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Title: Characterization of mobile genetic elements in antibiotic resistant Salmonella enterica isolates from food animals

Author
item MCMILLIAN, ELIZABETH - University Of Georgia
item GUPTA, SUSHIM - Orise Fellow
item WILLIAMS, LAURA - Former ARS Employee
item JOVE, THOMAS - Hospital And University Center Of Limoges
item Jackson, Charlene
item MCCLELLAND, MICHAEL - University Of California
item Frye, Jonathan

Submitted to: American Society for Microbiology Conference
Publication Type: Abstract Only
Publication Acceptance Date: 2/29/2016
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Antibiotic resistance (AR) is a major concern for the agricultural industry in the U.S. and globally. The problem of AR is further complicated by AR genes often being located on mobile genetic elements (MGEs) resulting in their spread among bacteria. In order to investigate the relationship between AR and MGEs, we identified AR genes, plasmids, and integrons in the genomes of Salmonella enterica isolated from animal sources. Salmonella enterica (n=194) isolated from beef and dairy cattle, chicken, swine, turkey, and their meat products representing 84 diverse serovars were selected based on their differing AR phenotypes. Isolates were sequenced using an Illumina HiSeq. Draft genomes were assembled using A5 and annotated with Prokka. Resistance genes were identified using ARG-ANNOT. Plasmid sequences were identified through in silico PCR identifying replicon and relaxase genes. Integrons were identified using INTEGRALL. The 194 isolates had a total of 883 resistance genes detected and at least one gene was detected per isolate. Plasmids were detected in 157 of 194 isolates. The most prevalent replicons detected were A/C, colE, F, HI1, HI2, and I. AR genes were detected on 110 plasmid sequences and 71 of those contained multiple AR genes. Class 1 integrons were detected in 66 isolates; no class 2, 3, or 4 integrons were detected. AR genes were found in 62 integrons, 55 of which had multiple AR genes detected. Twenty-six of the integrons were located on IncI1 plasmids and two on IncHI2 plasmids. Most isolates contained plasmids, integrons, or both. Many of the mobile elements and AR genes have been previously found in Salmonella, but not in animal associated isolates or in the rare serovars analyzed. The identification of AR genes on the same contiguous sequence as plasmid and/or integrons demonstrates linkage of MGEs and AR in these food animal associated Salmonella. Additionally, the localization of class 1 integrons on IncI1 and HI2 plasmids indicates the complex structure of MGEs and may suggest a mechanism for AR genes accumulation on plasmids. Future work will identify other MGEs and determine their relationships to AR.