Genotype diversity of Mycobacterium isolates from children in Jimma, Ethiopia

Pulmonary Tuberculosis and Rifampicin Resistant Mycobacterium Tuberculosis in Children and Adolescents using Gene Xpert MTB/RIF Assay in Tigray, Northern Ethiopia

Background

Tuberculosis (TB) continues to be a global health problem. While childhood TB contributes 10% to the global TB burden, the paucibacillary nature of TB disease in children and the absence of reliable diagnostic methods have made MTB diagnosis in children to be a great challenge. This study aimed to determine the prevalence of MTB and rifampicin-resistant MTB (RR-MTB) among children using Gene Xpert MTB/RIF Assay in Tigray, Ethiopia.

Methods

A retrospective database study was conducted among children in ten governmental hospitals in the Tigray region. Gene Xpert MTB/RIF results of sputum/gastric lavage samples from children with presumptive TB from January 2016 to December 2019 were extracted using a data extraction sheet. Data were collected and analyzed using Statistical Package for the Social Sciences version 21.

Results

The prevalence of bacteriologically confirmed MTB by Gene-Xpert in children with presumptive TB was 7.3% (95% CI: 6.7%-7.9%) and the proportion of those that were Gene-Xpert MTB positive who also have rifampicin resistance was 10.9% (95% CI: 8.2-13.6%). Older children aged 11-15 years [AOR = 1.76; 95% CI = 1.33-2.33, p < 0.001] and adolescents 16-17 years [AOR = 2.18; 95% CI = 1.63-2.92, p < 0.001] were more likely to be MTB positive. Relapse cases [AOR = 1.66; 95% CI = 1.09-2.51, p = 0.017] and lost/failure cases [AOR = 8.82; 95% CI = 3.94-19.76, p < 0.001] were more likely to have MTB compared to the new cases.

Conclusion

The proportion of MTB-positive among the TB presumptive patients was 7.3%. The proportion of rifampicin-resistant TB to all positive patients was 10.9%. Female participants had more MTB than males (or younger children). The result highlights the need for due attention in children because it is very helpful in determining the future control of the disease.

Genetic diversity and drug sensitivity profile of Mycobacterium tuberculosis among children in Ethiopia

BACKGROUND

Worldwide, tuberculosis (TB) affects about one million children every year. The burden of the disease is higher in developing countries. However, there is limited information on the lineages and drug sensitivity patterns of Mycobacterium tuberculosis (M. tuberculosis) infecting children in these countries, including Ethiopia. Thus, this study aimed to characterize the different lineages of the M. tuberculosis complex causing childhood pulmonary tuberculosis and evaluate the drug-sensitivity patterns to the first-line anti-TB drugs.

METHOD

A total of 54 stored cultures were used in this study. The region of difference 9 (RD9) based polymerase chain reaction (PCR) and spoligotyping were employed for the identification of the isolates at the species and lineages level respectively. Lineage identification was done by using the pre-existing database. Identification of clustering of the spoligotype patterns was by using the SPOLIDB3-based model. The result was retrieved by the most probable family format. Furthermore, the phenotypic, and genotypic drug-sensitivity test (DST) was performed using Mycobacterium Growth Indicator Tube (MGIT™ 960) and GenoTypeMTBDRplus assay respectively. Data analysis was done using SPSS version 27 software.

RESULT

Spoligotyping produced 39 interpretable results for M. tuberculosis. The majority (74.4%) of them were clustered into 7 groups, while the rest (25.6%) were single. The Euro-American (EA) lineage was the predominant lineage (64.1%) followed by the East-African Indian (EAI) (30.8%) and M. Africanum (5.1%) lineages. The most predominant subtypes were SIT37 (15.4%), SIT149 (12.8%), SIT25 (7.7%), and SIT53 (7.7%). Furthermore, of the identified SITs, T1 and CAS families consisted of 38.5% and 28.2% of the lineages respectively. Drug susceptibility was 91.9% by phenotypic method and 97.4% by molecular assay. The overall prevalence of any resistance was 7.8% and there was a single MDR-TB.

