The #history, #genome and #biology of NCTC 30: a non-pandemic #Vibrio cholerae isolate from #WW1 (Proc Roy Soc Biosci., abstract)

[Source: Proceedings of the Royal Society, Biological Sciences, full page: (LINK). Abstract, edited.]

The history, genome and biology of NCTC 30: a non-pandemic Vibrio cholerae isolate from World War One

Matthew J. Dorman, Leanne Kane, Daryl Domman, Jake D. Turnbull, Claire Cormie,Mohammed-Abbas Fazal, David A. Goulding, Julie E. Russell, Sarah Alexander
and Nicholas R. Thomson

Published: 10 April 2019 / DOI: https://doi.org/10.1098/rspb.2018.2025

 

Abstract

The sixth global cholera pandemic lasted from 1899 to 1923. However, despite widespread fear of the disease and of its negative effects on troop morale, very few soldiers in the British Expeditionary Forces contracted cholera between 1914 and 1918. Here, we have revived and sequenced the genome of NCTC 30, a 102-year-old Vibrio cholerae isolate, which we believe is the oldest publicly available live V. cholerae strain in existence. NCTC 30 was isolated in 1916 from a British soldier convalescent in Egypt. We found that this strain does not encode cholera toxin, thought to be necessary to cause cholera, and is not part of V. cholerae lineages responsible for the pandemic disease. We also show that NCTC 30, which predates the introduction of penicillin-based antibiotics, harbours a functional β-lactamase antibiotic resistance gene. Our data corroborate and provide molecular explanations for previous phenotypic studies of NCTC 30 and provide a new high-quality genome sequence for historical, non-pandemic V. cholerae.

Keywords: Antibiotics; Drugs Resistance; Penicillin; Beta-lactams; Vibrio cholerae.

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Estimating #cholera #incidence with cross-sectional #serology (Sci Transl Med., abstract)

[Source: Science Translational Medicine, full page: (LINK). Abstract, edited.]

Estimating cholera incidence with cross-sectional serology

Andrew S. Azman1,*, Justin Lessler1, Francisco J. Luquero2,3, Taufiqur Rahman Bhuiyan4, Ashraful Islam Khan4, Fahima Chowdhury4, Alamgir Kabir4, Marc Gurwith5, Ana A. Weil6,7, Jason B. Harris6,8,9, Stephen B. Calderwood6,7, Edward T. Ryan6,7,10, Firdausi Qadri4 and Daniel T. Leung11,12

1 Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA. 2 Epicentre, Paris 75012, France. 3 Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA. 4 Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh. 5 PaxVax Inc., Redwood City, CA 94065, USA. 6 Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA . 7 Department of Medicine, Harvard Medical School, Boston, MA 02115, USA. 8 Division of Global Health, Massachusetts General Hospital, Boston, MA 02114, USA. 9 Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA. 10 Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA. 11 Division of Infectious Diseases, University of Utah School of Medicine, Salt Lake City, UT 84132, USA. 12 Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, UT 84132, USA.

*Corresponding author. Email: azman@jhu.edu

Science Translational Medicine  20 Feb 2019: Vol. 11, Issue 480, eaau6242 / DOI: 10.1126/scitranslmed.aau6242

 

Estimating the true prevalence of cholera

Successful development of anti-cholera measures requires accurate estimates of infection incidence. Reporting of cholera cases, however, typically relies on clinical assessment at the time of patient presentation and can be problematized by lack of access to health care and variable, nonspecific symptomatology. Combining a small number of serological markers with machine learning methods, Azman et al. were able to accurately detect individuals who had had cholera infections within the previous year. Simulated serosurveys showed that this simple antibody-based approach could potentially be used as an alternative method to estimate cholera incidence in a population.

