Shewki Moga

Background: Drug-resistant tuberculosis (DR-TB) is a major challenge hindering global tuberculosis control. Ethiopia conducted a third national antituberculosis (TB) drug resistance survey, and this is the first survey to report on drug resistance using whole genome sequencing (WGS) in addition to genotypic and phenotypic test results. The aim of this study was to obtain up-to-date information regarding the magnitude and pattern of drug resistance in Ethiopia. Methods: A nationwide cross-sectional study was conducted in 217 health facilities across all Ethiopian regional states from August 2017 to January 2019. Sputum specimens were collected from patients with bacteriologically confirmed pulmonary TB to detect resistance to anti-TB drugs with Xpert MTB/RIF assay, culture-based phenotypic drug susceptibility testing (DST), and WGS with phylogenetic analysis. Results: The prevalence of rifampicin-resistant TB (RR-TB) was 1.07% (95% confidence interval [CI], .65%–1.74%) among new cases and 6.89% (95% CI, 4.02%–11.57%) among previously treated cases. The prevalence of isoniazid-resistant, rifampicin-susceptible TB was 4.15% (95% CI, 3.11%–5.53%) among new cases and 4.41% (95% CI, 1.97%–9.57%) among previously treated cases. While resistance to fluoroquinolones was detected in 1 RR-TB case, resistance to bedaquiline and linezolid was not detected in RR-TB cases. Mycobacterium tuberculosis lineage 4 was the most common, followed by lineage 3 and lineage 1, with sublineage 4.2.2 being the most frequent. Conclusions: The level of RR-TB remained low. Expanding baseline DST for isoniazid may help further lower the burden of DR-TB in Ethiopia.

BACKGROUND: Isoniazid-resistant, rifampicin-susceptible Mycobacterium tuberculosis (Hr-TB) is the most common form of drug-resistant TB (DR-TB). We investigated the prevalence of and risk factors for Hr-TB in Ethiopia. METHODS: A cross-sectional study was conducted to determine the magnitude of Hr-TB, and to compare characteristics of persons with Hr-TB to those with multidrug-resistant TB (MDR-TB) and INH/RMP-susceptible TB identified during the National Drug Resistance Survey from 2017–2019. RESULTS: Among 1927 M. tuberculosis isolates recovered from persons with pulmonary TB, the prevalence of Hr-TB was 4.1% (95% CI 3.2-5.1), whereas the prevalence of MDR-TB was 1.9%. (95% CI 1.3–2.6). Unlike MDR-TB, the occurrence of Hr-TB did not differ significantly between new and previously treated TB cases ( P = 0.67). The prevalence of Hr-TB cases was high in the Amhara (8.0%, 95% CI 4.8–12.5) region and Addis Ababa (7.1%, 95% CI 3.4–13.0). The proportion of Hr-TB increased with age (OR 1.02, 95% CI 1.01–1.04; P = 0.035). Compared to INH/RMP-susceptible TB, Hr-TB was more likely to harbor resistance to ethambutol, streptomycin and pyrazinamide ( P < 0.0001). CONCLUSIONS: Hr-TB is the most prevalent type of DR-TB in Ethiopia and varies among regional states. Given the lack of identifiable clinical factors associated with Hr-TB, we recommend screening all bacteriologically confirmed TB cases for INH resistance at baseline.

Background: Human migration significantly contributes to the global spread of infectious diseases. In recent years, Ethiopia has experienced an increased influx of returnees from the Kingdom of Saudi Arabia. These migrants were often held in densely populated and inadequately ventilated detention centers and faced a heightened risk of tuberculosis transmission. This study investigates the genotypic drug resistance and transmission clusters of M. tuberculosis among returnees from various detention centers in the Kingdom of Saudi Arabia. Whole genome sequencing (WGS) is employed to characterize the genotypic drug resistance patterns and transmission clusters of M. tuberculosis isolates in presumptive TB cases. Methodology: Following symptom screening for presumptive TB, sputum samples were collected from 161 Xpert MTB/RIF-confirmed returnees between August and December 2022. The samples were further cultured on Lowenstein-Jensen media, with 66.5% (107/161) yielding positive results. The M. tuberculosis strains were classified, and genotypic drug susceptibility was predicted. Transmission clusters were identified using a distance threshold of 12 single nucleotide polymorphisms (SNPs). Results: Among the 88 isolates, Lineage 4 was the most prevalent, representing 65.9% of M. tuberculosis cases among returnees. Sub-lineage 4.2.2.2 was the most dominant within this group, comprising 33% (29/88) of the isolates. Among the isolates, 40 gene mutations conferring resistance to first- and second-line anti-TB drugs were identified. Sixteen transmission clusters were identified, suggesting possible transmission events and a likely origin within the detention centers of the Kingdom of Saudi Arabia (KSA). The proportion of MDR-TB among newly diagnosed cases was 2.3% (2/88). Conclusion: The clustering patterns of M. tuberculosis strain among KSA returnees possibly suggest increased transmission rates in congregate settings. Most importantly, the identified prevalence of MDR-TB, particularly among newly diagnosed TB cases, underscores the need to strengthen robust screening practices for returning migrants before they reintegrate into the community to curb TB/DR-TB transmission.

