Genetic characteristics of Matlab variants of Vibrio cholerae O1 that are hybrids between classical and El Tor biotypes

Cholera rages in Africa and the Middle East: A narrative review on challenges and solutions

Background and Aim

Cholera is a life-threatening infectious disease that is still one of the most common acute watery diarrheal diseases in the world today. Acute diarrhea and severe dehydration brought on by cholera can cause hypovolemic shock, which can be fatal in minutes. Without competent clinical therapy, the rate of case fatality surpasses 50%. The purpose of this review was to highlight cholera challenges in Africa and the Middle East and explain the reasons for why this region is currently a fertile environment for cholera. We investigated cholera serology, epidemiology, and the geographical distribution of cholera in Africa and the Middle East in 2022 and 2023. We reviewed detection methods, such as rapid diagnostic tests (RDTs), and treatments, such as antibiotics and phage therapy. Finally, this review explored oral cholera vaccines (OCVs), and the vaccine shortage crisis.

Methods

We carried out a systematic search in multiple databases, including PubMed, Web of Science, Google Scholar, Scopus, MEDLINE, and Embase, for studies on cholera using the following keywords: ((Cholera) OR (Vibrio cholera) and (Coronavirus) OR (COVID-19) OR (SARS-CoV2) OR (The Middle East) OR (Africa)).

Results and Conclusions

Cholera outbreaks have increased dramatically, mainly in Africa and many Middle Eastern countries. The COVID-19 pandemic has reduced the attention devoted to cholera and disrupted diagnosis and treatment services, as well as vaccination initiatives. Most of the cholera cases in Africa and the Middle East were reported in Malawi and Syria, respectively, in 2022. RDTs are effective in the early detection of cholera epidemics, especially with limited advanced resources, which is the case in much of Africa. By offering both direct and indirect protection, expanding the use of OCV will significantly reduce the burden of current cholera outbreaks in Africa and the Middle East.

Emergence of multidrug resistant, ctx negative seventh pandemic Vibrio cholerae O1 El Tor sequence type (ST) 69 in coastal water of Kerala, India

Seventh pandemic Vibrio choleare O1 El Tor strain is responsible for the on-going pandemic outbreak of cholera globally. This strain evolved from non-pathogenic V. cholerae by acquiring seventh pandemic gene (VC 2346), pandemic Islands (VSP1 and VSP2), pathogenicity islands (VP1 and VP2) and CTX prophage region. The cholera toxin production is mainly attributed to the presence of ctx gene in these strains. However, several variants of this strain emerged as hybrid strains or atypical strains. The present study aimed to assess the aquatic environment of Cochin, India, over a period of 5 years for the emergence of multidrug resistant V. cholerae and its similarity with seventh pandemic strain. The continuous surveillance and monitoring resulted in the isolation of ctx negative, O1 positive V. cholerae isolate (VC6) from coastal water, Cochin, Kerala. The isolate possessed the biotype specific O1 El Tor tcpA gene and lacked other biotype specific ctx, zot, ace and rst genes. Whole genome analysis revealed the isolate belongs to pandemic sequence type (ST) 69 with the possession of pandemic VC2346 gene, pathogenic island VPI1, VPI2, and pandemic island VSP1 and VSP2. The isolate possessed several insertion sequences and the SXT/R391 family related Integrative Conjugative Elements (ICEs). In addition to this, the isolate genome carried virulence genes such as VgrG, mshA, ompT, toxR, ompU, rtxA, als, VasX, makA, and hlyA and antimicrobial resistance genes such as gyrA, dfrA1, strB, parE, sul2, parC, strA, VC1786ICE9-floR, and catB9. Moreover, the phylogenetic analysis suggests that the isolate genome is more closely related to seventh pandemic V. cholerae O1 N16961 strain. This study reports the first incidence of environmental ctx negative seventh pandemic V. choleare O1 El Tor isolate, globally and its presence in the aquatic system likely to induce toxicity in terms of public health point of view. The presence of this isolate in the aquatic environment warns the strict implementation of the epidemiological surveillance on the occurrence of emerging strains and the execution of flagship program for the judicious use of antibiotics in the aquatic ecosystem.

Polymyxin sensitivity/resistance cosmopolitan status, epidemiology and prevalence among O1/O139 and non-O1/non-O139 Vibrio cholerae: A meta-analysis

Resistance/sensitivity to polymyxin-B (PB) antibiotic has been employed as one among other epidemiologically relevant biotyping-scheme for Vibrio cholerae into Classical/El Tor biotypes. However, recent studies have revealed some pitfalls bordering on PB-sensitivity/resistance (PBR/S) necessitating study. Current study assesses the PBR/S cosmopolitan prevalence, epidemiology/distribution among O1/O139 and nonO1/nonO139 V. cholerae strains. Relevant databases (Web of Science, Scopus and PubMed) were searched to retrieve data from environmental and clinical samples employing the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). Random-effect-model (REM) and common-effect-model (CEM) of meta-analysis was performed to determine prevalence of PBR/S V. cholerae strains, describe the cosmopolitan epidemiological potentials and biotype relevance. Heterogeneity was determined by meta-regression and subgroup analyses. The pooled analyzed isolates from articles (7290), with sensitive and resistance are 2219 (30.44%) and 5028 (69.56%). Among these PB-sensitive strains, more than 1944 (26.67%) were O1 strains, 132 (1.81%) were nonO1 strains while mis-reported Classical biotype were 2080 (28.53) respectively indicating potential spread of variant/dual biotype. A significant PB-resistance was observed in the models (CEM = 0.66, 95% CI [0.65; 0.68], p-value = 0.001; REM = 0.83 [0.74; 0.90], p = 0.001) as both models had a high level of heterogeneity (I2 = 98.0%; d f = 33 2 = 1755.09 , Q p = 2.4932 ). Egger test (z = 5.4017, p < 0.0001) reveal publication bias by funnel plot asymmetry. The subgroup analysis for continents (Asia, Africa) and sources (acute diarrhea) revealed (98% CI (0.73; 0.93); 55% CI (0.20; 0.86)), and 92% CI (0.67; 0.98). The Epidemiological prevalence for El tor/variant/dual biotype showed 88% CI (0.78; 0.94) with O1 strains at 88% CI (0.78; 0.94). Such global prevalence, distribution/spread of phenotypes/genotypes necessitates updating the decades-long biotype classification scheme. An antibiotic stewardship in the post antibiotic era is suggestive/recommended. Also, there is need for holistic monitoring/evaluation of clinical/epidemiological relevance of the disseminating strains in endemic localities.

