Identifying Mycobacterium tuberculosis complex strain families using spoligotypes

Abstract

We present a novel approach for analysis of Mycobacterium tuberculosis complex (MTC) strain genotyping data. Our work presents a first step in an ongoing project dedicated to the development of decision support tools for tuberculosis (TB) epidemiologists exploiting both genotyping and epidemiological data. We focus on spacer oligonucleotide typing (spoligotyping), a genotyping method based on analysis of a direct repeat (DR) locus. We use mixture models to identify strain families of MTC based on their spoligotyping patterns. Our algorithm, SPOTCLUST, incorporates biological information on spoligotype evolution, without attempting to derive the full phylogeny of MTC. We applied our algorithm to 535 different spoligotype patterns identified among 7166 MTC strains isolated between 1996 and 2004 from New York State TB patients. Two models were employed and validated: a 36-component model based on global spoligotype database SpolDB3, and a randomly initialized model (RIM) containing 48 components. Our analysis both confirmed previously expert-defined families of MTC strains and suggested certain new families. SPOTCLUST, which is available online, can be further improved by incorporating data obtained using additional strain genetic markers and epidemiological information. We demonstrate on New York City (NYC) patient data how the resulting models can potentially form the basis of TB control tools using genotyping.3

SNP typing reveals similarity in Mycobacterium tuberculosis genetic diversity between Portugal and Northeast Brazil

“…To this end, part of the Potuguese and Brazilian datasets were also identified by their spoligotype profile using SPOTCLUST (Vitol et al, 2006). The spoligotyping identification was then compared with the group strains identified with SNP typing.…”

“…As for the 141 SNP typed Brazilian samples with complete information, we determine the spoligotyping pattern of each one. These 252 samples were identified through their spoligotype profile using SPOTCLUST (Vitol et al, 2006). Strain identification using spoligotyping was then compared with the group strains identified with SNP typing.…”

“…Spoligotyping has been shown not to be reliable for phylogenetic analysis, because its patterns may not reflect the evolution history of a strain and the "signature" pattern of the strain groups can be ambiguous or uninformative (Comas et al, 2009). To circumvent these problems we used a novel software that relies on an extensive Spolygotype database to assign new Spoligotype patterns to strain groups (SPOTCLUST, Vitol et al, 2006). Figure 5 shows a comparison between strain group identification in our collection using both types of molecular data, SNP typing and Spoligotyping.…”

“…These systems have limited use for phylogenetics and strain identification because, due to targeting polymorphisms with fast substitution rate and using limited number of markers, they may present events of convergent evolution, or homoplasy, (Comas et al, 2009). Furthermore, the use of Spoligotyping to identify genotype profiles absent from the reference database is debatable (but see Vitol et al, 2006). Nevertheless, their usage strongly shaped the classification of MTBC strains.…”

Evaluation of Two Molecular Assays for Rapid Detection of Mycobacterium tuberculosis Resistance to Fluoroquinolones in High-Tuberculosis and -Multidrug-Resistance Settings

“…Crude DNA extracts were isolated from cultures by heating (95°C, 30 min), followed by sonication (20 min). Isolates were genotyped using spoligotyping and variable-number tandem-repeat (VNTR) typing with a standardized panel of 24 loci as described previously (21,32,44,45). The VNTR loci 3232, 3336, 2163A, and 1982 were used, in addition to the standard panel (44).…”