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

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.

Keywords: Antimicrobial resistance; Historic; MLST; MRSA; Phylogeny; Switzerland; WGS.

Fig. 1

Epidemic distribution of MLST sequence types by collection year and dataset (A Public repositories, B Culture Collection of Switzerland, C Contemporary Swiss MRSA, D Legend). Samples with no collection year are not represented, n = 6. Contemporary STs with less than 100 isolates are only shown as “other” (gray). Be aware that each subfigure has a different y-axis

Fig. 2

MLST minimum spanning tree of all MRSAs (historic Swiss, historic international, and modern Swiss) generated by Ridom SeqSphere+ (n = 1761). Nodes colored by ST with CC superimposed. CCs are defined as all STs which match their central genotype (ST) in four or more loci. Branch labels show number of allelic differences

Fig. 3

cgMLST MST of CCoS and public repository genomes of MRSA (1960–1992, n = 554); nodes colored by sequence type and CCs are shaded. Clusters are shown with a maximal cluster distance of 24 allele differences and a minimal cluster size of 15. The earliest ST239 (1972) isolates are circled in red

Fig. 4

Predicted resistance/sensitivity, phenotypical resistance/sensitivity, and concordance between the two mapped to a maximum likelihood core genome SNP tree of ancient Swiss and international MRSA (1960–1992, n = 554). Leaves colored by sequence type. Outgroup (S. epidermis) line shortened through X-axis break for visualization purposes

Fig. 5

Virulence gene presence/absence heatmap mapped to a maximum likelihood core genes phylogenetic tree of historic Swiss and international MRSA (n = 554). Leaves colored by sequence type. Outgroup (S. epidermis) line shortened through X-axis break for visualization purposes