Molecular epidemiology and drug sensitivity pattern of Mycobacterium tuberculosis strains isolated from pulmonary tuberculosis patients in and around Ambo Town, Central Ethiopia

Epidemiology of Mycobacterium tuberculosis complex infections in cattle and humans in the remote pastoral settings of southern Ethiopia

Introduction

Mycobacterium tuberculosis complex (MTBC) infections are characterized by the development of granulomatous lesions in different parts of the bodies of animals and humans. MTBC infections cause significant economic and public health consequences in Ethiopia. However, there is a shortage of epidemiological data on MTBC infections in the pastoral regions of the country. The objective of the present study was to investigate the epidemiology of MTBC infections in cattle and humans in the remote pastoral setting of southern Ethiopia.

Methods

A cross-sectional study design was used to recruit 2,396 cattle and 1,200 human presumptive tuberculosis (TB) cases for this study from the southern pastoral districts of Ethiopia. The single intradermal comparative cervical tuberculin test (SICCTT) was used to screen for bovine TB in the cattle, while mycobacterial culture and spoligotyping were used to identify mycobacterial species and strains in the pastoralists.

Results

The herd and animal prevalences of bovine TB were 14.9% [95% confidence interval (CI) = 10.2-19.5%] and 3.2% (95% CI: 2.5-4.0), respectively. The herd prevalence was associated with the districts (χ 2 = 40.10, p < 0.001). Based on the multivariable binary logistic regression analysis, the male animals were 1.77 (95% CI: 1.02-3.05) times more likely to be TB positive than the female animals. Similarly, the cattle kept in the Dasenech and Benetsemi districts were 10.65 (95% CI: 2.47-45.87) and 22.94 (95% CI: 5.48-95.94) times more likely to be TB positive than the cattle kept in the Selamago district, respectively. Mycobacterial culture positivity was 13.4%, while spoligotyping identified Euro-American (EA), East African-Indian (EAI), Indo-Oceanic (IO), lineage 7, M. bovis, and M. africanum as the major lineages, with proportions of 67.3% (105/156), 22.4% (35/156), 6.4% (10/156), 1.9% (3/156), 1.3% (2/156), and 0.6% (1/156), respectively.

Conclusion

In general, the prevalence of bovine TB was relatively lower than that recorded in intensive dairy farms in central Ethiopia. Three species of MTBC, namely M. tuberculosis, M. africanum, and M. bovis, were isolated from the pastoralists of southern Ethiopia. The isolation of M. bovis from the pastoralists could suggest its zoonotic transmission from cattle to humans.

Isolation and genetic analysis of mycobacteria from suspect tuberculous lesions in slaughtered cattle from Wolaita, Ethiopia

Bovine tuberculosis (bTB), caused by Mycobacterium bovis and other members of the Mycobacterium tuberculosis complex (MTBC), is a significant concern for livestock and public health in Ethiopia. This study aimed to isolate and genetically characterize the causative agents of bTB in cattle from four abattoirs in the Wolaita zone of Ethiopia. A total of 2,251 cattle were examined post-mortem, and suspect tuberculous lesions were identified in 122 animals. From these animals, 180 tissue samples were collected and processed for bacteriological culture and genetic analysis, including the Loopamp™ commercial loop-mediated isothermal amplification kit, PCR targeting RD4 and RD9 loci and whole-genome sequencing (WGS). Bacteriological culture using mycobacteria growth indicator tube and Lowenstein-Jensen media ultimately identified 18 culture-positive samples, with WGS confirming M. bovis in lesions from four animals and M. tuberculosis in lesions from one animal. The M. bovis and M. tuberculosis isolates showed genetic similarity to previously identified MTBC lineages in Ethiopia. The presence of M. tuberculosis in cattle raises concerns about human-to-animal transmission. Additionally, non-tuberculous mycobacteria were isolated from lesions from multiple animals. Our study genetically characterized bacteria from suspect tuberculous lesions and provides the research community with new genome data for Ethiopian isolates of M. bovis and M. tuberculosis.

Genotypes and drug resistance pattern of Mycobacterium tuberculosis complex among clinically diagnosed pulmonary tuberculosis patients

Background

Clinically diagnosed pulmonary tuberculosis (TB) (CDPTB) patients account for a huge proportion of TB. However, little is known about the genetic diversity and drug resistance profile of Mycobacterium tuberculosis Complex (MTBC) strains in this group of patients.

Method

Unmatched case-control study was conducted among 313 PTB patients to compare the genetic diversity of MTBC and their drug resistance profiles among CDPTB (n = 173) and bacteriologically confirmed pulmonary TB (BCPTB) (n = 140) patients. Lowenstein-Jensen (LJ) culture, geneXpert and acid fast staining were performed on sputum specimen collected from both CDPTB and BCPTB patients. Spoligotyping, whole genome sequencing (WGS) and phenotypic drug resistance testing (DST) were done for a subset of LJ grown MTBC isolates. Data was analyzed by STATA version 17 software and a p-value <0.05 were considered statistically significant.