Antibiotic resistance and virulence genes profiling of Vibrio cholerae and Vibrio mimicus isolates from some seafood collected at the aquatic environment and wet markets in Eastern Cape Province, South Africa

The current study determines the density of Vibrio spp. and isolates V. cholerae and Vibrio mimicus from fish-anatomical-sites, prawn, crab and mussel samples recovered from fish markets, freshwater and brackish water. Virulence and antibiotic resistance profiling of isolates were carried out using standard molecular and microbiology techniques. Vibrio spp. was detected in more than 90% of samples [134/144] and its density was significantly more in fish than in other samples. Vibrio. cholerae and V. mimicus were isolated in at least one sample of each sample type with higher isolation frequency in fish samples. All the V. cholerae isolates belong to non-O1/non-O139 serogroup. One or more V. cholerae isolates exhibited intermediate or resistance against each of the eighteen panels of antibiotics used but 100% of the V. mimicus were susceptible to amikacin, gentamycin and chloramphenicol. Vibrio cholerae exhibited relatively high resistance against polymyxin, ampicillin and amoxicillin/clavulanate while V. mimicus isolates exhibited relatively high resistance against nitrofurantoin, ampicillin and polymixin. The multiple-antibiotic-resistance-index [MARI] for isolates ranges between 0 and 0.67 and 48% of the isolates have MARI that is >0.2 while 55% of the isolates exhibit MultiDrug Resistance Phenotypes. The percentage detection of acc, ant, drf18, sul1, mcr-1, blasvh, blaoxa, blatem, blaoxa48, gyrA, gyrB and parC resistance-associated genes were 2%, 9%, 14%, 7%, 2%, 25%, 7%, 2%, 2%, 32%, 25% and 27% respectively while that for virulence-associated genes in increasing other was ace [2%], tcp [11%], vpi [16%], ompU [34%], toxR [43%], rtxC [70%], rtxA [73%] and hyla [77%]. The study confirmed the potential of environmental non-O1/non-O139 V. cholerae and V. mimicus to cause cholera-like infection and other vibriosis which could be difficult to manage with commonly recommended antibiotics. Thus, regular monitoring of the environment to create necessary awareness for this kind of pathogens is important in the interest of public health.

Atypical and dual biotypes variant of virulent SA-NAG-Vibrio cholerae: an evidence of emerging/evolving patho-significant strain in municipal domestic water sources

Introduction and purpose

The recent cholera spread, new cases, and fatality continue to arouse concern in public health systems; however, interventions on control is at its peak yet statistics show continuous report. This study characterized atypical and patho-significant environmental Vibrio cholerae retrieved from ground/surface/domestic water in rural-urban-sub-urban locations of Amathole District municipality and Chris Hani District municipality, Eastern Cape Province, South Africa.

Methods

Domestic/surface water was sampled and 759 presumptive V. cholerae isolates were retrieved using standard microbiological methods. Virulence phenotypic test: toxin co-regulated pili (tcp), choleragen red, protease production, lecithinase production, and lipase test were conducted. Serotyping using polyvalent antisera (Bengal and Ogawa/Inaba/Hikojima) and molecular typing: 16SrRNA, OmpW, serogroup (Vc-O1/O139), biotype (tcpAClas/El Tor, HlyAClas/El Tor, rstRClas/El Tor, RS1, rtxA, rtxC), and virulence (ctxA, ctxB, zot, ace, cep, prt, toxR, hlyA) genes were targeted.

Result

Result of 16SrRNA typing confirmed 508 (66.9%) while OmpW detected/confirmed 61 (12.01%) V. cholerae strains. Phenotypic-biotyping scheme showed positive test to polymyxin B (68.9%), Voges proskauer (6.6%), and Bengal serology (11.5%). Whereas Vc-O1/O139 was negative, yet two of the isolates harbored the cholera toxin with a gene-type ctxB and hlyAClas: 2/61, revealing atypical/unusual/dual biotype phenotypic/genotypic features. Other potential atypical genotypes detected include rstR: 7/61, Cep: 15/61, ace: 20/61, hlyAElTor: 53/61, rtxA: 30/61, rtxC: 11/61, and prtV: 15/61 respectively.

Conclusion

Although additional patho-significant/virulent genotypes associated with epidemic/sporadic cholera cases were detected, an advanced, bioinformatics, and post-molecular evaluation is necessary. Such stride possesses potential to adequately minimize future cholera cases associated with dynamic/atypical environmental V. cholerae strains.

Epidemiological and pathogenic characteristics of Haitian variant V. cholerae circulating in India over a decade (2000-2018)

Vibrio cholerae, causative agent of the water-borne disease cholera still threatens a large proportion of world's population. The major biotypes of the pathogen are classical and El Tor. There have been recent reports of variant V. cholerae strains circulating around the world. In the present study, the epidemiological status of V. cholerae strains circulating in the country over a decade was assessed. Also, a comprehensive analysis of the difference in pathogenicity between the different biotypes of V. cholerae strains was evaluated both in-vitro and in-vivo. The amount of CT produced by different biotypes of V. cholerae strains were analyzed by GM₁ ELISA and the probable reasons for the difference in toxin production was discussed. MLST analysis grouped the isolates into a single Sequence Type (ST 69) whereas PFGE analysis clustered the isolates into ten different pulsotypes revealing molecular diversity. The circulating strains were identified to produce cholera toxin and CT mRNA intermediate to the classical and prototype El Tor strains. Also, the circulating strains were identified to possess four ToxR binding sequences. In-vivo pathogenicity analysis by rabbit ileal loop fluid accumulation assay revealed the Haitian variant strains to be more hyperemic than the prototype strains.

Characterization of Vibrio cholerae O1 isolates responsible for cholera outbreaks in Kenya between 1975 and 2017

Kenya is endemic for cholera with different waves of outbreaks having been documented since 1971. In recent years, new variants of Vibrio cholerae O1 have emerged and have replaced most of the traditional El Tor biotype globally. These strains also appear to have increased virulence, and it is important to describe and document their phenotypic and genotypic traits. This study characterized 146 V. cholerae O1 isolates from cholera outbreaks that occurred in Kenya between 1975 and 2017. Our study reports that the 1975-1984 strains had typical classical or El Tor biotype characters. New variants of V. cholerae O1 having traits of both classical and El Tor biotypes were observed from 2007 with all strains isolated between 2015 and 2017 being sensitive to polymyxin B and carrying both classical and El Tor type ctxB. All strains were resistant to Phage IV and harbored rstR, rtxC, hlyA, rtxA and tcpA genes specific for El Tor biotype indicating that the strains had an El Tor backbone. Pulsed field gel electrophoresis (PFGE) genotyping differentiated the isolates into 14 pulsotypes. The clustering also corresponded with the year of isolation signifying that the cholera outbreaks occurred as separate waves of different genetic fingerprints exhibiting different genotypic and phenotypic characteristics. The emergence and prevalence of V. cholerae O1 strains carrying El Tor type and classical type ctxB in Kenya are reported. These strains have replaced the typical El Tor biotype in Kenya and are potentially more virulent and easily transmitted within the population.

Tilapia (Oreochromis niloticus) as a Putative Reservoir Host for Survival and Transmission of Vibrio cholerae O1 Biotype El Tor in the Aquatic Environment

Studies have reported the occurrence of Vibrio cholerae in fish but little is known about the interaction between fish and toxigenic V. cholerae as opposed to phytoplankton, which are well-established aquatic reservoirs for V. cholerae. The present study determined the role of tilapia (Oreochromis niloticus) as a reservoir host for survival and transmission of V. cholerae in aquatic environments. Three experiments were performed with one repetition each, where O. niloticus (∼2 g) kept in beakers were inoculated with four V. cholerae strains (5 × 10⁷ cfu/mL). Firstly, infected tilapia were kept in stagnant water and fed live brine shrimp (Artemia salina) larvae daily. Secondly, infected tilapia were kept without feeding and water was changed every 24 h. Thirdly, infected tilapia were fed and water was renewed daily. Infected tilapia and non-infected controls were sacrificed on days 1, 2, 3, 7, and 14 post-inoculation and V. cholerae were enumerated in intestinal content and water. Another experiment assessed the transmission of V. cholerae from infected to non-infected tilapia. The study revealed that El Tor biotype V. cholerae O1 and V. cholerae non-O1 colonized tilapia intestines and persisted at stable concentrations during the second week of the experiment whereas the Classical biotype was undetectable after 1 week. In stagnant water with feeding, V. cholerae counts dropped to 10⁵ cfu/ml in water and from 10⁷ to 10⁴ cfu/intestine in fish after 14 days. When water was renewed, counts in water decreased from 10⁷ to 10³ cfu/ml and intestinal counts went from 10⁶ to 10² cfu/intestine regardless of feeding. All strains were transmitted from infected to naïve fish after 24 h of cohabitation. Tilapia like other fish may play an essential role in the survival and dissemination of V. cholerae O1 in aquatic environments, e.g., the seventh pandemic strains mostly. In this study, tilapia were exposed to high concentrations of V. cholerae to ensure initial uptake and follow-up studies with lower doses resembling natural concentrations of V. cholerae in the aquatic environment are needed to confirm our findings.

