Little is known about the genetic diversity of Salmonella enterica serovar Typhi (S. Typhi) circulating in Latin America. It has been observed that typhoid fever is still endemic in this part of the world; however, a lack of standardized blood culture surveillance across Latin American makes estimating the true disease burden problematic. The Colombian National Health Service established a surveillance system for tracking bacterial pathogens, including S. Typhi, in 2006. Here, we characterized 77 representative Colombian S. Typhi isolates collected between 1997 and 2018 using pulse field gel electrophoresis (PFGE; the accepted genotyping method in Latin America) and whole genome sequencing (WGS). We found that the main S. Typhi clades circulating in Colombia were clades 2.5 and 3.5. Notably, the sequenced S. Typhi isolates from Colombia were closely related in a global phylogeny. Consequently, these data suggest that these are endemic clades circulating in Colombia. We found that AMR in S. Typhi in Colombia was uncommon, with a small subset of organisms exhibiting mutations associated with reduced susceptibility to fluoroquinolones. This is the first time that S. Typhi isolated from Colombia have been characterized by WGS, and after comparing these data with those generated using PFGE, we conclude that PFGE is unsuitable for tracking S. Typhi clones and mapping transmission. The genetic diversity of pathogens such as S. Typhi is limited in Latin America and should be targeted for future surveillance studies incorporating WGS.

中文翻译：

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哥伦比亚伤寒沙门氏菌的基因组快照。


人们对拉丁美洲流行的肠伤寒沙门氏菌血清型伤寒菌（S. Typhi）的遗传多样性知之甚少。据观察，伤寒在世界这一地区仍然流行；然而，整个拉丁美洲缺乏标准化的血培养监测，使得估计真正的疾病负担变得困难。哥伦比亚国家卫生服务中心于 2006 年建立了一个追踪细菌病原体（包括伤寒沙门氏菌）的监测系统。在这里，我们使用脉冲场凝胶电泳（PFGE；公认的基因分型方法）对 1997 年至 2018 年期间收集的 77 个具有代表性的哥伦比亚伤寒沙门氏菌分离株进行了表征拉丁美洲）和全基因组测序（WGS）。我们发现哥伦比亚流行的伤寒沙门氏菌主要分支是 2.5 和 3.5 分支。值得注意的是，来自哥伦比亚的已测序伤寒沙门氏菌分离株在全球系统发育中密切相关。因此，这些数据表明这些是在哥伦比亚流行的地方性分支。我们发现哥伦比亚伤寒沙门氏菌中的抗菌素耐药性并不常见，一小部分生物体表现出与氟喹诺酮类药物敏感性降低相关的突变。这是首次通过全基因组测序（WGS）对从哥伦比亚分离的伤寒沙门氏菌进行表征，并将这些数据与使用 PFGE 生成的数据进行比较后，我们得出结论，PFGE 不适合追踪伤寒沙门氏菌克隆和绘制传播图谱。伤寒沙门氏菌等病原体的遗传多样性在拉丁美洲有限，应成为未来结合全基因组测序的监测研究的目标。