Mycobacterium tuberculosis Sub-Lineage 4.2.2/SIT149 as Dominant Drug-Resistant Clade in Northwest Ethiopia 2020–2022: In-silico Whole-Genome Sequence Analysis

Abstract

Introduction Drug resistance (DR) in Mycobacterium tuberculosis complex (MTBC) is mainly associated with certain lineages and varies across regions and countries. The Beijing genotype is the leading resistant lineage in Asia and western countries. M. tuberculosis (Mtb) (sub) lineages responsible for most drug resistance in Ethiopia are not well described. Hence, this study aimed to identify the leading drug resistance sub-lineages and characterize first-line anti-tuberculosis drug resistance-associated single nucleotide polymorphisms (SNPs). Methods A facility-based cross-sectional study was conducted in 2020–2022 among new and presumptive multidrug resistant-TB (MDR-TB) cases in Northwest Ethiopia. Whole-genome sequencing (WGS) was performed on 161 isolates using Illumina NovaSeq 6000 technology. The SNP mutations associated with drug resistance were identified using MtbSeq and TB profiler Bioinformatics softwares. Results Of the 146 Mtb isolates that were successfully genotyped, 20 (13.7%) harbored one or more resistance-associated SNPs. L4.2.2.ETH was the leading drug-resistant sub-lineage, accounting for 10/20 (50%) of the resistant Mtb. MDR-TB isolates showed extensive mutations against first-line anti-TB drugs. Ser450Leu/(tcg/tTg) for Rifampicin (RIF), Ser315Thr/(agc/aCc) for Isoniazid (INH), Met306Ile/(atg/atA(C)) for Ethambutol (EMB), and Gly69Asp for Streptomycin (STR) were the leading resistance associated mutations which accounted for 56.5%, 89.5%, 47%, and 29.4%, respectively. The presence of both clustered and non-clustered drug resistance (DR) isolates indicated that the epidemics is driven by both new DR development and acquired resistance. Conclusion The high prevalence of drug-resistant TB due to geographically restricted sub-lineages (L4.2.2.ETH) indicates the ongoing local micro epidemics. The Mtb drug resistance surveillance system must be improved. Further evolutionary analysis of L4.2.2.ETH strain is highly desirable to understand evolutionary forces that leads L4.2.2.ETH in to high level DR and transmissible sub-lineage.

Patterns and profiles of drug resistance-conferring mutations in Mycobacterium tuberculosis genotypes isolated from tuberculosis-suspected attendees of spiritual holy water sites in Northwest Ethiopia

“…Supporting our findings, the high clustering rate and predominance of drug-resistant SIT149/T3-ETH sublineages were reported in Ethiopia ( 56 , 63 , 76 , 77 ). In agreement with our findings, earlier studies in Ethiopia reported that SIT149/T3-ETH sublineages were predominantly linked with drug resistance, particularly MDR/XDR-TB ( 63 , 73–75 , 78 ). However, in contrast to our findings, a recent study in Ethiopia noted that “TUR-genotype (54%) was predominant in MDR-TB strains” ( 79 ).…”

“…The observed association between MTB genotypes and drug resistance in Ethiopia highlights the importance of understanding the genetic diversity of the pathogen in combating drug-resistant TB ( 63 , 73 , 74 ). The diversity of MTB genotypes circulating in the country, coupled with specific mutations conferring drug resistance, underscores the need for a comprehensive approach to TB control ( 73 , 75 ). A lack of comprehensive data on the molecular epidemiology of DR-TB strains in Ethiopia further complicates the implementation of molecular diagnostics.…”

“…However, in contrast to our findings, a recent study in Ethiopia noted that “TUR-genotype (54%) was predominant in MDR-TB strains” ( 79 ). This could be the fact that the T3-ETH/SIT149 Sublineages is an Ethiopian-specific genotype that predominantly circulates in the highlands of the country and plays an important role in TB disease transmission ( 73 ). Thus, a comprehensive study using improved genotyping techniques such as sequencing methods with high discriminatory power is warranted to tailor the clustering of these sublineages and their association with drug resistance.…”

Phenotypic and Genotypic Drug Resistance of Mycobacterium tuberculosis Strains Isolated from HIV-Infected Patients from a Third-Level Public Hospital in Mexico

“…These sublineages have been described in Mexico as part of the genetic diversity of M. tuberculosis [ 46 ]. The lineage that appeared most frequently in our results was Lineage 4, with different resistance phenotypes, this lineage has been associated with a high rate of MDR strains [ 47 ]. The Beijing sublineage has been described as having the highest rate of resistance [ 48 ] as occurred in our study.…”