypic typing techniques such as serotypes, biotypes, phage-types, and antibiograms lack the necessary sensitivity to distinguish between closely related pathogen strains, and therefore fail to adequately capture these critical variations for clinical applications. Gel-based techniques such as restriction fragment length polymorphism (RFLP) or cleaved amplified polymorphic sequences (CAPS) require a large amount of time and results are not easily compared or transferred among labs. Next-generation sequencing is an increasingly popular method of fully characterizing bacterial strains [1] and may be used for typing strains according to the sequences of a panel of housekeeping genes, as in multi-locus sequence typing (MLST) [2], but this approach is more commonly used to trace post hoc epidemic and phylogenetic relationships among clinical isolates. Furthermore, the complexity and quantity of sequencing data far exceeds the minimum information required to efficiently and accurately diagnose a patient. For example, bioinformatics studies suggest that a panel of just 30–50 single nucleotide variations (SNVs) could be used to uniquely identify thousands of strains of Mycobacterium tuberculosis [3, 4]. Yet SNVs are not the only source of variation among pathogens; polymorphisms from SNVs and short indels up to genetic changes as large as whole plasmids or sets of genes may be responsible for critical changes to pathogenicity. Thus there exists a clear clinical need for a novel approach to molecular typing that can quickly and simply screen patient samples for a panel of widely varying known genetic polymorphisms of dangerous pathogens.

Solid-state nanopores may be used to discriminate the lengths of unlabeled individual biopolymers such as DNA molecules across a wide range of lengths [5, 6]. Biopolymers are electrophoretically attracted and threaded through a voltage-biased nanoscale pore drilled in an ultrathin freestanding SiNx membrane [7, 8]. When a DNA molecule is threaded through a nanopore, it partially blocks the flow of ions moving through the pore, allowing real-time detection of the analyte by monitoring changes in the ion current. Nanopore sensing is biochemically simple, as it does not require labeling of the analyte with radioactive or fluorescent probes, yet it can be used to detect minute quantities of nucleic acid molecules, surpassing the sensitivity of bulk methods [8]. Moreover, nanopore sensing involves relatively simple instrumentation (primarily a current amplifier) and may be used to analyze thousands of molecules in just a few minutes, making this technique an ideal candidate for applications such as nucleic acid based diagnostics.

Here we describe and practice a novel detection scheme (Fig 1) for molecular typing of pathogens using solid-state nanopores, and demonstrate its ability to discriminate a wide range of critical genetic polymorphisms in closely related organisms with starkly different pathogenicities. In the first sensing mode of our approach (Mode I), large insertions or deletions are detected by directly classifying the length of DNA in the nanopore. In the second sensing mode (Mode II), small indels down to SNVs may be detected by sequence-specific digestion at the site of the polymorphism to produce either one or two DNA fragments, which are then detected in the nanopore. We first characterize the practical range of our nanopore system for detecting variation in DNA length, and show that fragment length differences are more readily apparent for shorter DNA lengths and for asymmetric cut sites. We then demonstrate that statistical analysis tools such as Bayesian classifiers, commonly used for automated classification, are highly effective for rapid and statistically robust discrimination among different lengths and combinations of DNA fragments translocating through a nanopore, even in cases where significant portions of these distributions overlap. We apply these techniques to demonstrate polymorphism discrimination down to the single nucleotide level in prototypical strains of Mycobacterium tuberculosis (virulent vs. avirulent) and Streptococcus aureus(methicillin-resistant vs. multi-drug resistant). This highly versatile combination of rapid length and digest discrimination, spanning several orders of magnitude of possible genomic variation size, in a single, parallelizable device, could be extended to probe a large panel of critical sites within a genome for point-of-care determination of critical pathogenic properties and sequence typing.

Fig 1.  Two Principal Modes for Nanopore Discrimination of Pathogen Genomic Variation.

http://journals.plos.org/plosone/article/figure/image?size=large&id=info:doi/10.1371/journal.pone.0142944.g001

Fig 1. Two Principal Modes for Nanopore Discrimination of Pathogen Genomic Variation.

