Trich-tracker - a practical tool to trace T. spiralis transmission based on rapid, cost-effective sampling of genome-wide genetic variation

Authors: BILSKA-ZAJAK, EWA - Non ARS Employee; Rosenthal, Benjamin; Thompson, Peter

Submitted to: International Journal for Parasitology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/18/2021
Publication Date: 9/17/2021
Citation: Bilska-Zajak, E., Rosenthal, B.M., Thompson, P.C. 2021. Trich-tracker - a practical tool to trace T. spiralis transmission based on rapid, cost-effective sampling of genome-wide genetic variation. International Journal for Parasitology. https://doi.org/10.1016/j.ijpara.2021.08.002.
DOI: https://doi.org/10.1016/j.ijpara.2021.08.002

Interpretive Summary: Strain typing has become an indispensable tool in tracing outbreaks of bacterial and viral pathogens, but less precedent exists for eukaryotic parasites, which typically reproduce sexually, evolve more slowly, and have much larger genomes. Accurate and timely source tracking would aid efforts to understand and control sources of human exposure to Trichinella spiralis. Reduced genome representation techniques provide means to sample many loci from throughout the genome. One such method, RADseq, produces DNA libraries for high-throughput sequencing using restriction enzymes that cut at specific motifs wherever they occur in the genome. Here, we developed a tool that makes efficient use of diagnostic variation distributed throughout this parasite’s genome to more rapidly, and conclusively, resolve connections and distinctions among focal outbreaks of T. spiralis. In particular, we rapidly characterized genetic variation among a sample of parasites from Polish farms and wildlife, sampling genomic variation using double digest restriction-site associated DNA sequencing (ddRADseq). We document a procedure affording unprecedented epidemiological resolution that can be completed in just days or weeks, and at an affordable cost. The results will aid veterinary and public health regulators, epidemiologists, livestock producers, and wildlife biologists.

Technical Abstract: Here, we introduce Trich-Tracker, a tool that makes efficient use of diagnostic variation distributed throughout the genome of Trichinella spiralis to more rapidly, and conclusively, resolve connections and distinctions among focal outbreaks of T. spiralis. In particular, we rapidly characterized genetic variation among a sample of parasites from Polish farms and wildlife, sampling genomic variation using double digest restriction-site associated DNA sequencing (ddRADseq). We document a procedure affording unprecedented epidemiological resolution that can be completed in just days or weeks, and at an affordable cost, identifying informative variation. By simultaneously sequencing many isolates at thousands of loci (~400,000 nucleotides per sample), we identified sufficient variation (within a metapopulation varying at ~ 1 base in 10,000). Trich-tracker is very flexible tool, quickly and inexpensively mining genomes of even highly inbred populations of T. spiralis to support outbreak investigations. The discriminating power of this tool is tunable and scalable, allowing application in a variety of epidemiological contexts. The simplicity of entire procedure, time effectivity and cost effectivity of Trich-tracker ensure opportunity of its practical application in ongoing Trichinella outbreaks.