Staphylococcus aureus (SA) is a common commensal in humans and animals, including livestock, and a major opportunistic pathogen responsible for infections ranging from skin lesions to fatal bacteremia (Park and Ronholm, 2021). Beyond its virulence, its significance lies in its remarkable ability to acquire antimicrobial resistance, particularly methicillin resistance (MRSA), and to spread across healthcare (HA), community (CA), and livestock-associated (LA) settings (Park and Ronholm, 2021; Kasela et al., 2023). In 2019, SA was the leading bacterial cause of death globally and the second in antimicrobial resistance (AMR)-related mortality, ranking first in the Americas. It also showed the sharpest increase in AMR-attributed deaths from 1990 to 2021 and is classified by WHO as a high-priority pathogen (GBD 2019 Antimicrobial Resistance Collaborators, 2022; GBD 2021 Antimicrobial Resistance Collaborators, 2024; Antimicrobial Resistance Collaborators, 2022, 2023; Sati et al., 2025).

Within the One Health framework, AMR is driven by antimicrobial use in human medicine, agriculture, and animal production, particularly pig farming, and by environmental stressors such as heavy metals, which facilitate the persistence and spread of AMR-bacteria and AMR-genes (ARGs) across human-animal-environmental sectors (Wang et al., 2023; Khairullah et al., 2023). In 2015, Argentina adopted the One Health approach and launched a national AMR strategy. In August 2022, legislation was passed to regulate antibiotic use and sales in both human and veterinary contexts.¹ In pig production, antimicrobials are widely used for treatment and prevention. Antibiotic growth promoters have been banned in several countries, including Argentina since 2024 (SNSyCAA/Res.445, 2024), but remain permitted elsewhere (Muurinen et al., 2021).

Although SA is endemic worldwide, the emergence of high-risk clones (HRCs), defined by enhanced transmissibility, virulence, and/or multidrug resistance (MDR), has accelerated its global spread (Aanensen et al., 2016). MDR HA-MRSA clones have circulated in hospitals since 1959. From the 1980s, distinct CA-MRSA clones emerged with regional variation and now also cause hospital-onset infections (Egea et al., 2014; Lakhundi and Zhang, 2018; Barcudi et al., 2020). LA-MRSA is a significant zoonotic pathogen of growing global public health concern. It was first isolated from bovine mastitis in 1972, and zoonotic transmission from pigs (ST398 lineage) was first reported in the Netherlands in 2005 (Wang et al., 2023). Today, pigs are recognized as important reservoirs of MDR LA-MRSA, primarily acting as asymptomatic carriers colonized on skin and mucosa. Direct animal contact is the main transmission route on farms, while contaminated environments and animal products further amplify dissemination (Khairullah et al., 2023; Wang et al., 2023). MRSA positivity in pig farms varies by region; in countries such as Denmark and the Netherlands, over 75% of farms are MRSA-positive (Sieber et al., 2018; EFSA and ECDC, 2023).

While the prevalence of MDR LA-MRSA remains lower than that of HA- or CA-MRSA, infections are increasing, sometimes in individuals without livestock contact, raising public health concerns, particularly in regions with intensive pig production (Chen et al., 2020; Matuszewska et al., 2022; Chen et al., 2023; Khairullah et al., 2023; Campana-Burguet et al., 2025) Human-to-human transmission has been reported, especially from farm workers to household members, and occasionally in healthcare settings (Avbersek et al., 2021; Crespo-Piazuelo and Lawlor, 2021; Wang et al., 2023). Reverse zoonosis from humans to pigs has also been documented (Narvaez-Bravo et al., 2016; Sahibzada et al., 2017).

Clonal complex (CC) 398 is the dominant LA-MRSA lineage worldwide, particularly in Europe, but has also been reported in the Americas, Asia, and Oceania (Sahibzada et al., 2017; Kruger-Haker et al., 2023; Khairullah et al., 2023; Gagetti et al., 2023b). Another key lineage, ST9/CC1, predominates in Asia and is emerging in the USA and Europe (Kasela et al., 2023; Wang et al., 2023; Khairullah et al., 2023). Both lineages commonly exhibit MDR and have been linked to zoonotic transmission, including cases without direct livestock contact (Chen et al., 2020; Jin et al., 2020; Chen et al., 2023; Kruger-Haker et al., 2023). Of particular concern is their resistance to oxazolidinones, last-resort drugs for Gram-positive infections in humans. Three transferable resistance genes, cfr, optrA, and poxtA, have been primarily identified in livestock-associated staphylococci and are notable for their cross-resistance, mobility, and co-selection potential (Schwarz et al., 2018; Schwarz et al., 2021; Timmermans et al., 2021).

