Mobile genetic elements drive the evolution and multidrug resistance of Salmonella infantis along the United States poultry production line

Authors: Zhang, Yujie; CHU, MACKENNA - Hispanic Association Of Colleges & Universities (HACU); SAMALA, SANGHVI - Hispanic Association Of Colleges & Universities (HACU); Salvador, Alexandra; Liao, Yen-Te; Wu, Vivian

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/29/2026
Publication Date: 3/3/2026
Citation: Zhang, Y., Chu, M., Samala, S., Salvador, A., Liao, Y., Wu, V.C. 2026. Mobile genetic elements drive the evolution and multidrug resistance of Salmonella infantis along the United States poultry production line. BMC Genomics. 27. Article 358. https://doi.org/10.1186/s12864-026-12607-z.
DOI: https://doi.org/10.1186/s12864-026-12607-z

Interpretive Summary: The poultry industry has grown drastically worldwide with the increasing demand for poultry consumption and other related food products. However, a common pathogen—Salmonella Infantis—has been widely found in the poultry production line and contributed to several foodborne outbreaks, posing food safety risks to human health. Additionally, there has been a rising concern regarding the antimicrobial resistance observed in S. Infantis strains due to the use of antibiotics in poultry production. The objectives of this study were to characterize antibiotic-resistant S. Infantis strains isolated from the poultry production line in the United States and to investigate the development of their antibiotic resistance. The results showed that 9 S. Infantis strains were resistant to two or more antibiotics. Additionally, each strain contained a plasmid of a large genome size. These plasmids harbored five or more antibiotic resistance genes and contributed to the bacterial antimicrobial resistance. The findings of this study provided insight into the role of large plasmids on the emergence and spread of antimicrobial-resistant S. Infantis in the United States poultry production.

Technical Abstract: Salmonella is the primary enteric pathogen related to foodborne illnesses worldwide, posing significant public health concerns. Amongst the diversity and pathogenicity of over 2000 Salmonella serotypes, Salmonella Infantis (S. Infantis) ranks among the top Salmonella serotypes implicated in foodborne outbreaks, with thousands of reported cases annually in the United States. Moreover, the incidence of S. Infantis infections has spread rapidly globally from the U.S. to Europe, where more than 50% of isolated S. Infantis strains have developed antibiotic resistance. Previous studies have shown that antibiotic resistance genes (ARGs), particularly those carried on by plasmids, contribute to the persistence and spread of multiple-drug resistant (MDR) Salmonella strains in various environments. However, there is less information regarding the multidrug resistance and spread of S. Infantis. Hence, the objectives of this study were to characterize antibiotic-resistant S. Infantis isolated from the poultry production line in the United States and to examine the correlation between mobile genetic elements and bacterial resistome evolution. A total of 9 S. Infantis strains were isolated from poultry production lines in 2022, including comminuted chicken, raw intact/nonintact chicken, and chicken carcass. These strains were further subject to the antimicrobial susceptibility test and the whole genome sequencing. The complete bacterial genome showed that all isolates had a dsDNA chromosome with a GC content of 52.3% and an average genome size of 4,730 kb, belonging to sequence type 32. Additionally, most strains showed phenotypic resistance to four or more antibiotics, except for SI-4897. The genomic characterization of S. Infantis isolates revealed each strain contained one IncFIB mega-plasmid with lengths from 289 to 327 kb. Five or more ARGs were detected in each strain, of which most ARGs were located in the mega-plasmids and bordered by diverse mobile genetic elements, including transposons, integrons, and prophages. Moreover, the majority of WGS-derived ARG profiles had concordant phenotypic traits. These findings demonstrate the genomic features and antimicrobial resistance profiles of S. Infantis strains from the poultry production lines in the United States, indicating the potential of mega-plasmids-driven S. Infantis resistome development.