Population dynamics and genomic characterization of Salmonella Infantis reveal poultry as a major reservoir of antimicrobial resistance genes and pESI megaplasmid

ABSTRACT Salmonella enterica serovar Infantis is one of the emerging multidrug-resistant serovars causing foodborne illness to humans. Here, we analyzed the genome sequences of 16,157 S . Infantis isolated globally to illustrate the population dynamics, risk of antimicrobial resistance, and pESI megaplasmid carriage rates. The population structure revealed that, irrespective of the source and location of isolation, greater than 95% of isolates were ST-32. S . Infantis from ST-32 was further analyzed using the ResFinder and PlasmidFinder databases in the Abricate platform. Population dynamics and odds ratios (OR) of antimicrobial resistance (AMR) across sources and continents were analyzed using logistic regression, with multiple comparisons assessed using Tukey’s HSD test and Benjamini-Hochberg false discovery rate (FDR) correction applied to both global and pairwise P -values. The significance level was set at 0.05. Analysis of ST-32 S . Infantis isolates revealed that the risk of harboring AMR genes was significantly higher in isolates collected from poultry compared to other sources, despite having variation in the number of genes and the magnitude of the odds ratio. Interestingly, irrespective of the source of isolation, almost all S . Infantis isolates possess aac (6 ′ )-Iaa genes, whereas the most prevalent AMR genes among poultry-sourced S . Infantis were tet(A ), followed by sul1 and ant (3 ′ )-Ia . Additionally, the carriage rate of the pESI-plasmid was higher in poultry (87.90%), followed by human isolates (26.98%). In conclusion, our work provides an insight into multilocus sequence typing (MLST), AMR, and carriage rates of the pESI-like plasmid among S . Infantis isolated globally from diverse isolation sources. IMPORTANCE Foodborne illness caused by Salmonella remains a major public health concern. Among >2,500 known Salmonella serovars, S . Infantis ranks among the top 10 serovars causing human illness. The significance of S . Infantis is further amplified by its ability to harbor and disseminate antimicrobial resistance (AMR) genes mediated by pESI-like megaplasmid. Therefore, understanding the population dynamics and assessing the risk of AMR gene carriage in S . Infantis isolates collected from diverse sources and geographic locations are critical. The findings from this analysis help identify high-risk reservoirs and track current AMR trends, enabling the development of streamlined treatment strategies and data-driven interventions aimed at limiting the global spread of multidrug-resistant S . Infantis.