Azarian Taj, Ali Afsar, Johnson Judith A, Mohr David, Prosperi Mattia, Veras Nazle M, Jubair Mohammed, Strickland Samantha L, Rashid Mohammad H, Alam Meer T, Weppelmann Thomas A, Katz Lee S, Tarr Cheryl L, Colwell Rita R, Morris J Glenn, Salemi Marco
McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA.
mBio. 2014 Dec 23;5(6):e01824-14. doi: 10.1128/mBio.01824-14.
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.
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.
全基因组单核苷酸多态性（SNP）数据的系统发育动力学分析是研究细菌流行病潜在进化过程的有力工具。该方法被用于研究2010年至2012年间从海地收集的65株霍乱弧菌临床和环境分离株。对从环境样本中分离出的菌株进行特征分析，共鉴定出4株产毒霍乱弧菌O1分离株、4株非O1/O139分离株以及1株带有经典tcpA基因的新型无毒霍乱弧菌O1分离株。在贝叶斯框架内，使用基于溯祖的群体模型从全基因组SNP推断菌株的系统发育。观察到临床和环境产毒霍乱弧菌O1菌株之间存在密切的系统发育关系。2010年10月至2012年8月霍乱在海地传播期间，群体规模最初增加，随后随时间波动。沿系统发育树内部分支的选择分析表明，同义替换稳定积累，非同义替换随时间逐渐增加，这表明多样化可能是由正选择驱动的。选择驱动的非同义替换的短期积累可能对毒力、传播动态乃至疫苗效力具有重要意义。
霍乱是由产毒霍乱弧菌引起的一种导致脱水腹泻的疾病，于2010年在海地出现；在过去100年里海地没有霍乱相关记录。尽管此次疫情在发病率和死亡率方面具有毁灭性，但它为研究霍乱弧菌的进化动态及其在环境中的存在提供了独特机会。本研究在先前工作的基础上进行了拓展，提供了一项深入的系统发育动力学分析；该分析是基于海地2年期间分散地理区域的临床和环境菌株的全基因组单核苷酸多态性推断得出的。我们的结果表明，即使在如此短的时间尺度内，海地的霍乱弧菌也经历了由正选择驱动的进化和多样化，这可能对理解该疾病的全球临床和流行病学模式具有重要意义。此外，流行菌株在海地水生环境中的持续存在对传播具有重要意义。