Phylogenetic evidence suggests that LA-CC398 originated from a human-associated methicillin-susceptible Staphylococcus aureus (MSSA) ancestor that acquired tet (M) and SCCmec elements after transmission to livestock, while losing the immune evasion cluster (IEC). IEC reacquisition facilitates re-adaptation to human, illustrating the bidirectional nature of zoonotic transmission. Notably, IEC gain/loss drives host shifts not only in CC398 but also in CC1/ST9, CC1, and CC5 (Matuszewska et al., 2022; Wang et al., 2023; Chen et al., 2020; Yu et al., 2021). Accordingly, CC398 comprises two major clades: a livestock-associated (LA) clade [IEC⁻, tet(M)⁺, mostly MRSA] and a human-associated (HuA) clade [IEC⁺, tet(M)⁻, mostly MSSA] (Wang et al., 2023). A recent study of over 3,000 CC398 genomes revealed geographically structured phylogroups across Asia, Europe, and the Americas, each with distinct resistance and virulence profiles (Fernandez et al., 2024), emphasizing the need for regional genomic surveillance of LA-SA.

In Argentina, SA infections have increased by 23.4% over the past decade, primarily driven by community-onset MSSA with rising macrolide and gentamicin resistance, particularly the CC398-t1451-erm(T)⁺ clone (Di Gregorio et al., 2023; Barcudi et al., 2024). Although MRSA incidence remained stable and mostly HA-related, a shift from ST5-I to diverse clones, CC5 (ST5-IV, ST100-IV), CC30 (ST30-IV), and minor lineages such as CC97 (ST97-IV) and CC8 (ST8-IV, ST72-IV); has been observed (Barcudi et al., 2024).

Pig farming is a key sector in Latin America, with pork consumption increasing by 57% between 2005 and 2022 (Roppa et al., 2024). Brazil and Mexico lead the sector, followed by Argentina and Colombia, which together contribute 14% of global exports. In Argentina, production is concentrated in Córdoba and Buenos Aires (24% each of national stock), and is highly fragmented: just 2% of farms (>2,500 sows) produce half the slaughter pigs (SAGyP, 2023). Despite the known role of pigs as MRSA reservoirs, data on circulating lineages in Argentine farms remain limited (Gagetti et al., 2023b).

This study aimed to: (i) identify and characterize MRSA strains from pig farm environments (feces/sludge and effluents) in the central region of Argentina (Córdoba Province); and (ii) characterize LA-MRSA lineages CC1/ST9 and CC398 using whole-genome sequencing, with a focus on resistome and virulome. Potential MRSA transmission within and between farms was also assessed. Additionally, a comparative phylogenetic analysis was performed using publicly available genomes from the Americas, Europe, and Asia to contextualize Argentine isolates globally.

Intensified livestock production and extensive antimicrobial use raise concerns about farm animals as reservoirs of antibiotic-resistant pathogens transmissible to humans (Rhouma et al., 2022; Kasela et al., 2023; Campana-Burguet et al., 2025). In this study, 80% of pig farms in central Argentina were MRSA-positive during February–March 2022, particularly nursery and finishing units, with co-occurrence of major LA-MRSA lineages CC398 and CC1/ST9. All farms had used multiple antimicrobials in the preceding 6 months, underscoring the widespread antimicrobial pressure in these systems. Although our survey covered only 6% of all farms with more than 100 sows in Córdoba (n: 166) (SAGyP, 2023), Argentina’s leading pig-producing province, the high MRSA prevalence aligns with reports from some European countries (Denmark, Netherland, Germany) where LA-MRSA rates reach 70–80%, and contrasts with lower prevalence in Italy (38%), Canada (45%), Sri Lanka (10%), and Japan (8.3–29.6%) (Sieber et al., 2018; Kalupahana et al., 2019; EFSA and ECDC, 2023; Khairullah et al., 2023; Kruger-Haker et al., 2023; Kawanishi et al., 2024). Consistent with previous studies, the fattening and nursery stages were most frequently MRSA-positive, likely driven by increased animal movements and suboptimal hygiene and disinfection practices facilitating bacterial spread (Crombe et al., 2013; Khairullah et al., 2023). A prior Argentine study also reported substantial nasal colonization (29.7%) in fattening pigs (Gagetti et al., 2023b), supporting our findings.