 

Abstract

The development of new approaches to cholera control relies on an accurate understanding of cholera epidemiology. However, most information on cholera incidence lacks laboratory confirmation and instead relies on surveillance systems reporting medically attended acute watery diarrhea. If recent infections could be identified using serological markers, cross-sectional serosurveys would offer an alternative approach to measuring incidence. Here, we used 1569 serologic samples from a cohort of cholera cases and their uninfected contacts in Bangladesh to train machine learning models to identify recent Vibrio cholerae O1 infections. We found that an individual’s antibody profile contains information on the timing of V. choleraeO1 infections in the previous year. Our models using six serological markers accurately identified individuals in the Bangladesh cohort infected within the last year [cross-validated area under the curve (AUC), 93.4%; 95% confidence interval (CI), 92.1 to 94.7%], with a marginal performance decrease using models based on two markers (cross-validated AUC, 91.0%; 95% CI, 89.2 to 92.7%). We validated the performance of the two-marker model on data from a cohort of North American volunteers challenged with V. cholerae O1 (AUC range, 88.4 to 98.4%). In simulated serosurveys, our models accurately estimated annual incidence in both endemic and epidemic settings, even with sample sizes as small as 500 and annual incidence as low as two infections per 1000 individuals. Cross-sectional serosurveys may be a viable approach to estimating cholera incidence.

Keywords: Vibrio cholerae; Cholera; Serology.

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Molecular basis for the potent #inhibition of the emerging #carbapenemase VCC-1 by #avibactam (Antimicrob Agents Chemother., abstract)

[Source: Antimicrobial Agents and Chemotherapy, full page: (LINK). Abstract, edited.]

Molecular basis for the potent inhibition of the emerging carbapenemase VCC-1 by avibactam

Chand S. Mangat, Grishma Vadlamani, Viktor Holicek, Mitchell Chu, Veronica Larmour, David J. Vocadlo, Michael R. Mulvey, Brian L. Mark

DOI: 10.1128/AAC.02112-18

 

ABSTRACT

In 2016 we identified a new class A carbapenemase, VCC-1, in nontoxigenic Vibrio cholerae that had been isolated from retail shrimp imported into Canada for human consumption. Shortly thereafter, seven additional VCC-1 producing V. cholerae were isolated along the German coastline. These isolates appear to have acquired the VCC-1 gene (blaVCC-1) independently from the Canadian isolate, suggesting blaVCC-1 is mobile and widely distributed. VCC-1 hydrolyzes penicillins, cephalothin, aztreonam, and carbapenems, and like the broadly disseminated class A carbapenemase KPC-2, is only weakly inhibited by clavulanic acid or tazobactam. Although VCC-1 has yet to observed in the clinic, its encroachment into aquaculture and other areas with human activity suggests the enzyme may be emerging as a public health threat. To pre-emptively address this threat, we examined the structural and functional biology of VCC-1 against the FDA approved non-β-lactam-based inhibitor avibactam. We found that avibactam restored the in vitro sensitivity of V. cholerae to meropenem, impenem and ertapenem. Acylation efficiency was lower for VCC-1 as compared to KPC-2 and akin to that of Pseudomonas aeruginosa PAO1 AmpC (k2/Ki=3.0 × 103 M-1sec-137). The tertiary structure of VCC-1 is similar to that of KPC-2 and they bind avibactam similarly; however, our analyses suggest that VCC-1 may be unable to degrade avibactam as has been found for KPC-2. Based on our prior genomics-based surveillance, we were able to target VCC-1 for detailed molecular studies to gain early insights that could be used to combat this carbapenemse in the future.

Copyright © 2019 American Society for Microbiology. All Rights Reserved.

Keywords: Antibiotics; Drugs resistance; Vibrio cholerae; Avibactam.

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#Niche #adaptation limits #bacteriophage #predation of #Vibrio cholerae in a nutrient-poor aquatic #environment (Proc Natl Acad Sci USA, abstract)

[Source: Proceedings of the National Academy of Sciences of the United States of America, full page: (LINK). Abstract, edited.]

