Comparison of in silico predicted Mycobacterium tuberculosis spoligotypes and lineages from whole genome sequencing data - Archive ouverte HAL
Article Dans Une Revue Scientific Reports Année : 2023

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

Résumé

Bacterial strain-types in the Mycobacterium tuberculosis complexunderlie tuberculosis disease, and have been associated with drugresistance, transmissibility, virulence, and host–pathogeninteractions. Spoligotyping was developed as a molecular genotypingtechnique used to determine strain-types, though recent advances inwhole genome sequencing (WGS) technology have led to theircharacterization using SNP-based sub-lineage nomenclature.Notwithstanding, spoligotyping remains an important tool and thereis a need to study the congruence between spoligotyping-based andSNP-based sub-lineage assignation. To achieve this, an in silicospoligotype prediction method (“Spolpred2”) was developed andintegrated into TB-Profiler. Lineage and spoligotype predictionswere generated for > 28 k isolates and the overlap betweenstrain-types was characterized. Major spoligotype families detectedwere 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 MTBClineages (L1-L7, plus animal). Conversely, at lower levels of thesub-lineage system, the relationship breaks down, with only 65% ofspoligotypes being perfectly associated with a sub-lineage at thesecond or subsequent levels of the hierarchy. Our work supports theuse of spoligotyping (membrane or WGS-based) for low-resolutionsurveillance, and WGS or SNP-based systems for higher-resolutionstudies.

Dates et versions

hal-04224785 , version 1 (02-10-2023)

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Citer

Taane G Clark, Gary Napier, David Couvin, Guislaine Refrégier, Christophe Guyeux, et al.. Comparison of in silico predicted Mycobacterium tuberculosis spoligotypes and lineages from whole genome sequencing data. Scientific Reports, 2023, 13, pp.11368 (7). ⟨10.1038/s41598-023-38384-3⟩. ⟨hal-04224785⟩
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