Genetic variation of Vibrio cholerae during outbreaks, Bangladesh, 2010-2011

The Viable but Non-Culturable (VBNC) State in Vibrio Species: Why Studying the VBNC State Now Is More Exciting than Ever

During periods that are not conducive for growth or when facing stressful conditions, Vibrios enter a dormant state called the Viable But Non-Culturable (VBNC) state. In this chapter, I will analyse the role of the VBNC state in Vibrio species survival and pathogenesis and the molecular mechanisms regulating this complex phenomenon. I will emphasise some of the novel findings that make studying the VBNC state now more exciting than ever and its significance in the epidemiology of these pathogens and critical role in food safety.

Epidemiological and molecular forensics of cholera recurrence in Haiti

Cholera has affected Haiti with damping waves of outbreaks since October 2010. However, mechanisms behind disease persistence during lull periods remain poorly understood. By mid 2014, cholera transmission seemed to only persist in the northern part of Haiti. Meanwhile, cholera appeared nearly extinct in the capital, Port-au-Prince, where it eventually exploded in September 2014. This study aimed to determine whether this outbreak was caused by local undetected cases or by re-importation of the disease from the north. Applying an integrated approach between November 2013 and November 2014, we assessed the temporal and spatial dynamics of cholera using routine surveillance data and performed population genetics analyses of 178 Vibrio cholerae O1 clinical isolates. The results suggest that the northern part of the country exhibited a persisting metapopulation pattern with roaming oligoclonal outbreaks that could not be effectively controlled. Conversely, undetected and unaddressed autochthonous low-grade transmission persisted in the Port-au-Prince area, which may have been the source of the acute outbreak in late-2014. Cholera genotyping is a simple but powerful tool to adapt control strategies based on epidemic specificities. In Haiti, these data have already yielded significant progress in cholera surveillance, which is a key component of the strategy to eventually eliminate cholera.

Vibrio cholerae genomic diversity within and between patients

Cholera is a severe, water-borne diarrhoeal disease caused by toxin-producing strains of the bacterium Vibrio cholerae. Comparative genomics has revealed 'waves' of cholera transmission and evolution, in which clones are successively replaced over decades and centuries. However, the extent of V. cholerae genetic diversity within an epidemic or even within an individual patient is poorly understood. Here, we characterized V. cholerae genomic diversity at a micro-epidemiological level within and between individual patients from Bangladesh and Haiti. To capture within-patient diversity, we isolated multiple (8 to 20) V. cholerae colonies from each of eight patients, sequenced their genomes and identified point mutations and gene gain/loss events. We found limited but detectable diversity at the level of point mutations within hosts (zero to three single nucleotide variants within each patient), and comparatively higher gene content variation within hosts (at least one gain/loss event per patient, and up to 103 events in one patient). Much of the gene content variation appeared to be due to gain and loss of phage and plasmids within the V. cholerae population, with occasional exchanges between V. cholerae and other members of the gut microbiota. We also show that certain intra-host variants have phenotypic consequences. For example, the acquisition of a Bacteroides plasmid and non-synonymous mutations in a sensor histidine kinase gene both reduced biofilm formation, an important trait for environmental survival. Together, our results show that V. cholerae is measurably evolving within patients, with possible implications for disease outcomes and transmission dynamics.

Comparative genomics of Vibrio cholerae O1 isolated from cholera patients in Bangladesh

Whole genome sequencing was utilized to investigate the genomic profile of Vibrio cholerae O1 strains, isolated from symptomatic patients in a low-income urban area of Dhaka, Bangladesh. Comparative genomics using bioinformatics tools were applied to identify major virulence factors, biotype and antimicrobial resistance genes in three V. cholerae O1 strains (VC-1, 2 and 3) isolated from two case patients. A phylogenetic SNP (single nucleotide polymorphism)-based analysis was conducted to infer the relatedness to V. cholerae O1 strains isolated elsewhere. The V. cholerae strains were the El Tor variant carrying ctxB1 (standard classical genotype). SNP-based global phylogeny revealed that the three isolates were strictly clonal and the closest neighbouring genomes were epidemic clones of V. cholerae O1 isolated in 2010 from cholera patients in Pakistan. All strains harboured the integrase gene of the SXT element (int_SXT ), antimicrobial resistance genes for aminoglycosides, phenicol, sulphonamide and trimethoprim except VC-1 that lacked sulphonamide resistance genes. The multilocus sequence typing (MLST) revealed that the strains belonged to sequence type, ST69. The study provides knowledge on current genetic traits of clinical V. cholerae O1 circulating in urban household clusters of Bangladesh which may help in predicting emergence of new pandemic strains in Bangladesh.

