Molecular epidemiology of the RDRio genotype of Mycobacterium tuberculosis in Ecuador: a tracking update for the years 2018 and 2023

Introduction The RDRio genotype of Mycobacterium tuberculosis (MTB), a major genotype within the Latin American-Mediterranean (LAM) family, has been associated with increased transmissibility and multidrug resistance (MDR). In Ecuador, a previous baseline study reported a low prevalence of 2.09% for 2012–2016, prior to the large influx of migrants from Venezuela—where RDRio is highly endemic—that has occurred since 2015. This study aimed to update the molecular epidemiology of the RDRio genotype in Ecuador. Methods We screened 699 clinical MTB isolates collected in 2018 (384) and 2023 (315) for the RDRio genotype by duplex PCR and further characterized them by 24-locus MIRU-VNTR typing, spoligotyping, and whole-genome sequencing (WGS). We conducted minimum spanning tree (MST) analyses based on MIRU-VNTR profiles to assess genetic relatedness. Results We identified 40 isolates (5.72%) as RDRio, with no significant difference in prevalence between 2018 ( n = 20; 5.21%) and 2023 ( n = 20; 6.35%). WGS confirmed that the dominant sublineages were 4.3.4.1 and 4.3.4.2, all within Lineage 4 (Euro-American). Genotypic resistance profiling classified 32.1% (9/28) of sequenced isolates as MDR-TB and 7.1% (2/28) as pre-XDR-TB. MST analysis showed that RDRio isolates from Ecuador segregated predominantly into distinct clonal complexes and remained largely isolated from international reference strains, including Venezuelan isolates. Discussion The overall RDRio prevalence of 5.72% represents a nearly three-fold increase relative to the 2.09% reported for the 2012–2016 baseline, although it remained stable across the 2018–2023 period and low compared with high-endemicity settings such as Venezuela. Despite this relatively low prevalence, the RDRio genotype was associated with a substantial burden of drug resistance. The genetic segregation of the predominant RDRio Ecuadorian clonal complex from international reference strains—including Venezuelan isolates—did not support recent importation associated with the Venezuelan diaspora. Despite their limitations, classical genotyping methods remain a valid, cost-effective approach to monitor MTB strains of interest associated with MDR-TB, such as RDRio, in low-resource settings like Ecuador.