CONCLUSION

Many of the isolates belong to the modern lineages (Euro American) representing the most common circulating strains in the country. More importantly, despites the tiny isolates tested, drug resistance is low. To fully describe the molecular epidemiology of MTBC lineages in children, we recommend a prospective large-scale study.

Mycobacterium tuberculosis Drug Resistance in Ethiopia: An Updated Systematic Review and Meta-Analysis

Background: Tuberculosis (TB) remains a significant global public health issue, despite advances in diagnostic technologies, substantial global efforts, and the availability of effective chemotherapies. Mycobacterium tuberculosis, a species of pathogenic bacteria resistant to currently available anti-TB drugs, is on the rise, threatening national and international TB-control efforts. This systematic review and meta-analysis aims to estimate the pooled prevalence of drug-resistant TB (DR-TB) in Ethiopia. Materialsand Methods: A systematic literature search was undertaken using PubMed/MEDLINE, HINARI, the Web of Science, ScienceDirect electronic databases, and Google Scholar (1 January 2011 to 30 November 2020). After cleaning and sorting the records, the data were analyzed using STATA 11. The study outcomes revealed the weighted pooled prevalence of any anti-tuberculosis drug resistance, any isoniazid (INH) and rifampicin (RIF) resistance, monoresistance to INH and RIF, and multidrug-resistant TB (MDR-TB) in newly diagnosed and previously treated patients with TB. Results: A total of 24 studies with 18,908 patients with TB were included in the final analysis. The weighted pooled prevalence of any anti-TB drug resistance was 14.25% (95% confidence interval (CI): 7.05–21.44%)), whereas the pooled prevalence of any INH and RIF resistance was found in 15.62% (95%CI: 6.77–24.47%) and 9.75% (95%CI: 4.69–14.82%) of patients with TB, respectively. The pooled prevalence for INH and RIF-monoresistance was 6.23% (95%CI: 4.44–8.02%) and 2.33% (95%CI: 1.00–3.66%), respectively. MDR-TB was detected in 2.64% (95%CI: 1.46–3.82%) of newly diagnosed cases and 11.54% (95%CI: 2.12–20.96%) of retreated patients with TB, while the overall pooled prevalence of MDR-TB was 10.78% (95%CI: 4.74–16.83%). Conclusions: In Ethiopia, anti-tuberculosis drug resistance is widespread. The estimated pooled prevalence of INH and RIF-monoresistance rates were significantly higher in this review than in previous reports. Moreover, MDR-TB in newly diagnosed cases remained strong. Thus, early detection of TB cases, drug-resistance testing, proper and timely treatment, and diligent follow-up of TB patients all contribute to the improvement of DR-TB management and prevention. Besides this, we urge that a robust, routine laboratory-based drug-resistance surveillance system be implemented in the country.

A glimpse into the genotype and clinical importance of non tuberculous mycobacteria among pulmonary tuberculosis patients: The case of Ethiopia

Laboratory identification of nontuberculous mycobacteria (NTM) species is not regularly performed while, they have a public health importance with a prevalence of more than 5% among pulmonary tuberculosis (PTB) patients in Ethiopia. Hence, this study aimed to identify the NTM species and their clinical significance among PTB patients. A retrospective study was conducted at the Ethiopian Public Health Institution’s (EPHI’s) national TB referral laboratory. Stored NTM isolates were genotyped using GenoType Mycobacterium CM/AS kit (Hain Life science, Germany). Data pertinent to the study was extracted from the EPHI’s database and patients’ medical records. Between January 2 & December 28 of 2017, a total of 3,834 samples were processed from 698 TB patients of whom 50% were female. Among 3,317 samples with mycobacterial culture results 7.3% were NTM and majority of them were identified from smear negative TB patients. M. simiae was the /predominant NTM among the genotyped isolates. All the studied NTM species were not clinically important however, considering the similarity of clinical and radiologic findings between NTM and MTBC infected patients, integrating NTM species identification in the routine TB laboratory diagnosis may augment clinicians’ decision particularly in DR-TB patients. Additional similar prospective study with a larger sample size is recommended. Moreover, urgent improvements on patients’ record keeping practice are required in the studied hospitals.

