Diagnostic and Research Institute for Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria.
Department of Periodontology and Operative Dentistry, University Hospital Münster, Münster, Germany.
J Clin Microbiol. 2024 Jun 12;62(6):e0172523. doi: 10.1128/jcm.01725-23. Epub 2024 May 23.
The environmental bacterium displays an alarming increase of antibiotic-resistant strains that frequently cause outbreaks in intensive care units. Due to its prevalence in the environment and opportunistic presence in humans, molecular surveillance (including resistance marker screening) and high-resolution cluster analysis are of high relevance. Furthermore, previously described in studies is rather a species complex (KoSC) than a single species comprising at least six closely related species that are not easily differentiated by standard typing methods. To reach a discriminatory power high enough to identify and resolve clusters within these species, whole genome sequencing is necessary. The resolution is achievable with core genome multilocus sequence typing (cgMLST) extending typing of a few housekeeping genes to thousands of core genome genes. CgMLST is highly standardized and provides a nomenclature enabling cross laboratory reproducibility and data exchange for routine diagnostics. Here, we established a cgMLST scheme not only capable of resolving the KoSC species but also producing reliable and consistent results for published outbreaks. Our cgMLST scheme consists of 2,536 core genome and 2,693 accessory genome targets, with a percentage of good cgMLST targets of 98.31% in 880 KoSC genomes downloaded from the National Center for Biotechnology Information (NCBI). We also validated resistance markers against known resistance gene patterns and successfully linked genetic results to phenotypically confirmed toxic strains carrying the gene cluster. In conclusion, our novel cgMLST enables highly reproducible typing of four different clinically relevant species of the KoSC and thus facilitates molecular surveillance and cluster investigations.
环境细菌显示出令人震惊的抗生素耐药菌株的增加，这些菌株经常在重症监护病房引发疫情。由于其在环境中的普遍性和在人类中的机会性存在，分子监测（包括耐药标记物筛查）和高分辨率聚类分析具有重要意义。此外，以前的研究描述的更像是一个物种复合体（KoSC），而不是一个由至少六个密切相关的物种组成的单一物种，这些物种不容易通过标准分型方法区分。为了达到足够高的分辨力，以识别和解决这些物种内的聚类，需要进行全基因组测序。通过核心基因组多位点序列分型（cgMLST），可以实现分辨率的提高，该方法将少数看家基因的分型扩展到数千个核心基因组基因。cgMLST 高度标准化，并提供了一个命名法，使常规诊断中的实验室间可重复性和数据交换成为可能。在这里，我们建立了一种 cgMLST 方案，不仅能够分辨 KoSC 物种，而且能够为已发表的疫情产生可靠和一致的结果。我们的 cgMLST 方案由 2536 个核心基因组和 2693 个辅助基因组靶标组成，从国家生物技术信息中心（NCBI）下载的 880 个 KoSC 基因组中，有 98.31%的良好 cgMLST 靶标。我们还针对已知的耐药基因模式对耐药标记进行了验证，并成功将遗传结果与携带 基因簇的表型确认的毒性菌株联系起来。总之，我们的新型 cgMLST 能够高度重现性地对 KoSC 的四个不同临床相关物种进行分型，从而促进了分子监测和聚类研究。