SIGNIFICANCE AND IMPACT OF THE STUDY

Vibrio cholerae has frequently experienced genetic changes with rapid evolution of pandemic clones in the Ganges Delta region. Whole genome sequencing can reveal genetic information of current pathogenic V. cholerae in Bangladesh which includes cefotaxime genotypes, virulence factors, altered antimicrobial resistance pattern as well as mobile genetic element compared to global pandemic strains. This study data could be used in planning future surveillance strategies in Ganges Delta region by informing new epidemiology of current outbreak strains.

A prospective cohort study comparing household contact and water Vibrio cholerae isolates in households of cholera patients in rural Bangladesh

Background

Household contacts of cholera patients are at a 100 times higher risk of developing cholera than the general population. The objective of this study was to examine the incidence of V. cholerae infections among household contacts of cholera patients in a rural setting in Bangladesh, to identify risk factors for V. cholerae infections among this population, and to investigate transmission pathways of V. cholerae using multilocus variable-number tandem-repeat analysis (MLVA).

Methodology/Principal findings

Stool from household contacts, source water and stored water samples were collected from cholera patient households on Day 1, 3, 5, and 7 after the presentation of the index patient at a health facility. Two hundred thirty clinical and water V. cholerae isolates were analyzed by MLVA. Thirty seven percent of households had at least one household contact with a V. cholerae infection. Thirteen percent of households had V. cholerae in their water source, and 27% had V. cholerae in stored household drinking water. Household contacts with V. cholerae in their water source had a significantly higher odds of symptomatic cholera (Odds Ratio (OR): 5.49, 95% Confidence Interval (CI): 1.07, 28.08). Contacts consuming street vended food had a significantly higher odds of a V. cholerae infection (OR: 9.45, 95% CI: 2.14, 41.72). Older age was significantly associated with a lower odds of a V. cholerae infection (OR: 0.96, 95% CI: 0.93, 0.99). Households with both water and clinical V. cholerae-positive samples all had isolates that were closely related by MLVA.

Conclusions/Significance

These findings emphasize the need for interventions targeting water treatment and food hygiene to reduce V. cholerae infections.

Household members of cholera patients are at a 100 times higher risk of developing cholera infections than the general population. This risk is highest during the seven days after the cholera patient presents at a health facility. In this study we investigated the rate of cholera transmission within cholera patient households, identified risk factors for household cholera transmission, and performed genetic characterization of cholera strains collected. Stool was collected from patients, their household members, and from water sources and stored water during the seven days after the cholera patient presented at the health facility. A total of 230 human and water V. cholerae strains were collected and analyzed. Thirty seven percent of households had at least one household member with a V. cholerae infection. Thirteen percent of households had V. cholerae in their water source, and 27% had V. cholerae in stored drinking water. A water source with V. cholerae, consuming street vended food, and younger age were risk factors for cholera infections for household members of cholera patients. All strains from within households with water and human samples were closely related. These results demonstrate the importance of interventions focusing on water treatment and food hygiene for prevention of cholera.

Genetic relatedness of Vibrio cholerae isolates within and between households during outbreaks in Dhaka, Bangladesh

Background

Household contacts of cholera patients have a 100 times higher risk of developing a cholera infection than the general population. To compare the genetic relatedness of clinical and water source Vibrio cholerae isolates from cholera patients’ households across three outbreaks, we analyzed these isolates using whole-genome-sequencing (WGS) and multilocus variable-number tandem-repeat analysis (MLVA).

