RESUMO
UNLABELLED: Phylodynamic analysis of genome-wide single-nucleotide polymorphism (SNP) data is a powerful tool to investigate underlying evolutionary processes of bacterial epidemics. The method was applied to investigate a collection of 65 clinical and environmental isolates of Vibrio cholerae from Haiti collected between 2010 and 2012. Characterization of isolates recovered from environmental samples identified a total of four toxigenic V. cholerae O1 isolates, four non-O1/O139 isolates, and a novel nontoxigenic V. cholerae O1 isolate with the classical tcpA gene. Phylogenies of strains were inferred from genome-wide SNPs using coalescent-based demographic models within a Bayesian framework. A close phylogenetic relationship between clinical and environmental toxigenic V. cholerae O1 strains was observed. As cholera spread throughout Haiti between October 2010 and August 2012, the population size initially increased and then fluctuated over time. Selection analysis along internal branches of the phylogeny showed a steady accumulation of synonymous substitutions and a progressive increase of nonsynonymous substitutions over time, suggesting diversification likely was driven by positive selection. Short-term accumulation of nonsynonymous substitutions driven by selection may have significant implications for virulence, transmission dynamics, and even vaccine efficacy. IMPORTANCE: Cholera, a dehydrating diarrheal disease caused by toxigenic strains of the bacterium Vibrio cholerae, emerged in 2010 in Haiti, a country where there were no available records on cholera over the past 100 years. While devastating in terms of morbidity and mortality, the outbreak provided a unique opportunity to study the evolutionary dynamics of V. cholerae and its environmental presence. The present study expands on previous work and provides an in-depth phylodynamic analysis inferred from genome-wide single nucleotide polymorphisms of clinical and environmental strains from dispersed geographic settings in Haiti over a 2-year period. Our results indicate that even during such a short time scale, V. cholerae in Haiti has undergone evolution and diversification driven by positive selection, which may have implications for understanding the global clinical and epidemiological patterns of the disease. Furthermore, the continued presence of the epidemic strain in Haitian aquatic environments has implications for transmission.
Assuntos
Cólera/epidemiologia , Cólera/microbiologia , Microbiologia Ambiental , Variação Genética , Seleção Genética , Vibrio cholerae O139/classificação , Vibrio cholerae O1/classificação , DNA Bacteriano/química , DNA Bacteriano/genética , Evolução Molecular , Haiti/epidemiologia , Mutação de Sentido Incorreto , Mutação Puntual , Polimorfismo de Nucleotídeo Único , Análise de Sequência de DNA , Vibrio cholerae O1/genética , Vibrio cholerae O1/isolamento & purificação , Vibrio cholerae O139/genética , Vibrio cholerae O139/isolamento & purificaçãoRESUMO
Vibrio cholerae O139 Bengal emerged as a second aetiologic agent of cholera in South Asia in late 1992. This new serogroup arose from a Vibrio cholerae O1 strain by deletion of the chromosomal region encoding O1 specificity and acquisition of a novel 35-kb region encoding the O139 specificity. Previous studies indicated significant phenotypic and genotypic changes in O139 isolates over the years since its first appearance. This prompted us to study possible polymorphism in the 35-kb novel region encoding the O139 specificity. A total of 17 V. cholerae O139 isolates originating from different countries and years in South Asia and China, and a single unrelated V. cholerae O139 isolate from Argentina were studied. The 35-kb chromosomal region was amplified as two fragments of 12 and 23 kb in an extended PCR from all isolates. These amplicons were then treated separately with seven different restriction enzymes and separated by agarose gel electrophoresis. The South Asian and Chinese isolates gave identical patterns for the same enzymes, but different patterns for different enzymes, thus exhibiting no polymorphism in the 35-kb region. However, the Argentine isolate gave distinct patterns for most of the enzymes confirming its different origin. This data indicated that the portion of the chromosome encoding the O139 antigen specificity is highly conserved. As found in previous studies, the early O139 isolates were resistant to trimethoprim-sulfamethoxazole (TMP-SMX) and vibriostatic compound, O/129, and CAMP- haemolysin positive. The isolates of later years diverged exhibiting different patterns by pulsed-field gel electrophoresis (PFGE), and becoming susceptible to TMP-SMX and O/129, and CAMP-haemolysin negative.