Résultats de la recherche

Antibiotic resistance in Vibrio cholerae: Understanding the ecology of resistance genes and mechanisms

Author(s): Bhabatosh Das | Jyoti Verma | Pawan Kumar | Amit Ghosh | Thandavarayan Ramamurthy

Date of Publication: July 2, 2019

Publication: Vaccine

Summary/Abstract: The unique genetic makeup and remarkable competency of Vibrio cholerae are the key factors that help the cholera pathogen adapt rapidly to adverse environmental conditions and resist the detrimental effect of antimicrobial agents. In the last few decades, V. cholerae that causes acute watery diarrhoeal disease cholera has emerged as a notorious multidrug resistant enteric pathogen. Although chromosomal mutations can contribute to antimicrobial resistance (AMR), the frequent acquisition of extrachromosomal mobile genetic elements from closely/distantly related bacterial species are major players in V. cholerae drug resistance. Whole genome sequence analysis of clinical and environmental V. cholerae strains revealed that the genome of most of the recent isolates harbour integrating conjugative elements, plasmids, superintegron, transposable elements and insertion sequences, which are the key carriers of genetic traits encoding antimicrobial resistance function. Different antimicrobial resistance genes identified in V. cholerae can contribute in antibiotic resistance by facilitating one of the following three mechanisms; reduced permeability or active efflux of the antibiotics, (alteration of the antibiotic targets by introducing post-transcriptional/translational modifications and (hydrolysis or chemical modification of antibiotics. We present an overview of the present insights on the emergence and mechanisms of AMR in V. cholerae.

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Whole genome sequence of Vibrio cholerae directly from dried spotted filter paper

Author(s): Angèle H. M. Bénard | Etienne Guenou | Maria Fookes | Jerome Ateudjieu | Watipaso Kasambara | Matthew Siever | Stanislas Rebaudet | Jacques Boncy | Paul Adrien | Renaud Piarroux | David A. Sack | Nicholas Thomson | Amanda K. Debes

Date of Publication: 2019-5-30

Publication: PLoS Neglected Tropical Diseases

Summary/Abstract: Cholera affects more than 4 million people globally every year; people predominantly living in poverty or in resource-constrained conditions including political crises or natural disasters. Cholera’s typical presentation is characterized by rapid onset of acute watery diarrhea and vomiting which can progress from watery stool to shock in as little as four hours. Laboratory conditions needed for culture confirmation and strain preservation are rarely to never present in these affected areas. In fact, many cholera endemic areas in Sub-Saharan African are so remote that even treatment response alone is often challenging. Here we present the genomic analysis of DNA extracted from dried filter paper, which is a low-cost, low-tech and sustainable method. Previously this method has facilitated cholera confirmation by PCR, but we demonstrate that this method is also suitable for whole genome sequencing and subsequent strain characterization by presenting the analysis of samples from an outbreak in a remote area of Cameroon. This method will facilitate the understanding of the molecular epidemiology in cholera-prone areas, which were previously too challenging to attempt. It also introduces a method that can be used on a broader scale for diarrheal disease surveillance, including providing a window into co-infection and microbiome analyses.

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

Author(s): Matthew J. Dorman | Leanne Kane | Daryl Domman | Jake D. Turnbull | Claire Cormie | Mohammed-Abbas Fazal | David A. Goulding | Julie E. Russell | Sarah Alexander | Nicholas R. Thomson

Date of Publication: 2019-4-10

Publication: Proceedings of the Royal Society B: Biological Sciences

Summary/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.