Results

The WGS analyses revealed that 80% of households had source water isolates that were more closely related to clinical isolates from the same household than to any other isolates. While in another 20% of households an isolate from a person was more closely related to clinical isolates from another household than to source water isolates from their own household. The mean pairwise differences in single nucleotide-variant (SNV) counts for isolates from the same household were significantly lower than those for different households (2.4 vs. 7.7 p < 0.0001), and isolates from the same outbreak had significantly fewer mean pairwise differences compared to isolates from different outbreaks (mean: 6.2 vs. 8.0, p < 0.0001). Based on MLVA in outbreak 1, we observed that the majority of households had clinical isolates with MLVA genotypes related to other clinical isolates and unrelated to water source isolates from the same household. While in outbreak 3, there were different MLVA genotypes between households, however within the majority of households, the clinical and water source isolates had the same MLVA genotypes. The beginning of outbreak 2 resembled outbreak 1 and the latter part resembled outbreak 3. We validated our use of MLVA by comparing it to WGS. Isolates with the identical MLVA genotype had significantly fewer mean pairwise SNV differences than those isolates with different MLVA genotypes (mean: 4.8 vs. 7.7, p < 0.0001). Furthermore, consistent with WGS results, the number of pairwise differences in the five MLVA loci for isolates within the same household was significantly lower than isolates from different households (mean: 1.6 vs. 3.0, p < 0.0001).

Conclusion

These results suggest that transmission patterns for cholera are a combination of person-to-person and water-to-person cholera transmission with the proportions of the two modes varying within and between outbreaks.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4254-9) contains supplementary material, which is available to authorized users.

Minimal genetic change in Vibrio cholerae in Mozambique over time: Multilocus variable number tandem repeat analysis and whole genome sequencing

Although cholera is a major public health concern in Mozambique, its transmission patterns remain unknown. We surveyed the genetic relatedness of 75 Vibrio cholerae isolates from patients at Manhiça District Hospital between 2002-2012 and 3 isolates from river using multilocus variable-number tandem-repeat analysis (MLVA) and whole genome sequencing (WGS). MLVA revealed 22 genotypes in two clonal complexes and four unrelated genotypes. WGS revealed i) the presence of recombination, ii) 67 isolates descended monophyletically from a single source connected to Wave 3 of the Seventh Pandemic, and iii) four clinical isolates lacking the cholera toxin gene. This Wave 3 strain persisted for at least eight years in either an environmental reservoir or circulating within the human population. Our data raises important questions related to where these isolates persist and how identical isolates can be collected years apart despite our understanding of high change rate of MLVA loci and the V. cholerae molecular clock.

Genetic Characterization of Vibrio cholerae O1 isolates from outbreaks between 2011 and 2015 in Tanzania

Background

Cholera outbreaks have occurred in Tanzania since 1974. To date, the genetic epidemiology of these outbreaks has not been assessed.

Methods

96 Vibrio cholerae O1 isolates from five regions were characterized, and their genetic relatedness assessed using multi-locus variable-number tandem-repeat analysis (MLVA) and whole genome sequencing (WGS).

Results

Of the 48 MLVA genotypes observed, 3 were genetically unrelated to any others, while the remaining 45 genotypes separated into three MLVA clonal complexes (CCs) - each comprised of genotypes differing by a single allelic change. In Kigoma, two separate outbreaks, 4 months apart (January and May, 2015), were each caused by genetically distinct strains by MLVA and WGS. Remarkably, one MLVA CC contained isolates from both the May outbreak and ones from the 2011/2012 outbreak in Dar-es-Salaam. However, WGS revealed the isolates from the two outbreaks to be distinct clades. The outbreak that started in August 2015 in Dar-es-Salaam and spread to Morogoro, Singida and Mara was comprised of a single MLVA CC and WGS clade. Isolates from within an outbreak were closely related differing at fewer than 5 nucleotides. All isolates were part of the 3^rd wave of the 7^th pandemic and were found in four clades related to isolates from Kenya and Asia.

Conclusions

We conclude that genetically related V. cholerae cluster in outbreaks, and distinct strains circulate simultaneously.

