Methicillin-resistant Staphylococcus aureus (MRSA) strains are associated with serious complications and poor clinical outcome. In Egypt, they contribute to more than 70% of S. aureus healthcare-associated infections. This study combined whole-genome sequencing, bioinformatics, and statistical analyses to identify the phylogeny, resistome, virulome and potential genotype–phenotype–clinical correlation among 18 clinical isolates of MRSA in a tertiary hospital in Cairo, Egypt. The ST1535-V MRSA clone was the most frequently isolated (16.6%), followed by ST5-VI, ST1-V and ST239-III (11.1% each). SCCmec V, VI, IV and III types were detected at frequencies of 50%, 16.6%, 11.1% and 11.1%, respectively. None of the tested virulence genes were detected in all isolates, but they ranged in distribution from 1/18 to 17/18. The Panton–Valentine leukocidin (PVL)-encoding genes were detected in only four isolates and were enriched in isolates causing non-severe cases. Phylogenetic analysis revealed relatedness between three ST1535-Vs, two ST5-VIs, two ST239-IIIs and two ST1-Vs; however, only the two genetically related ST1-V isolates were epidemiologically linked. While disease outcome and source of infection had no correlation with a particular genotypic pattern, the sequence type was the most correlated factor with phylogeny and genotypic patterns, and a few genes were associated with non-severe cases.

中文翻译：

---

三级医院通过高通量测序对耐甲氧西林金黄色葡萄球菌 (MRSA) 进行基因组表征

耐甲氧西林金黄色葡萄球菌 (MRSA) 菌株与严重的并发症和较差的临床结果有关。在埃及，它们导致了 70% 以上的金黄色葡萄球菌医疗保健相关感染。本研究结合全基因组测序、生物信息学和统计分析，确定了埃及开罗一家三级医院 18 株 MRSA 临床分离株之间的系统发育、耐药组、病毒组和潜在的基因型-表型-临床相关性。ST1535-V MRSA 克隆是最常分离的（16.6%），其次是 ST5-VI、ST1-V 和 ST239-III（各 11.1%）。SCCmec V、VI、IV 和 III 型的检测频率分别为 50%、16.6%、11.1% 和 11.1%。在所有分离株中均未检测到测试的毒力基因，但它们的分布范围为 1/18 至 17/18。Panton–Valentine leukocidin (PVL) 编码基因仅在四个分离株中检测到，并且在导致非严重病例的分离株中富集。系统发育分析揭示了三个 ST1535-V、两个 ST5-VI、两个 ST239-III 和两个 ST1-V 之间的相关性；然而，只有两个遗传相关的 ST1-V 分离株与流行病学有关。虽然疾病结果和感染源与特定的基因型模式无关，但序列类型是与系统发育和基因型模式最相关的因素，少数基因与非严重病例相关。只有两个遗传相关的 ST1-V 分离株在流行病学上有关联。虽然疾病结果和感染源与特定的基因型模式无关，但序列类型是与系统发育和基因型模式最相关的因素，少数基因与非严重病例相关。只有两个遗传相关的 ST1-V 分离株在流行病学上有关联。虽然疾病结果和感染源与特定的基因型模式无关，但序列类型是与系统发育和基因型模式最相关的因素，少数基因与非严重病例相关。