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High quality reference genomes for toxigenic and non-toxigenic Vibrio cholerae serogroup O139

Author(s): Matthew J. Dorman | Daryl Domman | Muhammad Ikhtear Uddin | Salma Sharmin | Mokibul Hassan Afrad | Yasmin Ara Begum | Firdausi Qadri | Nicholas R. Thomson

Date of Publication: 2019-4-10

Publication: Scientific Reports

Summary/Abstract: Toxigenic Vibrio cholerae of the O139 serogroup have been responsible for several large cholera epidemics in South Asia, and continue to be of clinical and historical significance today. This serogroup was initially feared to represent a new, emerging V. cholerae clone that would lead to an eighth cholera pandemic. However, these concerns were ultimately unfounded. The majority of clinically relevant V. cholerae O139 isolates are closely related to serogroup O1, biotype El Tor V. cholerae, and comprise a single sublineage of the seventh pandemic El Tor lineage. Although related, these V. cholerae serogroups differ in several fundamental ways, in terms of their O-antigen, capsulation phenotype, and the genomic islands found on their chromosomes. Here, we present four complete, high-quality genomes for V. cholerae O139, obtained using long-read sequencing. Three of these sequences are from toxigenic V. cholerae, and one is from a bacterium which, although classified serologically as V. cholerae O139, lacks the CTXφ bacteriophage and the ability to produce cholera toxin. We highlight fundamental genomic differences between these isolates, the V. cholerae O1 reference strain N16961, and the prototypical O139 strain MO10. These sequences are an important resource for the scientific community, and will improve greatly our ability to perform genomic analyses of non-O1 V. cholerae in the future. These genomes also offer new insights into the biology of a V. cholerae serogroup that, from a genomic perspective, is poorly understood.

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Wave 2 strains of atypical Vibrio cholerae El Tor caused the 2009-2011 cholera outbreak in Papua New Guinea

Author(s): Andrew R. Greenhill | Ankur Mutreja | Dieter Bulach | Matthew J. Belousoff | Marinjho H. Jonduo | Deirdre A. Collins | Monalisa P. Kas | Johanna Wapling | Torsten Seemann | Alice Lafana | Gordon Dougan | Mark V. Brown | Paul F. Horwood

Date of Publication: Mar 2019

Publication: Microbial Genomics

Summary/Abstract: Vibrio cholerae is the causative agent of cholera, a globally important human disease for at least 200 years. In 2009–2011, the first recorded cholera outbreak in Papua New Guinea (PNG) occurred. Genetic and phenotypic characterization of 21 isolates of V. cholerae was carried out, with whole-genome sequencing conducted on 2 representative isolates. The PNG outbreak was caused by an atypical El Tor strain harbouring a tandem repeat of the CTX prophage on chromosome II. Whole-genome sequence data, prophage structural analysis and the absence of the SXT integrative conjugative element was indicative that the PNG isolates were most closely related to strains previously isolated in South-East and East Asia with affiliations to global wave 2 strains. This finding suggests that the cholera outbreak in PNG was caused by an exotic (non-endemic) strain of V. cholerae that originated in South-East Asia.

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Genomic insights into the 2016–2017 cholera epidemic in Yemen

Author(s): François-Xavier Weill | Daryl Domman | Elisabeth Njamkepo | Abdullrahman A. Almesbahi | Mona Naji | Samar Saeed Nasher | Ankur Rakesh | Abdullah M. Assiri | Naresh Chand Sharma | Samuel Kariuki | Mohammad Reza Pourshafie | Jean Rauzier | Abdinasir Abubakar | Jane Y. Carter | Joseph F. Wamala | Caroline Seguin | Christiane Bouchier | Thérèse Malliavin | Bita Bakhshi | Hayder H. N. Abulmaali | Dhirendra Kumar | Samuel M. Njoroge | Mamunur Rahman Malik | John Kiiru | Francisco J. Luquero | Andrew S. Azman | Thandavarayan Ramamurthy | Nicholas R. Thomson | Marie-Laure Quilici

