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

Publication ,  Journal Article
Lapp, Z; Abel, L; Mangeni, J; Obala, AA; O'Meara, WP; Taylor, SM; Markwalter, CF
Published in: Methods in Ecology and Evolution
February 1, 2024

Measuring vector–human contact in a natural setting can inform precise targeting of interventions to interrupt transmission of vector-borne diseases. One approach 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 bloodmeals 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 matching 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 multisource samples containing DNA from 50 known human sources. Then, we applied it to match 777 newly field-collected mosquito bloodmeals to a database of 645 people. The R package implements four STR matching algorithms in user-friendly functions with clear documentation. bistro correctly matched 99% (187/188) of profiles 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 bloodmeal–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.

Duke Scholars

Published In

Methods in Ecology and Evolution

DOI

EISSN

2041-210X

Publication Date

February 1, 2024

Volume

15

Issue

2

Start / End Page

308 / 316

Related Subject Headings

  • 4104 Environmental management
  • 3109 Zoology
  • 3103 Ecology
  • 0603 Evolutionary Biology
  • 0602 Ecology
  • 0502 Environmental Science and Management
 

Citation

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Lapp, Z., Abel, L., Mangeni, J., Obala, A. A., O’Meara, W. P., Taylor, S. M., & Markwalter, C. F. (2024). bistro: An R package for vector bloodmeal identification by short tandem repeat overlap. Methods in Ecology and Evolution, 15(2), 308–316. https://doi.org/10.1111/2041-210X.14277
Lapp, Z., L. Abel, J. Mangeni, A. A. Obala, W. P. O’Meara, S. M. Taylor, and C. F. Markwalter. “bistro: An R package for vector bloodmeal identification by short tandem repeat overlap.” Methods in Ecology and Evolution 15, no. 2 (February 1, 2024): 308–16. https://doi.org/10.1111/2041-210X.14277.
Lapp Z, Abel L, Mangeni J, Obala AA, O’Meara WP, Taylor SM, et al. bistro: An R package for vector bloodmeal identification by short tandem repeat overlap. Methods in Ecology and Evolution. 2024 Feb 1;15(2):308–16.
Lapp, Z., et al. “bistro: An R package for vector bloodmeal identification by short tandem repeat overlap.” Methods in Ecology and Evolution, vol. 15, no. 2, Feb. 2024, pp. 308–16. Scopus, doi:10.1111/2041-210X.14277.
Lapp Z, Abel L, Mangeni J, Obala AA, O’Meara WP, Taylor SM, Markwalter CF. bistro: An R package for vector bloodmeal identification by short tandem repeat overlap. Methods in Ecology and Evolution. 2024 Feb 1;15(2):308–316.
Journal cover image

Published In

Methods in Ecology and Evolution

DOI

EISSN

2041-210X

Publication Date

February 1, 2024

Volume

15

Issue

2

Start / End Page

308 / 316

Related Subject Headings

  • 4104 Environmental management
  • 3109 Zoology
  • 3103 Ecology
  • 0603 Evolutionary Biology
  • 0602 Ecology
  • 0502 Environmental Science and Management