Results

The proportion of lineage 3 was larger among CDPTB patients (31%, 13/42) compared to BCPTB patients (15%, 11/74) (p-value <0.05). A higher proportion of MTBC isolates from CDPTB 16.6% (3/18) were phenotypically resistant to one or more anti-TB drugs than BCPTB 12% (4/33) (p-value >0.05). A single lineage 3 strain resistant to all the primary anti-TB drugs was detected in one CDPTB by both DST methods.

Conclusion

The observed differences in the genotypes of MTBC isolates between CDPTB and BCPTB patients may be attributed to challenges in the identification of CDPTB that requires further investigation on sequenced genome of the MTBC strains for better understanding and recommendation based on the current finding. There was also primary drug resistant TB among culture positive CDPTB patients which would be otherwise missed by current national protocols.

Genotypic and phenotypic drug resistance patterns of Mycobacterium tuberculosis isolated from presumptive pulmonary tuberculosis patients in Ethiopia: A multicenter study

BACKGROUND

The emergence of drug-resistant tuberculosis (DR-TB) has been a major obstacle to global tuberculosis control programs, especially in developing countries, including Ethiopia. This study investigated drug resistance patterns and associated mutations of Mycobacterium tuberculosis Complex (MTBC) isolates from the Amhara, Gambella, and Benishangul-Gumuz regions of Ethiopia.

METHODS

A cross-sectional study was conducted using 128 MTBC isolates obtained from patients with presumptive tuberculosis (TB). Phenotypic (BACTEC MGIT 960) and genotypic (MTBDRplus and MTBDRsl assays) methods were used for drug susceptibility testing. Data were entered into Epi-info and analyzed using SPSS version 25. Frequencies and proportions were determined to describe drug resistance levels and associated mutations.

RESULTS

Of the 127 isolates recovered, 100 (78.7%) were susceptible to four first-line anti-TB drugs. Any drug resistance, polydrug resistance, and multi-drug resistance (MDR) were detected in 21.3% (27), 15.7% (20), and 15% (19) of the isolates, respectively, by phenotypic and/or genotypic methods. Mono-resistance was observed for Isoniazid (INH) (2, 1.6%) and Streptomycin (STR) (2, 1.6%). There were two genotypically discordant RIF-resistant cases and one INH-resistant case. One case of pre-extensively drug-resistant TB (pre-XDR-TB) and one case of extensively drug-resistant TB (XDR-TB) were identified. The most frequent gene mutations associated with INH and rifampicin (RIF) resistance were observed in the katG MUT1 (S315T1) (20, 76.9%) and rpoB (S531L) (10, 52.6%) genes, respectively. Two MDR-TB isolates were resistant to second-line drugs; one had a mutation in the gyrA MUT1 gene, and the other had missing gyrA WT1, gyrA WT3, and rrs WT1 genes without any mutation.

CONCLUSIONS

The detection of a significant proportion of DR-TB cases in this study suggests that DR-TB is a major public health problem in Ethiopia. Thus, we recommend the early detection and treatment of DR-TB and universal full first-line drug-susceptibility testing in routine system.

Spiritual Holy Water Sites in Ethiopia: Unrecognized High-Risk Settings for Transmission of Pulmonary Tuberculosis

Ethiopia is a high-tuberculosis (TB) burden country with 157 new cases per 100,000 people, with 23,800 TB-related deaths in 2020. In Ethiopia, TB patients have different healthcare-seeking behaviors. They frequently visit spiritual places, such as holy water sites (HWSs), to seek treatment for their illness spiritually. This study examined the prevalence of pulmonary TB (PTB) and drug susceptibility profiles of Mycobacterium tuberculosis (MTB) isolates among spiritual HWS attendees in Northwest Ethiopia. A cross-sectional study was conducted from June 2019 to March 2020. Sputum samples were collected, processed, and cultured using Löwenstein-Jensen (LJ) culture medium. Second-generation line probe assays (LPAs), GenoType®MTBDRplus VER2.0 and GenoType®MTBDRsl VER2.0, were used to detect anti-TB drug-resistant isolates. STATA 17 was utilized to perform descriptive statistics, bivariate, and multivariate regression analyses. Of 560 PTB-symptomatic participants, 21.8% ((95% confidence interval (95 CI): 18.4-25.2%)) were culture-positive, resulting in a point prevalence of 1,183/100,000 attendees. Amongst HWS attendees, culture-positive TB occurred most commonly in persons 18-33 years of age (28.5% (95 CI 23.4-34.3%)). Other participant characteristics significantly associated with culture-positive PTB were as follows: rural residents (adjusted odds ratio (aOR) 2.65; 95 CI 1.38-5.10), married participants (aOR 2.43; 95 CI 1.28-4.63), family members >5 per household (aOR 1.84; 95 CI 1.04-3.24), and sharing living space (aOR 10.57; 95 CI 3.60-31.13). Also, among 438 participants followed for 12 months after showing negative TB culture results while at the HWS, 6.8% (95 CI 4.4-9.4%) developed or contracted culture-positive TB post-residency at the HWSs. Of the 122 tested isolates, 20 (16.4%) were isoniazid (INH) and/or rifampicin (RIF) resistant. Multidrug-resistant (MDR) TB was detected in 15 cases (12.3%), five of which were fluoroquinolones (FLQs) resistant. The findings from this study should raise a concern about HWSs as potential high-risk settings for TB transmission. It is recommended that appropriate control measures be instituted that include compulsory TB testing and tightened infection control at HWSs, where an increased risk exists for transmission of TB.