Niche adaptation limits bacteriophage predation of Vibrio cholerae in a nutrient-poor aquatic environment

Cecilia A. Silva-Valenzuela and Andrew Camilli

PNAS published ahead of print January 11, 2019 / DOI: https://doi.org/10.1073/pnas.1810138116

Edited by Lucia B. Rothman-Denes, The University of Chicago, Chicago, IL, and approved December 11, 2018 (received for review June 13, 2018)

 

Significance

Virulent phages can reduce populations of bacteria and help shape bacterial evolution. Here, we used three virulent phages to understand their equilibrium with V. cholerae in nutrient-limiting aquatic microcosms. It has been proposed that phages quench cholera outbreaks, but no direct evidence of phage predation in aquatic environments had been established. Here, we show that different phages possess varied abilities to infect in certain niches or stages of the host bacterial life cycle. Unveiling the phage/bacterial interactions in their natural setting is important to the understanding of cholera outbreaks and could be ultimately used to help develop a method for outbreak prediction and/or control.

 

Abstract

Vibrio cholerae, the causative agent of cholera, has reservoirs in fresh and brackish water where it interacts with virulent bacteriophages. Phages are the most abundant biological entity on earth and coevolve with bacteria. It was reported that concentrations of phage and V. cholerae inversely correlate in aquatic reservoirs and in the human small intestine, and therefore that phages may quench cholera outbreaks. Although there is strong evidence for phage predation in cholera patients, evidence is lacking for phage predation of V. choleraein aquatic environments. Here, we used three virulent phages, ICP1, ICP2, and ICP3, commonly shed by cholera patients in Bangladesh, as models to understand the predation dynamics in microcosms simulating aquatic environments. None of the phages were capable of predation in fresh water, and only ICP1 was able to prey on V. cholerae in estuarine water due to a requirement for salt. We conclude that ICP2 and ICP3 are better adapted for predation in a nutrient rich environment. Our results point to the evolution of niche-specific predation by V. cholerae-specific virulent phages, which complicates their use in predicting or monitoring cholera outbreaks as well as their potential use in reducing aquatic reservoirs of V. cholerae in endemic areas.

Vibrio cholerae – cholera – bacteriophage – aquatic reservoir – environment

 

Footnotes

1 To whom correspondence should be addressed. Email: andrew.camilli@tufts.edu.

Author contributions: C.A.S.-V. and A.C. designed research; C.A.S.-V. and A.C. performed research; C.A.S.-V. contributed new reagents/analytic tools; C.A.S.-V. and A.C. analyzed data; and C.A.S.-V. and A.C. wrote the paper.

The authors declare no conflict of interest.

This article is a PNAS Direct Submission.

This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1810138116/-/DCSupplemental.

Published under the PNAS license.

Keywords: Vibrio cholerae; Cholera; Bacteriophages.

—–

#Probiotic strains detect and suppress #cholera in mice (Sci Transl Med., abstract)

[Source: Science Translational Medicine, full page: (LINK). Abstract, edited.]

Probiotic strains detect and suppress cholera in mice

Ning Mao1,2,3,4,*,  Andres Cubillos-Ruiz1,2,3,*, D. Ewen Cameron1,*,† and James J. Collins1,2,3,‡

1 Institute for Medical Engineering and Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology (MIT), Cambridge, MA 02138, USA. 2 Broad Institute of MIT and Harvard, Cambridge, MA 02138, USA. 3 Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA. 4 Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA.

Corresponding author. Email: jimjc@mit.edu

* These authors contributed equally to this work.

† Present address: Flagship Pioneering, Cambridge, MA 02142, USA.

