High Throughput Equipment for Validation of Antimicrobial Resistance Data Analysis and Quality Control Procedures for Whole Genome Sequencing Using Commensal E. coli from Multiple Animal Species

Washington State University, Pullman WA

Investigators

Abstract

1 Project Summary: Veterinary diagnostic laboratories currently lack universal standardized 2 methods and quality control for WGS data analysis with regard to assessing AMR. Furthermore, 3 there is a paucity of high throughput WGS capacity and capability in the USA directed to AMR 4 surveillance testing and trend analysis in animals. As the FDA CVM is currently funding AMR 5 monitoring and whole genome sequencing (WGS) this is a significant gap. The purpose of this 6 project is to provide high throughput equipment to an ongoing FDA-VetLIRN project in our 7 laboratory to optimize and validate existing bioinformatics platforms and develop and validate 8 bioinformatics quality assurance/quality control procedures related to AMR using Escherichia 9 coli, a microbe commonly harbored in multiple animal species. The current project application 10 described herein is to utilize high throughput equipment to more broadly assess microbial 11 resistomes at the population level. Not only do resistant bacterial infections impact animal 12 health and welfare, but they also have significant potential for causing negative human health 13 consequences through transmission of resistant bacteria or resistance genes through food or 14 animal contact. The use of common classes of antimicrobials in humans and animals increases 15 the likelihood that drug resistance selected for in animal species could impact humans. 16 Therefore, monitoring AMR in animals has the potential to mitigate not only disease in animals 17 but human infections as well. Recent reductions in sequencing cost has provided an 18 opportunity for veterinary diagnostic laboratories to consider utilizing high throughput whole 19 genome sequencing technology for antimicrobial resistance assessment. Increases in 20 automation for sample preparation for whole genome sequencing (WGS) is a critical capacity 21 building effort for veterinary diagnostic laboratories. This will allow for better standardization 22 of sample preparation within the laboratory and potentially between Vet-LIRN sequencing core 23 laboratories as this technology is adopted. The project would incorporate automated 24 instrumentation into the whole genome sequencing workflow for AMR surveillance testing in 25 animal species. Funding from the current application, which will expand high throughput WGS 26 capacity and capability for FDA-VetLIRN, would increase the breadth of the current studies by 27 markedly increasing sample numbers, improving statistical evaluation, and expanding studies to 28 a broader geographical level. Areas of activity in the funding opportunity addressed by the 29 proposal include ?support purchase of equipment needed for testing?? and ?support 30 emergency surge capacity testing?.