The Mycobacterium tuberculosis complex (MTBC) includes several human- and animal-adapted pathogens. It is thought to have originated in East Africa from a recombinogenic Mycobacterium canettii-like ancestral pool. Here, we describe the discovery of a clinical tuberculosis strain isolated in Ethiopia that shares archetypal phenotypic and genomic features of M. canettii strains, but represents a phylogenetic branch much closer to the MTBC clade than to the M. canettii strains. Analysis of genomic traces of horizontal gene transfer in this isolate and previously identified M. canettii strains indicates a persistent albeit decreased recombinogenic lifestyle near the emergence of the MTBC. Our findings support that the MTBC emergence from its putative free-living M. canettii-like progenitor is evolutionarily very recent, and suggest the existence of a continuum of further extant derivatives from ancestral stages, close to the root of the MTBC, along the Great Rift Valley.

Background: Isoniazid (INH) resistant Mycobacterium tuberculosis (Hr-TB) is the most common type of drug resistant TB, and is defined as M tuberculosis complex (MTBC) strains resistant to INH but susceptible to rifampicin (RIF). Resistance to INH precedes RIF resistance in almost all multidrug resistant TB (MDR-TB) cases, across all MTBC lineages and in all settings. Therefore, early detection of Hr-TB is critical to ensure rapid initiation of appropriate treatment, and to prevent progression to MDR-TB. We assessed the performance of the GenoType MTBDRplus VER 2.0 line probe assay (LPA) in detecting isoniazid resistance among MTBC clinical isolates. Methods: A retrospective study was conducted among M. tuberculosis complex (MTBC) clinical isolates obtained from the third-round Ethiopian national drug resistance survey (DRS) conducted between August 2017 and December 2019. The sensitivity, specificity, positive predictive value, and negative predictive value of the GenoType MTBDRplus VER 2.0 LPA in detecting INH resistance were assessed and compared to phenotypic drug susceptibility testing (DST) using the Mycobacteria Growth Indicator Tube (MGIT) system. Fisher’s exact test was performed to compare the performance of LPA between Hr-TB and MDR-TB isolates. Results: A total of 137 MTBC isolates were included, of those 62 were Hr-TB, 35 were MDR-TB and 40 were INH susceptible. The sensitivity of the GenoType MTBDRplus VER 2.0 for detecting INH resistance was 77.4% (95% CI: 65.5–86.2) among Hr-TB isolates and 94.3% (95% CI: 80.4–99.4) among MDR-TB isolates (P = 0.04). The specificity of the GenoType MTBDRplus VER 2.0 for detecting INH resistance was 100% (95% CI: 89.6–100). The katG 315 mutation was observed in 71% (n = 44) of Hr-TB phenotypes and 94.3% (n = 33) of MDR-TB phenotypes. Mutation at position-15 of the inhA promoter region alone was detected in four (6.5%) Hr-TB isolates, and concomitantly with katG 315 mutation in one (2.9%) MDR-TB isolate. Conclusions: GenoType MTBDRplus VER 2.0 LPA demonstrated improved performance in detecting INH resistance among MDR-TB cases compared to Hr-TB cases. The katG315 mutation is the most common INH resistance conferring gene among Hr-TB and MDR-TB isolates. Additional INH resistance conferring mutations should be evaluated to improve the sensitivity of the GenoType MTBDRplus VER 2.0 for the detection of INH resistance among Hr-TB cases.