Predominance of the Mycobacterium tuberculosis Beijing strain amongst children from a high tuberculosis burden township in South Africa

The objective was to determine the molecular epidemiology and drug susceptibility patterns of Mycobacterium tuberculosis (MTB) of children and their household contacts (HHC) in Umlazi, a high TB-burden township in South Africa. Sixty eight MTBRifPLUS positive TB-infected children (TIC) (≤14 years) and 111 HHC were enrolled. Drug susceptibility testing (DST) was performed on sputum samples using the proportion method and GenoType® MTBDR. Genotyping of MTB was conducted using IS6110-restriction fragment length polymorphism (RFLP) and spoligotyping. Rifampicin (RIF) susceptibility was observed in 67/68 TIC. GenoType® MTBDRplus and phenotypic DST identified drug resistant strains in five of 16 culture-confirmed TIC. The Beijing strain was identified in six and the F15/LAM4/KZN strain in one of the 13 TIC respectively. Four patients with unknown RFLP strains belonged to spoligoclades S, T1, T3 variant and X2. The S-lineage and an unknown strain were identified in two HHC. MDR-TB and pre-XDR-TB were identified in one HHC each. Household transmission could not be determined as none of the culture-confirmed TIC resided with the six culture-confirmed contacts. The predominance of the hypervirulent Beijing strain and presence of drug-resistant strains must be considered in the implementation of effective TB control strategies and development of efficacious vaccines.

Detection of Mycobacterium tuberculosis and rifampicin resistance by Xpert® MTB/RIF assay among presumptive tuberculosis cases at Jimma University Medical Center, Southwest Ethiopia

Background

Rapid diagnosis of tuberculosis (TB) and detection of drug resistance are very important for timely and appropriate management of patients. Xpert MTB/RIF assay is approved for use in TB and rifampicin-resistance diagnosis. However, data are limited on the impact of Xpert MTB/RIF assay under routine clinical settings with a heterogeneous group of patients and sample types in Ethiopia.

Methods

A retrospective study was carried out in 2220 presumptive TB cases at Jimma University Medical Center. Data were gathered from the registration logbook using formatted data extraction tools and double entered to epidata version 3.1 and further transported to SPSS version 20 for analysis. Associations were determined using the Chi-square test and P-value <0.05 was considered statistically significant.

Results

Of 2220 cases enrolled, 1665 (75%) were adults and the remaining 555 (25%) were children aged less than 14 years. The majority, 1964 (88.46%), had pulmonary manifestation and 256 (11.54%) had extrapulmonary involvements. The overall, frequency of Mycobacterium tuberculosis (MTB) was 9.3% (206/2220), among this 10.27% (171/1665) and 6.3% (35/555) were adults and children, respectively. M. tuberculosis was detected from 171 (8.75%) of pulmonary patients and 35 (13.28%) of extrapulmonary manifested patients. Out of 206 M. tuberculosis positive cases, 7(3.4%) were rifampicin-resistant: four from pulmonary tuberculosis (PTB) patients and three from EPTB patients. In the Chi-square test, the age group of 15–24 years, previous history of TB, pus/lymph node sample, and being HIV positive were significantly associated with TB positivity by Xpert MTB/RIF (P-value <0.001).

Conclusion

These data suggest that the overall frequency of M. tuberculosis and rifampicin resistance was found to be relatively low compared to the previous reports in Ethiopia. Nevertheless, better diagnostic tools and approaches are still vital to halt the burden of TB and drug-resistant TB in the country.

Prevalence of drug resistance-conferring mutations associated with isoniazid- and rifampicin-resistant Mycobacterium tuberculosis in Ethiopia: a systematic review and meta-analysis

OBJECTIVES

Globally, the incidence and mortality of tuberculosis (TB) are declining; however, low detection of drug-resistant disease threatens to reverse current progress toward global TB control. Multiple rapid molecular diagnostic tests have recently been developed to detect genetic mutations in Mycobacterium tuberculosis (Mtb) known to confer drug resistance. However, their utility depends on the frequency and distribution of resistance-associated mutations in the pathogen population. This review aimed to assess the prevalence of gene mutations associated with rifampicin (RIF)- and isoniazid (INH)-resistant Mtb in Ethiopia.

