Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy.
Department of Biomedical and Clinical Sciences "L. Sacco", University of Milan, Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", Milan, Italy.
Microb Genom. 2020 Apr;6(4). doi: 10.1099/mgen.0.000347. Epub 2020 Mar 9.
In this work we compared the most frequently used typing methods: PFGE, cgMLST and coreSNP. We evaluated the discriminatory power of the three methods to confirm or exclude nosocomial transmission on strains isolated from January to December 2017, in the framework of the routine surveillance for multidrug-resistant organisms at the San Raffaele Hospital, in Milan. We compared the results of the different methods to the results of epidemiological investigation. Our results showed that cgMLST and coreSNP are more discriminant than PFGE, and that both approaches are suitable for transmission analyses. cgMLST appeared to be inferior to coreSNP in the CG258 phylogenetic reconstruction. Indeed, we found that the phylogenetic reconstruction based on cgMLST genes wrongly clustered ST258 clade1 and clade2 strains, conversely properly assigned by coreSNP approach. In conclusion, this study provides evidences supporting the reliability of both cgMLST and coreSNP for hospital surveillance programs and highlights the limits of cgMLST scheme genes for phylogenetic reconstructions.
在这项工作中，我们比较了最常用的分型方法：PFGE、cgMLST 和核心 SNP。我们评估了这三种方法在确认或排除 2017 年 1 月至 12 月期间从米兰圣拉斐尔医院多药耐药菌常规监测框架中分离的菌株的医院内传播方面的区分能力。我们将不同方法的结果与流行病学调查的结果进行了比较。我们的结果表明，cgMLST 和核心 SNP 比 PFGE 更具区分能力，并且这两种方法都适用于传播分析。cgMLST 在 CG258 系统发育重建中似乎不如核心 SNP。事实上，我们发现基于 cgMLST 基因的系统发育重建错误地将 ST258 分支 1 和分支 2 菌株聚类在一起，而核心 SNP 方法则正确地进行了分配。总之，这项研究为 cgMLST 和核心 SNP 用于医院监测计划提供了证据支持，并强调了 cgMLST 方案基因在系统发育重建方面的局限性。
