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Related Experiment Video

Updated: Jun 9, 2025

High-throughput Gene Tagging in Trypanosoma brucei

High-throughput Gene Tagging in Trypanosoma brucei

Published on: August 12, 2016

Detecting complex infections in trypanosomatids using whole genome sequencing.

João Luís Reis-Cunha¹, Daniel Charlton Jeffares²

¹York Biomedical Research Institute, Department of Biology and York Biomedical Research Institute, University of York, York, YO10 5DD, UK. joao.cunha@york.ac.uk.

|October 30, 2024

Summary

A new method identifies complex infections in trypanosomatid parasites, revealing that while multiclonality and polyploidy occur, they are infrequent in cultured samples. This tool aids in understanding parasite diversity and host-parasite interactions.

Keywords:

Aneuploidy Complex infections Multiplicity of infection Polyploidy Protozoan parasites Trypanosomatids

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Area of Science:

Genomics
Parasitology
Bioinformatics

Background:

Trypanosomatid parasites cause significant diseases in developing nations.
These protozoans exhibit complex adaptations, including polyploidy and multiplicity of infections (MOI), to survive in mammalian hosts.
Distinguishing between MOI and polyploidy is crucial for understanding parasite population dynamics.

Purpose of the Study:

To develop and validate a methodology for identifying multiclonal infections and polyploidy in trypanosomatid parasites.
To assess the prevalence of complex infections across different trypanosomatid clades using whole genome sequencing data.
To provide a user-friendly bioinformatic tool for analyzing infection complexity.

Main Methods:

Developed a method analyzing allelic read depth fluctuations in heterozygous positions from whole genome sequencing data.
Validated the methodology using simulated MOI and known polyploid isolates (Leishmania, Trypanosoma cruzi).
Applied the approach to genome-wide SNP data from 497 cultured trypanosomatid samples across four clades.

Main Results:

The method accurately estimates the complexity index (CI) and robustly detects complex infections with sufficient sequencing coverage and heterozygous SNPs.
Analysis of 497 trypanosomatid isolates revealed that approximately 7% of cultured samples exhibit complexity (multiclonality or polyploidy).
Multiclonality and polyploidy were observed across L. donovani/L. infantum, L. braziliensis, T. cruzi, and T. brucei clades.

Conclusions:

The developed method accurately identifies polyploid isolates and multiclonal infections under adequate sequencing conditions.
A user-friendly R script is available for analyzing variant call format (VCF) files to assess infection complexity.
While present in all studied clades, complex infections are not frequent in cultured trypanosomatids, with current estimates representing lower bounds.