Phenotype–Genotype Concordance and Coresistance Patterns in Multidrug-Resistant Salmonella enterica Serovar Choleraesuis from Diseased Pigs in Taiwan

Salmonella enterica serovar Choleraesuis (S. Choleraesuis) is a swine-adapted zoonotic pathogen for which multidrug resistance has become an increasing concern. An antimicrobial resistance profile and multidrug resistance pattern in S. Choleraesuis isolates from diseased pig in Taiwan have been reported. This study was designed as a secondary molecular and statistical analysis of 272 isolates recovered from diseased pigs in Taiwan whose minimum inhibitory concentration phenotypes had been reported previously. Using this isolate collection, we evaluated phenotype–genotype concordance and coresistance patterns by combining antimicrobial susceptibility data with targeted polymerase chain reaction screening and quinolone resistance-determining region sequencing. Multidrug resistance was detected in 97.8% of isolates. Among the screened acquired determinants, blaTEM was the most prevalent gene (94.5%), followed by floR (55.9%) and mcr-1 (12.9%); mcr-3 was detected in only one isolate. Significant phenotype–genotype concordance was observed for aphA-1 with kanamycin resistance and mcr-1 with colistin resistance. Sequence analysis of 60 enrofloxacin-resistant isolates revealed that high-level resistance was associated with combined gyrA and parC substitutions, with additional gyrB-region polymorphisms observed in isolates showing the highest minimum inhibitory concentrations. These findings demonstrate frequent coresistance patterns and complex resistance mechanisms in this lineage and support continued genomic surveillance and prudent antimicrobial stewardship in the swine sector.