Laboratory Culturing Techniques and Maintenance of Vibrio cholerae

Cholera is a severe diarrheal disease caused by the consumption of food or water contaminated with the aquatic gram-negative bacterium Vibrio cholerae. Infected hosts will experience vomiting and severe watery diarrhea and if not treated properly will ultimately succumb to death by dehydration. Due to the global prevalence and severity of cholera, V. cholerae has been extensively studied in both environmental and laboratory settings. Herein, we describe proper V. cholerae maintenance, in addition to classical and El Tor biotype culturing in a laboratory setting.

Genotypic and Phenotypic Assays to Distinguish Vibrio cholerae Biotype

Vibrio cholerae is a motile gram-negative bacterium found in brackish water and the etiological agent of the fecal-oral disease cholera. Classical and El Tor are two main biotypes that make up the V. cholerae O1 serogroup, which each display unique genotypic and phenotypic characteristics that allow for reliable biotype characterization. While treatment for cholera is much the same despite the causative strain's biotype, such classification can be imperative for laboratory experiments and may have broader impacts in the biomedical field. In the early 2000s, clinical isolates were identified that contained genotypic and phenotypic traits from both biotypes. The newly identified hybrids, termed El Tor variants, have caused clinical and environmental isolate biotype identification to be more complicated than previous single-assay identification. Herein, we describe a series of PCR-based genetic screens (tcpA and ctxB) and phenotypic assays (polymyxin B resistance, citrate metabolism, proteolytic activity, hemolytic activity, motility, and Voges-Proskauer). Together, these assays are used for reliable biotype characterization of V. cholerae clinical (and environmental) isolates.

Comparative genomics of Vibrio cholerae El Tor strains isolated at epidemic complications in Siberia and at the Far East

The territory of Siberia and the Far East of Russia is classified as epidemically safe for cholera; however, in the 1970s and 1990s a number of infection importation cases and acute outbreaks associated with the cholera importation were reported. Here, we analyze genomes of four Vibrio cholerae El Tor strains isolated from humans during epidemic complications (imported cases, an outbreak) in the 1990s. The analyzed strains harbor the classical allele of the cholera toxin subunit B gene (ctxB1); thus, belong to genetically altered variants of the El Tor biotype. Analysis of the genomes revealed their high homology with the V. cholerae N16961 reference strain: 85-93 SNPs were identified in the core genome as compared to the reference. The determined features of SNPs in the CTX prophage made it possible to propose the presence of a new subtype - CTX-2a in two strains; the other two strains carried the prophage of CTX-3 type. Results of phylogenetic analysis based on SNP-typing demonstrated that two strains belonged to the second wave, and two - to the early third wave of cholera dissemination in the world. Phylogenetic reconstruction in combination with epidemiological data permitted to trace the origin of the strains and the way of their importation to the Russian Federation directly or through temporary cholera foci.

Laboratory Techniques Used to Maintain and Differentiate Biotypes of Vibrio cholerae Clinical and Environmental Isolates

The aquatic Gram-negative bacterium Vibrio cholerae is the etiological agent of the infectious gastrointestinal disease cholera. Due to the global prevalence and severity of this disease, V. cholerae has been extensively studied in both environmental and laboratory settings, requiring proper maintenance and culturing techniques. Classical and El Tor are two main biotypes that compose the V. cholerae O1 serogroup, each displaying unique genotypic and phenotypic characteristics that provide reliable mechanisms for biotype characterization, and require distinct virulence inducing culturing conditions. Regardless of the biotype of the causative strain for any given infection or outbreak, the standard treatment for the disease involves rehydration therapy supplemented with a regimen of antibiotics. However, biotype classification may be necessary for laboratory studies and may have broader impacts in the biomedical field. In the early 2000's clinical isolates were identified which exhibit genotypic and phenotypic traits from both classical and El Tor biotypes. The newly identified hybrids, termed El Tor variants, have caused clinical and environmental isolate biotype identification to become more complex than previous traditional single assay identification protocols. In addition to describing V. cholerae general maintenance and culturing techniques, this manuscript describes a series of gene specific (ctxB and tcpA) PCR-based genetic screens and phenotypic assays (polymyxin B resistance, citrate metabolism, proteolytic activity, hemolytic activity, motility, and glucose metabolism via Voges-Proskauer assay) collectively used to characterize and/or distinguish between classical and El Tor biotypes. Together, these assays provide an efficient systematic approach to be used as an alternative, or in addition, to costly, labor-intensive experiments in the characterization of V. cholerae clinical (and environmental) isolates.

Identification of Atypical El TorV. cholerae O1 Ogawa Hosting SXT Element in Senegal, Africa

Vibrio cholerae O1 is the causative agent of cholera with classical and El Tor, two well-established biotypes. In last 20 years, hybrid strains of classical and El Tor and variant El Tor which carry classical ctxB have emerged worldwide. In 2004-2005, Senegal experienced major cholera epidemic with a number of cases totalling more than 31719 with approximately 458 fatal outcomes (CFR, 1.44%). In this retrospective study, fifty isolates out of a total of 403 V. cholerae biotype El Tor serovar Ogawa isolates from all areas in Senegal during the 2004-2005 cholera outbreak were randomly selected. Isolates were characterized using phenotypic and genotypic methods. The analysis of antibiotic resistance patterns revealed the predominance of the S-Su-TCY-Tsu phenotype (90% of isolates). The molecular characterization of antibiotic resistance revealed the presence of the SXT element, a self-transmissible chromosomally integrating element in all isolates. Most of V. cholerae isolates had an intact virulence cassette (86%) (ctx, zot, ace genes). All isolates tested gave amplification with primers for classical CT, and 10/50 (20%) of isolates carried classical and El Tor ctxB. The study reveals the presence of atypical V. cholerae O1 El Tor during cholera outbreak in Senegal in 2004-2005.