Drug Resistance in Tuberculous Lymphadenitis: Molecular Characterization

Background

Drug-resistant tuberculosis (TB) epidemic in high-TB-incidence countries, particularly Ethiopia, remains a significant challenge. As a result, we investigated the drug resistance, common gene mutation, and molecular characterization of mycobacterial isolates from patients with suspected tuberculous lymphadenitis (TBLN). Methodology. A cross-sectional study of 218 FNA samples from TBLN patients inoculated on Lowenstein-Jensen media was carried out. The culture isolates were identified as MTB by polymerase chain reaction (PCR) and the difference-9 (RD9) test region. In addition, the GenoType MTBDRplus assay tested the first and second-line MTB drugs, and the spoligotyping strain-dependent polymorphism test was determined.

Results

Among the 50 culture-positive isolates, 14% (7/50) had drug resistance caused by a gene mutation. Out of these, 4 (8%) isolates were mono-resistant to isoniazid drug, which is caused by a gene mutation in katG in the region of interrogated at codon 315 in the amino acid sequence of S315T1, and 3 (6%) isolates were resistant to both rifampicin and isoniazid drugs. The mutation was observed for katG (at codon 315 with a change in the sequence of amino acid S315T) and rpoB (at codon 530-533 with a change in the sequence of amino acid S531L (S450L)) genes. The most prevalent spoligotypes were orphan and SIT53 strains.

Conclusion

The predominance of INH mono-resistance poses a critical risk for the potential development of MDR-TB, as INH mono-resistance is a typical pathway to the occurrence of MDR-TB. The orphan and SIT53 (T) strains were the most common in the study area, and a drug-resistant strain caused by a common gene mutation could indicate the transmission of clonal-resistant strains in the community.

The Magnitude of MTB and Rifampicin Resistance MTB Using Xpert-MTB/RIF Assay Among Tuberculosis Suspected Patients in Gedeo Zone, Southern Ethiopia

Background

Tuberculosis (TB) remains a major global health problem causing death among millions of people each year. The new barrier that challenges the control of tuberculosis is the emerging and the increasing number of drug-resistant TB that becomes a world concern. This study aimed to determine the magnitude of rifampicin-resistant Mycobacterium tuberculosis (RR-MTB) among presumptive TB patients attending Dilla University Referral Hospital, Gedeo Zone, Ethiopia.

Methods

A retrospective cross-sectional study was conducted at Dilla University Referral Hospital from January 2014 to December 2020. Sputum results were done using Xpert MTB/RIF assay and other necessary data were collected from the registration logbooks using a standardized data extraction format and analyzed using SPSS version 23 statistical software.

Results

A total of 17,745 presumptive TB patients were included, of which 62.2% were males. The overall prevalence of Mycobacterium tuberculosis (MTB) was 11.8%, of which 5.1% were confirmed to have RR-MTB. Extra-pulmonary TB was reported in 1.5% of the study participants. The highest prevalence of MTB and RR-MTB was recorded in 2017 with a prevalence of 20.1% and 8.5%, respectively. All age groups were significantly associated with a higher prevalence of MTB (p < 0.036). TB patients with a history of previous treatment and HIV positive were significantly associated with MTB (P < 0.021), while RR-MTB was only significantly associated with patients with a history of previous treatment (P < 0.018).

Conclusion

A high magnitude of MTB and RR-MTB was reported among TB patients with HIV and a history of previous treatment. Therefore, coordinated efforts should be applied to the improvement of treatment adherence of known TB cases, and appropriate control and prevention methods to reduce the emergence and increase of MTB and RR-MTB cases.

Molecular Epidemiology of Mycobacterium tuberculosis strains isolated from pulmonary tuberculosis patients in south Ethiopia

Introduction:

Understanding the epidemiology of tuberculosis is limited by lack of genotyping data. We sought to characterize the drug susceptibility testing patterns and genetic diversity of M. tuberculosis isolates in southern Ethiopia.

Methodology:

A cross-sectional study was conducted among newly diagnosed sputum smear positive patients with tuberculosis visiting nine health facilities in southern Ethiopia from June 2015 to May 2016. Three consecutive sputum samples (spot-morning-spot) per patient were examined using acid-fast bacilli smear microscopy with all smear positive specimens having acid-fast bacilli cultures performed. M. tuberculosis isolates had drug susceptibility testing performed using indirect proportion method and were genotyped with RD9 deletion analysis and spoligotyping. Mapping of strain was made using geographic information system.

