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

TL;DR

This study identifies new antibiotic-resistant MRSA strains in Argentine pig farms, including a novel OptrA variant and a local ST9 lineage coexisting with global CC398 strains.

Contribution

The discovery of a novel OptrA variant and the regional emergence of an ST9 lineage in Argentina adds new insights into the genomic diversity and spread of LA-MRSA.

Findings

Two predominant LA-MRSA lineages (CC398 and CC1/ST9) were identified in Argentine pig farms.

A novel OptrA variant (OptrA/FDKFP) was discovered in MRSA isolates, marking the first report of optrA in Argentina.

Phylogenetic analysis revealed a distinct ST9 clade and multiple introductions of CC398 subgroups in the region.

Abstract

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.

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