Mode I: Direct length detection according to analyte translocation dwell time and depth enables discrimination of longer vs. shorter fragments; i.e: whether or not an insertion or deletion is present (left). Mode II: Prior to translocation, samples are exposed to a restriction enzyme that cuts at the site of a SNV or short indel or mutation. Detection of cleaved vs. uncleaved DNA fragments in the nanopore reveals whether or not the critical genomic variation is present.

http://dx.doi.org:/10.1371/journal.pone.0142944.g001

Detection of DNA Sequence Polymorphisms in Solid-State Nanopores  

The simplest form of nanopore translocation analysis involves the measurement of the depth of each current blockade (ΔIB) and the dwell time of each molecule within the pore (tD). Both parameters have been shown to grow nonlinearly with DNA length, forming the basis for fragment length separation in the nanopore system. The statistical distributions of these independently measured quantities may be used to distinguish between analytes of different lengths, such as DNAs [5, 6, 9], or proteins having identical molecular weight but slightly different charge or 3D structure [1013]. Variation in the translocation dwell-time (tD) in solid-state nanopores measured for different DNA lengths (l), are empirically described by a power law: tDlα where α = 1.38±0.02, which has been reproduced by multiple experimental approaches [5, 9, 14]. Using a log-scale distribution of translocation times to estimate the distribution of tD, note that the difference in log(tD) for two sequences (lengths l0 and l0 + Δl) is more apparent for shorter length l0 as compared with the insertions and deletions Δl (i.e. when Δl/l0 ∼ 1) according to Eq 1:(1)

If the presence of two fragment lengths must be identified from within a single sample, it is desirable that their distributions of ΔIB or tD should be as well-separated as possible. Furthermore, if the presence of a cut sample must be distinguished from an uncut sample, then by Eq 1 the peak produced by the shorter part of a cut sample will appear farther away from the uncut peak than the longer part of a cut sample. To statistically distinguish the samples, it is desirable for the peak of the shorter part to be as dissimilar as possible from the uncut peak. Therefore, asymmetrically cut DNA pieces from a restriction digest are more readily distinguished from the original uncut length than those produced by symmetrically positioned restriction sites, provided that the shorter piece is of sufficient length to be detected by the nanopore. In cases where separation between two similar length biopolymers (Δl/l0 ∼ 1) is required, the measured histograms of either ΔIB or tD may overlap significantly, making discrimination between these molecules difficult. Combinations of multiple fragment lengths within a sample pose additional challenges, as their more complicated distributions may overlap or otherwise preclude simple contour cluster separation.

In the context of sequence typing, identification of fragments by sizing will indicate the presence of specific insertions and deletions that may enhance or reduce pathogenicity or otherwise uniquely identify a pathogenic strain. Upper bounds on Δl are set by: 1) sample preparation parameters and limitations; for example, robust and fast PCR amplification is most easily achieved for fragment lengths of ~102–103 bp [15] and 2) nanopore stability considerations; for example, nanopores are more frequently clogged by very long DNA (>20 kbp). Lower bounds on l0 are set by nanopore sensitivity; while several groups have demonstrated detection of small DNA fragments (<50 bp) [16] we find that a minimum l0 on the order of ~100 bp is more reliable since it is readily detectable in small nanopores with no additional modifications [5], producing an extremely small fraction of missed events due to the finite system bandwidth. Thus a reasonable design range for sequence typing fragments is ~100 bp minimum length forl0, ranging up to a few thousand base pairs maximum length for l0 + Δl. Many types of common genetic variations used for strain typing fall within this size range. For example, one complete IS6110 (insertion-like sequence element) insertion in M. tuberculosis is 1358 bp [17]. At the other end of this range, multi-drug resistant strains of methicillin-resistant S. aureus (MRSA) have many insertions and deletions in the range 47 bp—643 bp that affect their pathogenicity [18]. To detect the smallest indels, which fall below the minimum detectable Δl, we turn to the exquisite sequence specificity of digestion by restriction enzymes, which can identify sequence polymorphisms down to a single nucleotide variation.

Using these design principles, we present here two alternative modes of detection that illustrate the wide range of genomic variations that may be detected using a single sensor. For large insertions or deletions (Fig 1: Mode I, left panel), a nanopore may be used to discriminate the raw change in DNA length caused by the presence or absence of this sequence according to the duration of translocation events. For short indels, mutations, or single nucleotide variations (SNVs) (Fig 1: Mode II, right panel), which are more difficult to identify solely by length as discussed above, we utilize a restriction enzyme. The sample is only cut in the presence (or absence) of the critical sequence, and subsequent detection in a nanopore reveals either one or two fragments in the nanopore according to the observed durations and blockage levels of translocation events.