METHODS

We searched the literature in PubMed/MEDLINE, Web of Science, Scopus and Cochrane Library. Data analysis was conducted in Stata 11.

RESULTS

Totally, 909 (95.8%) of 949 INH-resistant Mtb isolates had detectable gene mutations: 95.8% in katG315 and 5.9% in the inhA promoter region. Meta-analysis resulted in an estimated pooled prevalence of katGMUT1(S315T1) of 89.2% (95% CI 81.94-96.43%) and a pooled prevalence of inhAMUT1(C15T) of 77.5% (95% CI 57.84-97.13%). Moreover, 769 (90.8%) of 847 RIF-resistant strains had detectable rpoB gene mutations. Meta-analysis resulted in a pooled prevalence of rpoBMUT3(S531L) of 74.2% (95% CI 66.39-82.00%).

CONCLUSION

RIF-resistant Mtb were widespread, particularly those harbouring rpoB(S531L) mutation. Similarly, INH-resistant Mtb with katG(S315T1) and inhA(C15T) mutations were common. Tracking S531L, S315T1 and C15T mutations among RIF- and INH-resistant isolates, respectively, would be diagnostically and epidemiologically valuable. Rapid diagnosis of RIF- and INH-resistant Mtb would expedite modification of TB treatment regimens, and proper timely infection control interventions could reduce the risk of development and transmission of multidrug-resistant TB.

Rifampicin-resistant Mycobacterium tuberculosis by GeneXpert MTB/RIF and Associated Factors Among Presumptive Pulmonary Tuberculosis Patients in Nepal

Background

Mycobacterium tuberculosis(MTB) remains a major public health problem worldwide, and emergence of drug-resistant TB has become a significant obstacle to effective TB control. However, the rate of MTB and rifampicin resistant-MTB (RR-MTB) in the Nepalese setting has not been studied extensively. Therefore, the present study aims to assess the rate of MTB and RR-MTB and further determine the factors associated with it.

Methods

A retrospective cross-sectional study, among national representative data of 990 consecutive presumptive TB resister of patients subjected to the GeneXpert test that presented to the tuberculosis referral hospital, was conducted over a one year period from February 2018 to January 2019. Significance for the difference for categorical data was performed by Chi-square test and factors associated with MTB and RR-MTB were assessed using binary logistic regression yielding OR with 95%CI.

Results

Of total 990 presumptive tuberculosis analyzed cases, median ages of the patients were 39±19.09 years and two-thirds of the patients were male 653 (66.0%). The estimated prevalence of MTB in presumptive TB patients was 13.8% (95%CI: 11.88%–16.16%), and risk for MTB was significantly associated with previously treated patients: OR: 10.4 (P<0.001). The estimated prevalence of RR-MTB in MTB confirmed patients was 10.2% (4.97%–15.1%). Our study confirmed no association of RR-TB with age, sex, ethnicity, geographical diversity and previous history of treatment failure (P>0.05).

Conclusion

The overall prevalence of MTB and RR-MTB was high in Nepalese study population,  and that being previously treated with anti-TB drug remained significant predictors for MTB; proactive measures are urgently needed to address the challenge of prompt diagnosis, early management and improved monitoring of treatment to limit the emergence drug-resistant MTB strains in the community.

Molecular epidemiology of drug resistant Mycobacterium tuberculosis in Africa: a systematic review

Background

The burden of drug resistant tuberculosis in Africa is largely driven by the emergence and spread of multidrug resistant (MDR) and extensively drug resistant (XDR) Mycobacterium tuberculosis strains. MDR-TB is defined as resistance to isoniazid and rifampicin, while XDR-TB is defined as MDR-TB with added resistance to any of the second line injectable drugs and any fluoroquinolone.