Science Translational Medicine  13 Jun 2018: Vol. 10, Issue 445, eaao2586 / DOI: 10.1126/scitranslmed.aao2586

 

Designer bugs as drugs

The endemic persistence and outbreaks of Vibrio cholerae indicate a need for new methods of control; in this issue, two groups investigated the potential of engineered bacteria to mediate cholera resistance in animal models. Mao et al. discovered that lactic acid production by the probiotic Lactococcus lactis rendered the infant mouse gut hostile to V. cholerae and engineered L. lactis to detect breakthrough infection. Hubbard et al. extensively modified a contemporary V. cholerae strain for a live oral vaccine, which resulted in an attenuated strain that could protect infant rabbits from V. cholerae challenge within 24 hours of vaccine administration, indicating the protective effects were not dependent on adaptive immunity. These papers showcase innovative approaches to tackling cholera.

 

Abstract

Microbiota-modulating interventions are an emerging strategy to promote gastrointestinal homeostasis. Yet, their use in the detection, prevention, and treatment of acute infections remains underexplored. We report the basis of a probiotic-based strategy to promote colonization resistance and point-of-need diagnosis of cholera, an acute diarrheal disease caused by the pathogen Vibrio cholerae. Oral administration of Lactococcus lactis, a common dietary fermentative bacterium, reduced intestinal V. cholerae burden and improved survival in infected infant mice through the production of lactic acid. Furthermore, we engineered an L. lactis strain that specifically detects quorum-sensing signals of V. cholerae in the gut and triggers expression of an enzymatic reporter that is readily detected in fecal samples. We postulate that preventive dietary interventions with fermented foods containing natural and engineered L. lactis strains may hinder cholera progression and improve disease surveillance in populations at risk of cholera outbreaks.

Keywords: Probiotics; Vibrio cholerae; Animal Models; Lactococcus lactis.

——

#Vibriovulnificus – new insights into a deadly opportunistic #pathogen (Environ Microbiol., abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Environ Microbiol. 2017 Oct 13. doi: 10.1111/1462-2920.13955. [Epub ahead of print]

Vibrio vulnificus – new insights into a deadly opportunistic pathogen.

Baker-Austin C1, Oliver JD2.

Author information: 1 Centre for Environment, Fisheries and Aquaculture Science, Weymouth Laboratory, Weymouth, Dorset, England. 2 University of North Carolina at Charlotte, Charlotte, NC, USA.

 

Abstract

Vibrio vulnificus is a Gram-negative aquatic bacterium first isolated by the United States (US) Centers for Disease Control and Prevention (CDC) in 1964. This bacterium is part of the normal microbiota of estuarine waters and occurs in high numbers in molluscan shellfish around the world, particularly in warmer months. Infections in humans are derived from consumption of seafood produce and from water exposure. V. vulnificus is a striking and enigmatic human pathogen, yet many aspects related to its biology, genomics, virulence capabilities and epidemiology remain elusive and poorly understood. This pathogen is responsible for over 95% of seafood-related deaths in the USA, and carries the highest fatality rate of any food-borne pathogen. Indeed, infections associated with this pathogen that progress to primary septicaemia have a similar case fatality rate to category BSL 3 and 4 pathogens, such as anthrax, bubonic plague, Ebola, and Marburg fever. Interestingly, V. vulnificus infections disproportionately affect males (∼85% of cases) and older patients (> 40 years), especially those with underlying conditions such as liver diseases, diabetes and immune disorders. New insights from molecular studies and comparative genomic approaches have offered tantalising insights into this pathogen. A recent increase and geographical spread in reported infections, in particular wound cases, underlines the growing international importance of V. vulnificus, particularly in the context of coastal warming. We outline and explore here a range of current data gaps regarding this important pathogen, and provide some current thoughts on approaches to elucidate key aspects associated with this bacterium.

This article is protected by copyright. All rights reserved.

© 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

KEYWORDS: V. vulnificus; Vibrios; oysters; septicaemia; whole genome sequencing; wound

PMID: 29027375 DOI: 10.1111/1462-2920.13955

Keywords: Vibrio Vulnificus.

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#Origins of the current seventh #cholera #pandemic (Proc Natl Acad Sci USA, abstract)

[Source: Proceedings of the National Academy of Sciences of the United States of America, full page: (LINK). Abstract, edited.]

