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Research Project: Monitoring and Molecular Characterization of Antimicrobial Resistance in Foodborne Bacteria

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Title: Cassette structures associated with antibiotic resistance genes in Salmonella enterica isolated from processing plants, food animals, and retail meats

item MCMILLAN, ELIZABETH - University Of Georgia
item GUPTA, SUSHIM - Orise Fellow
item WILLIAMS, LAURA - Providence College
item JOVE, THOMAS - Inserm University Of Limoges
item Jackson, Charlene
item MCCLELLAND, MICHAEL - University Of California
item Frye, Jonathan

Submitted to: American Society for Microbiology General Meeting
Publication Type: Abstract Only
Publication Acceptance Date: 2/22/2018
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Slowing the spread of antibiotic resistance (AR) is one of the most urgent tasks currently facing the field of microbiology. Mobile genetic elements, like plasmids and integrons, allow AR genes to transfer horizontally, thus increasing the spread of AR genes. Determining which AR genes are found on particular mobile elements and whether AR genes occur with other genes more frequently will provide insight into how these AR genes are spreading and could identify points where interventions could slow their spread. In order to investigate these questions, Salmonella enterica isolates associated with US food animals were sequenced and analyzed. Salmonella enterica (n=194) isolated from beef and dairy cattle, chicken, swine, turkey, and their meat products representing 84 serotypes were selected based on their differing AR phenotypes and unique PFGE patterns. Isolates were analyzed by WGS using an Illumina HiSeq. Draft genomes were assembled using A5 and annotated with Prokka. Resistance genes were identified using ARG-ANNOT while plasmid sequences were identified through homology to other plasmid sequences. Contigs containing the same resistance genes were aligned using SnapGene. Sequences including AR genes with nearly identical flanking sequence in multiple unrelated isolates were classified as cassettes. A total of 922 AR genes were identified in the 194 isolates. Plasmids were found in 155/194 isolates and more than 12 different replicon types were detected. Five cassettes were identified that contained the following AR genes: 1. tetA, tetR, strAB, and sulII (n=25), 2. aac3IId (n=11), 3. aph, sph (n=13), 4. cmy (n=39) 5. aac3, aadA, sulI (n=44). All cassettes were located on a plasmid. None of the cassettes were exclusive to one replicon type, but cassettes 1, 3, and 4 were exclusive to two replicons types. Presence of cassettes containing multiple AR genes show that AR of multiple classes are linked and could be selected for one another and presence of the these cassettes on multiple replicon types shows that this is not due to expansion of a clonal plasmid. Knowing which AR genes are linked in these cassettes could predict useful interventions to slow the spread of resistance.