Approximately 9.4 million cases of foodborne illness occur annually in the United States, with Salmonella infections comprising about 1 million of these cases. Environmental reservoirs of Salmonella -- particularly those related to agricultural practices -- may contribute greatly to the dissemination of these potential human pathogens, though such reservoirs are not well characterized. Furthermore, the use of antibiotics in animal agriculture has potentially expanded the circulation of antibiotic resistance (AR) genes in the environment. Surveillance of environmental Salmonella is a critical step in monitoring the distribution of this pathogen and can be accomplished through whole-genome sequencing of isolates. Stream sediment from eight sites and chicken litter from five poultry houses in the Shenandoah Valley were sampled between October 2016 and September 2017. Modified FDA Bacteriological Analytical Manual methods of pre-enrichment, enrichment, and isolation were used to isolate 33 putative Salmonella. Twenty-eight were isolated from stream sediments and five from litter from a commercial chicken house. No Salmonella were isolated from small backyard chicken house litter. Putative Salmonella were confirmed by polymerase chain reaction amplification of the Salmonella-specific invA gene, and isolates were distinguished using rep-PCR BOX fingerprinting. Isolate genomes were sequenced using Illumina whole-genome shotgun sequencing and are in the process of being annotated, with a particular focus on mobile genetic elements and AR genes. AR profiles were determined both genotypically and phenotypically using ResFinder and NARMS Sensititre MIC assays, respectively. Additionally, isolates were genoserotyped using multiplex PCR and the service SeqSero 1.2. Isolates with AR and plasmids will also be sequenced on the Oxford Nanopore MinION. This will allow for hybrid assembly of Salmonella genomes and the differentiation of chromosomal and plasmid DNA. Combining genomic and more traditional approaches can provide a more complete understanding of the potential threat posed by environmental Salmonella.

Additional Abstract Information

Student(s): Charles P. Holmes II, Sophie Jurgensen

Department: Biology

Faculty Advisor: Dr. James Herrick

Type: Poster

Year: 2018

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