Abstract：
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.
摘要：
通过全基因组测序基于单核苷酸多态性（SNP）的系统发育分析被认为是探查医院传播的标准方法。然而,WGS的应用受到设备成本高和需要多种分析工具的限制，这限制了它在临床实验室环境中的广泛使用。在日本,基于PCR的开放阅读框分型(POT)用于追踪耐甲氧西林金黄色葡萄球菌(MRSA)传播途径的普遍使用归因于其简单易用.虽然POT的辨别力被认为不足以用于医院传播分析，缺乏支持这一概念的结论性数据。这项研究评估了SNP分析和POT对64种临床MRSA菌株的辨别能力。ST5/SCCmecIIa的所有21株MRSA，有超过16个SNP，展示了不同的克隆。相反，两个菌株共享相同的POT编号，并被鉴定为A组。在具有超过9个SNP的ST8/SCCmecIVl的12个MRSA菌株中，五人进入POTB组，将ST8/SCCmecIVa的4株MRSA菌株归入POTD组，尽管它们包括具有30多个SNP的菌株。在ST1/SCCmecIVa的27株MRSA菌株中，14人被归类为POT组。然而，除了两个簇(每个簇包含两个或三个菌株)，所有SNP计数均>10（图1-D）。对CC1/SCCmecIV中MRSA的SNP分析显示，几个菌株在POT数量中具有相同数量的SNP（106-183-37），即使在SNPs>100的细菌中，表明POT在详细的医院传播分析中的使用有限。