Results:

Among 250 newly diagnosed patients with tuberculosis, 4% were HIV co-infected. All 230 isolates tested were M. tuberculosis strains belonging to three lineages: Euro-American, 187 (81%), East-African-Indian, 31 (14%), and Lineage 7 (Ethiopian lineage), 8 (4%); categorized into 63 different spoligotype patterns, of which 85% fell into 28 clusters. M. tuberculosis strains were clustered by geographic localities. The dominant spoligotypes were SIT149 (21%) and SIT53 (19%). Drug susceptibility testing found that 14% of isolates tested were resistant to ≥ 1 first line anti- tuberculosis drugs and 11% to INH. SIT 149 was dominant among drug resistant isolates.

Conclusions:

The study revealed several clusters and drug resistant strains of M. tuberculosis in the study area, suggesting recent transmission including of drug resistant tuberculosis. Wider monitoring of drug susceptibility testing and geospatial analysis of transmission trends is required to control tuberculosis in southern Ethiopia.

Epidemiology of Mycobacterium tuberculosis lineages and strain clustering within urban and peri-urban settings in Ethiopia

Background

Previous work has shown differential predominance of certain Mycobacterium tuberculosis (M. tb) lineages and sub-lineages among different human populations in diverse geographic regions of Ethiopia. Nevertheless, how strain diversity is evolving under the ongoing rapid socio-economic and environmental changes is poorly understood. The present study investigated factors associated with M. tb lineage predominance and rate of strain clustering within urban and peri-urban settings in Ethiopia.

Methods

Pulmonary Tuberculosis (PTB) and Cervical tuberculous lymphadenitis (TBLN) patients who visited selected health facilities were recruited in the years of 2016 and 2017. A total of 258 M. tb isolates identified from 163 sputa and 95 fine-needle aspirates (FNA) were characterized by spoligotyping and compared with international M.tb spoligotyping patterns registered at the SITVIT2 databases. The molecular data were linked with clinical and demographic data of the patients for further statistical analysis.

Results

From a total of 258 M. tb isolates, 84 distinct spoligotype patterns that included 58 known Shared International Type (SIT) patterns and 26 new or orphan patterns were identified. The majority of strains belonged to two major M. tb lineages, L3 (35.7%) and L4 (61.6%). The observed high percentage of isolates with shared patterns (n = 200/258) suggested a substantial rate of overall clustering (77.5%). After adjusting for the effect of geographical variations, clustering rate was significantly lower among individuals co-infected with HIV and other concomitant chronic disease. Compared to L4, the adjusted odds ratio and 95% confidence interval (AOR; 95% CI) indicated that infections with L3 M. tb strains were more likely to be associated with TBLN [3.47 (1.45, 8.29)] and TB-HIV co-infection [2.84 (1.61, 5.55)].

Conclusion

Despite the observed difference in strain diversity and geographical distribution of M. tb lineages, compared to earlier studies in Ethiopia, the overall rate of strain clustering suggests higher transmission and warrant more detailed investigations into the molecular epidemiology of TB and related factors.

Prevalence of Mycobacterium tuberculosis (Rifampicin-Resistant MTB) and Associated Risk Actors Among Pulmonary Presumptive TB Patients in Eastern Amhara, Ethiopia: 2015-2019

INTRODUCTION

Tuberculosis (TB) is a major health problem, mainly in resource-limited settings. The aim of this study was to determine the prevalence of TB and rifampicin-resistant Mycobacterium tuberculosis (RR-MTB) among presumptive tuberculosis patients using Xpert MTB/RIF assay in Eastern Amhara, Ethiopia.

METHODS

A retrospective cross-sectional study was conducted among presumptive TB patients from three governmental hospitals in Amhara Regional State. Records of sputum sample results using Xpert MTB/RIF assay from January 2015 to December 2019 were investigated from registration books and analyzed using SPSS v.21.

RESULTS

Of the total of 26,656 (24,116 adults and 2540 children) TB presumptive patients included in the study, more than half, 14,624 (54.9%), were males and the median age was 36.87 (interquartile: 25.46-50.85 years). The majority of participants were new cases, 20,273 (76.1%), and with unknown HIV status, 18,981 (71.2%), respectively. MTB prevalence was 11% (95% CI: 9.34-12.08%) in all age groups, and 7.6% (95% CI 6.52-9.04%) among children. Of the MTB confirmed cases, prevalence of RR-MTB was 245 (8.3%) in adults and 14 (7.2%) in children. MTB infection was higher in the age groups of 18-35 years [adjusted odds ratio (AOR) = 2.17; 95% CI: 1.86-2.54, p < 0.001], 36-53 years (AOR = 1.31; 95% CI 1.11-1.54, p < 0.001), those who were relapse cases (AOR = 1.97; 95% CI 1.69-2.27, p < 0.0010), and failure cases (AOR = 4.67; 95% CI 3.36-6.50, p < 0.001). However, the age groups of 54-71 years (AOR = 0.79; 95% CI 0.65-0.95, p = 0.01) and over 71 years (AOR = 0.48; 95% CI 0.35-0.68, p < 0.001) were associated with lower MTB infection. Resistance to rifampicin was higher in the relapsed (AOR = 2.10; 95% CI 1.40-3.03, p < 0.001) and failure cases (AOR = 3.50; 95% CI 1.9-6.61, p < 001).

