Comparison of in silico predicted Mycobacterium tuberculosis spoligotypes and lineages from whole genome sequencing data

Bacterial strain-types in the Mycobacterium tuberculosis complex underlie tuberculosis disease, and have been associated with drug resistance, transmissibility, virulence, and host-pathogen interactions. Spoligotyping was developed as a molecular genotyping technique used to determine strain-types,...

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Bibliographic Details
Published in:	Scientific reports 2023-07, Vol.13 (1), p.11368-11368, Article 11368
Main Authors:	Napier, Gary, Couvin, David, Refrégier, Guislaine, Guyeux, Christophe, Meehan, Conor J, Sola, Christophe, Campino, Susana, Phelan, Jody, Clark, Taane G
Format:	Article
Language:	eng
Subjects:	Bacterial Typing Techniques Beijing Computer Science Cryptography and Security Distributed, Parallel, and Cluster Computing Drug Resistance Emerging Technologies Genomes Genotype Genotyping Geographical distribution Host-pathogen interactions Humans Modeling and Simulation Multiagent Systems Mycobacterium tuberculosis Nomenclature Single-nucleotide polymorphism Software Engineering Spoligotyping Tuberculosis Tuberculosis - microbiology Ubiquitous Computing Virulence Whole genome sequencing
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Summary:	Bacterial strain-types in the Mycobacterium tuberculosis complex underlie tuberculosis disease, and have been associated with drug resistance, transmissibility, virulence, and host-pathogen interactions. Spoligotyping was developed as a molecular genotyping technique used to determine strain-types, though recent advances in whole genome sequencing (WGS) technology have led to their characterization using SNP-based sub-lineage nomenclature. Notwithstanding, spoligotyping remains an important tool and there is a need to study the congruence between spoligotyping-based and SNP-based sub-lineage assignation. To achieve this, an in silico spoligotype prediction method ("Spolpred2") was developed and integrated into TB-Profiler. Lineage and spoligotype predictions were generated for > 28 k isolates and the overlap between strain-types was characterized. Major spoligotype families detected were Beijing (25.6%), T (18.6%), LAM (13.1%), CAS (9.4%), and EAI (8.3%), and these broadly followed known geographic distributions. Most spoligotypes were perfectly correlated with the main MTBC lineages (L1-L7, plus animal). Conversely, at lower levels of the sub-lineage system, the relationship breaks down, with only 65% of spoligotypes being perfectly associated with a sub-lineage at the second or subsequent levels of the hierarchy. Our work supports the use of spoligotyping (membrane or WGS-based) for low-resolution surveillance, and WGS or SNP-based systems for higher-resolution studies.
ISSN:	2045-2322 2045-2322