The detection of MDR MRSA in 80% of farms underscores its zoonotic potential, particularly for farm workers with daily animal contact, who may be exposed occupationally while also serving as carriers and vectors to their households and communities (Xin et al., 2022; Kasela et al., 2023; Wang et al., 2023). This risk is amplified by the environmental persistence of LA-MRSA in dust, manure, air, equipment, and improperly handled carcasses, which can also affect wildlife (Abdullahi et al., 2021), facilitating spread beyond farm boundaries and raising concerns for community and food-chain exposure (Xin et al., 2022; EFSA and ECDC, 2023). These findings, consistent with Argentina’s 2022 legislation promoting prudent antimicrobial use (enacted shortly after this study and providing a baseline for future evaluation), also reveal major surveillance gaps in livestock reservoirs, particularly pig farms, recognized hotspots for AMR transmission (Xin et al., 2022), where systematic monitoring is still lacking. Strengthening LA-MRSA surveillance within a One Health framework is therefore critical, encompassing antimicrobial stewardship to reduce selection pressure, enhanced farm biosecurity, including proper management of effluents and carcasses to minimize environmental contamination, regulation of animal movements, and occupational protection for workers (Wang et al., 2023; Khairullah et al., 2023; Sawodny et al., 2025). Together, these considerations highlight the broader public health importance of our findings and underscore the need for coordinated One Health strategies across the animal–human–environment interface to mitigate zoonotic risk and curb AMR dissemination.

LA-MRSA strains in pigs show regional variation: CC398 predominates in Europe, the Americas, Australia, and recently Asia, whereas ST9/CC1 dominates in Asia (particularly China) and occurs sporadically elsewhere, also emerging as LA-MSSA in North America (Randad et al., 2021; Yu et al., 2021; Li et al., 2022; Narongpun et al., 2023; Khairullah et al., 2023; Kawanishi et al., 2024; Campana-Burguet et al., 2025). Although less studied and less widespread than CC398, ST9 has also been implicated in human infections, including cases without direct animal contact (Schwarz et al., 2018; Chen et al., 2020; Avbersek et al., 2021; Yu et al., 2021; Chen et al., 2023). In central Argentina, however, both IEC¯ LA-MRSA lineages were identified: CC398 (spa-t034, spa-t571; ST398 and the novel ST8814) in five farms, and CC1/ST9 (spa-t16964) in three farms, co-occurring in one farm. The unusual coexistence of both globally dominant LA-MRSA clones raises public health concerns due to their potential for interspecies transmission and resistance gene exchange, highlighting the need for molecular surveillance to track lineage evolution, AMR dissemination, and zoonotic risk, which is essential for timely One Health interventions.

In line with previous studies (Richardson et al., 2018), phylogenetic analysis of MRSA isolates revealed lineage-based clustering: CC398 formed a distinct clade, while CC1/ST9 and CC8/ST72 grouped separately. Furthermore, the transmission analysis with core SNP showed intra-farm dissemination of ST398 and ST9 across pig-associated environments in Argentina’s central region, which accounts for 24% of national pig production. While both clones spread within farms, likely between pens or animal categories, only ST9 exhibited inter-farm transmission, highlighting the pig-environment as a reservoir for LA-MRSA, consistent with previous reports (Avbersek et al., 2021; Randad et al., 2021; Li et al., 2022; Li et al., 2022; Hu et al., 2023; Talim et al., 2024). LA-MRSA contaminates soil, water, air, and crops, mainly via manure and airborne particles, facilitating long-distance spread (Wang et al., 2023; Xin et al., 2022). Inter-farm transmission may be driven by animal movements, environmental contamination (e.g., feed, air, water, equipment), human mobility (e.g., farm-workers, veterinarians), and lineage-specific adaptability (Crombe et al., 2013; Kruger-Haker et al., 2022; Chen et al., 2023; Kasela et al., 2023). The restriction of inter-farm spread to ST9 may reflect its greater environmental or host adaptability. Understanding these lineage-specific dynamics is crucial for designing targeted interventions at the animal–environment–human interface, and larger-scale studies including molecular analysis of MRSA are needed to test this hypothesis.

Notably, CC398 exhibits high diversity in spa types, STs, and SCCmec elements, reflecting ongoing microevolution and evolutionary plasticity (Monecke et al., 2018; Kruger-Haker et al., 2023; Fernandez et al., 2024) as evidenced by the novel ST8814 identified in this study. Consistent with previous findings in pig-associated LA-MRSA (Avbersek et al., 2021; Matuszewska et al., 2022), WGS revealed that most LA-MRSA isolates (CC398 and ST9) carried SCCmecVc (5C2&5), particularly the complete form in CC398MRSA, typically encoding mecA, tet(K), and czrC, conferring resistance to β-lactams, tetracycline, and zinc (a common feed additive), thereby supporting the role of co-selection in maintaining resistant strains (Matuszewska et al., 2022; Rhouma et al., 2022; Khairullah et al., 2023). We also detected rare SCCmec variants: a Vc-like type with an additional ccrA1B1 complex and an IIIA-like type containing only the 3A component. Such variants, sporadically reported in CC398 from livestock or clinical isolates, underscore the remarkable plasticity of SCCmec (Nemeghaire et al., 2014; Peeters et al., 2015; Monecke et al., 2018; Kruger-Haker et al., 2023; Narongpun et al., 2023; Fernandez et al., 2024). Importantly, SCCmec excision and potential horizontal transfer raise concerns about dissemination to more virulent or clinically relevant S. aureus lineages, representing an emerging public health threat (Huber et al., 2022; Monecke et al., 2018). Continued surveillance and research are essential to elucidate the selective pressures driving SCCmec diversification and its implications for LA-MRSA control.