CONCLUSION

Prevalence of MTB and RR-MTB low. TB infection was higher in adult age groups and those who had previous TB treatment history. Similarly, resistance to rifampicin was higher among the relapsed and failure patients. Appropriate measurements in monitoring of TB treatment could reduce TB and RR-MTB in the study area.

Magnitude of Mycobacterium tuberculosis Infection and Its Resistance to Rifampicin Using Xpert-MTB/RIF Assay Among Presumptive Tuberculosis Patients at Motta General Hospital, Northwest Ethiopia

Background

Mycobacterium Tuberculosis (MTB) and its drug resistance form are the devastating infectious diseases in the world. It is the major cause of morbidity and mortality in low-income countries with Ethiopia carrying a heavy burden. Data on the magnitude of MTB and rifampicin resistance using Xpert- MTB/RIF assay is limited in the study area. Therefore, this study aimed to assess the prevalence of Mycobacterium tuberculosis and rifampicin resistance among presumptive TB patients using GeneXpert at Motta General Hospital, North West Ethiopia.

Methods

A retrospective cross-sectional study was conducted from 1st October to 30 November 2020 among patients tested for GeneXpert at Motta General Hospital, Northwest Ethiopia. Data recorded on GeneXpert test results were collected on laboratory registration book in Microbiology laboratory. Data were analyzed by using the Statistical Package for Social Sciences (SPSS) version 20.

Results

A total of 4109 specimens were tested using the GeneXpert automated system. Of these, the majority 2148 (52.3%) of participants were males and 1961 (47.7%) were females. Similarly, about 1553 (37.8%) were in the age range of 25-44 years followed by 1347 (32.8%) in 45-64 years. Moreover, about 2486 (60.5%) participants were from rural. The overall prevalence of M. tuberculosis was 346 (8.4%) among these, the majority 222 (5.4%) had unknown HIV status, 48 (1.2%) were HIV positive, and 314 (7.6%) was new MTB cases. The overall prevalence of rifampicin resistance was 15 (4.3%) and 8(1.7%) were intermediate. Among rifampicin resistance, 10 (2.9%) were males, 8(2.3%) lived in rural, 9 (2.6%) had unknown HIV status, 13 (3.8%) were new TB patients, and 13 (3.8%) had pulmonary tuberculosis.

Conclusion

The prevalence of M. tuberculosis was 8.4% and relatively higher rate of rifampicin-resistant M. tuberculosis was found.

Predictive study of tuberculosis incidence by time series method and Elman neural network in Kashgar, China

OBJECTIVES

Kashgar, located in Xinjiang, China has a high incidence of tuberculosis (TB) making prevention and control extremely difficult. In addition, there have been very few prediction studies on TB incidence here. We; therefore, considered it a high priority to do prediction analysis of TB incidence in Kashgar, and so provide a scientific reference for eventual prevention and control.

DESIGN

Time series study.

SETTING KASHGAR, CHINA

Kashgar, China.

METHODS

We used a single Box-Jenkins method and a Box-Jenkins and Elman neural network (ElmanNN) hybrid method to do prediction analysis of TB incidence in Kashgar. Root mean square error (RMSE), mean absolute error (MAE) and mean absolute percentage error (MAPE) were used to measure the prediction accuracy.

RESULTS

After careful analysis, the single autoregression (AR) (1, 2, 8) model and the AR (1, 2, 8)-ElmanNN (AR-Elman) hybrid model were established, and the optimal neurons value of the AR-Elman hybrid model is 6. In the fitting dataset, the RMSE, MAE and MAPE were 6.15, 4.33 and 0.2858, respectively, for the AR (1, 2, 8) model, and 3.78, 3.38 and 0.1837, respectively, for the AR-Elman hybrid model. In the forecasting dataset, the RMSE, MAE and MAPE were 10.88, 8.75 and 0.2029, respectively, for the AR (1, 2, 8) model, and 8.86, 7.29 and 0.2006, respectively, for the AR-Elman hybrid model.

CONCLUSIONS

Both the single AR (1, 2, 8) model and the AR-Elman model could be used to predict the TB incidence in Kashgar, but the modelling and validation scale-dependent measures (RMSE, MAE and MAPE) in the AR (1, 2, 8) model were inferior to those in the AR-Elman hybrid model, which indicated that the AR-Elman hybrid model was better than the AR (1, 2, 8) model. The Box-Jenkins and ElmanNN hybrid method therefore can be highlighted in predicting the temporal trends of TB incidence in Kashgar, which may act as the potential for far-reaching implications for prevention and control of TB.

