Investigation of the diversity of antibiotic resistance genes and mobile genetic elements in Salmonella associated with U.S. food animals

Authors: Frye, Jonathan; MCMILLAN, ELIZABETH - University Of Georgia; GUPTA, SUSHIM - Oak Ridge Institute For Science And Education (ORISE); JOVE, THOMAS - Hospital And University Center Of Limoges; MCCLELLAND, MICHAEL - University Of California; Jackson, Charlene

Submitted to: American Society for Microbiology Conference
Publication Type: Abstract Only
Publication Acceptance Date: 7/21/2016
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: With the emergence of antibiotic resistance (AR), multidrug resistance (MDR), and carbapenem resistant Enterobacteriaceae (CRE), the specter of widespread untreatable bacterial infections threatens human and animal health. The ability of these emerging resistances to transfer between bacteria on mobile genetic elements (MGEs) could cause the rapid establishment of MDR bacteria in animals leading to a foodborne risk to humans. To investigate this, we identified AR genes, plasmids, and integrons in the genomes of Salmonella enterica isolated from animal sources. To obtain the greatest variety of AR genes and MGEs, Salmonella enterica isolates (n=193) from beef and dairy cattle, chicken, swine, turkey, and their meat products were selected based on their resistance phenotypes, serovar, and PFGE patterns, resulting in 75 serovars and diverse PFGE patterns within a serovar being selected. Isolates were sequenced using an Illumina HiSeq. Draft genomes were assembled using A5miseq pipeline with an average of 115 contigs per isolate and annotated with Prokka. Resistance genes were identified using ARG-ANNOT and integrons were identified using INTEGRALL. Plasmid sequences were identified by the presence of replicon and relaxase genes or homology to known plasmids. A total of 913 AR genes were detected in the 193 isolates. Class I integrons were detected in 65/193 isolates. Forty-four integrons contained a single gene cassette (aadA of various alleles n=38, dfrA of various alleles n=5, and carb n=1). Nine integrons had multiple genes (five with aadB and cmlA, three with aadA and dfrA, and one with aadA and estX-3), two had no AR gene, six had incomplete AR gene sequences, and another six were novel AR gene cassettes. Plasmids were detected in 155/193 isolates. The most prevalent replicons detected in the isolates were A/C (n=32), colE (76), F (43), HI1 (4), HI2 (21), I (62), N (4), Q (7), and X (35). AR genes were found on most of the plasmids, with many of them encoding MDR. For example, 27 of the 32 A/C plasmids contained AR genes with 16 different patterns of AR genes and as many as ten AR genes detected (e.g. tetAR, strAB, sulII, cmy, floR, aadB, cmlA, and aph3). AR genes on the other plasmid replicons were also highly variable representing a diversity of AR and MDR genotypes resulting in their observed antibiotic resistances. Most isolates contained plasmids, integrons, or both encoding AR or MDR. Many of the mobile elements and AR genes have been previously found in Salmonella; however, they are arranged differently and have not previously been found in animal associated isolates or in the serovars analyzed. The identification of AR genes, plasmids, and integrons demonstrates linkage of MGEs and AR in these food animal associated Salmonella. This begins to reveal the complexity of AR and MGE assembly and spread among Salmonella in the food animal environment.