Both passive and active surveillance of drug resistance have an important role in tuberculosis (TB) control program. Surveillance data are important to estimate the magnitude of drug resistance TB, to know the trend of the disease, assess the performance of the program, and to forecast diagnosis and treatment supplies. Therefore, this study aimed to determine the prevalence and the proportion of drug resistant tuberculosis in Ethiopia based on passively collected data. A cross-sectional study was conducted at the National Tuberculosis Reference Laboratory and seven Regional TB laboratories in Ethiopia on a retrospective data collected from July 2017 to June, 2018. Data were collected by standardized checklist from TB culture laboratory registration book. Percentage of recovery rate, contamination rate, and prevalence of drug resistance TB were determined by Statistical Package for Social Science (SPSS) version 23. Of 10 134 TB suspected individuals included into this analysis, 1183 (11.7%) were culture positive. The overall contamination proportion was 5.3% and nontuberculous mycobacteria proportion was 0.98%. First-line drug susceptibility test was performed for 329 Mycobacterium tuberculosis complex isolates, and the proportion of resistance was 5.7 and 6.3% for isoniazid and rifampicin respectively. The proportion of multidrug-resistant tuberculosis (MDR-TB) was 4.3% in new patients, while 6.7% in previously treated patients. However, there was no category for 0.6% patients, and the overall proportion of MDR-TB was 11.6%. The result of this study indicated that MDR-TB is a serious public health problem in Ethiopia. Thus, strengthen prevention and control program is vital to halt the burden of drug resistant TB in the country.

Bacteriological confirmed active case detection remains the corner stone for diagnosing tuberculosis. Non-radiometric liquid culture system Mycobacterium Growth Indicator Tube with automated interface had been recommended by expert groups in addition to conventional solid culture media such as Lowenstein–Jensen. However in high burden resource limited countries advanced non-radiometric based tuberculosis diagnostic methods such as MGIT 960 is limited. Therefore we have evaluated the performance of MGIT 960 system compared to LJ for recovery of Mycobacterium complex (MTBC) from clinical specimens. A cross sectional study was conducted from a total of 908 samples between January 1st, 2013 to December 31st, 2014. Clinical specimens were processed following standard procedures and the final suspension was inoculated to MGIT tubes and LJ slant. Identification and confirmation of MTBC was done by ZN staining and SD Bioline test. Data was analyzed by SPSS version 20. The sensitivity, specificity, recovery rate and the average turnaround time to recover the organism was computed. From a total of 908 clinical specimens processed using both LJ and BACTEC MGIT liquid culture methods the recovery rate for LJ and MGIT, for smear positive samples was 66.7% (74/111) and 87.4% (97/ 111) respectively while for smear negative samples was 13.4% (108/797) and 17.4% (139/797) for LJ and MGIT methods respectively. The overall recovery rate for MGIT is significantly higher than LJ methods [26% (236/908; vs. 20%, 182/908, P = 0.002)]. The average turnaround time for smear positive samples was 16 and 31 days for MGIT and LJ respectively. Turnaround time for smear negative samples was 20 and 36 days for MGIT and LJ respectively. The overall agreement between MGIT and LJ was fairly good with Kappa value of 0.59 (P < 0.001). In the present study the contamination rate for MGIT is higher than the LJ methods, 15 and 9.3% respectively. The BACTEC MGIT liquid culture system has better MTBC recovery rate with shorter turnaround time for both smear positive and negative clinical specimens compared to Conventional LJ method. However, efforts should be made in order to reduce the high contamination rate in BACTEC MGIT system and to lesser extent to LJ methods.

Extended spectrum β-lactamases (ESBLs) have emerged as a major threat worldwide with limited treatment options. The prevalence of ESBL producing Escherichia coli and Klebsiella pneumoniae strains largely remain unknown in Ethiopia. The study was aimed at determining the occurrence of extended spectrum β-lactamase-producing E. coli and K. pneumoniae among inpatient and outpatient settings, their antimicrobial resistance profile and associated risk factors in Jimma University Specialized Hospital (JUSH). A total of 471 consecutive, non repetitive clinical specimens were collected among inpatients (n=314) and outpatients (n=157). Among these, 112 isolates of K. pneumoniae (n=27) and E. coli (n=85) were recovered. Overall prevalence of extended spectrum beta lactamase (ESBL) producers was 38.4% (n=43) of total isolates. Extended spectrum beta lactamases were found in 28.2% (n=24) of E. coli and 70.4% (n=19) of K. pneumoniae. Extended spectrum beta lactamase producers mediated very high resistance to both beta-lactams and non-betalactams, and they were significantly higher among in-patients (46.4%) than out-patients (14.3%). On Multivariate analysis, treatment with third generation cephalosporin was identified as a sole risk factor for acquisition of ESBL enzyme. Our findings confirmed that infection due to extended spectrum beta lactamase-producing E. coli and K. pneumonia is prevalent in JUSH and that exposure to third generation cephalosporin was associated with these infections. The magnitude of E. coli and K. pneumoniae infection was more in inpatients with higher levels of extended spectrum beta lactamase production than outpatients. Key words: Escherichia coli, Klebsiella pneumoniae, extended spectrum β-lactamases, inpatients, outpatients.