Prevalence and molecular epidemiology of methicillin-resistant Staphylococcus aureus in livestock farmers, livestock, and livestock products in southern Sri Lanka: A one health approach

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Methicillin-resistant Staphylococcus aureus (MRSA) colonization can lead to subsequent severe infections. Unlike community and hospital-associated types, Livestock-associated MRSA (LA-MRSA) transmits to humans through direct contact with livestock and contaminated livestock products. This study aimed to investigate MRSA prevalence and molecular epidemiology in livestock farmers, livestock, and livestock products, including LA-MRSA presence and MRSA abundance in human and animal nasal microbiome, in southern Sri Lanka using a One Health approach. Nasal swabs from farmers and livestock on 50 farms (Nov 2020 - Dec 2021) and livestock products were collected. MRSA was isolated and confirmed using standard microbiological techniques. Staphylococcal chromosomal cassette mec typing, spa typing, and multilocus sequence typing were performed. Identified clones were compared with hospital isolates. Metagenomics analysis was performed on selected samples. MRSA prevalence was 24.0 % (12/50) in farms, 7.9 % (12/152) in farmers, 2.1 % (5/240) in livestock, and 1.9 % (3/157) in products. Of 372 S. aureus collected from clinical cultures, 59.4 % were MRSA. MRSA clones were identified in farm personnel (CC5/ST5/t002, CC1/ST1/t127, and ST45/CC45/t026), livestock (CC5/ST5/t002), and clinical cultures (CC5/ST5/t002 and CC5/ST6/t304), with ST45/CC45/t026 and CC5/ST6/t304 reported for the first time in Sri Lanka. LA-MRSA clones (ST389/ST9) were not detected. Animals had more diverse nasal microbiomes and lower MRSA abundance (<1.4 %) compared to humans (>82.3 %). MRSA colonization prevalence in southern Sri Lanka was relatively low. Two new clones and no LA-MRSA clones were identified. This study highlights the importance of continuing MRSA surveillance under the One Health framework to identify MRSA transmission between humans, animals, and the environment. • There is a gap in knowledge in the epidemiology of MRSA in Southern Sri Lanka. • Utilized standard microbiological and advanced molecular techniques for the characterization of MRSA. • Relatively low MRSA colonization prevalence was observed indicating two new MRSA clones with no established LA-MRSA clones present. • The first reported metagenomics analysis of human and animal nasal microbiome linked to MRSA in Sri Lanka. • Emphasis on the need for ongoing MRSA surveillance under the One Health framework.

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