The highest burden of drug resistant TB is seen in countries further experiencing an HIV epidemic. The molecular mechanisms of drug resistance as well as the evolution of drug resistant TB strains have been widely studied using various genotyping tools. The study aimed to analyse the drug resistant lineages in circulation and transmission dynamics of these lineages in Africa by describing outbreaks, nosocomial transmission and migration. Viewed as a whole, this can give a better insight into the transmission dynamics of drug resistant TB in Africa.

Methods

A systematic review was performed on peer reviewed original research extracted from PubMed reporting on the lineages associated with drug resistant TB from African countries, and their association with outbreaks, nosocomial transmission and migration. The search terms “Tuberculosis AND drug resistance AND Africa AND (spoligotyping OR molecular epidemiology OR IS6110 OR MIRU OR DNA fingerprinting OR RFLP OR VNTR OR WGS)” were used to identify relevant articles reporting the molecular epidemiology of drug resistant TB in Africa.

Results

Diverse genotypes are associated with drug resistant TB in Africa, with variations in strain predominance within the continent. Lineage 4 predominates across Africa demonstrating the ability of “modern strains” to adapt and spread easily. Most studies under review reported primary drug resistance as the predominant type of transmission. Drug resistant TB strains are associated with community and nosocomial outbreaks involving MDR- and XDR-TB strains. The under-use of molecular epidemiological tools is of concern, resulting in gaps in knowledge of the transmission dynamics of drug resistant TB on the continent.

Conclusions

Genetic diversity of M. tuberculosis strains has been demonstrated across Africa implying that diverse genotypes are driving the epidemiology of drug resistant TB across the continent.

Nontuberculous mycobacterial infections in a Brazilian pediatric population: a seven-year survey

The aim of this study was to describe the frequency of nontuberculous mycobacteria (NTM) isolation and their related outcomes among pediatric patients of a Brazilian university hospital from 2012 to 2019. NTM were identified in different clinical samples by microbiological culture and molecular-based methods. NTM were isolated from 14 patients, out of whom four (27%) were infected and were treated accordingly. Two were infected with Mycobacterium avium complex (MAC), two with M. abscessus complex (MABSC) and one with M. intracellulare. Two patients had cystic fibrosis-related lung disease and improved after successful NTM eradication. One patient was HIV-positive and died. One patient had severe combined immunodeficiency (SCID)-related pneumonia and is currently being followed-up. We conclude that NTM frequency in our center was low among pediatric patients. Whether this is inherent to Brazilian patients, due to the broad coverage of the Bacille Calmette-Guérin (BCG) vaccine in Brazil, or a result of underdiagnosis remains to be elucidated.

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.

The Incidence of Non-Tuberculous Mycobacteria in Infants in Kenya

There is inadequate understanding of the epidemiology of Non-Tuberculous Mycobacteria (NTM) among infants in high tuberculosis burden countries. The objective of this study was to document the incidence and diversity of NTM disease or colonisation in sputum specimens from infants with presumptive TB, the risk factors, and clinical characteristics, in a high TB and HIV burden setting in Western Kenya. A cohort of 2900 newborns was followed for 1–2 years to assess TB incidence. TB investigations included collection of induced sputa and gastric aspirates for culture and speciation by HAIN®, Tuberculin Skin Testing (TST), HIV testing, and chest radiography. The American Thoracic Society Criteria (ATS) were applied to identify NTM disease. Among 927 (32% of 2900) with presumptive TB, 742 (80%) were investigated. NTM were isolated from 19/742 (2.6%) infants. M. fortuitum was most frequently speciated (32%). Total person-time was 3330 years. NTM incidence was 5.7/1,000 person-years, 95% CI (3.5, 8.7). Infants diagnosed with TB were more likely to have NTM isolation (odds ratio 11.5; 95% CI 3.25, 41.0). None of the infants with NTM isolated met the criteria for NTM disease. The incidence of NTM isolation was comparable to similar studies in Africa. NTM isolation did not meet ATS criteria for disease and could represent colonisation. TB disease appears to be structural lung disease predisposing to NTM colonisation.