Event Diagram Discrimination of Sample Length and Composition

We first experimentally illustrate the practical length resolution of the nanopore platform for identifying sample length and composition. We analyzed samples containing mixtures of DNA fragments composed of one or two well-defined lengths. The resulting event diagrams create unique fingerprints that can be used to distinguish different lengths of DNA (Mode I) or whether or not a fragment of DNA has been cut (Mode II). Fig 2A–2E show event diagrams for 100 bp, 200 bp, 900 bp, 1000 bp, and 100+900 bp DNA in a single nanopore (diameter 4.8 nm, effective height 7 nm) at +300 mV bias (for additional examples, see Figs B-E in S1 File). Here, each translocation event is represented by its corresponding ion current event amplitude (ΔIB) and dwell time (tD). From comparison of Fig 2A and 2D, it is evident that insertions and deletions Δl several times larger than the base length (here: Δl:l0 = 9:1) are indeed easily distinguishable (Fig C in S1 File). Comparison of Fig 2A and 2B illustrates that Δl = 100 bp results in reasonably distinct event diagrams for l0 = 100 bp, which may be distinguished to >95% confidence with just a few events each, taking both dwell time and current amplitude into consideration (Fig D in S1 File). However, at l0 = 900 bp a minimum of several hundred events are required to confidently (>95%) differentiate l0 (Fig 2C) from l0 + Δl (1000 bp, Fig 2D), since their event diagrams overlap significantly (Fig E in S1 File). Returning to Eq 1, for Δl = 100 bp, we expect Δlog(tD) = 0.415 for l0 = 100 bp, and Δlog(tD) = 0.063 for l0 = 900 bp. For the data shown in Fig 2F, Δlog(tD) = 0.1 for l0 = 100 bp, and Δlog(tD) = 0.03 for l0 = 900 bp. The inability to easily and quickly discriminate the 900 bp DNA from the 1000 bp DNA demonstrates the practical limits set on Mode I sample identification according to the size of the insertion or deletion that must be detected.

Fig 2.  Translocation Event Diagrams Uniquely Identify DNA Fragment Lengths in a Single Nanopore.

http://journals.plos.org/plosone/article/figure/image?size=large&id=info:doi/10.1371/journal.pone.0142944.g002

Fig 2. Translocation Event Diagrams Uniquely Identify DNA Fragment Lengths in a Single Nanopore.

(a) 100 bp at 1 nM. (b) 200 bp at 1 nM. (c) 900 bp at 1 nM. (d) 1000 bp at 1 nM. (e) 1:1 combination of 100 bp and 900 bp, total concentration 2 nM. (f) Semilog(x) distributions of translocation dwell times for all samples (a)-(e). Translocations for all samples were collected in a single nanopore (4.8 nm diameter, effective thickness ~7 nm) with a +300 mV bias relative to trans (open pore current: 13 nA). To facilitate visualization of population density, a random white noise offset below the acquisition rate of this data (-2 μs < Δt < +2 μs, acquisition rate 250 kHz) has been added to each tD.    http://dx.doi.org:/10.1371/journal.pone.0142944.g002

Fig 2E illustrates how Mode II may overcome these limitations by digesting DNA into fragments: here, a highly asymmetric ratio of lengths in a mixed sample (100+900 bp) clearly facilitates sample identification as compared to the full length 1000 bp DNA (Fig 2D). However, Mode II also presents a more challenging case for quantitative discrimination between an uncut and a cut sample. Whereas single-length samples can be identified using either their tD or Idistribution (as shown in Fig 2F), the longer fragment in a cut sample may share significant overlap with the uncut sample. This is particularly true in the case of a highly asymmetric cut site.

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http://journals.plos.org/plosone/article/figure/image?size=inline&id=info:doi/10.1371/journal.pone.0142944.g003

Fig 3. Gaussian Mixture Models for Mode II Classification of 1000 bp vs. 900+100 bp DNA Fragments.

(a) 2-D GMM for 1000 bp DNA fragment translocations. (b) 2-D GMM for 900+100 bp DNA fragment translocations. (c) Bayesian posterior estimates p(A|Θ) of correctly identifying a data set Θ as Case A, calculated for each increment of N points in Θ, repeated 1000 times (first 50 shown in gray) and averaged (blue), each using M = 1500 points in the model data set. (d) Bayesian posterior estimates p(B|Θ) of correctly identifying a data set Θ as Case B, calculated for each increment of N points in Θ, repeated 1000 times (first 50 shown in gray) and averaged (red), all using M = 1500 points in the model data set. (e) Bayesian posterior estimates p(A|Θ) for test data sets ofN points given a model based on data set size M. Each point represents the average of 1000 separate bootstrap simulations. (f) Bayesian posterior estimates p(A|Θ) for test data sets of N points given a model based on data set size M. Each point represents the average of 1000 separate bootstrap simulations. Insets: range of N for which p(A|Θ) reaches 0.95. See Methods and S1 File for complete numerical simulation details.    http://dx.doi.org:/10.1371/journal.pone.0142944.g003

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http://journals.plos.org/plosone/article/figure/image?size=inline&id=info:doi/10.1371/journal.pone.0142944.g004

Fig 4. Gaussian Mixture Models of DNA Fragments for Actual Mode II Pathogen Typing at the SNV Level.