Date of Publication: 2019/01

Publication: Nature

Summary/Abstract: Yemen is currently experiencing, to our knowledge, the largest cholera epidemic in recent history. The first cases were declared in September 2016, and over 1.1 million cases and 2,300 deaths have since been reported. Here we investigate the phylogenetic relationships, pathogenesis and determinants of antimicrobial resistance by sequencing the genomes of Vibrio cholerae isolates from the epidemic in Yemen and recent isolates from neighbouring regions. These 116 genomic sequences were placed within the phylogenetic context of a global collection of 1,087 isolates of the seventh pandemic V. cholerae serogroups O1 and O139 biotype El Tor. We show that the isolates from Yemen that were collected during the two epidemiological waves of the epidemic—the first between 28 September 2016 and 23 April 2017 (25,839 suspected cases) and the second beginning on 24 April 2017 (more than 1 million suspected cases)—are V. cholerae serotype Ogawa isolates from a single sublineage of the seventh pandemic V. cholerae O1 El Tor (7PET) lineage. Using genomic approaches, we link the epidemic in Yemen to global radiations of pandemic V. cholerae and show that this sublineage originated from South Asia and that it caused outbreaks in East Africa before appearing in Yemen. Furthermore, we show that the isolates from Yemen are susceptible to several antibiotics that are commonly used to treat cholera and to polymyxin B, resistance to which is used as a marker of the El Tor biotype.

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Expanding dynamics of the virulence-related gene variations in the toxigenic Vibrio cholerae serogroup O1

Author(s): Zhenpeng Li | Bo Pang | Duochun Wang | Jie Li | Jialiang Xu | Yujie Fang | Xin Lu | Biao Kan

Date of Publication: 12/2019

Publication: BMC Genomics

Summary/Abstract: Toxigenic Vibrio cholerae serogroup O1 is the causative pathogen in the sixth and seventh cholera pandemics. Cholera toxin is the major virulent factor but other virulence and virulence-related factors play certain roles in the pathogenesis and survival in the host. Along with the evolution of the epidemic strains, the virulence-related genes also experience variation, gain and loss, and lead to genetic divergence in different strains. In this study, we analyzed the virulence-related gene profiles in the toxigenic serogroup O1 strains isolated from 1923 to 2015, the genomes of which were publicly available. The virulence-related genes of the V. cholerae O1 strains were annotated based on the Virulence Factors Database (VFDB). An average of 230.1 virulence-related genes per strain were identified; significant differences in the average numbers were found between the classical and El Tor biotypes, and increasing trends in the number of virulence-related genes along with the isolation years were observed in the El Tor biotype strains. A total of 176 homologs of virulence-related genes were found from these strains, of which 25 belonged to the core genes, suggesting their conservative and necessary roles in V. cholerae pathogenesis. We described the diversities of the homologs by defining gene sequence type, and illustrated its association with gene duplication; we found that gene duplication clearly increased the complexity of the gene sequence types in the core virulence-related genes. In addition, we provided virulence-related gene profiles whose genetic characteristic depend on the isolation years from the view of gene gain and loss, variation, gene duplication and gene sequence type number. Our study reveals the comprehensive variation dynamics of the virulence-related genes in toxigenic V. cholerae serogroup O1 during epidemics. The increasing trend for the virulence-related genes may suggest the evolutional advantage of strains by gaining virulence-related genes with diverse functional categories.

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Long-Read-Based Genome Sequences of Pandemic and Environmental Vibrio cholerae Strains

Author(s): Noémie Matthey | Natália C. Drebes Dörr | Melanie Blokesch

Date of Publication: 2018-12-13

Publication: Microbiology Resource Announcements

Summary/Abstract: The bacterium Vibrio cholerae exhibits two distinct lifestyles, one as an aquatic bacterium and the other as the etiological agent of the pandemic human disease cholera. Here, we report closed genome sequences of two seventh pan- demic V. cholerae O1 El Tor strains, A1552 and N16961, and the environmental strain Sa5Y.