Frequency of MTB and rifampicin resistance MTB using Xpert-MTB/RIF assay among adult presumptive tuberculosis patients in Tigray, Northern Ethiopia: A cross sectional study

BACKGROUND

Multidrug-resistant tuberculosis (MDR-TB) continues to be a global health problem. Data on rifampicin resistance MTB using Xpert- MTB/RIF assay in Ethiopia, particularly in the study area is limited. The aim of this study was to determine the frequency of MTB and rifampicin resistant-MTB among presumptive tuberculosis patients in Tigray, Northern Ethiopia.

METHODS

A multicenter retrospective study was conducted among presumptive TB patients from five governmental hospitals and one comprehensive specialized teaching hospital in Tigray regional state. Records of sputum sample results of presumptive MTB patients with Xpert-MTB/RIF assay from January 2016 to December 2019 were investigated. Data extraction tool was used to collect data from registration books and analyzed using SPSS ver.21 statistical software. Statistical significance was set at p-value ≤ 0.05.

RESULTS

Of the 30,935 presumptive adult TB patients who have provided specimens for TB diagnosis from January 2016 to December 2019, 30,300 (98%) had complete data and were included in this study. More than half, 17,471 (57.7%) were males, and the age of the patients ranged from 18-112 years, with a median age of 40.65 (interquartile 29.4-56.5 years). Majority, 28,996 (95.7%) of the participants were treatment naïve, and 23,965 (79.1%) were with unknown HIV status. The overall frequency of MTB was 2,387 (7.9% (95% CI: 7.6-8.2%); of these, 215 (9% (95% CI: 7.9-10.2%) were rifampicin resistant-MTB. Age (18-29 years), HIV positive and previous TB treatment history were significantly associated with high MTB (p < 0.001), whereas gender (being female) was associated with low MTB (p < 0.001). Likewise, rifampicin resistant-MTB was more prevalent among relapse (p < 0.001) and failure cases (p = 0.025); while age group 30-39 years was significantly associated with lower frequency of rifampicin resistant-MTB (p = 0.008).

CONCLUSION

Frequency of MTB among tuberculosis presumptive patients was low; however, the problem of rifampicin resistant-MTB among the tuberculosis confirmed patients was high. The high frequency of MTB and RR-MTB among previously treated and HIV positive patients highlights the need for more efforts in TB treatment and monitoring program in the study area.

Molecular epidemiology of clinical Mycobacterium tuberculosis complex isolates in South Omo, Southern Ethiopia

BACKGROUND

Tuberculosis (TB) is caused by Mycobacterium tuberculosis complex (MTBC). Mapping the genetic diversity of MTBC in high TB burden country like Ethiopia is important to understand principles of the disease transmission and to strengthen the regional TB control program. The aim of this study was to investigate the genetic diversity of Mycobacterium tuberculosis complex (MTBC) isolates circulating in the South Omo, southern Ethiopia.

METHODS

MTBC isolates (N = 156) were genetically analyzed using spacer oligotyping (spoligotyping) and mycobacterial interspersed repetitive unit-variable number of tandem repeat (MIRU-VNTR) typing. Major lineages and lineages were identified using MTBC databases. Logistic regression was used to correlate patient characteristics with strain clustering.

RESULTS

The study identified Euro-American (EA), East-African-Indian (EAI), Indo-Oceanic (IO), Lineage_7/Aethiops vertus, Mycobacterium bovis and Mycobacterium africanum major lineages in proportions of 67.3% (105/156), 22.4% (35/156), 6.4% (10/156), 1.9% (3/156), 1.3% (2/156) and 0.6% (1/156), respectively. Lineages identified were Delhi/CAS 23.9% (37/155), Ethiopia_2 20.6% (32/155), Haarlem 14.2% (22/155), URAL 14.2%(22/155), Ethiopia_3 8.4% (13/155), TUR 6.5% (10/155), Lineage_7/Aethiops vertus 1.9% (3/155), Bovis 1.3% (2/155), LAM 1.3% (2/155), EAI 0.6% (1/155), X 0.6% (1/155) and Ethiopia H₃₇Rv-like strain 0.6% (1/155). Of the genotyped isolates 5.8% (9/155) remained unassigned. The recent transmission index (RTI) was 3.9%. Orphan strains compared to shared types (AOR: 0.09, 95% CI: 0.04-0.25) were associated with reduced odds of clustering. The dominant TB lineage in pastoral areas was EAI and in non-pastoral areas was EA.

CONCLUSION

The epidemiological data, highly diverse MTBC strains and a low RTI in South Omo, provide information contributing to the TB Control Program of the country.

