Staphylococcus epidermidis joint isolates: Whole-genome sequencing demonstrates evidence of hospital transmission and common antimicrobial resistance

Samantha J. Simon, Mohamad Sater, Ian Herriott, Miriam Huntley, Emma Briars, Brian L. Hollenbeck
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Abstract

Objective: We investigated genetic, epidemiologic, and environmental factors contributing to positive Staphylococcus epidermidis joint cultures. Design: Retrospective cohort study with whole-genome sequencing (WGS). Patients: We identified S. epidermidis isolates from hip or knee cultures in patients with 1 or more prior corresponding intra-articular procedure at our hospital. Methods: WGS and single-nucleotide polymorphism–based clonality analyses were performed, including species identification, in silico multilocus sequence typing (MLST), phylogenomic analysis, and genotypic assessment of the prevalence of specific antibiotic resistance and virulence genes. Epidemiologic review was performed to compare cluster and noncluster cases. Results: In total, 60 phenotypically distinct S. epidermidis isolates were identified. After removal of duplicates and impure samples, 48 isolates were used for the phylogenomic analysis, and 45 (93.7%) isolates were included in the clonality analysis. Notably, 5 S. epidermidis strains (10.4%) showed phenotypic susceptibility to oxacillin yet harbored mecA, and 3 (6.2%) strains showed phenotypic resistance despite not having mecA. Smr was found in all isolates, and mupA positivity was not observed. We also identified 6 clonal clusters from the clonality analysis, which accounted for 14 (31.1%) of the 45 S. epidermidis isolates. Our epidemiologic investigation revealed ties to common aspirations or operative procedures, although no specific common source was identified. Conclusions: Most S. epidermidis isolates from clinical joint samples are diverse in origin, but we identified an important subset of 31.1% that belonged to subclinical healthcare–associated clusters. Clusters appeared to resolve spontaneously over time, suggesting the benefit of routine hospital infection control and disinfection practices.
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表皮葡萄球菌关节分离株:全基因组测序显示医院传播和常见抗菌药耐药性的证据
目的:我们调查了导致表皮葡萄球菌关节培养阳性的遗传、流行病学和环境因素。设计:全基因组测序(WGS)的回顾性队列研究。患者:我们从髋关节或膝关节培养物中分离出了表皮葡萄球菌,这些患者曾在本院接受过一次或多次相应的关节内手术。方法:WGS 和单核苷酸测序:进行了 WGS 和基于单核苷酸多态性的克隆分析,包括物种鉴定、硅多焦点序列分型 (MLST)、系统发生组分析以及特定抗生素耐药性和毒力基因流行率的基因型评估。还进行了流行病学回顾,以比较集群病例和非集群病例。结果:共鉴定出 60 株表型不同的表皮葡萄球菌分离株。去除重复样本和不纯样本后,48 个分离株被用于系统发生组分析,45 个分离株(93.7%)被纳入克隆性分析。值得注意的是,5 株表皮葡萄球菌(10.4%)对奥沙西林表现出表型敏感性,但却携带有 mecA;3 株(6.2%)尽管没有 mecA,但却表现出表型耐药性。在所有分离株中都发现了 Smr,但未观察到 mupA 阳性。我们还从克隆性分析中发现了 6 个克隆群,在 45 株表皮葡萄球菌分离物中占 14 株(31.1%)。我们的流行病学调查显示,虽然没有发现具体的共同来源,但与常见的抽吸或手术过程有关。得出结论:大多数 S. 表皮真菌分离株与常见的抽吸或手术过程有关:从临床关节样本中分离出的大多数表皮葡萄球菌来源多种多样,但我们发现有31.1%的重要亚群属于亚临床医疗相关菌群。随着时间的推移,集群似乎会自发消退,这表明常规医院感染控制和消毒措施是有益的。
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