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A Metagenomic Approach to Evaluating Surface Water Quality in Haiti

Author(s): Monika A. Roy | Jean M. Arnaud | Paul M. Jasmin | Steve Hamner | Nur A. Hasan | Rita R. Colwell | Timothy E. Ford

Date of Publication: 2018-10

Publication: International Journal of Environmental Research and Public Health

Summary/Abstract: The cholera epidemic that occurred in Haiti post-earthquake in 2010 has resulted in over 9000 deaths during the past eight years. Currently, morbidity and mortality rates for cholera have declined, but cholera cases still occur on a daily basis. One continuing issue is an inability to accurately predict and identify when cholera outbreaks might occur. To explore this surveillance gap, a metagenomic approach employing environmental samples was taken. In this study, surface water samples were collected at two time points from several sites near the original epicenter of the cholera outbreak in the Central Plateau of Haiti. These samples underwent whole genome sequencing and subsequent metagenomic analysis to characterize the microbial community of bacteria, fungi, protists, and viruses, and to identify antibiotic resistance and virulence associated genes. Replicates from sites were analyzed by principle components analysis, and distinct genomic profiles were obtained for each site. Cholera toxin converting phage was detected at one site, and Shiga toxin converting phages at several sites. Members of the Acinetobacter family were frequently detected in samples, including members implicated in waterborne diseases. These results indicate a metagenomic approach to evaluating water samples can be useful for source tracking and the surveillance of pathogens such as Vibrio cholerae over time, as well as for monitoring virulence factors such as cholera toxin.

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Defining endemic cholera at three levels of spatiotemporal resolution within Bangladesh

Author(s): Daryl Domman | Fahima Chowdhury | Ashraful I. Khan | Matthew J. Dorman | Ankur Mutreja | Muhammad Ikhtear Uddin | Anik Paul | Yasmin A. Begum | Richelle C. Charles | Stephen B. Calderwood | Taufiqur R. Bhuiyan | Jason B. Harris | Regina C. LaRocque | Edward T. Ryan | Firdausi Qadri | Nicholas R. Thomson

Date of Publication: 2018-7

Publication: Nature genetics

Summary/Abstract: While much focus is placed on cholera epidemics, the greatest burden occurs in settings where cholera is endemic, including areas of South Asia, Africa, and now Haiti. Dhaka, Bangladesh is a megacity that is hyper-endemic for cholera, and experiences two regular seasonal outbreaks of cholera each year. Despite this, a detailed understanding of the diversity of Vibrio cholerae strains circulating in this setting, and their relationships to annual outbreaks, has not yet been obtained. In this study, we performed whole-genome sequencing of V. cholerae across several levels of focus and scale, at the maximum possible resolution. We analyzed bacterial isolates to define cholera dynamics at multiple levels, ranging from infection within individuals, to disease dynamics at the household level, to regional and intercontinental cholera transmission. Our analyses provide a genomic framework for understanding cholera diversity and transmission in an endemic setting.

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Antibiotic resistance in Vibrio cholerae: Understanding the ecology of resistance genes and mechanisms

Author(s): Bhabatosh Das | Jyoti Verma | Pawan Kumar | Amit Ghosh | Thandavarayan Ramamurthy

Date of Publication: July 2, 2019

Publication: Vaccine

Summary/Abstract: The unique genetic makeup and remarkable competency of Vibrio cholerae are the key factors that help the cholera pathogen adapt rapidly to adverse environmental conditions and resist the detrimental effect of antimicrobial agents. In the last few decades, V. cholerae that causes acute watery diarrhoeal disease cholera has emerged as a notorious multidrug resistant enteric pathogen. Although chromosomal mutations can contribute to antimicrobial resistance (AMR), the frequent acquisition of extrachromosomal mobile genetic elements from closely/distantly related bacterial species are major players in V. cholerae drug resistance. Whole genome sequence analysis of clinical and environmental V. cholerae strains revealed that the genome of most of the recent isolates harbour integrating conjugative elements, plasmids, superintegron, transposable elements and insertion sequences, which are the key carriers of genetic traits encoding antimicrobial resistance function. Different antimicrobial resistance genes identified in V. cholerae can contribute in antibiotic resistance by facilitating one of the following three mechanisms; reduced permeability or active efflux of the antibiotics, (alteration of the antibiotic targets by introducing post-transcriptional/translational modifications and (hydrolysis or chemical modification of antibiotics. We present an overview of the present insights on the emergence and mechanisms of AMR in V. cholerae.