Electronic supplementary material

The online version of this article (doi:10.1186/s12879-017-2252-9) contains supplementary material, which is available to authorized users.

Comparison of inferred relatedness based on multilocus variable-number tandem-repeat analysis and whole genome sequencing of Vibrio cholerae O1

Vibrio cholerae causes cholera, a severe diarrheal disease. Understanding the local genetic diversity and transmission of V. cholerae will improve our ability to control cholera. Vibrio cholerae isolates clustered in genetically related groups (clonal complexes, CC) by multilocus variable tandem-repeat analysis (MLVA) were compared by whole genome sequencing (WGS). Isolates in CC1 had been isolated from two geographical locations. Isolates in a second genetically distinct group, CC2, were isolated only at one location. Using WGS, CC1 isolates from both locations revealed, on average, 43.8 nucleotide differences, while those strains comprising CC2 averaged 19.7 differences. Strains from both MLVA-CCs had an average difference of 106.6. Thus, isolates comprising CC1 were more closely related (P < 10(-6)) to each other than to isolates in CC2. Within a MLVA-CC, after removing all paralogs, alternative alleles were found in all possible combinations on separate chromosomes indicative of recombination within the core genome. Including recombination did not affect the distinctiveness of the MLVA-CCs when measured by WGS. We found that WGS generally reflected the same genetic relatedness of isolates as MLVA, indicating that isolates from the same MLVA-CC shared a more recent common ancestor than isolates from the same location that clustered in a distinct MLVA-CC.

Evaluation in Cameroon of a Novel, Simplified Methodology to Assist Molecular Microbiological Analysis of V. cholerae in Resource-Limited Settings

Background

Vibrio cholerae is endemic in South Asia and Africa where outbreaks of cholera occur widely and are particularly associated with poverty and poor sanitation. Knowledge of the genetic diversity of toxigenic V. cholerae isolates, particularly in Africa, remains scarce. The constraints in improving this understanding is not only the lack of regular cholera disease surveillance, but also the lack of laboratory capabilities in endemic countries to preserve, store and ship isolates in a timely manner. We evaluated the use of simplified sample preservation methods for molecular characterization using multi-locus variable-number tandem-repeat analysis (MLVA) for differentiation of Vibrio cholerae genotypes.

Methods and Findings

Forty-seven V. cholerae isolates and 18 enriched clinical specimens (e.g. stool specimens after enrichment in broth) from cholera outbreaks in Cameroon were preserved on Whatman filter paper for DNA extraction. The samples were collected from two geographically distinct outbreaks in the Far North of Cameroon (FNC) in June 2014 and October 2014. In addition, a convenience sample of 14 isolates from the Philippines and 8 from Mozambique were analyzed. All 87 DNAs were successfully analyzed including 16 paired samples, one a cultured isolate and the other the enriched specimen from which the isolate was collected. Genotypic results were identical between 15 enriched specimens and their culture isolates and the other pair differed at single locus. Two closely related, but distinct clonal complexes were identified among the Cameroonian specimens from 2014.

Conclusions

Collecting V. cholerae using simplified laboratory methods in remote and low-resource settings allows for subsequent advanced molecular characterization of V. cholerae O1. These simplified DNA preservation methods identify V. cholerae and make possible timely information regarding the genetic diversity of V. cholerae; our results set the stage for continued molecular epidemiological research to better understand the transmission and dissemination of V. cholerae in Africa and elsewhere worldwide.

Cholera, caused by the bacterium Vibrio cholerae, causes an estimated 3–5 million cases every year and more than 100,000 deaths. The highest disease burden is reported from Africa, however, the epidemic potential and transmission patterns among circulating strains is scarcely understood. The challenges of disease surveillance are constrained by the costs associated with laboratory confirmation and sample preservation. To improve the ability to identify the cholera disease burden, to subsequently understand the molecular epidemiology of circulating cholera strains, and to elucidate transmission patterns, we applied simplified collection methodologies to facilitate timely molecular characterization of V. cholerae isolates from Cameroon, Mozambique and the Philippines. Enriched specimens as well as cultured isolates were examined, demonstrating that enriched specimens provide sufficient material for genetic analysis. The results of the genetic analyses did not suggest significant genetic diversity within two distinct outbreaks in Cameroon. The study detected a possible relationship between isolates present in Cameroon and two isolates from Mozambique, two geographically distant nations in Africa. Whole genome sequencing can test whether this hypothesis is correct. Our findings set the stage for surveillance and molecular characterization in these areas to elucidate more fully the relationship and disease transmission patterns.

