Results
A retrospective MIRU-VNTR analysis of 42 MTB isolates collected in Colon (January-August 2018) initially revealed that 40.5% (17/42) belonged to a major cluster of pansusceptible Beijing strains (cluster Beijing A). Most isolates (12/17) shared an identical 28-loci MIRU-VNTR pattern, and four different single-locus variants (SLVs) were detected (two of them involving a hypervariable locus), represented by 1, 2, 1 and 1 isolates (Table 1). Only four of the remaining non-Beijing isolates were clustered and distributed in different families: Haarlem (23.8%), H37RV-like (16.7%), LAM (16.7%), and S (2. 4%).
Next, a prospective sample of MTB isolates from 68 incident cases in Colon (September 2018-March 2020) was analysed, applying a Beijing A-specific PCR. The band-pattern expected for the Beijing A strain was obtained in 30 isolates (44.1%).
To assess whether the Beijing A strain -highly represented in Colon- was also present in other regions in the country, we selected another Panamanian province, Chiriquí (278 Km from Colon) and applied strain-specific PCR on a sample of 21 incident cases (cases from 2019). No amplification was obtained for two cases and the Beijing A strain pattern was not detected in any of the 19 amplified isolates.
Thirty Beijing A isolates, retrospectively and prospectively identified, for which appropriate quality DNA was available, were analyzed by WGS, and 25 of them offered enough coverage depth (>20X) to perform SNP calls, from which a network of relationships was built (Figure 1). We detected noticeable SNP-based diversity, most isolates with long pairwise genetic distances and distributed along different branches. The maximum SNP-distance was 38 and the median shortest SNP distance between two strains was five. Five not-sampled nodes (median vectors) were detected. Some small subgroups within the network shared shorter pairwise genetic distances (2-7 SNPs) and only two pairs of isolates showed 0 SNPs between them. Only one of the isolates with SLVs in MIRU-VNTR offered enough coverage and occupied an independent branch in the network (Figure 1).