The prime goal of molecular epidemiology is to identify the origin and evolution of pathogens, which can potentially influence the public health worldwide. Traditional methods provide limited information which is not sufficient for outbreak investigation and studying transmission dynamics. The recent advancement of next-generation sequencing had a major impact on molecular epidemiological studies. Currently, whole-genome sequencing (WGS) has become the gold standard typing method, especially for clinically significant pathogens. Here, we aimed to describe the application of appropriate molecular typing methods for global antimicrobial resistance surveillance system pathogens based on the level of discrimination and epidemiological settings. This shows that sequence-based methods such as multi-locus sequence typing (MLST) are widely used due to cost-effectiveness and database accessibility. However, WGS is the only method of choice for studying Escherichia coli and Shigella spp. WGS is shown to have higher discrimination than other methods in typing Klebsiella pneumoniae, Acinetobacter baumannii and Salmonella spp. due to its changing accessory genome content. For Gram positives such as Streptococcus pneumoniae, WGS would be preferable to understand the evolution of the strains. Similarly, for Staphylococcus aureus, combination of MLST, staphylococcal protein A or SCCmec typing along with WGS could be the choice for epidemiological typing of hospital- and community-acquired strains. This review highlights that combinations of different typing methods should be used to get complete information since no one standalone method is sufficient to study the varying genome diversity.

中文翻译：

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全球抗菌素耐药性监测系统病原体的局部到全球水平分子流行病学特征的当前策略。

分子流行病学的主要目标是确定病原体的起源和进化，这可能会影响全世界的公共卫生。传统方法提供的信息有限，不足以进行疫情调查和传播动力学研究。新一代测序的最新进展对分子流行病学研究产生了重大影响。目前，全基因组测序（WGS）已成为金标准分型方法，特别是对于临床上重要的病原体。在这里，我们的目的是根据歧视程度和流行病学背景，描述适当的分子分型方法在全球抗菌素耐药性监测系统病原体中的应用。这表明基于序列的方法，例如多位点序列分型（MLST），由于成本效益和数据库可访问性而被广泛使用。然而，全基因组测序是研究大肠杆菌和志贺氏菌的唯一选择方法。在对肺炎克雷伯菌、鲍曼不动杆菌和沙门氏菌进行分型时，全基因组测序显示出比其他方法更高的辨别力。由于其附属基因组内容的变化。对于肺炎链球菌等革兰氏阳性菌，全基因组测序更适合了解菌株的进化。同样，对于金黄色葡萄球菌，MLST、葡萄球菌蛋白 A 或 SCCmec 分型与 WGS 的组合可能是医院和社区获得性菌株流行病学分型的选择。这篇综述强调，应该使用不同分型方法的组合来获取完整的信息，因为没有一种独立的方法足以研究不同的基因组多样性。