Department of Clinical Laboratory, Toho University Omori Medical Center, 6-11-1, Omori-nishi, Ota-ku, Tokyo, 143-8541, Japan; Department of Microbiology and Infectious Diseases, Toho University School of Medicine, 5-21-16, Omori-nishi, Ota-ku, Tokyo, 143-8540, Japan.
Department of Microbiology and Infectious Diseases, Toho University School of Medicine, 5-21-16, Omori-nishi, Ota-ku, Tokyo, 143-8540, Japan.
J Infect Chemother. 2024 Sep;30(9):951-954. doi: 10.1016/j.jiac.2024.02.021. Epub 2024 Mar 2.
Phylogenetic analysis based on single-nucleotide polymorphism (SNP)-based through whole-genome sequencing is recognized as the standard method for probing nosocomial transmission. However, the application of WGS is constrained by the high cost of equipment and the need for diverse analysis tools, which limits its widespread use in clinical laboratory settings. In Japan, the prevalent use of PCR-based open reading frame typing (POT) for tracing methicillin-resistant Staphylococcus aureus (MRSA) transmission routes is attributed to its simplicity and ease of use. Although POT's discriminatory power is considered insufficient for nosocomial transmission analysis, conclusive data supporting this notion is lacking. This study assessed the discriminatory capabilities of SNP analysis and POT across 64 clinical MRSA strains. All 21 MRSA strains of ST5/SCCmec IIa, having more than 16 SNPs, demonstrated distinct clones. Conversely, two strains shared the same POT number and were identified as group A. Among the 12 MRSA strains of ST8/SCCmec IVl with over nine SNPs, five fell into POT group B, and five into POT group C. All four MRSA strains of ST8/SCCmec IVa were classified into POT group D, although they included strains with more than 30 SNPs. Among the 27 MRSA strains of ST1/SCCmec IVa, 14 were classified into POT group E. However, except for two clusters (each comprising two or three strains), all had SNP counts >10 (Fig. 1-D). SNP analysis of MRSA in CC1/SCCmec IV showed that several strains had the same number of SNPs in POT number (106-183-37), even among bacteria with >100 SNPs, indicating POT's limited use in detailed nosocomial transmission analysis.
基于单核苷酸多态性（SNP）的全基因组测序的系统发育分析被认为是探测医院感染传播的标准方法。然而，WGS 的应用受到设备成本高和需要多样化分析工具的限制，这限制了其在临床实验室环境中的广泛应用。在日本，基于聚合酶链反应的开放阅读框分型（POT）被广泛用于追踪耐甲氧西林金黄色葡萄球菌（MRSA）的传播途径，这归因于其简单易用。尽管 POT 的分辨力被认为不足以用于医院感染传播分析，但缺乏支持这一观点的确凿数据。本研究评估了 SNP 分析和 POT 在 64 株临床 MRSA 菌株中的区分能力。所有 21 株 ST5/SCCmec IIa 的 MRSA 菌株，具有超过 16 个 SNP，表现出明显的克隆。相反，两个菌株具有相同的 POT 编号，被归为 A 组。在 12 株 ST8/SCCmec IVl 的 MRSA 菌株中，有超过 9 个 SNP 的 5 株属于 POT 组 B，5 株属于 POT 组 C。所有 4 株 ST8/SCCmec IVa 的 MRSA 菌株均归入 POT 组 D，尽管它们包括 SNP 计数超过 30 的菌株。在 27 株 ST1/SCCmec IVa 的 MRSA 菌株中，14 株归入 POT 组 E。然而，除了两个聚类（每个聚类包含两个或三个菌株）外，所有菌株的 SNP 计数均大于 10（图 1-D）。CC1/SCCmec IV 中的 MRSA 的 SNP 分析表明，即使在 SNP 数大于 100 的细菌中，一些菌株的 POT 数的 SNP 数相同（106-183-37），表明 POT 在详细的医院感染传播分析中的应用有限。
