Abstract
Systematic molecular/genomic epidemiology studies for tuberculosis surveillance cannot be implemented in many countries. We selected Panama as a model for an alternative strategy. Mycobacterial interspersed repetitive unit–variable-number tandem-repeat (MIRU-VNTR) analysis revealed a high proportion (50%) of Mycobacterium tuberculosis isolates included in 6 clusters (A–F) in 2 provinces (Panama and Colon). Cluster A corresponded to the Beijing sublineage. Whole-genome sequencing (WGS) differentiated clusters due to active recent transmission, with low single-nucleotide polymorphism–based diversity (cluster C), from clusters involving long-term prevalent strains with higher diversity (clusters A, B). Prospective application in Panama of 3 tailored strain–specific PCRs targeting marker single-nucleotide polymorphisms identified from WGS data revealed that 31.4% of incident cases involved strains A–C and that the Beijing strain was highly represented and restricted mainly to Colon. Rational integration of MIRU-VNTR, WGS, and tailored strain–specific PCRs could be a new model for tuberculosis surveillance in countries without molecular/genomic epidemiology programs.
Highlights
Systematic molecular/genomic epidemiology studies for tuberculosis surveillance cannot be implemented in many countries
PCR-based molecular epidemiology approaches, namely mycobacterial interspersed repetitive unit–variable-number tandem-repeat (MIRU-VNTR), are being replaced by genomic epidemiology approaches. These approaches are based on the identification of single-nucleotide polymorphisms (SNPs) using whole-genome sequencing (WGS), which offers higher discriminatory power and precision in assigning transmission clusters [4,5,6]
Design of allele-specific oligonucleotide PCR (ASO-PCR) For MIRU-VNTR–defined clusters A, B, and C, we identified the strain-specific SNPs after comparing Whole-genome sequencing (WGS) data with a database containing 4,598 sequence genomes from strains circulating throughout the world
Summary
Systematic molecular/genomic epidemiology studies for tuberculosis surveillance cannot be implemented in many countries. García de Viedma); Instituto de Investigación Sanitaria Gregorio Marañón, Madrid Comas); Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Madrid PCR-based molecular epidemiology approaches, namely mycobacterial interspersed repetitive unit–variable-number tandem-repeat (MIRU-VNTR), are being replaced by genomic epidemiology approaches These approaches are based on the identification of single-nucleotide polymorphisms (SNPs) using whole-genome sequencing (WGS), which offers higher discriminatory power and precision in assigning transmission clusters [4,5,6]. Panama is an example of a country that, despite recently being classified in the upper-income category, has not implemented a systematic molecular/genomic epidemiology–based surveillance program [7] The lack of such a program, together with other limitations, means that Panama has the second highest incidence of TB in Central America and the highest TB death rate [8]. We based our effort on a rational application of MIRU-VNTR, subsequent WGS analysis of clustered representatives, and final tailoring of allele-specific oligonucleotide PCR (ASO-PCR) for local prospective targeted surveillance of TB cases
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