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- Title
Multilocus Sequence Typing (MLST) for Lineage Assignment and High Resolution Diversity Studies in Trypanosoma cruzi.
- Authors
Yeo, Matthew; Mauricio, Isabel L.; Messenger, Louisa A.; Lewis, Michael D.; Llewellyn, Martin S.; Acosta, Nidia; Bhattacharyya, Tapan; Diosque, Patricio; Carrasco, Hernan J.; Miles, Michael A.
- Abstract
Background: Multilocus sequence typing (MLST) is a powerful and highly discriminatory method for analysing pathogen population structure and epidemiology. Trypanosoma cruzi, the protozoan agent of American trypanosomiasis (Chagas disease), has remarkable genetic and ecological diversity. A standardised MLST protocol that is suitable for assignment of T. cruzi isolates to genetic lineage and for higher resolution diversity studies has not been developed. Methodology/Principal Findings: We have sequenced and diplotyped nine single copy housekeeping genes and assessed their value as part of a systematic MLST scheme for T. cruzi. A minimum panel of four MLST targets (Met-III, RB19, TcGPXII, and DHFR-TS) was shown to provide unambiguous assignment of isolates to the six known T. cruzi lineages (Discrete Typing Units, DTUs TcI-TcVI). In addition, we recommend six MLST targets (Met-II, Met-III, RB19, TcMPX, DHFR-TS, and TR) for more in depth diversity studies on the basis that diploid sequence typing (DST) with this expanded panel distinguished 38 out of 39 reference isolates. Phylogenetic analysis implies a subdivision between North and South American TcIV isolates. Single Nucleotide Polymorphism (SNP) data revealed high levels of heterozygosity among DTUs TcI, TcIII, TcIV and, for three targets, putative corresponding homozygous and heterozygous loci within DTUs TcI and TcIII. Furthermore, individual gene trees gave incongruent topologies at inter- and intra-DTU levels, inconsistent with a model of strict clonality. Conclusions/Significance: We demonstrate the value of systematic MLST diplotyping for describing inter-DTU relationships and for higher resolution diversity studies of T. cruzi, including presence of recombination events. The high levels of heterozygosity will facilitate future population genetics analysis based on MLST haplotypes. Author Summary: The single-celled parasite Trypanosoma cruzi occurs in animals and insect vectors in the Americas. When transmitted to humans it causes a major public health problem, Chagas disease (American trypanosomiasis). T. cruzi is genetically diverse and currently split into six groups, known as TcI to TcVI. Multilocus sequence typing (MLST) is a method used for studying the population structure and diversity of pathogens. MLST involves sequencing the DNA of several different genes and comparing the sequences between isolates. MLST has not yet been developed and systematically applied to T. cruzi. He, we sequence nine T. cruzi genes, selecting a panel of four for lineage assignment and six for higher resolution studies of genetic diversity. Our results showed that one of the T. cruzi genetic groups is further subdivided into North and South American subpopulations. Furthermore, comparative analyses of the gene sequences gave new evidence of genetic exchange in T. cruzi. Application of MLST for assigning field isolates of T. cruzi to genetic groups and for detailed investigation of diversity provides a valuable approach to understanding the taxonomy, population structure, genetics, ecology and epidemiology of this important human pathogen.
- Subjects
TRYPANOSOMA cruzi; CHAGAS' disease; SINGLE nucleotide polymorphisms; POPULATION genetics; GENETIC variation; BASE pairs
- Publication
PLoS Neglected Tropical Diseases, 2011, Vol 5, Issue 6, p1
- ISSN
1935-2727
- Publication type
Article
- DOI
10.1371/journal.pntd.0001049