Ecuador Study Reveals Ultra-Low Prevalence of a Drug-Resistant Beijing Tuberculosis Strain

A comprehensive molecular epidemiological study conducted in Ecuador between 2018 and 2023 has revealed that the Mycobacterium tuberculosis Beijing sublineage, a global public health concern known for its increased transmissibility and multidrug resistance (MDR), remains exceptionally rare within the country, with no evidence of active community transmission clusters.

The Beijing sublineage, often referred to as Lineage 2, is recognized worldwide as a significant threat due to its inherent selective advantages, including hypervirulence and a strong association with MDR and extensively drug-resistant (XDR) strains. While this lineage is dominant in East Asia, its presence in South America has historically been low, generally below 5%. However, Ecuador’s unique geographic position, sharing open borders with Peru and Colombia—nations where local prevalences of the Beijing lineage have reached concerning levels of 16.4% and 15.6%, respectively—necessitated an update on the local molecular epidemiology. This research aimed to analyze 699 clinical M. tuberculosis isolates collected in 2018 and 2023 to assess shifts in the prevalence and transmission patterns of this high-risk lineage.

The methodology employed was highly sophisticated, utilizing a stepwise genotyping approach designed to maximize detection and confirm lineage assignment with high resolution. The study began by screening all 699 isolates using allele-specific SNP-PCR, targeting the Rv2154724 (G526A) marker, which serves as a rapid, cost-effective first-line tool for identifying the Beijing-specific genetic signature. Isolates that tested positive via SNP-PCR were then subjected to more discriminatory techniques, including 24-locus MIRU-VNTR typing and traditional spoligotyping. To achieve the highest level of certainty and to characterize the pathogen’s resistance profile, whole-genome sequencing (WGS) was performed on the Beijing-positive isolate.

The results demonstrated an ultra-low prevalence of the Beijing sublineage. Out of 384 strains analyzed in 2018, only one isolate (0.26%) was identified as belonging to the M. tuberculosis Beijing sublineage. Furthermore, screening of 315 strains collected in 2023 showed no detection of the Beijing sublineage via SNP-PCR. This single isolate, collected in 2018 from Machala in the El Oro province, was rigorously confirmed as Beijing by SNP-PCR and MIRU-24 analysis, and subsequent WGS confirmed its classification as sublineage 2.2.1. The genetic relatedness of this isolate to other previously reported Ecuadorian Beijing strains was assessed using Minimum Spanning Tree (MST) analysis. This analysis, which incorporated all 12 previously reported M. tuberculosis Beijing isolates in Ecuador alongside international reference isolates, revealed moderate genetic diversity but crucially showed no active transmission clusters or temporal groupings among the Ecuadorian Beijing strains.

The identified M. tuberculosis Beijing isolate exhibited a genotypically predicted MDR profile, posing a significant clinical threat. WGS analysis confirmed resistance to rifampicin, isoniazid, ethambutol, and streptomycin. The presence of canonical resistance-associated mutations in genes encoding targets of first-line anti-tuberculosis drugs—such as rpoB p. His445Tyr for rifampicin resistance and katG p. Ser315Thr for high-level isoniazid resistance—underscores the potential severity of this strain. No mutations associated with resistance to fluoroquinolones, second-line injectable agents, bedaquiline, linezolid, delamanid, or pretomanid were detected, placing it firmly in the MDR-TB category without evidence of pre-XDR or XDR-associated resistance markers.

The MST analysis provided critical insights into the local dynamics of the Beijing lineage. By analyzing the 24-locus MIRU-VNTR profiles, researchers observed that the circulating strains, both in the present study and historical reports, showed moderate genetic diversity. The network visualization indicated that isolates from different geographic regions were distributed throughout the network rather than forming province-specific clusters. Similarly, the distribution of resistant and susceptible isolates was scattered across different branches of the tree, suggesting that the strains represent sporadic, independent introductions or reactivations of long-standing latent infections, rather than a consolidated community outbreak driven by active transmission from neighboring countries like Peru or Colombia. This finding challenges the global consensus regarding the hyper-adaptability and rapid expansion of Beijing strains within the South American context.

Methodologically, the study highlighted the necessity of a multi-tiered approach to accurately monitor high-risk lineages. The initial identification of the isolate was complex; while SNP-PCR and MIRU-VNTR confirmed its Beijing status, spoligotyping did not match any registered pattern in the SITVIT/SpolDB4 database, and the MIRU-VNTRplus database assigned it to the Delhi/CAS lineage. This misidentification underscores the limitations of spoligotyping, which relies on repetitive elements prone to convergent evolution. The subsequent use of WGS was essential to provide high-resolution confirmation of the Beijing lineage 2.2.1 classification and to accurately infer the genotypic drug-resistance profile. This underscores the study’s conclusion that genomic surveillance, specifically WGS, must be strengthened and expanded to avoid misclassifying or missing high-risk lineages.

The authors acknowledge several limitations inherent in the study design. First, the identification of only a single Beijing isolate precludes population-level inference about genetic diversity or transmission dynamics. Second, the screening relied on SNP-PCR, and since negative isolates were not sequenced, the study cannot formally exclude the presence of Beijing strains below the detection threshold of the screening assay. Third, the resistance profile was inferred genotypically rather than confirmed by phenotypic drug-susceptibility testing, although the genotypic prediction showed high concordance with known MDR phenotypes. Finally, the analyzed isolates primarily correspond to culture-positive strains from coastal provinces, which may not fully represent the national distribution of TB cases in Ecuador. Despite these limitations, the finding of an MDR-TB strain in a high-risk border province like El Oro is a critical indicator that continued molecular monitoring is vital for detecting potential shifts in transmission dynamics.

Subject of Research: Molecular epidemiology and prevalence of the Mycobacterium tuberculosis Beijing sublineage in Ecuador.

Article Title: Monitoring changes in the prevalence of the Beijing lineage of Mycobacterium tuberculosis in Ecuador: 2018 and 2023

Article References: Rodríguez-Pazmiño, Á. S., Pozo-Estupiñán, L. P., Cedeño-Vásquez, M. P., Trejo Cedeño, I., Cárdenas-Franco, G., Salcedo Maldonado, A. B., Jiménez-Pizarro, N., Hermoso de Mendoza, J., Orlando, S. A., Franco-Sotomayor, G., & Garcia-Bereguiain, M. Á. (2026). Monitoring changes in the prevalence of the Beijing lineage of Mycobacterium tuberculosis in Ecuador: 2018 and 2023. Frontiers in Public Health, 14, Article 1967382. https://doi.org/10.3389/fpubh.2026.1967382

Image Credits: AI Generated

DOI: 10.3389/fpubh.2026.1967382

Keywords: Mycobacterium tuberculosis, Beijing sublineage, Drug resistance, Molecular epidemiology, Whole-genome sequencing, Ecuador, Public health, SNP-PCR, MIRU-VNTR, Monitoring, changes, prevalence