Vibrio cholerae O1 with Reduced Susceptibility to Ciprofloxacin and Azithromycin Isolated from a Rural Coastal Area of Bangladesh

Cholera outbreaks occur each year in the remote coastal areas of Bangladesh and epidemiological surveillance and routine monitoring of cholera in these areas is challenging. In this study, a total of 97 Vibrio cholerae O1 isolates from Mathbaria, Bangladesh, collected during 2010 and 2014 were analyzed for phenotypic and genotypic traits, including antimicrobial susceptibility. Of the 97 isolates, 95 possessed CTX-phage mediated genes, ctxA, ace, and zot, and two lacked the cholera toxin gene, ctxA. Also both CTX⁺ and CTX⁻V. cholerae O1 isolated in this study carried rtxC, tcpA^ET, and hlyA. The classical cholera toxin gene, ctxB1, was detected in 87 isolates, while eight had ctxB7. Of 95 CTX⁺V. cholerae O1, 90 contained rstR^ET and 5 had rstR^CL. All isolates, except two, contained SXT related integrase intSXT. Resistance to penicillin, streptomycin, nalidixic acid, sulfamethoxazole-trimethoprim, erythromycin, and tetracycline varied between the years of study period. Most importantly, 93% of the V. cholerae O1 were multidrug resistant. Six different resistance profiles were observed, with resistance to streptomycin, nalidixic acid, tetracycline, and sulfamethoxazole-trimethoprim predominant every year. Ciprofloxacin and azithromycin MIC were 0.003–0.75 and 0.19–2.00 μg/ml, respectively, indicating reduced susceptibility to these antibiotics. Sixteen of the V. cholerae O1 isolates showed higher MIC for azithromycin (≥0.5 μg/ml) and were further examined for 10 macrolide resistance genes, erm(A), erm(B), erm(C), ere(A), ere(B), mph(A), mph(B), mph(D), mef(A), and msr(A) with none testing positive for the macrolide resistance genes.

Characterization and Genetic Variation of Vibrio cholerae Isolated from Clinical and Environmental Sources in Thailand

Cholera is still an important public health problem in several countries, including Thailand. In this study, a collection of clinical and environmental V. cholerae serogroup O1, O139, and non-O1/non-O139 strains originating from Thailand (1983 to 2013) was characterized to determine phenotypic and genotypic traits and to investigate the genetic relatedness. Using a combination of conventional methods and whole genome sequencing (WGS), 78 V. cholerae strains were identified. WGS was used to determine the serogroup, biotype, virulence, mobile genetic elements, and antimicrobial resistance genes using online bioinformatics tools. In addition, phenotypic antimicrobial resistance was determined by the minimal inhibitory concentration (MIC) test. The 78 V. cholerae strains belonged to the following serogroups O1: (n = 44), O139 (n = 16) and non-O1/non-O139 (n = 18). Interestingly, we found that the typical El Tor O1 strains were the major cause of clinical cholera during 1983–2000 with two Classical O1 strains detected in 2000. In 2004–2010, the El Tor variant strains revealed genotypes of the Classical biotype possessing either only ctxB or both ctxB and rstR while they harbored tcpA of the El Tor biotype. Thirty O1 and eleven O139 clinical strains carried CTXϕ (Cholera toxin) and tcpA as well four different pathogenic islands (PAIs). Beside non-O1/non-O139, the O1 environmental strains also presented chxA and Type Three Secretion System (TTSS). The in silico MultiLocus Sequence Typing (MLST) discriminated the O1 and O139 clinical strains from other serogroups and environmental strains. ST69 was dominant in the clinical strains belonging to the 7^th pandemic clone. Non-O1/non-O139 and environmental strains showed various novel STs indicating genetic variation. Multidrug-resistant (MDR) strains were observed and conferred resistance to ampicillin, azithromycin, nalidixic acid, sulfamethoxazole, tetracycline, and trimethoprim and harboured variants of the SXT elements.

For the first time since 1986, the presence of V. cholerae O1 Classical was reported causing cholera outbreaks in Thailand. In addition, we found that V. cholerae O1 El Tor variant and O139 were pre-dominating the pathogenic strains in Thailand. Using WGS and bioinformatic tools to analyze both historical and contemporary V. cholerae circulating in Thailand provided a more detailed understanding of the V. cholerae epidemiology, which ultimately could be applied for control measures and management of cholera in Thailand.

Single Nucleotide Polymorphisms in Regulator-Encoding Genes Have an Additive Effect on Virulence Gene Expression in a Vibrio cholerae Clinical Isolate

Cholera, an infectious disease of the small intestine caused by the aquatic bacterium Vibrio cholerae, often results in vomiting and acute watery diarrhea. If left untreated or if the response is too slow, the symptoms can quickly lead to extreme dehydration and ultimately death of the patient. Recent anecdotal evidence of cholera patients suffering from increasingly severe symptoms and of disease progression at a much higher rate than previously observed has emerged. As recent cholera outbreaks caused by increasingly virulent strains have resulted in higher mortality rates, the need to investigate the mechanism(s) allowing this observed increased virulence is apparent. The significance of our research is in identifying the mechanism for increased virulence capabilities, which will allow the development of a model that will greatly enhance our understanding of cholera disease and V. cholerae pathogenesis, leading to broader biomedical impacts, as cholera serves as a model for other enteric diarrheal diseases.

Vibrio cholerae is the etiological agent of the infectious disease cholera, which is characterized by vomiting and severe watery diarrhea. Recently, V. cholerae clinical isolates have demonstrated increased virulence capabilities, causing more severe symptoms with a much higher rate of disease progression than previously observed. We have identified single nucleotide polymorphisms (SNPs) in four virulence-regulatory genes (hapR, hns, luxO, and vieA) of a hypervirulent V. cholerae clinical isolate, MQ1795. Herein, all SNPs and SNP combinations of interest were introduced into the prototypical El Tor reference strain N16961, and the effects on the production of numerous virulence-related factors, including cholera toxin (CT), the toxin-coregulated pilus (TCP), and ToxT, were analyzed. Our data show that triple-SNP (hapR hns luxO and hns luxO vieA) and quadruple-SNP combinations produced the greatest increases in CT, TCP, and ToxT production. The hns and hns luxO SNP combinations were sufficient for increased TCP and ToxT production. Notably, the hns luxO vieA triple-SNP combination strain produced TCP and ToxT levels similar to those of MQ1795. Certain SNP combinations (hapR and hapR vieA) had the opposite effect on CT, TCP, and ToxT expression. Interestingly, the hns vieA double-SNP combination strain increased TCP production while decreasing CT production. Our findings suggest that SNPs identified in the four regulatory genes, in various combinations, are associated with increased virulence capabilities observed in V. cholerae clinical isolates. These studies provide insight into the evolution of highly virulent strains.

IMPORTANCE Cholera, an infectious disease of the small intestine caused by the aquatic bacterium Vibrio cholerae, often results in vomiting and acute watery diarrhea. If left untreated or if the response is too slow, the symptoms can quickly lead to extreme dehydration and ultimately death of the patient. Recent anecdotal evidence of cholera patients suffering from increasingly severe symptoms and of disease progression at a much higher rate than previously observed has emerged. As recent cholera outbreaks caused by increasingly virulent strains have resulted in higher mortality rates, the need to investigate the mechanism(s) allowing this observed increased virulence is apparent. The significance of our research is in identifying the mechanism for increased virulence capabilities, which will allow the development of a model that will greatly enhance our understanding of cholera disease and V. cholerae pathogenesis, leading to broader biomedical impacts, as cholera serves as a model for other enteric diarrheal diseases.

Phenotypic and genotypic characteristics of Vibrio cholerae O1 isolated from the Sierra Leone cholera outbreak in 2012

BACKGROUND

This study describes phenotypic, genotypic and antibiotic susceptibility patterns of the strains isolated from the 2012 Sierra Leone cholera outbreak. Rectal swabs were collected from patients and cultured for Vibrio cholerae O1.

