Background: Routine non-therapeutic antimicrobial use and overcrowding in animal farming may facilitate the propagation of methicillin-resistant Staphylococcus aureus  (MRSA). This study aimed to examine the carriage prevalence and phenotype–genotype characteristics of MRSA and methicillin-susceptible S. aureus  isolated from pigs.
Methods: Nasal swabs were collected from 1,458 pigs in 9 pig farms and 3 slaughterhouses. All strains were tested for antimicrobial susceptibility, resistance genes, and virulence genes, and characterized by multilocus sequence typing. The correspondence analysis was conducted to explore the relationships between multiple phenotypic and molecular characteristics of S. aureus  isolates.
Results: In the 1,458 pigs, the carriage prevalence was 9.5% for S. aureus , 3.3% for MRSA, and 9.3% for multidrug-resistant S. aureus . Notably, 97.1% S. aureus  isolates were multidrug resistant, and the predominant resistance pattern was non-susceptible to clindamycin, tetracycline, and erythromycin. The predominant genotype was CC9 (ST9) for S. aureus  and MRSA isolates. Importantly, all S. aureus  isolates were negative for the scn  gene and resistant to tetracycline. Notably, all 9 linezolid-resistant isolates were classified as multidrug resistance, including 1 expressing the cfr  gene and 6 expressing the optrA  gene. The correspondence analysis showed a significant relationship between clonal complexes and resistance pattern or virulence genes. For example, CC9 was associated with extensive drug-resistance and co-carrying chp , sak , and hlb , and CC1 was associated with multidrug resistance and co-carrying sak  and hlb .
Conclusion: The significant correspondence relationship between multiple characteristics provides some implication for vaccine strategies and new ideas for monitoring new epidemiologic clones.
Keywords: livestock, animals, Staphylococcus aureus , antimicrobial susceptibility, multidrug resistance, molecular characterization