Epidemiology and genomics of azithromycin-resistant extensively drug-resistant Salmonella enterica serovar Typhimurium in Taiwan

ABSTRACT The recent emergence of azithromycin-resistant extensively drug-resistant (AziR-XDR) Salmonella enterica serovar Typhimurium ( S . Typhimurium) in Taiwan poses a significant public health concern. To investigate the genetic basis and the evolutionary dynamics, we analyzed 60 isolates collected between 2007 and 2024, comprising multidrug-resistant (MDR, n = 45) and AziR-XDR ( n = 15) isolates from human and animal sources. Whole-genome sequencing analysis revealed that 36 of 45 MDR isolates and all AziR-XDR isolates belonged to the HC50_13 subclone (differing by ≤ 50 core genes) and clustered within the HC20_152604 cluster (differing by ≤ 20 core genes) and the SNP cluster PDS000042202. All HC50_13 MDR isolates and AziR-XDR isolates carried core resistance genes including aac(3)-IId , aph(3’’)-Ib , aph(6)-Id , blaTEM-1 , floR , sul2 , tet(A ) on type 2 IncC plasmids, and AziR-XDR isolates carried additional antimicrobial resistance genes (ARGs) on the plasmids, including blaDHA-1 , dfrA17 , mph(A ), qnrB , and sul1 , conferring additional resistance to azithromycin, trimethoprim, third-generation cephalosporins, and fluoroquinolones. AziR-XDR S. Typhimurium strains belonging to the HC50_13 subclone were initially identified in 2016 and have notably increased in Taiwan since 2021. The subclone was likely evolved from MDR ancestor strains by multiple IS 26 -mediated acquisitions of additional resistance cassettes. Our findings demonstrate how MDR S . Typhimurium can evolve locally into highly resistant strains. This underscores the need for genomic surveillance and coordinated antimicrobial stewardship in Taiwan and globally to prevent further dissemination of the highly resistant HC20_152604 clade.