Journal of global antimicrobial resistance · 2026
Complete genome sequences and structural variants of pESI-like plasmids in multidrug-resistant Salmonella Infantis carrying blaCTX-M-65 from retail chicken meat in South Korea.
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La Tae-Min, Kim Taesoo, Lee Sang-Won, Hyeon Ji-Yeon
Аннотация
OBJECTIVE: This study reports complete chromosome and pESI-like megaplasmid sequences of multidrug-resistant Salmonella enterica serovar Infantis (S. Infantis) isolates obtained from retail chicken meat in South Korea in 2023 and characterizes their antimicrobial resistance (AMR) gene repertoire and the structural diversity of their pESI-like plasmids.
METHODS: Twenty-one multidrug-resistant S. Infantis isolates were subjected to whole-genome sequencing using Illumina NextSeq and Oxford Nanopore MinION platforms. Hybrid assemblies were generated using Trycycler v0.5.0 and corrected using Polypolish v1.2.3. AMR genes were identified, and plasmid structures were reconstructed and visualized using Proksee.
RESULTS: All isolates belonged to sequence type ST32 and carried pESI-like megaplasmid encoding multiple AMR genes. Conserved resistance genes included aac(3)-IVa, aph(4)-Ia, blaCTX-M-65, and tet(A), while ant(3″)-Ia, aph(3')-Ia, dfrA14, floR, and sul1 were variably present. Comparative plasmid analysis revealed six plasmid structural variants (Types A-F), primarily distinguished by deletions within AMR regions. Type A retained all resistance loci, whereas Types B-F exhibited partial loss of regions harbouring aph(3')-Ia, dfrA14, floR, or sul1. Comparative plasmid mapping showed that the Korean pESI-like plasmids exhibited high overall structural similarity to internationally reported pESI-like plasmids, including those from the UK and USA.
CONCLUSIONS: These complete genome sequences expand the current knowledge of pESI-like plasmid diversity in S. Infantis and highlight their role in the dissemination of multidrug resistance in the poultry sector. Continued genomic surveillance is warranted to monitor the emergence and spread of high-risk S. Infantis clones across the food chain.
METHODS: Twenty-one multidrug-resistant S. Infantis isolates were subjected to whole-genome sequencing using Illumina NextSeq and Oxford Nanopore MinION platforms. Hybrid assemblies were generated using Trycycler v0.5.0 and corrected using Polypolish v1.2.3. AMR genes were identified, and plasmid structures were reconstructed and visualized using Proksee.
RESULTS: All isolates belonged to sequence type ST32 and carried pESI-like megaplasmid encoding multiple AMR genes. Conserved resistance genes included aac(3)-IVa, aph(4)-Ia, blaCTX-M-65, and tet(A), while ant(3″)-Ia, aph(3')-Ia, dfrA14, floR, and sul1 were variably present. Comparative plasmid analysis revealed six plasmid structural variants (Types A-F), primarily distinguished by deletions within AMR regions. Type A retained all resistance loci, whereas Types B-F exhibited partial loss of regions harbouring aph(3')-Ia, dfrA14, floR, or sul1. Comparative plasmid mapping showed that the Korean pESI-like plasmids exhibited high overall structural similarity to internationally reported pESI-like plasmids, including those from the UK and USA.
CONCLUSIONS: These complete genome sequences expand the current knowledge of pESI-like plasmid diversity in S. Infantis and highlight their role in the dissemination of multidrug resistance in the poultry sector. Continued genomic surveillance is warranted to monitor the emergence and spread of high-risk S. Infantis clones across the food chain.