Development of a SNP barcode to genotype < i > Babesia microti < /i > infections

by Mary Lynn Baniecki, Jade Moon, Kian Sani, Jacob E. Lemieux, Stephen F. Schaffner, Pardis C. SabetiBabesia microti is tick-borne disease that is an emerging threat to public health due to increasing prevalence and expanding geographic range. Detection and constant surveillance of babesiosis is imperative for predicting pathogen expansion. Leveraging our whole genome sequence (WGS) analyses ofB.microti, we developed a single nucleotide polymorphism (SNP)-based high resolution melt (HRM) surveillance tool. We developed our HRM assay using available sequence data and identified 775 SNPs. From these candidate SNPs, we developed a 32-SNP barcode that is robust and differentiates geographically distinct populations; it contains SNPs that are putatively neutral, located in nuclear, mitochondrial, and apicoplastal regions. The assays are reproducible and robust, requiring a small quantity of DNA (limit of detection as low as 10 pg.). We analyzed the performance of our HRM assay using 26B.microti clinical samples used in our WGS study from babesiosis endemic regions in the United States. We identified a minimal barcode consisting of 25 SNPs that differentiate geographically distinct populations across all clinical samples evaluated (average minor allele frequency> 0.22). Supporting our previous WGS findings, our 25-SNP barcode identified distinct barcode signatures that segregateB.microti into two lineages: Northeast and Midwest, with the Northeast having three subpopulations: Conne...

Source: PLoS Neglected Tropical Diseases - March 24, 2019 Category: Tropical Medicine Authors: Mary Lynn Baniecki Source Type: research