Consistent with previous reports (Khairullah et al., 2023; EFSA and ECDC, 2023; Wang et al., 2023), we detected a community-associated MRSA lineage (CC8/ST72-t3092-SCCmecIVa, IEC⁺) in one farm. Sporadic detection of CA- and HA-MRSA clones primarily associated with humans (e.g., ST5, ST8, ST22, ST30, ST45) in pig-associated environments likely reflects human-to-animal transmission, with potential subsequent host adaptation through MGEs, mutations, or recombination events (Richardson et al., 2018; Matuszewska et al., 2022). Thus, MRSA distribution in pigs is shaped not only by livestock factors but also by regional human clones (Kasela et al., 2023; Khairullah et al., 2023), as illustrated by ST93 dominating in Australia (Sahibzada et al., 2017), USA100 in Canada (Narvaez-Bravo et al., 2016), and an animal-adapted ST5-IV-IEC¯ variant in Japan (Kaku et al., 2022; Kawanishi et al., 2024). In our study, ST72/CC8 was detected on one farm; although still minor in Argentina (Barcudi et al., 2024), it is increasing in Chile (Martinez et al., 2023) and is the predominant CA-MRSA in South Korea, where it circulates among humans, pigs, and the environment (Moon et al., 2019). WGS revealed a novel νSaα variant (type X-like) in ST72 that, similar to other MGEs carrying ARGs and virulence genes in SA (Ba et al., 2023), may facilitate persistence across hosts and environments (Moon et al., 2016). These findings underscore the need for genomic surveillance to monitor the adaptation and potential establishment of MRSA ST72/CC8 in pig farms.

LA-MRSA strains from pigs show resistance to multiple antibiotics commonly used in animal production and human medicine, primarily mediated by MGEs (Matuszewska et al., 2022; Khairullah et al., 2023; Wang et al., 2023; Talim et al., 2024). In this study, all pig-environment MRSA isolates displayed MDR phenotypes, with LA-MRSA showing the broadest profiles, spanning 4–7 antimicrobial classes; over 50% were resistant to six or more, including β-lactams, tetracyclines, phenicols, fluoroquinolones, macrolide-lincosamides, trimethoprim/sulfamethoxazole, and aminoglycosides. In contrast, the two CA-MRSA ST72/CC8 strains exhibited narrower resistance spectra, although broader than those of CA-MRSA lineages circulating in humans in Argentina (Barcudi et al., 2024). Extensive antimicrobial use on these farms and prolonged environmental persistence of some of these, particularly tetracyclines, likely drove the emergence and spread of MDR strains (Rhouma et al., 2022). This represents a significant public health concern, as pig-to-human transmission of LA-MRSA, with broader resistance profiles than HA- or CA-MRSA in Argentina (Barcudi et al., 2024), could further limit treatment options.

Resistance profiles aligned with characteristic ARG patterns of pig-derived SA (Kruger-Haker et al., 2023; Narongpun et al., 2023; Talim et al., 2024; Randad et al., 2021; Ji et al., 2021; Li et al., 2022). These included both commonly reported ARGs in animal-associated staphylococci (e.g., tet, erm, blaZ, mecA) and less common or novel determinants such as those conferring resistance to aminocyclitols (spc-v, spw), fosfomycin (fosB), lincosamides–pleuromutilins–streptogramin A [vga(A), lsa(E)], trimethoprim (dfrK), and phenicols–oxazolidinones (optrA). Many were linked to MGEs, primarily transposons, small plasmids, or the spw-cluster of probable enterococcal origin (Schwarz et al., 2018; Fessler et al., 2018c; Ji et al., 2022; Kruger-Haker et al., 2023). Co-occurrence of multiple ARGs conferring resistance to the same antimicrobial class was frequent, likely due to their co-localization on MGEs (Schwarz et al., 2018; Kruger-Haker et al., 2023). In addition to mecA and blaZ, shared resistance elements across lineages included erm(C), fexA, optrA, and the gyrA(S84L) mutation, all previously reported in LA-MRSA (Yu et al., 2021; Chen et al., 2023; Fernandez et al., 2024). The plasmid-borne erm(C), the most common MLS_B gene in staphylococci, was located on a pDLK1-like RepL-type plasmid in both lineages, supporting horizontal transfer. Such plasmids facilitate erm(C) dissemination among staphylococci and other Firmicutes, likely driven by macrolide use (e.g., tylosin) in livestock (Lanza et al., 2015; Fessler et al., 2018a, 2018c). The fexA gene, encoding an MFS efflux pump for chloramphenicol/florfenicol, was carried on chromosomal Tn558, likely reflecting selective pressure from florfenicol use in food animals (Rhouma et al., 2022).

