Investigating the Diversity of Tuberculosis Spoligotypes with Dimensionality Reduction and Graph Theory

Abstract

The spoligotype is a graphical description of the CRISPR locus present in Mycobacterium tuberculosis, which has the particularity of having only 68 possible spacers. This spoligotype, which can be easily obtained either in vitro or in silico, allows to have a summary information of lineage or even antibiotic resistance (when known to be associated to a particular cluster) at a lower cost. The objective of this article is to show that this representation is richer than it seems, and that it is under-exploited until now. We first recall an original way to represent these spoligotypes as points in the plane, allowing to highlight possible sub-lineages, particularities in the animal strains, etc. This graphical representation shows clusters and a skeleton in the form of a graph, which led us to see these spoligotypes as vertices of an unconnected directed graph. In this paper, we therefore propose to exploit in detail the description of the variety of spoligotypes using a graph, and we show to what extent such a description can be informative.

Mycobacterium tuberculosis complex drug-resistance, phylogenetics, and evolution in Nigeria: Comparison with Ghana and Cameroon

“…The global genotypic resistance profile per country, as extracted from TB-Annotator (>94.694 isolates) is provided in Table 3 [16]. The same trend as the one found in the 165 patients Northern Nigeria cohort, or the trend found in our sequenced isolates is observed in the genomic mutations found in TB-Annotator.…”

“…Sequencing was performed using the Miniseq High Output Kit [Illumina, San Diego, USA] generating paired-end reads of 150 bp. Quality of reads was then analyzed by fastqc and a combination of web-based analysis (TB-Profiler) (available at https://tbdr.lshtm.ac.uk) or through a proprietary pipeline (TB-Annotator) [16].…”

“…Variant calling of the fastq data has been performed using TB-Annotator (91,465 isolates version, [16]), after integration of the newly sequenced isolates in the database. Lineage attribution has been done by using the robust SNP barcode for typing Mycobacterium tuberculosis complex isolates of Coll et al [4], as developed in the TB-Annotator platform.…”

Special Issue: New Advances in Bioinformatics and Biomedical Engineering Using Machine Learning Techniques, IWBBIO-2022

“…Finally, in the paper by Gaetan Senelle et al [ 9 ], with title: “Investigating the Diversity of Tuberculosis Spoligotypes with Dimensionality Reduction and Graph Theory”, analyze the spoligotype. The spoligotype is a graphical description of the CRISPR locus present in Mycobacterium tuberculosis, which has the peculiarity of having only 68 possible spacers.…”