Molecular detection of multidrug resistance pattern and associated gene mutations in M. tuberculosis isolates from newly diagnosed pulmonary tuberculosis patients in Addis Ababa, Ethiopia

INTRODUCTION

Multi-drug resistance is a major challenge in the control of tuberculosis. Despite newer modalities for diagnosis and treatment, people are still suffering from this disease. Understanding the common gene mutations conferring rifampicin and isoniazid resistance is crucial for the implementation of effective molecular tools at local and national levels. Hence, this study aimed to evaluate the molecular detection of rifampicin and isoniazid-resistant gene mutations in M.tuberculosis isolates in Addis Ababa, Ethiopia.

METHOD

Health Center-based cross-sectional study was conducted between January and September 2017 in Addis Ababa, Ethiopia. The collected sputum samples were processed for mycobacterial isolation and Region of difference 9 based polymerase chain reaction for species identification. To characterize the rifampicin and isoniazid-resistant M. tuberculosis isolates, a molecular genetic assay (GenoType MTBDRplus) was used; the assay is based on DNA-STRIP technology.

RESULT

Culture positivity was confirmed in 82.6% (190/230) of smear-positive newly diagnosed pulmonary tuberculosis cases enrolled in the study. From 190 isolates 93.2% were sensitive for both rifampicin and isoniazid, and 6.8% of the isolates were resistant to at least one of the tested anti-TB drugs. Gene mutations were observed in all studied multidrug resistance-associated gene loci (rpoB, katG, and inhA). Two isolates exhibited heteroresistance, a mutated, as well as wild type sequences, were detected in the respective strains. MDR-TB case was observed in 1.1% (2/190) of the cases. All the MDR-TB cases were positive for HIV and found to have a history of prior hospital admission.

CONCLUSION

In our finding a relatively high prevalence of any drug resistance was observed and the overall prevalence of multidrug-resistant tuberculosis was 1.1%.The majority of drug-resistant isolates demonstrated common mutations. Heteroresistant strains were detected, signaling the existence of an M.tuberculosis population with variable responses to anti-tuberculosis drugs or of mixed infections.

Exploring the usefulness of molecular epidemiology of tuberculosis in Africa: a systematic review

BACKGROUND

Tuberculosis (TB) is caused by Mycobacterium tuberculosis complex (MTBC) and remains a serious global public health threat, especially in resource-limited settings such as the African region. Recent developments in molecular epidemiology tools have significantly improved our understanding of TB transmission patterns and revealed the high genetic diversity of TB isolates across geographical entities in Africa. This study reports the results of a systematic review of current knowledge about MTBC strain diversity and geographical distribution in African regions.

METHODS

Search tools (PubMed, Embase, Popline, OVID and Africa Wide Information) were employed to identify the relevant literature about prevalence, strain diversity, and geographic distribution of MTBC infection in Africa.

RESULTS

A total of 59 articles from 739 citations met our inclusion criteria. Most articles reported about patients with presumptive pulmonary TB (73%), fewer reports were on retreatment and treatment failure cases (12%), and presumptive drug resistance cases (3%). Spoligotyping was the most used, alone in 21 studies and in parallel with either the Mycobacterial Interspersed Repetitive Units Variable Number of Tandem Repeats or the Restriction Fragment Length Polymorphism. Various TB lineages were observed across the African continent, with the originally European lineage 4 spotted in all countries studied.

CONCLUSION

TB molecular epidemiology tools have substantially improved our understanding of the MTBC circulating isolates, their evolution, and diversity in this highly endemic region of Africa. We found that only TB lineage 4 is present throughout all the continent and the clusters identified provides an extended insight into the disease transmission dynamics.

Frequency of mutations associated with resistance to first- and second-line drugs in multidrug-resistant Mycobacterium tuberculosis isolates

INTRODUCTION

Tuberculosis is considered one of the most fatal diseases worldwide, with an estimation of 10.1 million cases. In this study, whole-genome sequencing was used to determine the genomic characterisation of 40 Mycobacterium tuberculosis isolates from patients with different nationalities hospitalised in the Czech Republic.

MATERIALS AND METHODS

Susceptibility testing for first-line drugs was performed. DNA was sequenced using the Illumina MiSeq platform. Spoligotype single-nucleotide polymorphisms and mutations in antibiotic-resistant genes were detected, and phylogenetic analysis was performed.

RESULTS

Samples showing phenotypic resistance to at least one drug were 12 to streptomycin, 11 to isoniazid, 7 to rifampicin, 6 to ethambutol and 5 to pyrazinamide. Phenotypic and genotypic profiles did not match in all cases, suggesting the presence of a novel mutation in some cases and a low expression of resistant genes in others. The presented phylogeny enables the correct assignation of M. tuberculosis lineages and sublineages. Our results suggest that the most dominant lineage in our samples was lineage 4 (33/40).

CONCLUSION

To our knowledge, this is the first study using this approach to be done in the Czech Republic. Lineage 4 was the predominant lineage identified among our samples. Nevertheless, the dominance of Lineage 4 along with other lineages suggests that infections can originate from different sources.