The optrA gene, which confers transferable resistance to phenicols and oxazolidinones, is concerning as it may compromise linezolid, a last-resort antibiotic (Schwarz et al., 2021; Timmermans et al., 2021; Li et al., 2022). In Argentina, optrA-mediated resistance was recently reported in clinical E. faecalis (Gagetti et al., 2023a). We detected optrA in six isolates (five ST398 from ID1, one ST9 from ID7), all resistant to chloramphenicol with borderline linezolid MICs (2–4 μg/mL). WGS revealed a novel OptrA variant (OptrA/FDKFP_SA7603-7633), not previously described (Morroni et al., 2017; Schwarz et al., 2021), in both lineages, suggesting mobilization via MGEs. Variant-specific mutations appeared to variably influence linezolid MICs, suggesting that resistance may depend not only on OptrA but also on additional, unidentified factors (Zhu et al., 2020; Schwarz et al., 2021). Thus, the clinical significance of optrA in S. aureus with MICs near the susceptibility breakpoint remains uncertain. optrA was found on short contigs (99.6% identity to the E. faecalis pL14 plasmid), limiting contextual resolution. Notably, only the optrA-positive isolates carried the plasmid-borne bleO gene and an Inc18-type plasmid. Similar optrA contexts, sometimes co-localized with cfr, have been reported on plasmids in S. sciuri, E. casseliflavus, and LA-MRSA (ST9, ST398) from humans and animals, particularly in China (Schwarz et al., 2021; Li et al., 2022; Dos Santos et al., 2023). Consequently, our results suggest that optrA is MGE-associated in both LA-MRSA lineages studied, though hybrid assemblies are needed for confirmation. Our study provides the first evidence of optrA-positive S. aureus in Argentina, highlighting pig farms as potential reservoirs. Further research is required to elucidate its clinical relevance, zoonotic and environmental dissemination, genetic context, and detection strategies, ultimately defining its public health impact.

In line with previous studies (Ji et al., 2021), CC398 and ST9 displayed distinct AMR profiles and lineage-specific ARG repertoires and contexts, reflecting intra-lineage homogeneity and differential adaptation to antimicrobial use (Fessler et al., 2018b; Jiang et al., 2019; Narongpun et al., 2023). CC398, particularly the novel ST8814, exhibited broader resistance spectra (6–7 classes), with higher rates to minocycline [tet(M)], trimethoprim-sulfamethoxazole (dfrG), and gentamicin (aacA-aphD), linked to a greater number of plasmid- or transposon-borne ARGs promoting horizontal transfer and co-selection (Fessler et al., 2018a). Enriched ARGs included erm(T), lnu(B)-lsa(E), tet(M)/(K), aadD, aac(6′)-aph(2″), spw, dfrG/K, and grlA(S80Y), many within MGEs such as the enterococcal-derived aadE-spw-lsa(E)-lnu(B) MDR cluster, reported in CC398 and ST9 from pigs and humans in Europe and Asia (Wendlandt et al., 2013; Wendlandt et al., 2014; Yu et al., 2021; Kruger-Haker et al., 2023). This cluster was plasmid-borne in most isolates and chromosomally integrated in one spa-t034 strain via Tn560, a Tn554-family transposon described in Chinese porcine ST398 LA-MRSA (Ji et al., 2022; Kruger-Haker et al., 2023). All spa-t571 strains exclusively carried aac(6′)-aph(2″) on plasmid-borne Tn4001, erm(T) on a pKKS25-like plasmid, plasmid-borne dfrG, and an additional plasmid-borne blaZ operon copy. The pKKS25 plasmid, first identified in a porcine ST398 strain from Germany (Kadlec and Schwarz, 2010), harbors erm(T), dfrK, and tet(L), flanked by ISSau10, key to ARGs dissemination. Intensive use of β-lactams, tetracyclines, aminoglycosides, and macrolides in local pig production likely drove ARGs selection and MGE-mediated co-selection in CC398, especially in the spa-t571 group. Consistently, fosB subtypes, common in staphylococci (Fu et al., 2016; Hu et al., 2023), were detected in two farms with prior fosfomycin use: fosB6 in spa-t571 strains closely-related from farm ID2, suggesting within-farm transmission, and fosB3 in spa-t034 strains from farm ID6, likely acquired via plasmid transfer or interspecies exchange with enterococci under selective pressure. Similar findings in Chinese duck farms (Hu et al., 2023) underscore farms, as reservoirs of fosB-positive MRSA.

In contrast, the plasmids pVGA/[vga(A)] and pG38-like, and the grlA(S80F) fluoroquinolone-resistance mutation, were restricted to ST9 MRSA. pG38-like, carrying aadD, tet(T), and tet(L), confers tetracycline-resistance via ribosomal protection/[tet(T)] and efflux/[tet(L)], is rare in SA, and likely also reflects selection pressure from intensive tetracycline use (Fessler et al., 2018b; Jiang et al., 2019; Narongpun et al., 2023).