Source link
Whole genome sequence of Vibrio cholerae directly from dried spotted filter paper

Author(s): Angèle H. M. Bénard | Etienne Guenou | Maria Fookes | Jerome Ateudjieu | Watipaso Kasambara | Matthew Siever | Stanislas Rebaudet | Jacques Boncy | Paul Adrien | Renaud Piarroux | David A. Sack | Nicholas Thomson | Amanda K. Debes

Date of Publication: 2019-5-30

Publication: PLoS Neglected Tropical Diseases

Summary/Abstract: Cholera affects more than 4 million people globally every year; people predominantly living in poverty or in resource-constrained conditions including political crises or natural disasters. Cholera’s typical presentation is characterized by rapid onset of acute watery diarrhea and vomiting which can progress from watery stool to shock in as little as four hours. Laboratory conditions needed for culture confirmation and strain preservation are rarely to never present in these affected areas. In fact, many cholera endemic areas in Sub-Saharan African are so remote that even treatment response alone is often challenging. Here we present the genomic analysis of DNA extracted from dried filter paper, which is a low-cost, low-tech and sustainable method. Previously this method has facilitated cholera confirmation by PCR, but we demonstrate that this method is also suitable for whole genome sequencing and subsequent strain characterization by presenting the analysis of samples from an outbreak in a remote area of Cameroon. This method will facilitate the understanding of the molecular epidemiology in cholera-prone areas, which were previously too challenging to attempt. It also introduces a method that can be used on a broader scale for diarrheal disease surveillance, including providing a window into co-infection and microbiome analyses.

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

Author(s): Matthew J. Dorman | Leanne Kane | Daryl Domman | Jake D. Turnbull | Claire Cormie | Mohammed-Abbas Fazal | David A. Goulding | Julie E. Russell | Sarah Alexander | Nicholas R. Thomson

Date of Publication: 2019-4-10

Publication: Proceedings of the Royal Society B: Biological Sciences

Summary/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.

Source link
High quality reference genomes for toxigenic and non-toxigenic Vibrio cholerae serogroup O139

Author(s): Matthew J. Dorman | Daryl Domman | Muhammad Ikhtear Uddin | Salma Sharmin | Mokibul Hassan Afrad | Yasmin Ara Begum | Firdausi Qadri | Nicholas R. Thomson

Date of Publication: 2019-4-10

Publication: Scientific Reports

Summary/Abstract: Toxigenic Vibrio cholerae of the O139 serogroup have been responsible for several large cholera epidemics in South Asia, and continue to be of clinical and historical significance today. This serogroup was initially feared to represent a new, emerging V. cholerae clone that would lead to an eighth cholera pandemic. However, these concerns were ultimately unfounded. The majority of clinically relevant V. cholerae O139 isolates are closely related to serogroup O1, biotype El Tor V. cholerae, and comprise a single sublineage of the seventh pandemic El Tor lineage. Although related, these V. cholerae serogroups differ in several fundamental ways, in terms of their O-antigen, capsulation phenotype, and the genomic islands found on their chromosomes. Here, we present four complete, high-quality genomes for V. cholerae O139, obtained using long-read sequencing. Three of these sequences are from toxigenic V. cholerae, and one is from a bacterium which, although classified serologically as V. cholerae O139, lacks the CTXφ bacteriophage and the ability to produce cholera toxin. We highlight fundamental genomic differences between these isolates, the V. cholerae O1 reference strain N16961, and the prototypical O139 strain MO10. These sequences are an important resource for the scientific community, and will improve greatly our ability to perform genomic analyses of non-O1 V. cholerae in the future. These genomes also offer new insights into the biology of a V. cholerae serogroup that, from a genomic perspective, is poorly understood.

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