METHODS

The isolates were subjected to multiplex PCR, mismatch amplification mutation assay (MAMA) PCR, pulsed field gel electrophoresis (PFGE), and antibiotic sensitivity tests using disk diffusion and minimum inhibitory concentration (MIC) E-test following standard procedures.

RESULTS

Out of 17 rectal swabs tested, 15 yielded V. cholerae O1 biotype El Tor, serotype Ogawa. All the strains belonged to 'altered' variants as MAMA PCR result showed the presence of classical cholera toxin B. PFGE result revealed four pulse types. Using antibiotic disk diffusion, all the isolates were resistant to erythromycin, chloramphenicol, furazolidone, and trimethoprim/sulfamethoxazole (SXT) except SL1 which was sensitive to chloramphenicol and SXT. All the isolates were sensitive to nalidixic acid, tetracycline, doxycycline, azithromycin, and ciprofloxacin except SL2 which was resistant to nalidixic acid. However, variable sensitivity patterns were observed for kanamycin. The ranges of MIC were 0.125-0.50 mg/l, 0.003-0.023 mg/l and 0.38-0.75 mg/l for azithromycin, ciprofloxacin and tetracycline, respectively.

CONCLUSIONS

This study demonstrates that altered variants of V. cholerae O1 of four clonal types were responsible for the 2012 outbreak of cholera in Sierra Leone.

Dynamics in genome evolution of Vibrio cholerae

Vibrio cholerae, the etiological agent of the acute secretary diarrheal disease cholera, is still a major public health concern in developing countries. In former centuries cholera was a permanent threat even to the highly developed populations of Europe, North America, and the northern part of Asia. Extensive studies on the cholera bug over more than a century have made significant advances in our understanding of the disease and ways of treating patients. V. cholerae has more than 200 serogroups, but only few serogroups have caused disease on a worldwide scale. Until the present, the evolutionary relationship of these pandemic causing serogroups was not clear. In the last decades, we have witnessed a shift involving genetically and phenotypically varied pandemic clones of V. cholerae in Asia and Africa. The exponential knowledge on the genome of several representatives V. cholerae strains has been used to identify and analyze the key determinants for rapid evolution of cholera pathogen. Recent comparative genomic studies have identified the presence of various integrative mobile genetic elements (IMGEs) in V. cholerae genome, which can be used as a marker of differentiation of all seventh pandemic clones with very similar core genome. This review attempts to bring together some of the important researches in recent times that have contributed towards understanding the genetics, epidemiology and evolution of toxigenic V. cholerae strains.

Genomic science in understanding cholera outbreaks and evolution of Vibrio cholerae as a human pathogen

Modern genomic and bioinformatic approaches have been applied to interrogate the V. cholerae genome, the role of genomic elements in cholera disease, and the origin, relatedness, and dissemination of epidemic strains. A universal attribute of choleragenic strains includes a repertoire of pathogenicity islands and virulence genes, namely the CTXϕ prophage and Toxin Co-regulated Pilus (TCP) in addition to other virulent genetic elements including those referred to as Seventh Pandemic Islands. During the last decade, the advent of Next Generation Sequencing (NGS) has provided highly resolved and often complete genomic sequences of epidemic isolates in addition to both clinical and environmental strains isolated from geographically unconnected regions. Genomic comparisons of these strains, as was completed during and following the Haitian outbreak in 2010, reveals that most epidemic strains appear closely related, regardless of region of origin. Non-O1 clinical or environmental strains may also possess some virulence islands, but phylogenic analysis of the core genome suggests they are more diverse and distantly related than those isolated during epidemics. Like Haiti, genomic studies that examine both the Vibrio core and pan-genome in addition to Single Nucleotide Polymorphisms (SNPs) conclude that a number of epidemics are caused by strains that closely resemble those in Asia, and often appear to originate there and then spread globally. The accumulation of SNPs in the epidemic strains over time can then be applied to better understand the evolution of the V. cholerae genome as an etiological agent.

Zebrafish as a natural host model for Vibrio cholerae colonization and transmission

The human diarrheal disease cholera is caused by the aquatic bacterium Vibrio cholerae. V. cholerae in the environment is associated with several varieties of aquatic life, including insect egg masses, shellfish, and vertebrate fish. Here we describe a novel animal model for V. cholerae, the zebrafish. Pandemic V. cholerae strains specifically colonize the zebrafish intestinal tract after exposure in water with no manipulation of the animal required. Colonization occurs in close contact with the intestinal epithelium and mimics colonization observed in mammals. Zebrafish that are colonized by V. cholerae transmit the bacteria to naive fish, which then become colonized. Striking differences in colonization between V. cholerae classical and El Tor biotypes were apparent. The zebrafish natural habitat in Asia heavily overlaps areas where cholera is endemic, suggesting that zebrafish and V. cholerae evolved in close contact with each other. Thus, the zebrafish provides a natural host model for the study of V. cholerae colonization, transmission, and environmental survival.

Large outbreak of cholera caused by El Tor variant Vibrio cholerae O1 in the eastern coast of Odisha, India during 2009

A large outbreak of cholera reported during April-July 2009 in the Kendrapada district of Odisha, India was investigated. Forty-one rectal swabs and 41 water samples, collected from diarrhoeal patients and from different villages were bacteriologically analysed for the isolation of bacterial enteriopathogens, antibiogram profile and detection of various toxic genes. The bacteriological analysis of rectal swabs and environmental water samples revealed the presence of V. cholerae O1 Ogawa biotype El Tor. The V. cholerae strains were resistant to ciprofloxacin, co-trimoxazole, chloramphenicol, streptomycin, ampicillin, furazolidone and nalidixic acid. The multiplex polymerase chain reaction (PCR) assay on V. cholerae strains revealed the presence of ctxA and tcpA genes. The mismatch amplification of mutation assay (MAMA) PCR on clinical and environmental isolates of V. cholerae revealed that the strains were El Tor biotype, which harboured the ctxB gene of the classical strain. The random amplified polymorphic DNA PCR analysis and pulsed-field gel electrophoresis results indicated that the V. cholerae isolates belonged to the same clone. This investigation gives a warning that the El Tor variant of V. cholerae has spread to the coastal district causing a large outbreak that requires close monitoring and surveillance on diarrhoeal outbreaks in Odisha.

Molecular diversity of CTX prophage in Vibrio cholerae

AIMS

The objective of this study was to investigate the molecular diversity of CTX genetic element within toxigenic Vibrio cholerae genomes and to determine the genetic diversity of V. cholerae population collected in a 6-year period (2004-2009) in Iran.

METHODS AND RESULTS

The results of mismatch amplification mutation assay (MAMA)-PCR and sequencing showed cytosine nucleotide in positions 203 and 115 in all 50 El Tor V. cholerae strains, which is the same as classical ctxB sequence. One strain yielded amplicons with both El Tor and classical biotype primers in MAMA-PCR indicative of presence of two copies of CTX phages with different genotypes (rstR(ET) ctxB(class) and rstR(ET) ctxB(ET)) integrated within the genome of this isolate, which suggested the integration of two different CTX phages at different occasions or point mutation in one copy of CTX. Sequencing and PCR analysis indicated the presence of hybrid CTX genotype (rstR(ET) ctx(class)) in 70.6% of the isolates; however, only El Tor RS1 phage has been integrated in flanking to the CTX phages with different genotypes.

