Phylodynamic Analysis of Clinical and Environmental <named-content content-type="genus-species">Vibrio cholerae</named-content> Isolates from Haiti Reveals Diversification Driven by Positive Selection
ABSTRACT 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 Hai...
Guardado en:
| Autores principales: | , , , , , , , , , , , , , , , |
|---|---|
| Formato: | article |
| Lenguaje: | EN |
| Publicado: |
American Society for Microbiology
2014
|
| Materias: | |
| Acceso en línea: | https://doaj.org/article/804f55a9a3d049a7867db3f81f4d3780 |
| Etiquetas: |
Agregar Etiqueta
Sin Etiquetas, Sea el primero en etiquetar este registro!
|
| id |
oai:doaj.org-article:804f55a9a3d049a7867db3f81f4d3780 |
|---|---|
| record_format |
dspace |
| spelling |
oai:doaj.org-article:804f55a9a3d049a7867db3f81f4d37802021-11-15T15:47:03ZPhylodynamic Analysis of Clinical and Environmental <named-content content-type="genus-species">Vibrio cholerae</named-content> Isolates from Haiti Reveals Diversification Driven by Positive Selection10.1128/mBio.01824-142150-7511https://doaj.org/article/804f55a9a3d049a7867db3f81f4d37802014-12-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.01824-14https://doaj.org/toc/2150-7511ABSTRACT 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.Taj AzarianAfsar AliJudith A. JohnsonDavid MohrMattia ProsperiNazle M. VerasMohammed JubairSamantha L. StricklandMohammad H. RashidMeer T. AlamThomas A. WeppelmannLee S. KatzCheryl L. TarrRita R. ColwellJ. Glenn MorrisMarco SalemiAmerican Society for MicrobiologyarticleMicrobiologyQR1-502ENmBio, Vol 5, Iss 6 (2014) |
| institution |
DOAJ |
| collection |
DOAJ |
| language |
EN |
| topic |
Microbiology QR1-502 |
| spellingShingle |
Microbiology QR1-502 Taj Azarian Afsar Ali Judith A. Johnson David Mohr Mattia Prosperi Nazle M. Veras Mohammed Jubair Samantha L. Strickland Mohammad H. Rashid Meer T. Alam Thomas A. Weppelmann Lee S. Katz Cheryl L. Tarr Rita R. Colwell J. Glenn Morris Marco Salemi Phylodynamic Analysis of Clinical and Environmental <named-content content-type="genus-species">Vibrio cholerae</named-content> Isolates from Haiti Reveals Diversification Driven by Positive Selection |
| description |
ABSTRACT 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. |
| format |
article |
| author |
Taj Azarian Afsar Ali Judith A. Johnson David Mohr Mattia Prosperi Nazle M. Veras Mohammed Jubair Samantha L. Strickland Mohammad H. Rashid Meer T. Alam Thomas A. Weppelmann Lee S. Katz Cheryl L. Tarr Rita R. Colwell J. Glenn Morris Marco Salemi |
| author_facet |
Taj Azarian Afsar Ali Judith A. Johnson David Mohr Mattia Prosperi Nazle M. Veras Mohammed Jubair Samantha L. Strickland Mohammad H. Rashid Meer T. Alam Thomas A. Weppelmann Lee S. Katz Cheryl L. Tarr Rita R. Colwell J. Glenn Morris Marco Salemi |
| author_sort |
Taj Azarian |
| title |
Phylodynamic Analysis of Clinical and Environmental <named-content content-type="genus-species">Vibrio cholerae</named-content> Isolates from Haiti Reveals Diversification Driven by Positive Selection |
| title_short |
Phylodynamic Analysis of Clinical and Environmental <named-content content-type="genus-species">Vibrio cholerae</named-content> Isolates from Haiti Reveals Diversification Driven by Positive Selection |
| title_full |
Phylodynamic Analysis of Clinical and Environmental <named-content content-type="genus-species">Vibrio cholerae</named-content> Isolates from Haiti Reveals Diversification Driven by Positive Selection |
| title_fullStr |
Phylodynamic Analysis of Clinical and Environmental <named-content content-type="genus-species">Vibrio cholerae</named-content> Isolates from Haiti Reveals Diversification Driven by Positive Selection |
