Genomic insights into methicillin-resistant Staphylococcus aureus from Swiss wastewater and clinical samples

Objectives: To determine whether methicillin-resistant Staphylococcus aureus (MRSA) recov-ered from wastewater, as a proxy for community carriage, and clinical settings represent distinct populations and whether their comparison provides insight into distinctions between healthcare-associated (HA-) and community-associated (CA-) MRSA. Methods: We analyzed whole-genome sequences from 115 MRSA isolates collected in Switzer-land between 2021 and 2024, including 89 from three hospitals and 26 from six wastewater treatment plants serving the hospital catchment areas. We compared the phylogenetic relatedness, sequence types (STs), SCCmec types, spa types, antimicrobial resistance genes (ARGs), and viru-lence factors between the two sources. Results: Amongst all isolates, few were closely genetically related, with only 5% (273/6,105) of the pairwise comparisons differing by [≤]15 core-genome single nucleotide polymorphisms. Amongst the 89 clinical isolates, there were 23 STs and 46 spa types as compared to 6 STs and 9 spa types amongst the 26 wastewater isolates. All wastewater isolates (100%, or 26/26) and most clinical isolates (64%, or 57/89) were SCCmec IV, historically associated with CA-MRSA. Pan-ton-Valentine Leukocidin genes, which historically indicated virulence associated with CA-MRSA, were detected in 37% (43/115) of isolates, including 40% (36/89) of clinical isolates and 27% (7/26) of wastewater isolates. One wastewater ST (ST97, 6/26 isolates) was phylogenetically distinct from all clinical isolates and corresponds to a known livestock-associated MRSA lineage, while other STs identified in wastewater are known to circulate in livestock or communities (ST22, ST88, ST1482). Conclusions: Our findings highlight the effectiveness of clinical surveillance in monitoring MRSA epidemiology in Switzerland, with most major lineages, antimicrobial resistance determi-nants, and virulence factors identified in wastewater also present among clinical isolates. Notably, wastewater isolates shared sequence types with known livestock and CA-MRSA lineages. This suggests wastewater supplements traditional methods in understanding community circulation but provides limited unique insight into clinical circulation.