Class 1 integrons in clinical and swine industry isolates of Salmonella Typhimurium from Colombia, dating 1997 to 2017

Abstract

Background. Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) has been linked to outbreaks of foodborne gastroenteritis disease, and the emergence of antimicrobial-resistant clones. In Colombia, laboratory surveillance of Salmonella spp. between 1997-2018 revealed that S. Typhimurium was the most ubiquitous serovar (27.57% of all Salmonella isolates), with increasing levels of antimicrobial resistance to several families of antibiotics. Hypothesis. Resistant isolates of S. Typhimurium recovered from clinical and swine samples carry class 1 integrons that are linked to antimicrobial resistance genes. Aim. Identify class 1 integrons, and investigate their association with other mobile genetic elements, and their relationship to the antimicrobial resistance of Colombian S. Typhimurium isolates. Methods. In this study, 392 clinical isolates of S. Typhimurium were analyzed, of which 237 were obtained from blood culture, 155 from non-invasive sources and 50 isolates from swine of which 32 were obtained from a slaughterhouse, 10 from a point of sale and 8 from cutting plant. Class 1 integrons and plasmid incompatibility groups were analyzed by PCR and Whole Genome Sequencing (WGS), and the region surrounding of the integrons identified by WGS. The phylogenetic relationship was established by MLST and SNP analysis. Results. Overall, 39.03% (153/392) of the clinical isolates and 22% (11/50) of the swine S. Typhimurium isolates carried complete class 1 integrons. Twelve types of gene cassette arrays were identified, including dfr7-aac-blaOXA-2 (Int1-Col1) as the most frequent in clinical isolates (75.2% = 115/153). Clinical and swine isolates that carried class 1 integrons were resistant to up to 5 and up to 3 antimicrobial families, respectively. The Int1-Col1 integron was most prevalent in stool isolates and was associated with Tn21. The most common plasmid incompatibility group was IncA/C. Conclusions. The widespread presence of the integron (IntI1-Col1) in Colombia since 1997 was striking. We speculate that the relationship between integrons, source and mobile elements favors the dispersion of antibiotic resistance determinants in Colombian S. Typhimurium isolates.