Collectively, these findings support the hypothesis that CC398, likely due to the absence of a type I restriction-modification system in νSaβ, is more prone to acquiring exogenous ARGs, enhancing its adaptability (Ji et al., 2021; Kruger-Haker et al., 2022).

Overall, pig-environment LA-MRSA CC398 and ST9/CC1 isolates showed similar virulence profiles, lacking IEC genes (sak, chp, scn), consistent with animal adaptation (Wang et al., 2023). Although they did not carry major virulence factors such as Panton-Valentine leukocidin or toxic-shock-syndrome toxin-1, both harbored genes linked to adhesion, colonization, biofilm formation, and diverse infections. They also contained multiple hemolysins and the SaPIpig1 element, a SaPIbov4 variant within νSaα type V, encoding vwb (von Willebrand factor-binding protein), which promotes plasma clotting in pigs, sheep, and cattle, enhancing colonization in pigs and its transmission between individuals (Ji et al., 2021). SaPIpig1 also carries scn (staphylococcal-complement-inhibitor), potentially facilitating human colonization (Fernandez et al., 2024), underscoring its role in host adaptation and dissemination of ST398 and ST9 (Ji et al., 2021; Fernandez et al., 2024). Lineage-specific virulence traits were identified: CC1/ST9 strains carried additional sel genes (sel27 within νSaβ type XIII with the egc cluster, as well as selv and sely), which together with MDR may increase pathogenic potential and foodborne risk (Schwendimann et al., 2021; Klaui et al., 2019). In contrast, CC398 strains harbored cna, encoding a collagen-binding protein linked to osteomyelitis and arthritis (Madani et al., 2017), and a hysA homolog within νSaβ type V, previously detected in a human LA-MRSA ST398 endocarditis case and associated with greater virulence than CC1/ST9 (Ji et al., 2021). Collectively, these features highlight the invasive potential of pig-associated LA-MRSA and their public health threat, particularly for immunocompromised individuals or those with comorbidities (Ji et al., 2021; Li et al., 2022; Kasela et al., 2023).

The whole-genome phylogenetic analysis of pig-environment CC398 isolates from Argentina, placed in a global framework, revealed their distribution across two major clades: A (spa-t571) and C (spa-t034). Both belonged to the LA clade and clustered with C6 clade reference strains (Fernandez et al., 2024), a group driving CC398 dissemination in Europe through the European MRSA phylogroups EP3, EP4, and EP5, and also reported in Asia and the Americas as part of the American–Asian phylogroup (AAP). Within clade A (spa-t571), MRSA from Córdoba (farms ID2, ID9), including the novel ST8814, clustered with MSSA strains from a local river and previously identified C6/AAP strains (Fernandez et al., 2024). This group also included a pig isolate from Santa Fe province (Gagetti et al., 2023b) and strains from China and South Korea (Li et al., 2022). These spa-t571 MRSA formed a distinct lineage, separated by over 3,600 SNPs from other clades, consistent with earlier studies (Li et al., 2022; Fernandez et al., 2024). The AAP phylogroup, predominantly spa-t571, includes both MSSA and MRSA primarily from pigs and humans in Asia and the Americas. These strains lack IEC and pvl but carry multiple MGE-associated ARGs, enhancing bloodstream survival, host adaptation, and dissemination (Fernandez et al., 2024; Ba et al., 2023). The ARG profile of Argentina spa-t571 isolates aligned with that of the AAP phylogroup, including Tn558 carrying the florfenicol-chloramphenicol exporter (fexA), predominantly found in AAP strains (Fernandez et al., 2024). While most AAP strains harbor SaPIpig2 within νSaα, one U. S. MSSA isolate carries SaPIpig1 (Fernandez et al., 2024), both variants of SaPIbov4. Strikingly, all Argentine CC398 isolates carried SaPIpig1, underscoring complex evolutionary dynamics and local adaptation.

Five pig-environment MRSA spa-t034 isolates from Córdoba clustered within clade C, specifically with C6/EP4 phylogroup representative strains (Fernandez et al., 2024). EP4 comprises Danish pig lineages L1–L4 and the Italian L5 (spa-t899), which have spread beyond their original region and exhibit diverse ARG profiles. Four isolates (farms ID6, ID1) grouped within subgroup C1, alongside a Buenos Aires pig isolate (Gagetti et al., 2023b), a Brazilian human LA-MRSA, and a German cattle strain (C6/EP4/L1) (Fernandez et al., 2024). These carried L1-typical ARG profiles, including optrA and SCCmec types Vc, Vc-like A1B1, and IIIA-like. In contrast, one isolate from farm ID7 clustered in subgroup C2 with C6/EP4/L3 strains and carried an ARG profile consistent with L3. Thus, spa-t034 Argentine pig-environment MRSA showed close relatedness to EP4 lineages L1 and L3, which include isolates detected in pigs and humans (some IEC⁺) in Denmark, Hungary, and Germany, in pigs from China (L3 only), and also reported in Brazil (Fernandez et al., 2024).