Origins of the current seventh cholera pandemic

Dalong Hu a,b,1,2, Bin Liu a,c,1, Lu Feng a,b,d, Peng Ding a, Xi Guo a, Min Wanga, Boyang Cao a,b,d, Peter R. Reeves e,3, and Lei Wang a,b,d,f,3

Author Affiliations: a TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area, Tianjin 300457, People’s Republic of China; b The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin 300457, People’s Republic of China; c Tianjin Research Center for Functional Genomics and Biochip, Tianjin 300457, People’s Republic of China; d Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin 300457, People’s Republic of China; e School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia; f State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, People’s Republic of China

Edited by John J. Mekalanos, Harvard Medical School, Boston, MA, and approved October 11, 2016 (received for review June 2, 2016)

 

Significance

Cholera, a major disease in human history, has terrorized the world through seven pandemics. The seventh pandemic started in Indonesia in 1961 and spread globally, currently infecting 3–5 million people annually. By combining all available historical records and genomic analysis of available preseventh pandemic and some early pandemic strains, we revealed the complex six-step evolution of the pandemic strain from its probable origin in South Asia to its nonpathogenic form in the Middle East in ∼1900 to Indonesia in ∼1925, where it evolved into a pandemic strain before becoming widespread in 1961. This pathway relates to human traffic routes, including the annual Hajj pilgrimage, and involved novel niches that provided gene sources and the driving forces for stepwise evolution.

 

Abstract

Vibrio cholerae has caused seven cholera pandemics since 1817, imposing terror on much of the world, but bacterial strains are currently only available for the sixth and seventh pandemics. The El Tor biotype seventh pandemic began in 1961 in Indonesia, but did not originate directly from the classical biotype sixth-pandemic strain. Previous studies focused mainly on the spread of the seventh pandemic after 1970. Here, we analyze in unprecedented detail the origin, evolution, and transition to pandemicity of the seventh-pandemic strain. We used high-resolution comparative genomic analysis of strains collected from 1930 to 1964, covering the evolution from the first available El Tor biotype strain to the start of the seventh pandemic. We define six stages leading to the pandemic strain and reveal all key events. The seventh pandemic originated from a nonpathogenic strain in the Middle East, first observed in 1897. It subsequently underwent explosive diversification, including the spawning of the pandemic lineage. This rapid diversification suggests that, when first observed, the strain had only recently arrived in the Middle East, possibly from the Asian homeland of cholera. The lineage migrated to Makassar, Indonesia, where it gained the important virulence-associated elements Vibrio seventh pandemic island I (VSP-I), VSP-II, and El Tor type cholera toxin prophage by 1954, and it then became pandemic in 1961 after only 12 additional mutations. Our data indicate that specific niches in the Middle East and Makassar were important in generating the pandemic strain by providing gene sources and the driving forces for genetic events.

Vibrio cholerae – pandemic – evolution – comparative genomics

 

Footnotes

1 D.H. and B.L. contributed equally to this work.

2 Present address: School of Life and Environmental Sciences, Charles Perkins Centre, D17, University of Sydney, Sydney, NSW 2006, Australia.

3 To whom correspondence may be addressed. Email: wanglei@nankai.edu.cn or peter.reeves@sydney.edu.au.

Author contributions: L.F., P.R.R., and L.W. designed research; D.H., B.L., P.D., X.G., M.W., and B.C. performed research; D.H., B.L., L.F., P.R.R., and L.W. analyzed data; and B.L., P.R.R., and L.W. wrote the paper.

The authors declare no conflict of interest.

This article is a PNAS Direct Submission.

Data deposition: The sequences reported in this paper have been deposited in the GenBank database (accession nos. CP013301–CP013320).

This article contains supporting information online at http://www.pnas.org/lookup/suppl/doi:10.1073/pnas.1608732113/-/DCSupplemental.

Keywords: Cholera; Pandemics; Vibrio Cholerae.

——