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

Zena Lapp1, Lucy Abel2, Judith Mangeni3

  • 1Duke Global Health Institute, Duke University, Durham, NC, USA.

Methods in Ecology and Evolution
|July 4, 2024
PubMed
Summary

A new R package, bistro, improves vector-human contact analysis by accurately matching DNA from bloodmeals to individuals, enhancing disease transmission studies.

Keywords:
DNA matchingbloodmealbloodmeal matchingmalariamatchshort tandem repeatstrvector-borne disease

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Area of Science:

  • Epidemiology
  • Genetics
  • Bioinformatics

Background:

  • Accurate measurement of vector-human contact is crucial for controlling vector-borne diseases.
  • Existing methods for matching human DNA in vector bloodmeals to individuals have limitations, especially with incomplete or mixed DNA profiles.

Purpose of the Study:

  • To develop and evaluate "bistro", a novel R package and algorithm for improved matching of human DNA short tandem repeat (STR) profiles from vector bloodmeals to human sources.
  • To enhance the accuracy and robustness of analyses of vector-human contact in natural settings.

Main Methods:

  • Development of the "bistro" R package implementing four STR matching algorithms, including a new algorithm utilizing forensic likelihood ratio calculations and a dynamic threshold.
  • Evaluation of algorithm accuracy using a public dataset of 188 single-source and 100 multi-source DNA samples from 50 known human sources.
  • Application of the "bistro" package to match 777 field-collected mosquito bloodmeals against a database of 645 individuals.

Main Results:

  • The "bistro" algorithm achieved high accuracy, correctly matching 99% of single-source profiles and 62% of multi-source profiles.
  • Compared to existing methods, "bistro" demonstrated a sensitivity of 0.75 (vs. < 0.51) and a specificity of 0.9998.
  • The package successfully identified 79% of all possible matches for field-derived mosquitoes, yielding 1.4 times more matches than previous algorithms.

Conclusions:

  • The "bistro" R package significantly improves the identification of vector-human contact by enabling more accurate and comprehensive matching of bloodmeal DNA to individuals.
  • This advancement facilitates more precise targeting of interventions to interrupt vector-borne disease transmission.
  • The user-friendly design and clear documentation of the "bistro" package promote its widespread adoption in ecological and epidemiological research.