Data from: Comparative genomics of Methicillin-resistant Staphylococcus aureus ST239: distinct geographical variants in Beijing and Hong Kong

Background: The ST239 lineage is a globally disseminated, multiply drug-resistant hospital-associated methicillin-resistant Staphylococcus aureus (HA-MRSA). We performed whole-genome sequencing of representative HA-MRSA isolates of the ST239 lineage from bacteremic patients in hospitals in Hong Kong (HK) and Beijing (BJ) and compared them with three published complete genomes of ST239, namely T0131, TW20 and JKD6008. Orthologous gene group (OGG) analyses of the Hong Kong and Beijing cluster strains were also undertaken. Results: Homology analysis, based on highest-percentage nucleotide identity, indicated that HK isolates were closely related to TW20, whereas BJ isolates were more closely related to T0131 from Tianjin. Phylogenetic analysis, incorporating a total of 30 isolates from different continents, revealed that strains from HK clustered with TW20 into the ‘Asian clade’, whereas BJ isolates and T0131 clustered closely with strains of the ‘Turkish clade’ from Eastern Europe. HK isolates contained the typical φSPβ-like prophage with the SasX gene similar to TW20. In contrast, BJ isolates contained a unique 15 kb PT1028-like prophage but lacked φSPβ-like and φSA1 prophages. Besides distinct mobile genetic elements (MGE) in the two clusters, OGG analyses and whole-genome alignment of these clusters highlighted differences in genes located in the core genome, including the identification of single nucleotide deletions in several genes, resulting in frameshift mutations and the subsequent predicted truncation of encoded proteins involved in metabolism and antimicrobial resistance. Conclusions: Comparative genomics, based on de novo assembly and deep sequencing of HK and BJ strains, revealed different origins of the ST239 lineage in northern and southern China and identified differences between the two clades at single nucleotide polymorphism (SNP), core gene and MGE levels. The results suggest that ST239 strains isolated in Hong Kong since the 1990s belong to the Asian clade, present mainly in southern Asia, whereas those that emerged in northern China were of a distinct origin, reflecting the complexity of dissemination and the dynamic evolution of this ST239 lineage.

背景：ST239谱系是一种全球传播的多重耐药医院相关性耐甲氧西林金黄色葡萄球菌（HA-MRSA）。本研究对来自中国香港（HK）与北京（BJ）医院血流感染患者的ST239谱系代表性HA-MRSA分离株进行全基因组测序，并与已发表的3株ST239完整基因组（T0131、TW20及JKD6008）进行比对分析；同时针对香港与北京的聚类菌株开展直系同源基因簇（OGG）分析。结果：基于最高核苷酸同源性的同源性分析显示，香港分离株与TW20亲缘关系密切，而北京分离株则与来自天津的T0131亲缘关系更近。整合来自各大洲的共30株分离株的系统发育分析显示，香港分离株与TW20共同聚类为"亚洲进化枝"，而北京分离株与T0131则与来自东欧的"土耳其进化枝"菌株紧密聚类。香港分离株携带与TW20类似的、携带SasX基因的典型φSPβ样前噬菌体。与之相反，北京分离株携带独特的15kb PT1028样前噬菌体，但缺失φSPβ样及φSA1前噬菌体。除两聚类菌株间存在显著差异的可移动遗传元件（MGE）外，OGG分析及全基因组比对还揭示了核心基因组基因的差异，包括在多个基因中鉴定出单核苷酸缺失，该缺失可导致移码突变，进而使参与代谢与抗菌耐药的编码蛋白发生预测性截短。结论：基于香港与北京菌株的从头组装与深度测序的比较基因组学分析，揭示了ST239谱系在中国南北地区的不同起源，并鉴定出两个进化枝在单核苷酸多态性（SNP）、核心基因及可移动遗传元件水平上的差异。研究结果表明，自20世纪90年代以来在香港分离的ST239菌株属于主要分布于南亚的亚洲进化枝，而在中国北方出现的ST239菌株则起源不同，这反映了该ST239谱系的传播复杂性与动态进化特征。