CONCLUSIONS

Enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR) and ribosomal gene spacer-PCR (RS-PCR) showed a relatively homogenous population in different years. Our findings indicate that sequence analysis of RS and ctxB regions has more discriminative power than restriction-based methods.

SIGNIFICANCE AND IMPACT OF THE STUDY

Investigating the molecular diversity of CTX prophage among V. cholerae strains helps to establish a new valuable database of genetic information about isolates, which is of great importance for epidemiologic studies in Iran and other countries encountering cholera epidemics.

Vibrio cholerae O1 biotype El Tor strains isolated in 1992 from Varanasi, India harboured El Tor CTXΦ and classical ctxB on the chromosome-I and classical CTXΦ and classical ctxB on the chromosome-II

In this study, we report the presence of the El Tor CTXΦ and classical CTXΦ in Vibrio cholerae O1 strains isolated from Varanasi, India. Polymerase chain reaction, DNA sequencing and restriction fragment length polymorphism revealed that, although ctx-positive strains isolated after 1990 contain CTXΦ harbouring El Tor type of rstR and classical ctxB, strains isolated before 1990 contain El Tor type of rstR and El Tor ctxB. Two V. cholerae O1 strains (VC104 and VC106) represent an altered/hybrid strain containing the RS1 element followed by CTXΦ prophage harbouring El Tor type rstR and classical ctxB on the chromosome-I and RS2 element followed by second copy of CTXΦ prophage harbouring classical type rstR and classical ctxB on the chromosome-II. This is the first report of occurrence of El Tor CTXΦ harbouring classical ctxB and classical CTXΦ harbouring classical ctxB in chromosome-I and -II, respectively in diarrhoeal isolates of V. cholerae O1 El Tor strains from Varanasi, India, and that had been isolated in 1992.

Characterization of Vibrio cholerae O1 El Tor biotype variant clinical isolates from Bangladesh and Haiti, including a molecular genetic analysis of virulence genes

Vibrio cholerae serogroup O1, the causative agent of the diarrheal disease cholera, is divided into two biotypes: classical and El Tor. Both biotypes produce the major virulence factors toxin-coregulated pilus (TCP) and cholera toxin (CT). Although possessing genotypic and phenotypic differences, El Tor biotype strains displaying classical biotype traits have been reported and subsequently were dubbed El Tor variants. Of particular interest are reports of El Tor variants that produce various levels of CT, including levels typical of classical biotype strains. Here, we report the characterization of 10 clinical isolates from the International Centre for Diarrhoeal Disease Research, Bangladesh, and a representative strain from the 2010 Haiti cholera outbreak. We observed that all 11 strains produced increased CT (2- to 10-fold) compared to that of wild-type El Tor strains under in vitro inducing conditions, but they possessed various TcpA and ToxT expression profiles. Particularly, El Tor variant MQ1795, which produced the highest level of CT and very high levels of TcpA and ToxT, demonstrated hypervirulence compared to the virulence of El Tor wild-type strains in the infant mouse cholera model. Additional genotypic and phenotypic tests were conducted to characterize the variants, including an assessment of biotype-distinguishing characteristics. Notably, the sequencing of ctxB in some El Tor variants revealed two copies of classical ctxB, one per chromosome, contrary to previous reports that located ctxAB only on the large chromosome of El Tor biotype strains.

Clonal transmission, dual peak, and off-season cholera in Bangladesh

Vibrio cholerae is an estuarine bacterium associated with a single peak of cholera (March–May) in coastal villages of Bangladesh. For an unknown reason, however, cholera occurs in a unique dual peak (March–May and September–November) pattern in the city of Dhaka that is bordered by a heavily polluted freshwater river system and flood embankment. In August 2007, extreme flooding was accompanied by an unusually severe diarrhea outbreak in Dhaka that resulted in a record high illness. This study was aimed to understand the unusual outbreak and if it was related to the circulation of a new V. cholerae clone. Nineteen V. cholerae isolated during the peak of the 2007 outbreak were subjected to extensive phenotypic and molecular analyses, including multi-locus genetic screening by polymerase chain reaction (PCR), sequence-typing of the ctxB gene, and pulsed-field gel electrophoresis (PFGE). Factors associated with the unusual incidence of cholera were determined and analysis of the disease severity was done. Overall, microbiological and molecular data confirmed that the hypervirulent V. cholerae was O1 biotype El Tor (ET) that possessed cholera toxin (CT) of the classical biotype. The PFGE (NotI) and dendrogram clustering confirmed that the strains were clonal and related to the pre-2007 variant ET from Dhaka and Matlab and resembled one of two distinct clones of the variant ET confirmed to be present in the estuarine ecosystem of Bangladesh. Results of the analyses of both diarrheal case data for three consecutive years (2006–2008) and regional hydroclimatology over three decades (1980–2009) clearly indicate that the pattern of cholera occurring in Dhaka, and not seen at other endemic sites, was associated with flood waters transmitting the infectious clone circulating via the fecal-oral route during and between the dual seasonal cholera peaks in Dhaka. Circular river systems and flood embankment likely facilitate transmission of infectious V. cholerae throughout the year that leads to both sudden and off-season outbreaks in the densely populated urban ecosystem of Dhaka. Clonal recycling of hybrid El Tor with increasing virulence in a changing climate and in a region with a growing urban population represents a serious public health concern for Bangladesh.

Genetic Screens and Biochemical Assays to Characterize Vibrio cholerae O1 Biotypes: Classical and El Tor

Vibrio cholerae serogroup O1 has two biotypes, classical and El Tor, the latter of which has displaced the prior and has been the causative agent for the ongoing seventh pandemic. However, reports since 2001 have identified clinical isolates of El Tor that have classical O1 biotype genetic and phenotypic characteristics. These El Tor variants have been emerging in clinical settings with increased frequency, including the 2010 cholera outbreak in Haiti. The emergence of El Tor variants warrants the proper and timely identification of clinical (or environmental) isolates' biotype. This unit describes some quick and simple genetic screens and phenotypic assays (biochemical characterization), to be performed simultaneously, commonly used to distinguish biotype and initiate characterization of any clinical (or environmental) isolates of Vibrio cholerae O1.

Molecular characterization reveals involvement of altered El Tor biotype Vibrio cholerae O1 strains in cholera outbreak at Hyderabad, India

Thirty-four Vibrio cholerae isolates collected from a cholera outbreak in Hyderabad, South India were found to belong to serogroup Ol biotype El Tor serotype Ogawa. The genotype of all the isolates was confirmed by PCR assays. All the isolates were found PCR positive for ctxAB, ompW, rflOl, rtxC, and tcpA genes. All the isolates but one harboured rstR ( El Tor ) allele. However, one isolate carried both rstR ( EL Tor ) as well as rstR ( Classical ) alleles. Cholera toxin (ctxB) genotyping of the isolates confirmed the presence of altered cholera toxin B of classical biotype in all the isolates. All the isolates except VCH35 harboured an RS1-CTX prophage array on the large chromosome. The isolate VCH35 contained a tandem repeat of classical CTX prophage on the small chromosome. The clonal relationship among the V. cholerae isolates as carried out by enterobacterial repetitive intergenic consensus sequences PCR, BOX PCR and randomly amplified polymorphic DNA, uniformly showed a genetic relationship among the outbreak isolates. The results of this study suggest that altered El Tor biotype V. cholerae with the classical cholera toxin gene are involved in cholera outbreaks in India.

