Methicillin-resistant Staphylococcus aureus (MRSA) is a multi-drug resistant and opportunistic pathogen. The emergence of new clones of MRSA in both healthcare settings and the community warrants serious attention and epidemiological surveillance. However, epidemiological data of MRSA isolates from Pakistan are limited. We performed a whole-genome-based comparative analysis of two (P10 and R46) MRSA strains isolated from two provinces of Pakistan to understand the genetic diversity, sequence type (ST), and distribution of virulence and antibiotic-resistance genes. The strains belong to ST113 and harbor the SCCmec type IV encoding mecA gene. Both the strains contain two plasmids, and three and two complete prophage sequences are present in P10 and R46, respectively. The specific antibiotic resistance determinants in P10 include two aminoglycoside-resistance genes, aph(3’)-IIIa and aad(6), a streptothrin-resistance gene sat-4, a tetracycline-resistance gene tet(K), a mupirocin-resistance gene mupA, a point mutation in fusA conferring resistance to fusidic acid, and in strain R46 a specific plasmid associated gene ant(4’)-Ib. The strains harbor many virulence factors common to MRSA. However, no Panton-Valentine leucocidin (lukF-PV/lukS-PV) or toxic shock syndrome toxin (tsst) genes were detected in any of the genomes. The phylogenetic relationship of P10 and R46 with other prevailing MRSA strains suggests that ST113 strains are closely related to ST8 strains and ST113 strains are a single-locus variant of ST8. These findings provide important information concerning the emerging MRSA clone ST113 in Pakistan and the sequenced strains can be used as reference strains for the comparative genomic analysis of other MRSA strains in Pakistan and ST113 strains globally.

中文翻译：

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从巴基斯坦三级医院分离出的耐甲氧西林金黄色葡萄球菌 ST113 菌株的基因组研究

耐甲氧西林金黄色葡萄球菌（MRSA）是一种多重耐药和机会致病菌。在医疗机构和社区中出现新的 MRSA 克隆值得认真关注和流行病学监测。然而，来自巴基斯坦的 MRSA 分离株的流行病学数据有限。我们对从巴基斯坦两个省分离的两种（P10 和 R46）MRSA 菌株进行了基于全基因组的比较分析，以了解遗传多样性、序列类型 (ST) 以及毒力和抗生素抗性基因的分布。这些菌株属于 ST113 并具有编码mecA的 SCCmec IV 型基因。两种菌株都含有两个质粒，三个和两个完整的原噬菌体序列分别存在于 P10 和 R46 中。P10 中的特定抗生素抗性决定因素包括两个氨基糖苷类抗性基因aph(3')-IIIa和aad (6)、一个链霉菌素抗性基因sat-4、一个四环素抗性基因tet(K)、一个莫匹罗星抗性基因mupA ， fusA中的点突变赋予对夫西地酸的抗性，而在菌株R46中，特定的质粒相关基因ant(4')-Ib。这些菌株含有许多 MRSA 共有的毒力因子。然而，没有 Panton-Valentine leucocidin ( lukF-PV/lukS-PV）或中毒性休克综合征毒素（tsst）基因在任何基因组中检测到。P10和R46与其他流行MRSA菌株的系统发育关系表明ST113菌株与ST8菌株密切相关，ST113菌株是ST8的单基因座变体。这些发现提供了有关巴基斯坦新出现的 MRSA 克隆 ​​ST113 的重要信息，测序菌株可用作参考菌株，用于巴基斯坦其他 MRSA 菌株和全球 ST113 菌株的比较基因组分析。