Serotyping has traditionally been used for subtyping of non-typhoidal Salmonella (NTS) isolates. However, its discriminatory power is limited, which impairs its use for epidemiological investigations of source attribution. Whole-genome sequencing (WGS) analysis allows more accurate subtyping of strains. However, because of the relative newness and cost of routine WGS, large-scale studies involving NTS WGS are still rare. We aimed to revisit the big picture of subtyping NTS with a public health impact by using traditional serotyping (i.e. reaction between antisera and surface antigens) and comparing the results with those obtained using WGS. For this purpose, we analysed 18 282 sequences of isolates belonging to 37 serotypes with a public health impact that were recovered in the USA between 2006 and 2017 from multiple sources, and were available at the National Center for Biotechnology Information (NCBI). Phylogenetic trees were reconstructed for each serotype using the core genome for the identification of genetic subpopulations. We demonstrated that WGS-based subtyping allows better identification of sources potentially linked with human infection and emerging subpopulations, along with providing information on the risk of dissemination of plasmids and acquired antimicrobial resistance genes (AARGs). In addition, by reconstructing a phylogenetic tree with representative isolates from all serotypes (n=370), we demonstrated genetic variability within and between serotypes, which formed monophyletic, polyphyletic and paraphyletic clades. Moreover, we found (in the entire data set) an increased detection rate for AARGs linked to key antimicrobials (such as quinolones and extended-spectrum cephalosporins) over time. The outputs of this large-scale analysis reveal new insights into the genetic diversity within and between serotypes; the polyphyly and paraphyly of certain serotypes may suggest that the subtyping of NTS to serotypes may not be sufficient. Moreover, the results and the methods presented here, leading to differentiation between genetic subpopulations based on their potential risk to public health, as well as narrowing down the possible sources of these infections, may be used as a baseline for subtyping of future NTS infections and help efforts to mitigate and prevent infections in the USA and globally.

中文翻译：

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比较血清分型与全基因组测序对非伤寒肠沙门氏菌亚型的分析：对美国具有公共卫生影响的 37 种血清型进行的大规模分析。


血清分型传统上用于非伤寒沙门氏菌(NTS) 分离株的亚型分型。然而，其歧视力有限，这损害了其在流行病学调查来源归因中的应用。全基因组测序 (WGS) 分析可以更准确地对菌株进行亚型分析。然而，由于常规 WGS 相对新颖且成本较高，涉及 NTS WGS 的大规模研究仍然很少。我们的目的是通过使用传统的血清分型（即抗血清和表面抗原之间的反应）并将结果与​​使用全基因组测序获得的结果进行比较，重新审视对公共健康影响的 NTS 亚型分型的总体情况。为此，我们分析了 2006 年至 2017 年间在美国从多个来源回收的 18 282 个分离株序列，这些序列属于 37 种血清型，对公共卫生有影响，这些序列可在美国国家生物技术信息中心 (NCBI) 获取。使用核心基因组重建每种血清型的系统发育树，以鉴定遗传亚群。我们证明，基于全基因组测序的亚型可以更好地识别与人类感染和新兴亚群潜在相关的来源，并提供有关质粒和获得性抗菌素耐药性基因（AARG）传播风险的信息。此外，通过重建具有所有血清型（ n =370）的代表性分离株的系统发育树，我们证明了血清型内部和血清型之间的遗传变异性，形成了单系、多系和并系进化枝。此外，我们发现（在整个数据集中）随着时间的推移，与关键抗菌药物（例如喹诺酮类和广谱头孢菌素）相关的 AARG 检出率有所增加。 这项大规模分析的结果揭示了对血清型内部和血清型之间遗传多样性的新见解；某些血清型的多系和并系可能表明 NTS 对血清型的亚型可能不够充分。此外，本文提出的结果和方法，根据其对公共健康的潜在风险来区分遗传亚群，并缩小这些感染的可能来源，可用作未来 NTS 感染和分型的基线。帮助美国和全球减轻和预防感染的努力。