Clonal expansion of chromosome-borne CTX-M-55 extended-spectrum β-lactamase-producing Salmonella enterica serovar Agona, Taiwan.

We investigated emerging multidrug-resistant (MDR) Salmonella enterica serovar Agona in Taiwan. These MDR strains commonly harbored the efflux pump activator gene ramAp and up to 15 resistance genes, including aac (3)-IId, aadA22, aph(3')-Ia, aph (6)-Id, arr-2, bla CTX-M-55, bla LAP-2, bla TEM-1, dfrA14, floR, lnu(F), qnrS13, sul2, sul3, and tet(A), within IncHI2-IncHI2A plasmids or diverse chromosomal resistance genomic islands (RGIs). These newly emerging MDR strains comprised 44.9% and 74.4% of S. Agona isolates collected in 2023 and 2024, respectively. Through analysis of chromosomal insertion sites, we identified 11 distinct RGIs. Strains containing RGI_SA11 became predominant, comprising 59.2% of S. Agona isolates collected in 2024.IMPORTANCEThe emergence and clonal expansion of MDR S. Agona represent a growing public health concern. This study identifies a significant shift in resistance mechanisms, driven by chromosomally integrated resistance genomic islands (RGIs), which likely originated from IncHI2-IncHI2A plasmids. The chromosomal integration of antimicrobial resistance genes enhances the evolutionary fitness of these strains, facilitating their persistence and dissemination in both human and animal populations. These findings underscore the urgent need for enhanced surveillance, targeted interventions, and global antimicrobial stewardship to curb the spread of MDR pathogens and safeguard public health.