Prevalence of rifampicin resistant Mycobacterium tuberculosis among presumptive tuberculosis patients in selected governmental hospitals in Addis Ababa, Ethiopia

BACKGROUND

Rapid detection of rifampicin resistance is essential for early management and prevention of transmission of multidrug-resistant tuberculosis (MDR-TB). We studied the prevalence of rifampicin resistance of Mycobacterium tuberculosis (MTB) among presumptive TB patients in Addis Ababa, Ethiopia.

METHODS

A retrospective cross sectional study was conducted in three referral hospitals and the regional laboratory in Addis Ababa city from March 2015 to October 2017. Data was collected by data-extraction sheet from registration books. It was analyzed using SPSS version 20. Statistically significant association was taken with P < 0.05.

RESULTS

A total of 12,414 (11,672 adults and 742 paediatrics) TB presumptive patients were included in the study. The overall prevalence of TB was 15.11% (1876/12414) in all age groups and 13.6%(101/742) among paediatric population. Rifampicin resistant TB was 9.9% (186/1876) in all TB confirmed cases and 7.9% (8/101) in paediatric TB patients. The prevalence of rifampicin resistant TB among new and previously treated was 7.6 and 27.4%, respectively. Sex (being female) and previous TB treatment were significantly associated with rifampicin resistant TB.

CONCLUSIONS

Rifampicin-resistant TB is prevalent both among adult and paediatric TB patients. The strong association of rifampicin resistance with previous treatment in this study suggests the need to improve and monitor the treatment to limit the emergence of drug resistant TB.

Spoligotype-based population structure of Mycobacterium tuberculosis in the Jimma Zone, southwest Ethiopia

Background

To understand the population dynamics and propose more effective preventive strategies, defining the population structure of the circulating Mycobacterium tuberculosis strains is important.

Methods

A total of 177 M. tuberculosis complex isolates from pulmonary tuberculosis (TB) cases in southwest Ethiopia were genotyped by spoligotyping. Of the strains included in this study, 126 were pan‐susceptible strains while the remaining 51 isolates were resistant to one or more first‐line anti‐TB drugs. The genotyping results were compared to the international spoligotyping (SITVIT) database of the Pasteur Institute of Guadeloupe and the newly revised publicly available international multi‐marker database (SITVITWEB/SPOLDB4). An online tool Run TB‐Lineage was also used to predict the major lineages using a conformal Bayesian network analysis.

Results

The spoligotyping of the 177 isolates resulted in 69 different spoligotype patterns of which 127 (71.8%) were clustered into 19 spoligoclusters (with clustering rate of 61.02%). Each cluster contains 2–29 isolates. Of the isolates with corresponding SIT in SITVIT/SDB4, the predominant strains identified were SIT 37 of the T3 subfamily with 29 isolates followed by SIT 53 of the T1 subfamily with 20 isolates. SIT 777 of the H4 subfamily and SIT 25 of the CAS1_DELHI subfamily each consisting of six isolates were identified. Eighty spoligotype patterns were orphan as they were not recorded in the SITVIT2/SPDB4 database. Further classification of the isolates on the basis of major lineages showed that 82.5% and 14.1% of the isolates belonged to Euro‐American and East African Indian lineages, respectively, while 2.8% of the isolates belonged to Mycobacterium africanum and 0.6% to Indo‐Oceanic.

Conclusion

The ill‐defined T and H clades were predominant around Jimma. The substantial number of orphans recorded in the study area warrants for additional studies with genotyping methods with better resolution and covering whole areas of southwest Ethiopia.

The present study has shown the dominance of ill‐defined T and H clades in the study area. Moreover, a substantial number of isolates were Orphan warranting for additional studies covering the whole geographic area of the southwest Ethiopia and genotypic methods with better resolution.

Spoligotyping based genetic diversity of Mycobacterium tuberculosis in Ethiopia: a systematic review

BACKGROUND

Understanding the types of strains and lineages of Mycobacterium tuberculosis (M. tuberculosis) circulating in a country is of paramount importance for tuberculosis (TB) control program of that country. The main aim of this study was to review and compile the results of studies conducted on strains and lineages of M. tuberculosis in Ethiopia.