Molecular tools in understanding the evolution of Vibrio cholerae

Vibrio cholerae, the etiological agent of cholera, has been a scourge for centuries. Cholera remains a serious health threat for developing countries and has been responsible for millions of deaths globally over the past 200 years. Identification of V. cholerae has been accomplished using a variety of methods, ranging from phenotypic strategies to DNA based molecular typing and currently whole genomic approaches. This array of methods has been adopted in epidemiological investigations, either singly or in the aggregate, and more recently for evolutionary analyses of V. cholerae. Because the new technologies have been developed at an ever increasing pace, this review of the range of fingerprinting strategies, their relative advantages and limitations, and cholera case studies was undertaken. The task was challenging, considering the vast amount of the information available. To assist the study, key references representative of several areas of research are provided with the intent to provide readers with a comprehensive view of recent advances in the molecular epidemiology of V. cholerae. Suggestions for ways to obviate many of the current limitations of typing techniques are also provided. In summary, a comparative report has been prepared that includes the range from traditional typing to whole genomic strategies.

A metalloprotease secreted by the type II secretion system links Vibrio cholerae with collagen

Vibrio cholerae is autochthonous to various aquatic niches and is the etiological agent of the life-threatening diarrheal disease cholera. The persistence of V. cholerae in natural habitats is a crucial factor in the epidemiology of cholera. In contrast to the well-studied V. cholerae-chitin connection, scarce information is available about the factors employed by the bacteria for the interaction with collagens. Collagens might serve as biologically relevant substrates, because they are the most abundant protein constituents of metazoan tissues and V. cholerae has been identified in association with invertebrate and vertebrate marine animals, as well as in a benthic zone of the ocean where organic matter, including collagens, accumulates. Here, we describe the characterization of the V. cholerae putative collagenase, VchC, encoded by open reading frame VC1650 and belonging to the subfamily M9A peptidases. Our studies demonstrate that VchC is an extracellular collagenase degrading native type I collagen of fish and mammalian origin. Alteration of the predicted catalytic residues coordinating zinc ions completely abolished the protein enzymatic activity but did not affect the translocation of the protease by the type II secretion pathway into the extracellular milieu. We also show that the protease undergoes a maturation process with the aid of a secreted factor(s). Finally, we propose that V. cholerae is a collagenovorous bacterium, as it is able to utilize collagen as a sole nutrient source. This study initiates new lines of investigations aiming to uncover the structural and functional components of the V. cholerae collagen utilization program.

Circulation and transmission of clones of Vibrio cholerae during cholera outbreaks

Cholera is still a major public health problem. The underlying bacterial pathogen Vibrio cholerae (V. cholerae) is evolving and some of its mutations have set the stage for outbreaks. After V. cholerae acquired the mobile elements VSP I & II, the El Tor pandemic began and spread across the tropics. The replacement of the O1 serotype encoding genes with the O139 encoding genes triggered an outbreak that swept across the Indian subcontinent. The sxt element generated a third selective sweep and most recently a fourth sweep was associated with the exchange of the El Tor ctx allele for a classical ctx allele in the El Tor background. In Kenya, variants of this fourth selective sweep have differentiated and become endemic residing in and emerging from environmental reservoirs. On a local level, studies in Bangladesh have revealed that outbreaks may arise from a nonrandom subset of the genetic lineages in the environment and as the population of the pathogen expands, many novel mutations may be found increasing the amount of genetic variation, a phenomenon known as a founder flush. In Haiti, after the initial invasion and expansion of V. cholerae in 2010, a second outbreak occurred in the winter of 2011-2012 driven by natural selection of specific mutations.