Optimized Multilocus Sequence Typing (MLST) scheme for Trypanosoma cruzi

Diosque, P. et al. (2014) Optimized Multilocus Sequence Typing (MLST) scheme for Trypanosoma cruzi. PLoS Neglected Tropical Diseases, 8(8), e3117. (doi:10.1371/journal.pntd.0003117) (PMID:25167160) (PMCID:PMC4148231)

Diosque, P. et al. (2014) Optimized Multilocus Sequence Typing (MLST) scheme for Trypanosoma cruzi. PLoS Neglected Tropical Diseases, 8(8), e3117. (doi:10.1371/journal.pntd.0003117) (PMID:25167160) (PMCID:PMC4148231)

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Abstract

Trypanosoma cruzi, the aetiological agent of Chagas disease possess extensive genetic diversity. This has led to the development of a plethora of molecular typing methods for the identification of both the known major genetic lineages and for more fine scale characterization of different multilocus genotypes within these major lineages. Whole genome sequencing applied to large sample sizes is not currently viable and multilocus enzyme electrophoresis, the previous gold standard for T. cruzi typing, is laborious and time consuming. In the present work, we present an optimized Multilocus Sequence Typing (MLST) scheme, based on the combined analysis of two recently proposed MLST approaches. Here, thirteen concatenated gene fragments were applied to a panel of T. cruzi reference strains encompassing all known genetic lineages. Concatenation of 13 fragments allowed assignment of all strains to the predicted Discrete Typing Units (DTUs), or near-clades, with the exception of one strain that was an outlier for TcV, due to apparent loss of heterozygosity in one fragment. Monophyly for all DTUs, along with robust bootstrap support, was restored when this fragment was subsequently excluded from the analysis. All possible combinations of loci were assessed against predefined criteria with the objective of selecting the most appropriate combination of between two and twelve fragments, for an optimized MLST scheme. The optimum combination consisted of 7 loci and discriminated between all reference strains in the panel, with the majority supported by robust bootstrap values. Additionally, a reduced panel of just 4 gene fragments displayed high bootstrap values for DTU assignment and discriminated 21 out of 25 genotypes. We propose that the seven-fragment MLST scheme could be used as a gold standard for T. cruzi typing, against which other typing approaches, particularly single locus approaches or systematic PCR assays based on amplicon size, could be compared.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Llewellyn, Dr Martin
Authors: Diosque, P., Tomasini, N., Lauthier, J.J., Messenger, L.A., Monje Rumi, M.M., Ragone, P.G., Alberti-D'Amato, A. M., Pérez Brandán, C., Barnabé, C., Tibayrenc, M., Lewis, M.D., Llewellyn, M. S., Miles, M.A., and Yeo, M.
College/School:College of Medical Veterinary and Life Sciences
Journal Name:PLoS Neglected Tropical Diseases
Publisher:Public Library of Science
ISSN:1935-2735
ISSN (Online):1935-2735
Copyright Holders:Copyright © 2014 Diosque et al
First Published:First published in PLoS Neglected Tropical Diseases 8(8):e3117
Publisher Policy:Reproduced under a Creative Commons License

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