METHODS

A systematic search and review of articles published on M. tuberculosis strains and lineages in Ethiopia were made. PubMed and Google Scholar databases were considered for the search while the keywords used were M. tuberculosis, molecular epidemiology, molecular typing spoligotyping and Ethiopia.

RESULT

Twenty-one studies were considered in this review and a total of 3071 M. tuberculosis isolates and 3067 strains were included. These studies used spoligotyping and identified five lineages including Indo-Ocean, East Asian/Beijing, East African-Indian, Euro-American and Ethiopian in a proportion of 7.1%, 0.2%, 23.0%, 64.8%, and 4.1%, respectively. Thus, Euro-American was the most frequently (64.8%) occurring Lineage while East Asian was the least (0.2%) frequently occurring Lineage in the country. Surprisingly, the Ethiopian Lineage seemed to be localized to northeastern Ethiopia. In addition, the top five clades identified by this review were T, CAS, H, Manu and Ethiopian comprising of 48.0%, 23.0%, 11.0%, 6.0% and 4.1% of the strains, respectively. Furthermore, predominant shared types (spoligotype patterns) identified were SIT149, SIT53, SIT25, SIT37, and SIT21, each consisting of 420, 343, 266, 162 and 102 isolates, respectively, while, on the other hand, 15% of the strains were orphan.

CONCLUSION

According to the summary of the results of this review, diversified strains and lineages of M. tuberculosis were found in Ethiopia, and the frequencies of occurrence of these strains and lineages were variable in different regions of the country. This systematic review is registered in the PRISMA with the registration number of 42017059263.

Microbead-based spoligotyping of Mycobacterium tuberculosis from Ziehl-Neelsen-stained microscopy preparations in Ethiopia

The worldwide dissemination of Mycobacterium tuberculosis strains has led to the study of their genetic diversity. One of the most used genotyping methods is spoligotyping, based on the detection of spacers in the clustered regularly interspaced short palindromic repeats (CRISPR) locus. This study assessed the performance of a microbead-based spoligotyping assay using samples extracted from Ziehl-Neelsen-stained smear-microscopy preparations and described the genetic diversity of Mycobacterium tuberculosis among new TB patients in Southern Nations, Nationalities and Peoples’ Region (SNNPR) in Ethiopia. Among the 91 samples analysed, 59 (64.8%) generated spoligotyping patterns. Fifty (84.7%) samples were classified into 12 clusters (mostly Lineage 4 or 3) comprising 2–11 samples and nine had unique spoligotyping patterns. Among the 59 spoligotyping patterns, 25 belonged to the T1 sublineage, 11 to the T3-ETH, 5 to the URAL, 4 to the H3 and 14 to other L4 sublineages. There was a remarkable variation in genetic distribution in SNNPR compared to other regions of the country. Microbead-based spoligotyping is an easy-to-perform, high-throughput assay that can generate genotyping information using material obtained from smear microscopy preparations. The method provides an opportunity to obtain data of the M. tuberculosis genetic epidemiology in settings with limited laboratory resources.

Non-tuberculous Mycobacteria isolated from Pulmonary samples in sub-Saharan Africa - A Systematic Review and Meta Analyses

Pulmonary non-tuberculous mycobacterial (NTM) disease epidemiology in sub-Saharan Africa is not as well described as for pulmonary tuberculosis. Earlier reviews of global NTM epidemiology only included subject-level data from one sub-Saharan Africa country. We systematically reviewed the literature and searched PubMed, Embase, Popline, OVID and Africa Wide Information for articles on prevalence and clinical relevance of NTM detection in pulmonary samples in sub-Saharan Africa. We applied the American Thoracic Society/Infectious Disease Society of America criteria to differentiate between colonisation and disease. Only 37 articles from 373 citations met our inclusion criteria. The prevalence of pulmonary NTM colonization was 7.5% (95% CI: 7.2%–7.8%), and 75.0% (2325 of 3096) occurred in males, 16.5% (512 of 3096) in those previously treated for tuberculosis and Mycobacterium avium complex predominated (27.7% [95% CI: 27.2–28.9%]). In seven eligible studies, 27.9% (266 of 952) of participants had pulmonary NTM disease and M. kansasii with a prevalence of 69.2% [95% CI: 63.2–74.7%] was the most common cause of pulmonary NTM disease. NTM species were unidentifiable in 29.2% [2,623 of 8,980] of isolates. In conclusion, pulmonary NTM disease is a neglected and emerging public health disease and enhanced surveillance is required.

