Enrichment of Helminth Mitochondrial Genomes From Faecal Samples Using Hybridisation Capture
Anderson, Roy M Cools, Piet Mekonnen, Zeleke Cantacessi, Cinzia Doyle, Stephen R
Anderson, Roy M
Cools, Piet
Mekonnen, Zeleke
Cantacessi, Cinzia
Doyle, Stephen R
Citations
Altmetric:
Advisors
Editors
Other Contributors
Affiliation
EPub Date
Issue Date
2025-07-09
Submitted Date
2025-02-25
Subject Terms
genome-skimming
hybridisation capture
soil-transmitted helminths
target enrichment
whole genome sequencing
hybridisation capture
soil-transmitted helminths
target enrichment
whole genome sequencing
Collections
Research Projects
Organizational Units
Journal Issue
Other Titles
Abstract
ABSTRACT: New approaches are urgently needed to enrich rare or low‐abundant DNA in complex samples. Soil‐transmitted helminths (STHs) inhabit heterogeneous environments, including the gastrointestinal tract of their host as adults and are excreted as eggs and larvae in faeces, complicating our understanding of their biology and the use of genetic tools for species monitoring and population tracking. We have developed a hybridisation capture approach to enrich mitochondrial genome sequences of two STH species, the roundworm <jats:italic>Ascaris lumbricoides</jats:italic> and whipworm <jats:italic>Trichuris trichiura,</jats:italic> from extracted DNA from faecal material and worm specimens. Employing ~1000 targeted probes, we achieved > 6000 and > 12,000 fold enrichment for <jats:italic>A. lumbricoides</jats:italic> and <jats:italic>T. trichiura,</jats:italic> respectively, relative to direct whole genome shotgun (WGS) sequencing. Sequencing coverage was highly concordant with probe targets and correlated with the number of eggs per gram (EPG) of parasites present, from which DNA from as few as 336 EPG for <jats:italic>Ascaris</jats:italic> and 48 EPG for <jats:italic>Trichuris</jats:italic> were efficiently captured and sufficient to provide effective mitochondrial genome data. Finally, allele frequencies were highly concordant between WGS and hybridisation capture, suggesting little genetic information is lost with additional sample processing required for enrichment. Our hybridisation capture design and approach enable sensitive and flexible STH mitochondrial genome sampling from faecal DNA extracts and pave the way for broader hybridisation capture‐based genome‐wide applications and molecular epidemiology studies of STHs.
Citation
Papaiakovou, M., A. Waeschenbach, R. M. Anderson, et al. 2025. “ Enrichment of Helminth Mitochondrial Genomes From Faecal Samples Using Hybridisation Capture.” Molecular Ecology Resources e70005. https://doi.org/10.1111/1755-0998.70005.
Publisher
Journal
Research Unit
PubMed ID
PubMed Central ID
Embedded videos
Type
Journal Article
Item Description
Copyright © 2025 The Author(s). Molecular Ecology Resources published by John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium,provided the original work is properly cited. The linked file is the published version of the article.
NHM Repository
NHM Repository
Series/Report no.
ISSN
1755-098X
EISSN
1755-0998
ISBN
ISMN
GovDoc
Test Link
License
openAccess