Integron-Mediated Antimicrobial Resistance and Virulence Factors in Salmonella Typhimurium Isolated from Poultry

Abstract

This study investigates antimicrobial-resistant (AMR) Salmonella Typhimurium in poultry, focusing on how class I integrons contribute to AMR and virulence. Using whole genome sequencing, researchers analyzed 26 S. Typhimurium isolates from U.S. poultry, finding that three isolates contained integrons (1000 base pairs each). These integron-positive isolates exhibited significantly higher resistance to beta-lactams, phenicols, and tetracyclines compared to integron-free isolates (p = 0.004, 0.009, and 0.02, respectively) and harbored genes like ges, imp, and oxa, which are linked to extended-spectrum beta-lactamase resistance. Most AMR gene classes (64%) were chromosome-based, with integron-positive isolates showing a broader array of resistance genes, including catB and tetA. Integron-bearing isolates had higher occurrences of bacteriocin genes and specific AMR genes like aminoglycoside and beta-lactam resistance genes, while integron-free isolates had more fimbrial and pilus genes. The presence of integrons may trend with increased AMR genes and virulence factors, highlighting the role of integron screening in enhancing AMR surveillance and reducing the need for high-priority antimicrobial treatments in poultry. These findings could support better AMR stewardship practices in poultry production, potentially lowering infection risks in humans and livestock.

Keywords: Salmonella Typhimurium; antimicrobial resistance; integrons; poultry; virulence factors.

Figure 1

Distribution of antimicrobial resistance genes identified on the chromosome of S. Typhimurium isolated from poultry (n = 26) grouped by presence or absence of integrons. Rows are grouped by antimicrobial resistance gene classes. Each column shows the gene profile of an individual S. Typhimurium isolates. Each box shows one gene. Red boxes indicate gene presence, and yellow boxes indicate that the gene was not detected in the individual S. Typhimurium isolate. Abbreviations: I = Integron Present; NI = Integron Absent.

Figure 2

Distribution of antimicrobial resistance genes identified on the plasmid of S. Typhimurium isolated from poultry (n = 26) grouped by presence or absence of integrons. Rows are grouped by antimicrobial resistance gene classes. Each column shows the gene profile of an individual S. Typhimurium isolates. Each box shows one gene. Red boxes indicate gene presence, and yellow boxes indicate that the gene was not detected in the individual S. Typhimurium isolate. Abbreviations: I = Integron Present; NI = Integron Absent.

Figure 3

Distribution of antimicrobial resistance gene class prevalences when comparing S. Typhimurium isolates with versus without integrons. Blue bars represent isolates with integrons (n = 3), and green bars represent isolates without integrons (n = 23). Panel (a) shows gene class distribution prevalences on the chromosome, and (b) shows gene class distributions on the plasmid. Prevalences were compared between isolates with and without integrons using Fisher’s exact test, and significance was defined as p < 0.05. Significance is denoted with an *.

Figure 4

Distribution of virulence factor genes identified on the chromosome (a) and plasmid (b) of S. Typhimurium isolated from poultry (n = 26) grouped by presence or absence of integrons. Rows are grouped by antimicrobial resistance gene classes. Each column shows the gene profile of an individual S. Typhimurium isolates. Each box shows one gene. Red boxes indicate gene presence, and white boxes indicate that the gene was not detected in the individual S. Typhimurium isolate. Abbreviations: I = Integron Present; NI = Integron Absent.

Figure 5

Distribution of virulence factor gene class prevalences when comparing S. Typhimurium isolates with versus without integrons. Blue bars represent isolates with integrons (n = 3), and green bars represent isolates without integrons (n = 23). Panel (a) shows gene class distribution prevalences on the chromosome, and (b) shows gene class distribution prevalences on the plasmid. Abbreviations: LPS = Lipopolysaccharide; T3SS = Type 3 secretion system; T5SS = Type 5 secretion system; T6SS = Type 6 secretion system. Prevalences were compared between isolates with and without integrons using Fisher’s exact test, and significance was defined as p < 0.05.