(a) Diagram of the main steps in sample preparation, detection, and classification: PCR fragments from isolated pathogens are subjected to a restriction digest, which recognizes and cuts only one genomic variant. Nanopore translocations are used to classify the pathogen according to the combination of fragment lengths detected. (b) ThemazG gene of the avirulent M. tuberculosis strain H37Ra is not cut by NaeI (942 bp), while the same gene in the closely related virulent strain H37Rv, which differs by only a single A-to-C mutation, is cut by NaeI (621bp + 321 bp). (c) Gaussian mixture model (one component) fit to translocations of mazG fragments from H37Ra. (d) Gaussian mixture model (two components) fit to translocations of mazG fragments from H37Rv. (e) Posterior probabilities for correctly identifying the H37Ra and H37Rv strains as a function of number of translocation events collected from an unknown sample, simulated using bootstrap sampling from nanopore translocation data. (f) The parC gene of the multi-drug-resistant MRSA strain FPR3757 is not cut by BseRI (886 bp) due to a single C-to-A mutation, while the closely related and less resistant strain HOU-MR is cut by BseRI (640bp + 245 bp). (g) Gaussian mixture model (one component) fit to translocations of parC fragments from FPR3757. (h) Gaussian mixture model (two components) fit to translocations of parC fragments from HOU-MR. (i) Posterior probabilities for correctly identifying the FPR3757 and HOU-MR strains as a function of number of translocation events collected from an unknown sample, simulated using bootstrap sampling from nanopore translocation data.    http://dx.doi.org:/10.1371/journal.pone.0142944.g004

Conclusion

Solid-state nanopore based biosensing is a rapidly growing field due to its practical and conceptual simplicity, portability and versatility. To date, few reports have demonstrated the utility of the method towards clinical diagnostic applications. Yet as we have shown here, nanopores are well-suited to make statistically robust diagnostic classifications among different DNA lengths with real single-molecule data, even in cases where the distributions significantly overlap. Utilizing a Bayesian statistical model, we have demonstrated that nanopore sensing can be used to discriminate among pathogens based on well-known genomic variations. Both large indels (Mode I) or short indels and single nucleotide variations (Mode II) can be targeted using proper sequence-specific digestion with off-the-shelf restriction enzymes. Furthermore, the Bayesian classifiers indicate the statistical confidence of each classification as a function of the number of nanopore events obtained in each measurement. Even at this preliminary stage of development we find that only a few tens of events (obtained in just a few minutes using a single pore) are sufficient to produce a statistically reliable result with well-defined and small error margins.

Our method is general and can be adapted to address many different “multiple-choice” clinical questions using a nanopore biosensor or other single molecule approaches. Future extensions of this work may seek to design and implement large panels of critical sites that represent the minimum sets necessary to characterize genomic variation for various applications in healthcare and research, and to develop additional sensing modalities. Although the primary design challenge currently remains linked to the location and availability of restriction digestion sites, we expect that the ongoing development of designer restriction enzymes, for example systems based on modular zinc fingers [27], TALENs [28], or CRISPR-like proteins will provide additional design flexibility for this technique.

The nanopore fingerprinting approach presented here addresses clear needs in clinical molecular diagnostics for a rapid and simple sensor that can identify a wide range of genomic variation in pathogens to inform treatment options. We have shown here discrimination of both large and small scale genomic variations between pathogen strains, down to single SNVs. The large, flexible sample design space for lengths, cut sites, and enzyme selection at each critical locus ensures that the technique is highly customizable for different genomic variation panels that could profile pathogenicity, antibiotic resistance, or even sequence type. The inherent scalability, minimal sample requirements, speed, and simple readout of the nanopore platform would all facilitate on-site and perhaps even automated use: As successive events are recorded, an increasingly clear fingerprint of translocation times and blockage levels will permit online software to “call” the sample as soon as enough events have been accumulated. Our technique is highly portable and customizable, and the binary data would be readily transferrable among different labs.

 

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