Preferred Name

Noah Greenman

Creative Commons License

Creative Commons License
This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 4.0 License.

Date of Graduation


Document Type


Degree Name

Master of Science (MS)


Department of Biology


James B. Herrick


Multidrug resistant Salmonella enterica present in stream sediment and poultry litter represent a critical health concern. A small number of S. enterica serotypes are responsible for most lab-confirmed infections in the US each year. To assess the prevalence of these significant strains, we isolated 88 S. enterica from stream sediment and poultry litter. Sequence data for all isolates were generated using an Illumina® sequencing platform, with long-reads for some isolates from the Oxford Nanopore MinION™ used in a hybrid genome assembly approach. Isolates were typed according to their serotype and multi-locus sequence type using SeqSero/SISTR and Enterobase respectively. Antibiotic resistance genes were annotated using ABRicate and Prokka. Thirty-one isolates possessed one or more antibiotic resistance genes, with resistance genes located exclusively on plasmids identified by MOB_Suite in 26 of those isolates. Eight of the 26 isolates with plasmids containing antibiotic resistance genes displayed phenotypic resistance to multiple antibiotics. Multiple plasmids were found to contain tra and/or pil gene cassettes, implicating them as conjugative in solid and/or liquid mediums. Septic Salmonella infections require antibiotic intervention, and the existence of multiple antibiotic resistance genes on transmissible plasmids in Salmonella isolated from streams and litter may indicate that a significant reservoir for transmissible resistance occurs in these environments. Infections with multidrug resistant Salmonella be difficult to treat, and plasmid-borne resistance may be transmissible to other, potentially even more pathogenic bacteria in these environments.



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