Ristro: An R package for vector bloodmeal identification by short tandem repeat overlap

Abstract

Measuring vector–human contact in a natural setting can inform precise target- ing of interventions to interrupt transmission of vector-borne diseases. One ap- proach is to directly match human DNA in vector bloodmeals to the individuals who were bitten using genotype panels of discriminative short tandem repeats (STRs). Existing methods for matching STR profiles in blood meals to the people bitten preclude the ability to match most incomplete profiles and multisource bloodmeals to bitten individuals.We developed bistro, an R package that implements three pre-existing STR match- ing methods as well as the package's namesake, bistro, a new algorithm described here. bistro employs forensic analysis methods to calculate likelihood ratios and match human STR profiles in bloodmeals to people using a dynamic threshold. We evaluated the algorithm's accuracy and compared it to existing matching approaches using a publicly available panel of 188 single-source and 100 multi source samples containing DNA from 50 known human sources. Then, we applied it to match 777 newly field-collected mosquito blood meals to a database of 645 people.The R package implements four STR matching algorithms in user-friendly func- tions with clear documentation. bistro correctly matched 99% (187/188) of pro- files in single-source samples, and 62% (224/359) of profiles from multisource samples, resulting in a sensitivity of 0.75 (vs. <0.51 for other algorithms). The specificity of bistro was 0.9998 (vs. 1 for other algorithms). Furthermore, bistro identified 79% (720/906) of all possible matches for field-derived mosquitoes, yielding 1.4× more matches than existing algorithms.bistro identifies more correct blood meal–human matches than existing approaches, enabling more accurate and robust analyses of vector–human contact in natural settings. The bistro R package and corresponding documentation allow for straightforward uptake of this algorithm by others.