Simplified Model to Survey Tuberculosis Transmission in Countries Without Systematic Molecular Epidemiology Programs

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.

Phylogenomic Perspective on a Unique Mycobacterium bovis Clade Dominating Bovine Tuberculosis Infections among Cattle and Buffalos in Northern Brazil

“…This set of specific SNPs identified in this study therefore has the potential to be incorporated in molecular screening strategies aimed at detecting the Marajó M. bovis strain at a global level using in silico approaches or, at the state or national level in M. bovis strain biobanks to further evaluate the dissemination of this clade to other regions in Brazil and to assess the risk to human health. This type of approach, using allele-specific PCR amplification has been successfully used to evaluate the dissemination of specific strains outside its endemic region, understand the transmission dynamics at the cross-border level or enable the evaluation of TB transmission in settings without routine or universal molecular typing 31 .…”

Probable long-term prevalence for a predominant Mycobacterium tuberculosis clone of a Beijing genotype in Colon, Panama

“…To help solve the lack of a systematic molecular epidemiology program in Panama, we introduced (Dominguez et al, 2019) a novel strategy as follows: i) fast MIRU-VNTR-based snapshots of the most prevalent strains, ii) targeted WGS on these major clones, and iii) tailored PCRs to identify marker SNPs for prevalent strains (Dominguez et al, 2019). This allowed us to determine that six strains were responsible for 50% of MTB cases in Panama City and Colon.…”

“…Specific targeted alleles and PCR conditions for BeijingMycobacterium tuberculosis strain A (Beijing A) were as described elsewhere (Dominguez et al, 2019). In brief, PCR reaction mixtures included a final volume of 25 μl: 1.25 μl of 5 U/μl HotStarTaq ® DNA polymerase (Qiagen, Hilden, Germany), 0.4 μl of 25 mM MgCl2, 2.5 μl of 10x PCR buffer with 15 mM MgCl2, 5 μl of 5x of Q solution, primer pool concentration (2.5 μl mix: 2μM, 6 μM, 5 μM), 0.2 μl of 25 mM dNTPs, water, and the DNA target.…”

“…An additional set of four hypervariable loci was added for the Beijing isolates (Allix-Beguec et al, 2014). WGS on the Illumina MiSeq platform, mapping, and single nucleotide polymorphism (SNP) calling was performed as detailed elsewhere (Dominguez et al, 2019). The median-joining network was constructed from the SNP matrix generated for each case using the NETWORK 5.0.0.1 program Sequences were deposited in EMBL-EBI database (Accession numbers PRJEB39699, PRJEB23681 and PRJEB29408).…”

“…The purpose of this study was to complete a preliminary information (Dominguez et al, 2019) on the presence of this lineage in Panama. We focused our efforts on Colon, a Panamanian province with the highest TB incidence rate (MINSA, 2018).…”