Molecular evidence of cholera outbreak caused by a toxigenic Vibrio cholerae O1 El tor variant strain in Kelantan, Malaysia

A total of 20 Vibrio cholerae isolates were recovered for investigation from a cholera outbreak in Kelantan, Malaysia, that occurred between November and December 2009. All isolates were biochemically characterized as V. cholerae serogroup O1 Ogawa of the El Tor biotype. They were found to be resistant to multiple antibiotics, including tetracycline, erythromycin, sulfamethoxazole-trimethoprim, streptomycin, penicillin G, and polymyxin B, with 35% of the isolates being resistant to ampicillin. All isolates were sensitive to ciprofloxacin, norfloxacin, chloramphenicol, gentamicin, and kanamycin. Multiplex PCR analysis confirmed the biochemical identification and revealed the presence of virulence genes, viz., ace, zot, and ctxA, in all of the isolates. Interestingly, the sequencing of the ctxB gene showed that the outbreak strain harbored the classical cholera toxin gene and therefore belongs to the newly assigned El Tor variant biotype. Clonal analysis by pulsed-field gel electrophoresis demonstrated that a single clone of a V. cholerae strain was responsible for this outbreak. Thus, we present the first molecular evidence that the toxigenic V. cholerae O1 El Tor variant has invaded Malaysia, highlighting the need for continuous monitoring to facilitate early interventions against any potential epidemic by this biotype.

Cholera between 1991 and 1997 in Mexico was associated with infection by classical, El Tor, and El Tor variants of Vibrio cholerae

Vibrio cholerae O1 biotype El Tor (ET), the cause of the current 7th pandemic, has recently been replaced in Asia and Africa by an altered ET biotype possessing cholera toxin (CTX) of the classical (CL) biotype that originally caused the first six pandemics before becoming extinct in the 1980s. Until recently, the ET prototype was the biotype circulating in Peru; a detailed understanding of the evolutionary trend of V. cholerae causing endemic cholera in Latin America is lacking. The present retrospective microbiological, molecular, and phylogenetic study of V. cholerae isolates recovered in Mexico (n = 91; 1983 to 1997) shows the existence of the pre-1991 CL biotype and the ET and CL biotypes together with the altered ET biotype in both epidemic and endemic cholera between 1991 and 1997. According to sero- and biotyping data, the altered ET, which has shown predominance in Mexico since 1991, emerged locally from ET and CL progenitors that were found coexisting until 1997. In Latin America, ET and CL variants shared a variable number of phenotypic markers, while the altered ET strains had genes encoding the CL CTX (CTX(CL)) prophage, ctxB(CL) and rstR(CL), in addition to resident rstR(ET), as the underlying regional signature. The distinct regional fingerprints for ET in Mexico and Peru and their divergence from ET in Asia and Africa, as confirmed by subclustering patterns in a pulsed-field gel electrophoresis (NotI)-based dendrogram, suggest that the Mexico epidemic in 1991 may have been a local event and not an extension of the epidemics occurring in Asia and South America. Finally, the CL biotype reservoir in Mexico is unprecedented and must have contributed to the changing epidemiology of global cholera in ways that need to be understood.

Effect of storage and sodium chloride on excision of CTXPhi or pre-CTXPhi and CTXPhi from Vibrio cholerae O139 strains

We examined the effect of storage and sodium chloride on excision of CTXPhi or pre-CTXPhi and CTXPhi from Vibrio cholerae O139 strains. We found that one strain of V. cholerae O139 VO146P showed loss of the complete phage array, and other strain VO170P showed partial loss of the phage array giving rise to altered strains designated as VO146N and VO170N. Results of PCR and RFLP analysis revealed that both strains (VO146P and VO170P) possessed a single copy of pre-CTX(ET)Phi and two copies of CTXPhi comprising CTX(Class)Phi and CTX(Calc)Phi arranged in tandem, and integrated in the large chromosome. The presence of classical ctxB was detected in CTX(Calc)Phi of both V. cholerae O139 strains. Nucleotide sequencing of three housekeeping genes showed no difference between parent and altered strains of V. cholerae O139.

Multilocus variable-number tandem repeat analysis of Vibrio cholerae O1 El Tor strains harbouring classical toxin B

Atypical Vibrio cholerae O1 strains - hybrid strains (strains that cannot be classified either as El Tor or classical biotype) and altered strains (El Tor biotype strains that produce classical cholera toxin) - are currently prevalent in Asia and Africa. A total of 74 hybrid and altered strains that harboured classical cholera toxin were investigated by multilocus variable-number tandem repeat analysis (MLVA). The results showed that the hybrid/altered strains could be categorized into three groups and that they were distant from the El Tor strain responsible for the seventh cholera pandemic. Hybrid/altered strains with a tandem repeat of the classical CTX prophage on the small chromosome were divided into two MLVA groups (group I: Mozambique/Bangladesh group; group III: Vietnam group), and altered strains with the RS1-CTX prophage containing the El Tor type rstR and classical ctxB on the large chromosome were placed in two MLVA groups (group II: India/Bangladesh group; group III: India/Vietnam group).

Classification of hybrid and altered Vibrio cholerae strains by CTX prophage and RS1 element structure

Analysis of the CTX prophage and RS1 element in hybrid and altered Vibrio cholera O1 strains showed two classifiable groups. Group I strains contain a tandem repeat of classical CTX prophage on the small chromosome. Strains in this group either contain no element(s) or an additional CTX prophage or RS1 element(s) on the large chromosome. Group II strains harbor RS1 and CTX prophage, which has an E1 Tor type rstR and classical ctxB on the large chromosome.

Sequence analysis of Vibrio cholerae orfU and zot from pre-CTXΦ and CTXΦ reveals multiple origin of pre-CTXΦ and CTXΦ

A multiplex PCR was developed to detect pre-CTXΦ and CTXΦ in Vibrio cholerae. A total of 115 V. cholerae were tested, of which 42 V. cholerae O1 and 18 V. cholerae O139 contained CTXΦ. Six V. cholerae O139 contained only pre-CTXΦ and three V. cholerae O1 and 23 V. cholerae O139 contained both pre-CTXΦ and CTXΦ. None of the V. cholerae non-O1 and non-O139 that were tested had pre-CTXΦ or CTXΦ. Results of Restriction Fragment Length Polymorphism (RFLP) analysis revealed the V. cholerae isolates possessed single or multiple copies of pre-CTXΦ and CTXΦ, always proceeded by a tandemly arranged RS1 element. Comparative nucleotide sequence analyses of the core region genes, orfU and zot, of 15 V. cholerae showed pre-CTX(ET) Φ and CTX(ET) Φ lineage with V. cholerae El Tor and pre-CTX(Class) Φ, pre-CTX(Calc) Φ, and CTX(Calc) Φ with classical V. cholerae O1 and O139. Two distinct types of ctxB were detected in V. cholerae O139. Multi-locus Sequence Typing (MLST) of seven V. cholerae housekeeping genes indicated clonal origin, irrespective of the presence of pre-CTXΦ and/or CTXΦ.