These findings reveal multiple introductions and circulation of international CC398 phylogroups in Argentine pig farms, including C6/AAP and C6/EP4. Local isolates cluster with strains from Asia, Europe, and the Americas, highlighting the global spread of CC398, likely facilitated by animal trade, and the establishment of foreign clones with zoonotic potential. Although Argentina has largely local pig production, live pig imports, mainly from Brazil (91.1% in 2022) (SAGyP, 2023), may have introduced AAP and EP4, both reported in Brazil. Importantly, these results underscore the need to implement or reinforce strategies to prevent LA-MRSA transmission, particularly via animal trade (Sawodny et al., 2025). On the other hand, detection of MSSA CC398 in river water from the same region, assigned to the AAP phylogroup, further suggests environmental reservoirs and possible local MSSA-to-MRSA evolution. Broader SA genomic studies from farm workers, animals, and environments are warranted to explore these dynamics.

Contemporaneous MSSA CC398 isolates from humans and cattle in Córdoba clustered within the HuA clade (subgroup G3), corresponding to the C2/susceptible phylogroup (C2/SP) described by Fernandez et al. (2024). The subgroup G3 isolates, IEC⁺ and predominantly spa-t571 and spa-t1451, carried erm(T) (Fernandez et al., 2024) and shared features with Argentina’s main MSSA clone (MSSA398-erm(T)-spa-t1451) (Di Gregorio et al., 2023; Barcudi et al., 2024). The C2/SP phylogroup is widespread in human colonization and infections across China, Europe, and the Americas, often in individuals without livestock contact (Bonnet et al., 2018; Wardyn et al., 2018; Fernandez et al., 2024), and has also been reported in cattle, pigs, and cats (Tegegne et al., 2022; Fernandez et al., 2024). Our findings reveal co-circulation of distinct MSSA CC398 lineages, C6/AAP (spa-t571) and C2/SP (spa-t571, spa-t1451), in the same region, each with distinct ARGs profiles and molecular traits. This diversity may reflect differences in host adaptation and transmission, underscoring the need to investigate MSSA CC398 under a One Health framework.

Similar to CC398, diverse SCCmec elements (e.g., types III, IV, V, IX, XI, XII/XII-like, with multiple ccr complexes, and non-typeable variants) have been reported within CC1/ST9 across studies. Their distribution appears region-specific: ST9 from Europe often carry SCCmecIV, while those from China typically harbor SCCmecXII (Chuang and Huang, 2015; Jiang et al., 2021; Ji et al., 2021; Yu et al., 2021; Chen et al., 2023).

Global phylogenetic analysis of Argentine ST9/CC1 pig-environment isolates confirmed the strong regional clustering of LA-ST9 lineages (Jiang et al., 2021; Yu et al., 2021; Randad et al., 2021; Ji et al., 2021). Ninety-six percent of ST9 genomes clustered within clade II, comprising human-associated MSSA (IIA, IEC⁺) and livestock-associated clusters IIB and IIC (IEC¯). The two antimicrobial-susceptible ST9 MSSA human isolates from this study grouped within the human-associated IIA clade, while the ST9 MRSA strains from pig environments and food clustered within the LA clade (IIB3). Clade IIB split into three geographically-associated subclades: IIB1 (European MRSA) (Yu et al., 2021), IIB2 (North American MDR-MSSA) (Randad et al., 2021), and IIB3, composed exclusively of Argentine MRSA isolates. Bidirectional pig–human transmission of clades IIB2 and IIC, with potential for community spread, has been reported (Randad et al., 2021; Yu et al., 2021), supporting the zoonotic potential of clade IIB3. IIB3 isolates, carried spa-t16964 or related types, SaPIpig1, and exhibited an MDR profile enriched, compared to IIB2, for erm(C), aadE, fexA, and fruorquinolone-resistance mutations grlAS80F and gyrA S84L. Notably, fexA on Tn558, aadE, and MRSA (SCCmecV) status were exclusive to IIB3, a pattern also observed in the Chinese IIC lineage, which harbors the highest ARG burden (Randad et al., 2021; Yu et al., 2021). The spa-t16964 detected here, also reported in MSSA from Germany (Ridom SpaServer), differs by one repeat from spa-t1430, previously associated with ST9 MSSA and MRSA from pigs, humans, and meat (Yu et al., 2021; Abdullahi et al., 2023).

