Bridging the gap between molecular and genomic epidemiology in tuberculosis: inferring MIRU-VNTR patterns from genomic data

• Published in: Journal of clinical microbiology 2024-09, Vol.62 (9), p.e0074124
• Main Authors: Buenestado-Serrano, Sergio, Martínez-Lirola, Miguel, Dippenaar, Anzaan, Sanz-Pérez, Amadeo, Garrido-Cárdenas, José Antonio, Esteban-García, Ana Belén, García-Toledo, Adriana Justine, Rodríguez-Grande, Cristina, Herranz-Martín, Marta, Saleeb, Sheri M, Muñoz, Patricia, Warren, Robin M, Pérez-Lago, Laura, García de Viedma, Darío
• Format: Article
• Language: English
• Subjects: Genomics; Genotype; Humans; Minisatellite Repeats - genetics; Molecular Epidemiology - methods; Mycobacteriology; Mycobacteriology and Aerobic Actinomycetes; Mycobacterium tuberculosis - classification; Mycobacterium tuberculosis - genetics; Reproducibility of Results; South Africa - epidemiology; Spain - epidemiology; Tuberculosis - epidemiology; Tuberculosis - microbiology
• ISSN: 0095-1137; 1098-660X; 1098-660X
• DOI: 10.1128/jcm.00741-24

The transition from MIRU-VNTR-based epidemiology studies in tuberculosis (TB) to genomic epidemiology has transformed how we track transmission. However, short-read sequencing is poor at analyzing repetitive regions such as the MIRU-VNTR loci. This causes a gap between the new genomic data and the large amount of information stored in historical databases. Long-read sequencing could bridge this knowledge gap by allowing analysis of repetitive regions. However, the feasibility of extracting MIRU-VNTRs from long reads and linking them to historical data has not been evaluated. In our study, an arm, consisting of inference of MIRU patterns from long-read sequences (using MIRUReader program), was compared with an experimental arm, involving standard amplification and fragment sizing. We analyzed overall performance on 39 isolates from South Africa and confirmed reproducibility in a sample enriched with 62 clustered cases from Spain. Finally, we ran 25 consecutive incident cases, demonstrating the feasibility of correctly assigning new clustered/orphan cases by linking data inferred from genomic analysis to MIRU-VNTR databases. Of the 3,024 loci analyzed, only 11 discrepancies (0.36%) were found between the two arms: three attributed to experimental error and eight to misassigned alleles from long-read sequencing. A second round of analysis of these discrepancies resulted in agreement between the experimental and arms in all but one locus. Adjusting the MIRUReader program code allowed us to flag potential misassignments due to suboptimal coverage or unfixed double alleles. Our study indicates that long-read sequencing could help address potential chronological and geographical gaps arising from the transition from molecular to genomic epidemiology of tuberculosis. The transition from molecular epidemiology in tuberculosis (TB), based on the analysis of repetitive regions (VNTR-based genotyping), to genomic epidemiology transforms in the precision with which we track transmission. However, short-read sequencing, the most common method for performing genomic analysis, is poor at analyzing repetitive regions. This means that we face a gap between the new genomic data and the large amount of information stored in historical databases, which is also an obstacle to cross-national surveillance involving settings where only molecular data are available. Long-read sequencing could help bridge this knowledge gap by allowing analysis of repetitive regions. Our study demon