A genomic snapshot of Salmonella enterica serovar Typhi in Colombia.
A genomic snapshot of Salmonella enterica serovar Typhi in Colombia.
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哥伦比亚伤寒沙门氏菌的基因组快照。
DOI：
10.1371/journal.pntd.0009755
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发表时间：
2021-09
影响因子：
3.8
通讯作者：
Baker S
中科院分区：
文献类型：
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作者：
Guevara PD;Maes M;Thanh DP;Duarte C;Rodriguez EC;Montaño LA;Dan THN;Nguyen TNT;Carey ME;Campos J;Chinen I;Perez E;Baker S
在拉丁美洲流行的伤寒沙门氏菌（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是地方性疾病；然而，整个拉丁美洲缺乏标准化的血液培养监测使得估计真正的疾病负担变得困难。2006年，哥伦比亚国家卫生局建立了一个监测系统，用于追踪包括伤寒沙门氏菌在内的细菌病原体。在这里，我们使用脉冲场凝胶电泳（PFGE，拉丁美洲公认的基因分型方法）和全基因组测序（WGS）对1997年至2018年间收集的77株具有代表性的哥伦比亚伤寒沙门氏菌进行了分析。我们发现在哥伦比亚流行的主要伤寒沙门氏菌分支是2.5和3.5分支。值得注意的是，经测序的哥伦比亚伤寒沙门氏菌分离株在全球系统发育上密切相关。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易感性降低相关的突变。这是首次使用WGS对哥伦比亚分离的伤寒沙门氏菌进行鉴定，并将这些数据与使用PFGE产生的数据进行比较，我们得出结论，PFGE不适合用于追踪伤寒沙门氏菌克隆和绘制传播图。伤寒沙门氏菌等病原体的遗传多样性在拉丁美洲是有限的，应该成为未来纳入WGS的监测研究的目标。伤寒沙门氏菌是伤寒的病原体，每年有900万至1300万例病例和116,800例相关死亡。伤寒仍然是一个公共卫生问题，主要发生在低收入和中等收入国家，包括拉丁美洲，其模拟发病率高达每10万人年169例（32-642例）。一些国际研究旨在填补关于伤寒全球分布和遗传格局的数据空白；然而，尽管作出了这些努力，拉丁美洲的代表人数仍然不足。用于追踪拉丁美洲伤寒暴发的公认方法（PFGE）无法检测到全球优势的伤寒沙门氏菌谱系（例如H58），它们通常携带多药耐药（MDR）质粒，氟喹诺酮类药物敏感性降低，现在又携带阿奇霉素耐药。我们将PFGE与全基因组序列（WGS）进行比较，发现两者相关性较差，导致病例过度聚类。我们还发现，与大多数流行国家不同，哥伦比亚的伤寒沙门氏菌对抗菌素高度敏感，并且仅限于有限数量的基因型，而这些基因型在其他伤寒沙门氏菌流行国家中并不常见。我们的研究首次利用WGS数据调查了哥伦比亚的种群结构，并确定了主要的流行基因型，为哥伦比亚伤寒沙门氏菌的分子流行病学提供了第一个增强的见解。我们的工作表明，整合WGS的常规监测不仅对于改善疾病负担估算，而且对于跟踪伤寒沙门氏菌的国家和区域传播动态是必要的。
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. Salmonella Typhi is the causative agent of typhoid fever, with between 9–13 million cases and 116,800 associated deaths annually. Typhoid fever is still a public health problem mainly in low and middle-income countries (LMICs), including in Latin America, which has a modelled incidence of up to 169 (32–642) cases per 100,000 person-years. Several international studies have aimed to fill data gaps regarding the global distribution and genetic landscape of typhoid; however, in spite of these efforts Latin America is still underrepresented. The globally dominant lineages of S. Typhi (e.g., H58), which often carry multi-drug resistance (MDR) plasmids, decreased fluoroquinolone susceptibility, and now azithromycin resistance, are not detectable by the accepted method (PFGE) used to track outbreaks of typhoid in Latin America. We compared PFGE with whole genome sequence (WGS) and found it correlated poorly, resulting in the over clustering of cases. We additionally found that unlike in most endemic countries, S. Typhi in Colombia are highly antimicrobial susceptible and restricted to a limited number of genotypes that are not as commonly identified in other S. Typhi endemic countries. Our study provides the first enhanced insights into the molecular epidemiology of S. Typhi in Colombia, using WGS data for the first time to investigate the population structure in Colombia and identifying predominant circulating genotypes. Our work demonstrates that routine surveillance with the integration of WGS is necessary not only to improve disease burden estimates, but also to track the national and regional transmission dynamics of S. Typhi.
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影响因子：
--
作者：
Castor, Mei L;Whitney, Cynthia G;Como-Sabetti, Kathryn;Facklam, Richard R;Ferrieri, Patricia;Bartkus, Joanne M;Juni, Billie A;Cieslak, Paul R;Farley, Monica M;Dumas, Nellie B;Schrag, Stephanie J;Lynfield, Ruth
通讯作者：
Lynfield, Ruth
多次介绍了肠道沙门氏菌鼠伤寒小鼠H58，其氟喹诺酮易感性降低了智利。
影响因子：
11.8
作者：
Maes M;Dyson ZA;Higginson EE;Fernandez A;Araya P;Tennant SM;Baker S;Lagos R;Levine MM;Hormazabal JC;Dougan G
通讯作者：
Dougan G
影响因子：
34.3
作者：
Marks, Florian;von Kalckreuth, Vera;Wierzba, Thomas F.
通讯作者：
Wierzba, Thomas F.
影响因子：
3.8
作者：
Kariuki, Samuel;Mbae, Cecilia;Dougan, Gordon
通讯作者：
Dougan, Gordon
影响因子：
5.8
作者：
Stamatakis, Alexandros
通讯作者：
Stamatakis, Alexandros