Sample pooling methods for efficient pathogen screening: Practical implications

Tara N. Furstenau, Jill H. Cocking, Crystal M. Hepp, Viacheslav Y. Fofanov

Research output: Contribution to journalArticlepeer-review

2 Scopus citations

Abstract

Due to the large number of negative tests, individually screening large populations for rare pathogens can be wasteful and expensive. Sample pooling methods improve the efficiency of large-scale pathogen screening campaigns by reducing the number of tests and reagents required to accurately categorize positive and negative individuals. Such methods rely on group testing theory which mainly focuses on minimizing the total number of tests; however, many other practical concerns and tradeoffs must be considered when choosing an appropriate method for a given set of circumstances. Here we use computational simulations to determine how several theoretical approaches compare in terms of (a) the number of tests, to minimize costs and save reagents, (b) the number of sequential steps, to reduce the time it takes to complete the assay, (c) the number of samples per pool, to avoid the limits of detection, (d) simplicity, to reduce the risk of human error, and (e) robustness, to poor estimates of the number of positive samples. We found that established methods often perform very well in one area but very poorly in others. Therefore, we introduce and validate a new method which performs fairly well across each of the above criteria making it a good general use approach.

Original languageEnglish (US)
Article numbere0236849
JournalPLoS ONE
Volume15
Issue number11 November
DOIs
StatePublished - Nov 2020

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

Fingerprint

Dive into the research topics of 'Sample pooling methods for efficient pathogen screening: Practical implications'. Together they form a unique fingerprint.

Cite this