Historic methicillin-resistant Staphylococcus aureus: expanding current knowledge using molecular epidemiological characterization of a Swiss legacy collection.

IF 10.4 1区生物学 Q1 GENETICS & HEREDITY

Genome Medicine Pub Date : 2024-02-05 DOI:10.1186/s13073-024-01292-w

Vanni Benvenga, Aline Cuénod, Srinithi Purushothaman, Gottfried Dasen, Maja Weisser, Stefano Bassetti, Tim Roloff, Martin Siegemund, Ulrich Heininger, Julia Bielicki, Marianne Wehrli, Paul Friderich, Reno Frei, Andreas Widmer, Kathrin Herzog, Hans Fankhauser, Oliver Nolte, Thomas Bodmer, Martin Risch, Olivier Dubuis, Sigrid Pranghofer, Romana Calligaris-Maibach, Susanne Graf, Vincent Perreten, Helena M B Seth-Smith, Adrian Egli

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引用次数: 0

Abstract

Background: Few methicillin-resistant Staphylococcus aureus (MRSA) from the early years of its global emergence have been sequenced. Knowledge about evolutionary factors promoting the success of specific MRSA multi-locus sequence types (MLSTs) remains scarce. We aimed to characterize a legacy MRSA collection isolated from 1965 to 1987 and compare it against publicly available international and local genomes.

Methods: We accessed 451 historic (1965-1987) MRSA isolates stored in the Culture Collection of Switzerland, mostly collected from the Zurich region. We determined phenotypic antimicrobial resistance (AMR) and performed whole genome sequencing (WGS) using Illumina short-read sequencing on all isolates and long-read sequencing on a selection with Oxford Nanopore Technology. For context, we included 103 publicly available international assemblies from 1960 to 1992 and sequenced 1207 modern Swiss MRSA isolates from 2007 to 2022. We analyzed the core genome (cg)MLST and predicted SCCmec cassette types, AMR, and virulence genes.

Results: Among the 451 historic Swiss MRSA isolates, we found 17 sequence types (STs) of which 11 have been previously described. Two STs were novel combinations of known loci and six isolates carried previously unsubmitted MLST alleles, representing five new STs (ST7843, ST7844, ST7837, ST7839, and ST7842). Most isolates (83% 376/451) represented ST247-MRSA-I isolated in the 1960s, followed by ST7844 (6% 25/451), a novel single locus variant (SLV) of ST239. Analysis by cgMLST indicated that isolates belonging to ST7844-MRSA-III cluster within the diversity of ST239-MRSA-III. Early MRSA were predominantly from clonal complex (CC)8. From 1980 to the end of the twentieth century, we observed that CC22 and CC5 as well as CC8 were present, both locally and internationally.

Conclusions: The combined analysis of 1761 historic and contemporary MRSA isolates across more than 50 years uncovered novel STs and allowed us a glimpse into the lineage flux between Swiss-German and international MRSA across time.

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历史上的耐甲氧西林金黄色葡萄球菌：利用瑞士遗留菌种的分子流行病学特征扩展现有知识。

背景：耐甲氧西林金黄色葡萄球菌（MRSA）在全球出现初期的测序结果寥寥无几。有关促进特定 MRSA 多焦点序列类型（MLST）成功的进化因素的知识仍然很少。我们的目的是描述从 1965 年到 1987 年分离出来的 MRSA 的特征，并将其与公开的国际和本地基因组进行比较：我们访问了保存在瑞士菌种保藏中心（Culture Collection of Switzerland）的 451 株历史（1965-1987 年）MRSA 分离物，其中大部分采集自苏黎世地区。我们确定了表型抗菌药耐药性（AMR），并使用 Illumina 短线程测序技术对所有分离株进行了全基因组测序（WGS），同时使用牛津纳米孔技术对部分分离株进行了长线程测序。为了解背景情况，我们纳入了从 1960 年到 1992 年的 103 个公开可用的国际汇编，并对从 2007 年到 2022 年的 1207 个现代瑞士 MRSA 分离物进行了测序。我们分析了核心基因组（cg）MLST和预测的SCCmec盒类型、AMR和毒力基因：结果：在 451 例瑞士 MRSA 历史分离株中，我们发现了 17 种序列类型（ST），其中 11 种之前已有描述。两个 ST 是已知位点的新组合，6 个分离株携带以前未提交的 MLST 等位基因，代表 5 个新 ST（ST7843、ST7844、ST7837、ST7839 和 ST7842）。大多数分离株（376/451，占 83%）代表了 20 世纪 60 年代分离的 ST247-MRSA-I，其次是 ST7844（25/451，占 6%），它是 ST239 的新型单基因座变异株（SLV）。cgMLST 分析表明，属于 ST7844-MRSA-III 的分离物聚集在 ST239-MRSA-III 的多样性中。早期的 MRSA 主要来自克隆复合体（CC）8。从 1980 年到 20 世纪末，我们观察到 CC22、CC5 和 CC8 在本地和国际上都存在：通过对 50 多年来 1761 株历史和当代 MRSA 分离物的综合分析，我们发现了新的 STs，并得以一窥瑞士-德国和国际 MRSA 之间不同时期的血统变化。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Genome Medicine GENETICS & HEREDITY-

CiteScore

20.80

自引率

0.80%

发文量

128

审稿时长

6-12 weeks

期刊介绍： Genome Medicine is an open access journal that publishes outstanding research applying genetics, genomics, and multi-omics to understand, diagnose, and treat disease. Bridging basic science and clinical research, it covers areas such as cancer genomics, immuno-oncology, immunogenomics, infectious disease, microbiome, neurogenomics, systems medicine, clinical genomics, gene therapies, precision medicine, and clinical trials. The journal publishes original research, methods, software, and reviews to serve authors and promote broad interest and importance in the field.

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