Evaluation of the iSeq platform for E. coli pathotyping

Project Summary/AbstractThere is a growing need for veterinary and public health laboratories to perform whole genome sequencing formonitoring antimicrobial resistance and protecting the safety of people and animals. The FDA Vet-LIRN iscurrently assessing a small benchtop sequencing platform (Illumina iSeq) that could potentially be deployedacross their network. Thus far, it has only been tested with Salmonella, and further methods optimization andevaluation is needed to ensure that the platform can be used by other laboratories that have less familiaritywith sequencing technologies.E. coli is the most common pathogen tested for antibiotic susceptibility in veterinary diagnostic labs. It is alsoone of the most concerning for multi-drug resistance; several isolates captured thus far in Vet-LIRN activesurveillance are predicted to be pan-resistant to all drugs used in human or animal medicine. Because themethods for susceptibility testing are not standardized, and specific drug panels are used for animal isolatesthat do not cover all antibiotics used in humans, it was not until these strains were sequenced that the severitywas fully appreciated. Having sequencing capacity for this organism in more labs will facilitate rapidsurveillance and better equip labs to participate in pet food contamination cases, which are now heavilyfocused on sequencing results. This directly supports the mission of FDA to ensure the safety of our nation'sfood supply and protect public health.Since E. coli is commonly found in people and animals, another critical need is the ability to discern thepotential virulence of different strains using molecular subtyping. Unfortunately, no bioinformatic tools currentlyexist that will provide interpretations that are host specific for animals while still conforming to the pathogenicprofiles used for humans. The capacity to perform advanced molecular characterization of bacterial isolates ina reliable manner is critical to our ability to respond quickly to suspected microbiological contamination andmonitor antimicrobial resistance in animals and feed. The proposed studies will have important impacts forboth human and veterinary health and will improve the capabilities of the Vet-LIRN to perform effectivesurveillance for food-borne pathogens.