| title_full_unstemmed |
Phylodynamic Analysis of Clinical and Environmental <named-content content-type="genus-species">Vibrio cholerae</named-content> Isolates from Haiti Reveals Diversification Driven by Positive Selection |
| title_sort |
phylodynamic analysis of clinical and environmental <named-content content-type="genus-species">vibrio cholerae</named-content> isolates from haiti reveals diversification driven by positive selection |
| publisher |
American Society for Microbiology |
| publishDate |
2014 |
| url |
https://doaj.org/article/804f55a9a3d049a7867db3f81f4d3780 |
| work_keys_str_mv |
AT tajazarian phylodynamicanalysisofclinicalandenvironmentalnamedcontentcontenttypegenusspeciesvibriocholeraenamedcontentisolatesfromhaitirevealsdiversificationdrivenbypositiveselection AT afsarali phylodynamicanalysisofclinicalandenvironmentalnamedcontentcontenttypegenusspeciesvibriocholeraenamedcontentisolatesfromhaitirevealsdiversificationdrivenbypositiveselection AT judithajohnson phylodynamicanalysisofclinicalandenvironmentalnamedcontentcontenttypegenusspeciesvibriocholeraenamedcontentisolatesfromhaitirevealsdiversificationdrivenbypositiveselection AT davidmohr phylodynamicanalysisofclinicalandenvironmentalnamedcontentcontenttypegenusspeciesvibriocholeraenamedcontentisolatesfromhaitirevealsdiversificationdrivenbypositiveselection AT mattiaprosperi phylodynamicanalysisofclinicalandenvironmentalnamedcontentcontenttypegenusspeciesvibriocholeraenamedcontentisolatesfromhaitirevealsdiversificationdrivenbypositiveselection AT nazlemveras phylodynamicanalysisofclinicalandenvironmentalnamedcontentcontenttypegenusspeciesvibriocholeraenamedcontentisolatesfromhaitirevealsdiversificationdrivenbypositiveselection AT mohammedjubair phylodynamicanalysisofclinicalandenvironmentalnamedcontentcontenttypegenusspeciesvibriocholeraenamedcontentisolatesfromhaitirevealsdiversificationdrivenbypositiveselection AT samanthalstrickland phylodynamicanalysisofclinicalandenvironmentalnamedcontentcontenttypegenusspeciesvibriocholeraenamedcontentisolatesfromhaitirevealsdiversificationdrivenbypositiveselection AT mohammadhrashid phylodynamicanalysisofclinicalandenvironmentalnamedcontentcontenttypegenusspeciesvibriocholeraenamedcontentisolatesfromhaitirevealsdiversificationdrivenbypositiveselection AT meertalam phylodynamicanalysisofclinicalandenvironmentalnamedcontentcontenttypegenusspeciesvibriocholeraenamedcontentisolatesfromhaitirevealsdiversificationdrivenbypositiveselection AT thomasaweppelmann phylodynamicanalysisofclinicalandenvironmentalnamedcontentcontenttypegenusspeciesvibriocholeraenamedcontentisolatesfromhaitirevealsdiversificationdrivenbypositiveselection AT leeskatz phylodynamicanalysisofclinicalandenvironmentalnamedcontentcontenttypegenusspeciesvibriocholeraenamedcontentisolatesfromhaitirevealsdiversificationdrivenbypositiveselection AT cherylltarr phylodynamicanalysisofclinicalandenvironmentalnamedcontentcontenttypegenusspeciesvibriocholeraenamedcontentisolatesfromhaitirevealsdiversificationdrivenbypositiveselection AT ritarcolwell phylodynamicanalysisofclinicalandenvironmentalnamedcontentcontenttypegenusspeciesvibriocholeraenamedcontentisolatesfromhaitirevealsdiversificationdrivenbypositiveselection AT jglennmorris phylodynamicanalysisofclinicalandenvironmentalnamedcontentcontenttypegenusspeciesvibriocholeraenamedcontentisolatesfromhaitirevealsdiversificationdrivenbypositiveselection AT marcosalemi phylodynamicanalysisofclinicalandenvironmentalnamedcontentcontenttypegenusspeciesvibriocholeraenamedcontentisolatesfromhaitirevealsdiversificationdrivenbypositiveselection |
| _version_ |
1718427528412004352 |