Spoligotyping and drug sensitivity of Mycobacterium tuberculosis isolated from pulmonary tuberculosis patients in the Arsi Zone of southeastern Ethiopia

Tuberculosis (TB) is one of the leading causes of morbidity and mortality in different zones of Ethiopia. This study was undertaken to identify the strains of Mycobacterium tuberculosis and evaluate their drug sensitivity profiles in the Arsi Zone. A total of 111 isolates of M. tuberculosis from individuals with pulmonary TB were included and speciation and strain identification were performed using Region of difference 9 and spoligotyping, respectively. The drug sensitivity patterns were assessed using Bactec MGIT 960 SIRE and GenoType MTBDRplus line probe assays. Of 111 isolates, 83% were interpretable and 56 different spoligotype patterns were identified. From these, 22 patterns were shared types while the remaining 34 were orphans. The predominant shared types were spoligotype international type (SIT) 149 and SIT53, comprising 12 and 11 isolates, respectively. Euro-American lineage was the dominant lineage followed by East-African-Indian. Phenotypically, 17.2% of tested isolates were resistant to any first-line drugs and 3.1% were multidrug-resistant. Higher (6.2%) mono-resistance was observed to streptomycin, and no resistance was observed to rifampicin or ethambutol. Genotypically, five (5.4%) isolates were resistant to isoniazid and mutated at codon S315T1 of katG. In contrast, only 1.1% of the isolates were resistant to rifampicin and were mutated at codon S531L of rpoB gene. In this study, a high proportion of orphan strains were isolated, which could suggest the presence of new strains and a high percentage of mono-resistance, warranting the need to strengthen control efforts.

Molecular epidemiology of M. tuberculosis in Ethiopia: A systematic review and meta-analysis

The molecular epidemiology of Mycobacterium tuberculosis (M. tuberculosis, Mtb) is poorly documented in Ethiopia. The data that exists has not yet been collected in an overview metadata form. Thus, this review summarizes available literature on the genomic diversity, geospatial distribution and transmission patterns of Mtb lineages (L) and sublineages in Ethiopia. Spoligotyping and Mycobacterial Interspersed Repetitive Units-Variable Number Tandem Repeats (MIRU-VNTR) based articles were identified from MEDLINE via PubMed and Scopus. The last date of article search was done on 12th February 2019. Articles were selected following the PRISMA flow diagram. The proportion of (sub)lineages was summarized at national level and further disaggregated by region. Clustering and recent transmission index (RTI) were determined using metan command and random effect meta-analysis model. The meta-analysis was computed using Stata 14 (Stata Corp. College Station, TX, USA). Among 4371 clinical isolates, 99.5% were Mtb and 0.5% were M. bovis. Proportionally, L4, L3, L1 and L7 made up 62.3%, 21.7%, 7.9% and 3.4% of the total isolates, respectively. Among sublineages, L4.2. ETH/SIT149, L4.10/SIT53, L3. ETH1/SIT25 and L4.6/SIT37 were the leading clustered isolates accounting for 14.4%, 9.7%, 7.2% and 5.5%, respectively. Based on MIRU-VNTR, the rate of clustering was 41% and the secondary case rate from a single source case was estimated at 29%. Clustering and recent transmission index was higher in eastern and southwestern Ethiopia compared with the northwestern part of the country. High level of genetic diversity with a high rate of clustering was noted which collectively mirrored the phenomena of micro-epidemics and super-spreading. The largest set of clustered strains deserves special attention and further characterization using whole genome sequencing (WGS) to better understand the evolution, genomic diversity and transmission dynamics of Mtb.

Multi-drug resistant Mycobacterium tuberculosis in Port Harcourt, Nigeria

Background

In past years, much focus has been on tackling the scourge and spread of tuberculosis worldwide. The recent emergence of multi-drug resistant (MDR) tuberculosis has, however, negatively threatened progress made so far. Nigeria ranks fourth out of the 22 high tuberculosis burden countries in the world and has the highest burden of tuberculosis in Africa. It is therefore necessary to monitor the MDR tuberculosis situation in the country.

Objectives

This study set out to assess the proportions of MDR tuberculosis in patients attending six directly observed treatment short-course centres in Port Harcourt, Nigeria, from October 2015 to October 2016.

Methods

Six hundred and nine participants between the ages of 18 and 75 years were enrolled in this study and comprised suspected and newly diagnosed tuberculosis cases. Sputum samples obtained from the participants were screened for the presence of Mycobacterium tuberculosis using standard culture and phenotypic biochemical techniques, and drug susceptibility testing was carried out using the 1% proportion conventional method.

Results

Of the 609 participants enrolled, 30 (4.9%) were confirmed as M. tuberculosis-positive cases. A high prevalence of drug resistant tuberculosis was noted in this study (14/30, 46.7%), with 26.7% of isolates resistant to streptomycin. MDR tuberculosis, defined as being resistant to isoniazid and rifampicin, was detected in only one case (3.3%).

Conclusion

This study reports a low rate of MDR tuberculosis and contributes to the sparse data on drug resistant tuberculosis in Nigeria.