Molecular characterisation of Vibrio cholerae O1 strains carrying an SXT/R391-like element from cholera outbreaks in Kenya: 1994-2007

BACKGROUND

Over the last decade, cholera outbreaks in parts of Kenya have become common. Although a number of recent studies describe the epidemiology of cholera in Kenya, there is paucity of information concerning the diversity and occurrence of mobile genetic elements in Vibrio cholerae strains implicated in these outbreaks. A total of 65 Vibrio cholerae O1 El Tor serotype Inaba isolated between 1994 and 2007 from various outbreaks in Kenya were investigated for mobile genetic elements including integrons, transposons, the integrating conjugative elements (ICEs), conjugative plasmids and for their genotypic relatedness.

RESULTS

All the strains were haemolytic on 5% sheep blood and positive for the Vibrio cholerae El Tor-specific haemolysin toxin gene (hylA) by PCR. They all contained strB, sulII, floR and the dfrA1 genes encoding resistance to streptomycin, sulfamethoxazole, chloramphenicol and trimethoprim respectively. These genes, together with an ICE belonging to the SXT/R391 family were transferable to the rifampicin-resistant E. coli C600 en bloc. All the strains were negative for integron class 1, 2 and 3 and for transposase gene of transposon Tn7 but were positive for integron class 4 and the trpM gene of transposon Tn21. No plasmids were isolated from any of the 65 strains. All the strains were also positive for all V. cholera El Tor pathogenic genes except the NAG- specific heat-stable toxin (st) gene. None of the strains were positive for virulence genes associated with the V. cholerae classical biotype. All the strains were positive for El Tor-specific CTXphi bacteriophage rstrR repressor gene (CTXETPhi) but negative for the Classical, Calcutta, and the Environmental repressor types. Pulse Field Gel Electrophoresis (PFGE) showed that regardless of the year of isolation, all the strains bearing the SXT element were clonally related.

CONCLUSIONS

This study demonstrates that the V. cholerae O1 strains carrying an SXT/R391-like element implicated in recent cholera outbreaks in Kenya has not changed significantly between 1994 and 2007 and are clonally related.

Evolution of new variants of Vibrio cholerae O1

Vibrio cholerae typically contains a prophage that carries the genes encoding the cholera toxin, which is responsible for the major clinical symptoms of the disease. In recent years, new pathogenic variants of V. cholerae have emerged and spread throughout many Asian and African countries. These variants display a mixture of phenotypic and genotypic traits from the two main biotypes (known as 'classical' and 'El Tor'), suggesting that they are genetic hybrids. Classical and El Tor biotypes have been the most epidemiologically successful cholera strains during the past century, and it is believed that the new variants (which we call here 'atypical El Tor') are likely to develop successfully in a manner similar to these biotypes. Here, we describe recent advances in our understanding of the epidemiology and evolution of the atypical El Tor strains.

Peruvian Vibrio cholerae O1 El Tor strains possess a distinct region in the Vibrio seventh pandemic island-II that differentiates them from the prototype seventh pandemic El Tor strains

A collection of environmental and clinical strains of Vibrio cholerae O1 isolated from the beginning of the Latin American epidemic of cholera in 1991 to 2003 from multiple locations in Peru were characterized and compared with V. cholerae O1 El Tor strains of the seventh pandemic from the rest of the world (Asia, Africa, Australia and Europe) using a multilocus virulence gene profiling strategy and DNA sequencing. Peruvian strains differed from El Tor strains from the rest of the world by the failure of PCR to amplify genes VC0512, VC0513, VC0514 and VC0515 in the Vibrio seventh pandemic island-II (VSP-II) gene cluster. Sequencing of the VSP-II gene cluster and its flanking regions in one Peruvian strain (PERU-130) confirmed the PCR results, indicating that the Peruvian strain had low DNA homology (46.6 %) compared to the reference strain N16961 within the VSP-II region encompassing genes VC0511 to VC0515. Based on these differences in VSP-II, and based on the overall similarity between the pulsotypes of the Peruvian strains and the El Tor reference strain N16961, we concluded that the Peruvian, Eurasian and African strains belonged to the same clonal complex, and that the Peruvian strains represented variants that had independently evolved for a relatively short time. Since these ORFs in VSP-II of Peruvian strains are unique and conserved, they could form the basis for tracking the origin of the Peruvian strains and therefore of the Latin American pandemic.

Cholera outbreaks caused by an altered Vibrio cholerae O1 El Tor biotype strain producing classical cholera toxin B in Vietnam in 2007 to 2008

Vibrio cholerae O1 isolates collected during cholera outbreaks occurring from late 2007 to early 2008 in northern Vietnam were revealed to represent an altered strain containing the RS1 element followed by a CTX prophage harboring El Tor type rstR and classical ctxB on the large chromosome.

Multilocus genetic analysis reveals that the Australian strains of Vibrio cholerae O1 are similar to the pre-seventh pandemic strains of the El Tor biotype

Episodes of cholera stemming from indigenous Vibrio cholerae strains in Australia are mainly associated with environmental sources. In the present study, 10 V. cholerae O1 strains of Australian origin were characterized. All of the strains were serogroup O1 and their conventional phenotypic traits categorized them as belonging to the El Tor biotype. Genetic screening of 12 genomic regions that are associated with virulence in V. cholerae showed variable results. Analysis of the ctxAB gene showed that the Australian environmental reservoir contains both toxigenic and non-toxigenic V. cholerae strains. DNA sequencing revealed that all of the toxigenic V. cholerae strains examined were of ctxB genotype 2. Whole genome PFGE analysis revealed that the environmental toxigenic V. cholerae O1 strains were more diverse than the non-toxigenic environmental O1 strains, and the absence of genes that make up the Vibrio seventh pandemic island-I and -II in all of the strains indicates their pre-seventh pandemic ancestry.

Vibrio cholerae O1 clinical strains isolated in 1992 in Kolkata with progenitor traits of the 2004 Mozambique variant

Retrospective analysis led to the detection of two Vibrio cholerae variant O1 strains (VC51 and VC53), which were isolated in 1992 in Kolkata from clinical cases, with identical traits to 2004 Mozambique variant O1 strains. The Mozambique O1 strains that caused a huge outbreak in 2004 have been shown to have phenotypic traits of both classical and El Tor biotypes, and thereby have been reported as variant. Our study demonstrated that two O1 strains isolated in Kolkata during 1992 were of the El Tor background as evidenced by polymyxin B (50 U ml−1) resistance, positivity in Voges–Proskauer reactions and sensitivity to biotype-specific vibrio phages. With the features of classical CTX prophage, localization in the small chromosome, and an absence of RS1 and pTLC, both Mozambique and Kolkata strains appeared to be identical. Furthermore, two Kolkata strains exhibited an identical ribotype to that of the Mozambique variant, displaying ribotype pattern RI that had been assigned to Kolkata V. cholerae O1 strains isolated on or before 1992. NotI pulsotype analysis indicated that these 1992 Kolkata strains along with the Mozambique variant O1 belonged to very closely related clones. Considering the chronological events, and the typical identity at the phenotypic and the genotypic level between the two O1 strains isolated during 1992 from Kolkata and during 2004 from Mozambique, we propose that some of the 1992 Kolkata O1 strains might have acted as progenitors for Mozambique variant O1 strains.

Development and validation of a mismatch amplification mutation PCR assay to monitor the dissemination of an emerging variant of Vibrio cholerae O1 biotype El Tor

A mismatch amplification mutation PCR assay was developed and validated for rapid detection of the biotype specific cholera toxin B subunit of V. cholerae O1. This assay will enable easy monitoring of the spread of a new emerging variant of the El Tor biotype of V. cholerae O1.