Host adaptation of S. aureus after human-to-animal jumps has been associated with genes or MGEs acquisition and recombination enhancing transmission, colonization, and virulence (Lowder et al., 2009; Richardson et al., 2018; Murray et al., 2017). The clustering of two Argentinean human MSSA ST9 IEC⁺ isolates within clade IIA, which includes IEC⁺ human MSSA of diverse spa-types from several countries and corresponds to the ancestral clades described by Yu et al. (2021), supports a human MSSA origin of regional ST9 LA-MRSA clones. This host shift likely involved loss of human-specific virulence factors (IEC), acquisition animal-associated factors such as vwb on SaPIpig1 (a SaPIbov4-like element) within the νSaα island, and subsequent antimicrobial-driven evolution through the acquisition of resistance determinants (including SCCmec types) across spa types. Our data further suggest that IIB2 and IIB3 diverged from a common ancestor, possibly in the Americas, and evolved as independent, geographically segregated clades distinct from the dominant Asian IIC, reflecting region-specific antimicrobial selection (Randad et al., 2021; Yu et al., 2021).

Notably, the co-circulation of two ST9 sublineages in Argentina, non-MDR MSSA in humans and MDR-MRSA in pigs, also demonstrated here, highlights the importance of molecular surveillance to monitor interspecies transmission and ongoing genomic adaptation of this emerging LA-MRSA clone.

Finally, the MDR profile of this regional ST9 LA-MRSA lineage (clade IIB3), combined with its high farm-to-farm transmissibility, detection in ready-to-eat chicken, and co-circulation with international CC398 phylogroups, underscores the need to identify and implement the most effective combination of targeted interventions, including enhanced biosecurity, reduced antimicrobial use, routine pig screening, environmental decontamination, and controlled animal movement, to control LA-MRSA spread in this region and prevent potential zoonotic spillover within a One Health framework (Kasela et al., 2023; Khairullah et al., 2023; Sawodny et al., 2025).

In conclusion, this study reveals a high burden of LA-MRSA in pig farms environments in central Argentina, with 80% of farms testing positive, particularly in nursery and finishing units, during early 2022. Antimicrobial use was widespread, with most farms reporting the use of more than seven drug classes and up to 18 different antimicrobials in the previous 6 months. Molecular characterization identified the co-circulation of two dominant multidrug-resistant lineages: CC398 (ST398 and the novel ST8814) and CC1/ST9, each associated with SCCmec Vc variants and pig-adapted resistance profiles. Notably, this is the first report of the phenicol-oxazolidinone resistance gene optrA in SA in Argentina, detected in both ST398 and ST9 MRSA isolates. WGS revealed a novel optrA variant (OptrA/FDKFP_SA7603-7633), likely linked to a MGE, raising concerns about unrecognized reservoirs and potential environmental dissemination. Phylogenetic analysis in a global context showed the emergence of a unique regional ST9 lineage in Argentina, composed exclusively of MRSA from pigs, pig environments, and food, with evidence of intra- and inter-farm transmission. In contrast, CC398 strains clustered within internationally recognized subgroups (C6/AAP and C6/EP4), suggesting multiple introductions and successful local establishment.

This study’s strengths include its prospective design, the comprehensive molecular and genomic characterization of pig–environment MRSA isolates and the identification of a novel optrA variant. The integration of recent on-farm antimicrobial use data adds valuable context. Importantly, to our knowledge, this is the first study to estimate the regional prevalence of MRSA-positive pig farms in central Argentina, a major swine-producing area with previously limited data. It also provides insights into LA-MRSA transmission dynamics within and between farms and situates Argentinean pig–environment LA-MRSA lineages within a global phylogenetic framework.

This work has several limitations. First, the small farms sample size (n: 10) limits broader extrapolation. Nonetheless, our findings are supported by a previous study reporting 29.7% nasal MRSA colonization in pigs from farms in three other provinces, with four sequenced strains clustering with those from this study. Second, analyzing only 1–2 MRSA colonies per environmental sample may have underestimated farm-level MRSA diversity and missed co-occurrence of ST398 and ST9. Third, the exclusive use of environmental samples likely led to under detection; including pig nasal samples could have increased the number of positive farms. However, the high proportion of MRSA-positive farms among those sampled highlights the relevance of our findings. Although the detected strains carry genetic features linked to human colonization and infection, no human samples were included to assess zoonotic transmission. Finally, hybrid sequencing will be required to fully characterize the optrA genetic context and SCCmec variants through complete genome assemblies.

This genomic and molecular analysis of pig–environment MRSA in central Argentina expands current knowledge by highlighting the pig environment as an emerging reservoir of LA-MRSA and ARM. Given their zoonotic potential and capacity for dissemination across farms and human populations, strengthening One Health surveillance and implementing integrated biosecurity and control measures are essential to limit LA-MRSA spread and the AMR dissemination. Addressing MRSA in pig farming is therefore not only an animal health issue but also critical for protecting public health and ecological integrity.