Phylogenomic insights into LA-MRSA from Argentine pig farm environments: novel OptrA variant and regional emergence of a ST9 lineage co-circulating with international CC398 lineages

María José González^1,2Julián Parada^3,4Enrique Blasko^1,2Ezequiel Jorge Sosa⁵Geehan Suleyman⁶Kaur Jagjeet⁶Gina Maki⁶Tyler Prentiss⁷Maite Corti Isgro^3,4Natalia Pereyra^3,4Rocío González¹Agostina Dagatti⁸Paula Gagetti⁹Fernanda Pacharoni¹⁰Ricardo Toselli^1,2Davor Nicolas Martinovic¹¹Cesar Bonetto^12,13Carolina Del Bo¹⁴Carina Porporatto^12,13Dario Fernández Do Porto¹⁵Laura Decca⁸José Luis Bocco^1,2María Valeria Amé^1,2Alejandra Corso⁹Alicia Isabel Carranza^3,4Marcus Zervos⁶Claudia Sola^1,2*

• ¹Departamento de Bioquímica Clínica, Universidad Nacional de Cordoba Facultad de Ciencias Quimicas, Córdoba, Argentina
• ²CONICET Centre for Research in Clinical Biochemistry and Immunology (CIBICI), Cordoba, Argentina
• ³Departamento de Patología Animal, Universidad Nacional de Rio Cuarto Facultad de Agronomia y Veterinaria, Río Cuarto, Argentina
• ⁴Instituto de Ciencias Veterinarias (INCIVET), CONICET, Río Cuarto, Argentina
• ⁵Universidad Tecnologica Nacional Facultad Regional Buenos Aires, Buenos Aires, Argentina
• ⁶Division of Infectious Diseases, Henry Ford Hospital, Detroit, United States
• ⁷The Global Health Initiative, Henry Ford Health,, Detroit, United States
• ⁸Laboratorio de Microbiología, Clínica Regional del SUD-Río IV, Río Cuarto, Argentina
• ⁹(INEI)-ANLIS “Dr. Carlos G. Malbrán”, Instituto Nacional de Enfermedades Infecciosas Servicio Antimicrobianos, Buenos Aires, Argentina
• ¹⁰Unidad de Microbiología. CEPROCOR. Ministerio de Producción, Ciencia e Innovación Tecnológica de Córdoba, Córdoba, Argentina
• ¹¹Laboratorio de Microbiología, Hospital Guillermo Rawson, Córdoba, Argentina
• ¹²Instituto Académico Pedagógico de Ciencias Básicas y Aplicadas, Universidad Nacional de Villa Maria, Villa María, Argentina
• ¹³Instituto Multidisciplinario de Investigación y Transferencia Agroalimentaria y Biotecnológica (IMITAB) CONICET, Villa María, Argentina
• ¹⁴Unidad de Microbiología. CEPROCOR. Ministerio de Producción, Ciencia e Innovación Tecnológica de Córdoba. Córdoba. Argentina, Córdoba, Argentina
• ¹⁵Departamento de Química Biológica, Universidad de Buenos Aires Facultad de Ciencias Exactas y Naturales, Buenos Aires, Argentina

Staphylococcus aureus (SA) colonizes both humans and animals. The spread of livestock-associated methicillin-resistant S. aureus (LA-MRSA) in farms and the environment poses a public health concern. While CC398 is globally predominant, regional variation exists, and data from Argentina remain scarce. This study investigated the presence, antimicrobial resistance (AMR), and genomic features of pig-associated MRSA in central Argentina, including transmission dynamics and the global phylogenetic context of LA-MRSA lineages CC398 and CC1/ST9. Between February and March 2022, 41 MRSA isolates were recovered from 50 fecal and effluent samples collected from 8 of 10 (80%) farrow-to-finish pig farms in Córdoba province, Argentina. Phenotypic susceptibility was assessed by disk diffusion and Vitek2 (CLSI 2023). Genotypic characterization included PCR for antimicrobial resistance genes (ARGs) and the immune evasion cluster (IEC), as well as PFGE, spa typing, SCCmec typing, and MLST. Twenty-four isolates underwent whole-genome sequencing (Illumina NovaSeq 6000) for resistome, virulome, and phylogenomic analysis. Antimicrobial use was extensive, with most farms reporting use of more than seven drug classes and up to 18 compounds in the previous six months. Two predominant IEC¯ LA-MRSA lineages were identified, mostly associated to SCCmecV: CC398 (53.7%, n:22), comprising ST398 (n:17, spa-types t034/t571) and ST8814 (n:5, t571); and CC1/ST9 (41.5%, n:17, spa-t16964). One IEC+ CA-MRSA lineage (CC8/ST72, n:2, SCCmecIVa) was also detected. All isolates were multidrug-resistant (MDR), with LA-MRSA showing broader resistance across 4–7 antimicrobial classes. Multiple ARGs matched phenotypic resistance, except optrA, found in ST398 (n:5) and ST9 (n:1) despite borderline linezolid MICs (2–4 µg/mL), representing the first report of optrA in S. aureus in Argentina. WGS revealed a novel optrA variant (OptrA/FDKFP), likely linked to a mobile genetic element. Phylogenetic analysis revealed the local emergence of a distinct ST9 clade and multiple introductions of CC398 within internationally recognized subgroups (C6/AAP and C6/EP4). These findings underscore pig farms as emerging reservoirs of multidrug-resistant MRSA both locally and globally, reinforcing the need for targeted surveillance and control strategies at the animal–human interface