Nontyphoidal Salmonella (NTS) are among the most common etiological agents of diarrheal diseases worldwide and have become the most commonly detected bacterial pathogen in children hospitalized with diarrhea in Vietnam. Aiming to better understand the epidemiology, serovar distribution, antimicrobial resistance (AMR), and clinical manifestation of NTS gastroenteritis in Vietnam, we conducted a clinical genomics investigation of NTS isolated from diarrheal children admitted to one of three tertiary hospitals in Ho Chi Minh City. Between May 2014 and April 2016, 3,166 children hospitalized with dysentery were recruited into the study; 478 (∼15%) children were found to be infected with NTS by stool culture. Molecular serotyping of the 450 generated genomes identified a diverse collection of serogroups (B, C1, C2 to C3, D1, E1, G, I, K, N, O, and Q); however, Salmonella enterica serovar Typhimurium was the most predominant serovar, accounting for 41.8% (188/450) of NTS isolates. We observed a high prevalence of AMR to first-line treatments recommended by WHO, and more than half (53.8%; 242/450) of NTS isolates were multidrug resistant (MDR; resistant to ≥3 antimicrobial classes). AMR gene detection positively correlated with phenotypic AMR testing, and resistance to empirical antimicrobials was associated with a significantly longer hospitalization (0.91 days; P = 0.04). Our work shows that genome sequencing is a powerful epidemiological tool to characterize the serovar diversity and AMR profiles in NTS. We propose a revaluation of empirical antimicrobials for dysenteric diarrhea and endorse the use of whole-genome sequencing for sustained surveillance of NTS internationally.

中文翻译：

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越南胡志明市住院儿童的非伤寒沙门氏菌肠胃炎的基因组血清型，临床表现和抗药性。

非伤寒沙门氏菌（NTS）是全世界腹泻病最常见的病原体之一，并且已成为越南住院腹泻儿童中最常见的细菌病原体。为了更好地了解越南NTS肠胃炎的流行病学，血清分布，抗菌素耐药性（AMR）和临床表现，我们进行了从胡志明市三所三级医院之一入院的腹泻儿童中分离出的NTS的临床基因组学调查。2014年5月至2016年4月，招募了3166名因痢疾住院的儿童。发现有478名（〜15％）儿童通过粪便培养感染了NTS。450个产生的基因组的分子血清分型确定了血清群的不同集合（B，C1，C2至C3，D1，E1，G，I，K，N，O和Q）；然而，鼠伤寒沙门氏菌是鼠伤寒沙门氏菌中最主要的，占NTS分离株的41.8％（188/450）。我们观察到WHO推荐的一线治疗对AMR的患病率很高，并且超过一半（53.8％; 242/450）的NTS分离株具有多重耐药性（MDR；对≥3种抗菌药具有耐药性）。AMR基因检测与表型AMR检测呈正相关，对经验性抗菌药物的耐药性与住院时间显着延长（0.91天；P =0.04）。我们的工作表明，基因组测序是表征NTS中血清多样性和AMR谱的强大流行病学工具。我们提议对痢疾性腹泻的经验性抗菌药物进行重新评估，并支持使用全基因组测序技术对国际上的NTS进行持续监测。