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Subtyping of Campylobacter jejuni ssp. doylei Isolates Using Mass Spectrometry-based PhyloProteomics (MSPP)
Published on: October 30, 2016
Strain classification of Mycobacterium tuberculosis: congruence between large sequence polymorphisms and spoligotypes
M Kato-Maeda1, S Gagneux, L L Flores
1Francis J Curry National Tuberculosis Center, Division of Pulmonary and Critical Care Medicine, San Francisco General Hospital, University of California San Francisco, California 94110, USA. midori.kato-maeda@ucsf.edu
Summary
Spoligotyping accurately classifies Mycobacterium tuberculosis strains into families, which represent sub-lineages within major lineages. This method aids molecular epidemiology by identifying reliable strain patterns for tuberculosis research.
Area of Science:
- Microbiology
- Genetics
- Epidemiology
Background:
- Spoligotyping is a widely used method in molecular epidemiology for Mycobacterium tuberculosis (Mtb) strain identification.
- Signature patterns from spoligotyping have historically identified Mtb strain families.
- Homoplasy in spoligotyping markers can lead to misclassification of phylogenetically distinct strains.
Purpose of the Study:
- To determine the accuracy of spoligotyping for Mtb strain classification.
- To validate spoligotyping against a gold standard based on large sequence and single nucleotide polymorphism (SNP)-defined lineages.
- To assess the phylogenetic relationship between spoligotype families and established Mtb lineages.
Main Methods:
- Analysis of 919 Mycobacterium tuberculosis isolates.
- Classification of isolates into spoligotype families.
- Comparison of spoligotype-based classification with six large sequence and SNP-defined lineages.
- Evaluation of marker homoplasy and its impact on strain classification.
Main Results:
- 870 out of 919 (95%) Mtb isolates were successfully classified into a spoligotype family.
- All strains within a specific spoligotype family belonged to the same major lineage.
- No instances of convergence, where unrelated strains shared the same spoligotype, were observed.
- Spoligotype families were found to represent distinct sub-lineages within the broader Mtb lineages.
Conclusions:
- Spoligotyping is a reliable method for classifying Mycobacterium tuberculosis strains into distinct families.
- These spoligotype families represent robust sub-lineages within the main phylogenetic lineages of Mtb.
- The findings support the continued use of spoligotyping in molecular epidemiological studies of tuberculosis, with an understanding of its relationship to deeper phylogenetic structures.
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