García-Basteiro A, Augusto OJ, Fraile O, Bulo H, Ira T, Gondo K, van Ingen J, Naniche D, Sacarlal J, Alonso PL. High Rates of Non-Tuberculous Mycobacteria Isolation in Mozambican Children with Presumptive Tuberculosis

INTRODUCTION

Non-tuberculous mycobacteria (NTM) can cause disease which can be clinically and radiologically undistinguishable from tuberculosis (TB), posing a diagnostic and therapeutic challenge in high TB settings. We aim to describe the prevalence of NTM isolation and its clinical characteristics in children from rural Mozambique.

METHODS

This study was part of a community TB incidence study in children <3 years of age. Gastric aspirate and induced sputum sampling were performed in all presumptive TB cases and processed for smear testing using fluorochrome staining and LED Microscopy, liquid and solid culture, and molecular identification by GenoType® Mycobacterium CM/AS assays.

RESULTS

NTM were isolated in 26.3% (204/775) of children. The most prevalent NTM species was M. intracellulare (N = 128), followed by M. scrofulaceum (N = 35) and M. fortuitum (N = 9). Children with NTM were significantly less symptomatic and less likely to present with an abnormal chest radiograph than those with M. tuberculosis. NTM were present in 21.6% of follow-up samples and 25 children had the same species isolated from ≥2 separate samples. All were considered clinically insignificant and none received specific treatment. Children with NTM isolates had equal all cause mortality and likelihood of TB treatment as those with negative culture although they were less likely to have TB ruled out.

CONCLUSIONS

NTM isolation is frequent in presumptive TB cases but was not clinically significant in this patient cohort. However, it can contribute to TB misdiagnosis. Further studies are needed to understand the epidemiology and the clinical significance of NTM in children.

Clinical, molecular and drug sensitivity pattern of mycobacterial isolates from extra-pulmonary tuberculosis cases in Addis Ababa, Ethiopia

BACKGROUND

In conjunction with the spread of HIV infection, tuberculosis (TB) remains a major cause of illness and death worldwide. The Ethiopian national report reveals that extra pulmonary tuberculosis is on the rise and that case detection rate is exceeding that of smear positive or negative cases in many parts of the country. Different studies indicated that host and/or pathogen related factors are associated with the rise of extra pulmonary cases. However, the reason for this is not clearly known in our setting.

METHODS

Specimens were taken from clinically suspected extra pulmonary patients and confirmed by cytology, histopathology and culture. Deletion typing and Spoligotyping was utilized to identify the strains. The isolates were then assigned to lineage using conformal Bayesian network (rules model) algorithm and dendrograms were drawn using UPGMA methods. In addition, drug sensitivity test was done using the indirect proportion and 24 well plate methods.

RESULTS

Out of the 200 clinically suspected extra pulmonary tuberculosis patients, 106 (53 %) were between 15 and 35 years of age and 167 (83.5 %) were new while 33 (16.5 %) were retreatment cases. The culture yield was 29.5 % (59). Of these only one was M. bovis and 58 were M. tuberculosis strains with 31 different spoligotype patterns grouped into seven clusters. The largest cluster (ST53) comprised 12 (20.3 %) isolates. There was higher clustering of CAS isolates in TBLN than in any other form of extra pulmonary tuberculosis cases. Resistance to rifampicin was higher (22 %) than that for INH, STM and EMB (8.1 %, 5 % and 3 % respectively). Out of the 37 isolates tested for resistance, only 2 isolates were resistant for both STM and INH and no MDR strain was found.

CONCLUSIONS

There is an ongoing active recent transmission among extra pulmonary tuberculosis in the study areas as shown by the presence of clusters. Although no MDR case was observed, there is a risk of emergence of MDR as noted from the high proportion of resistance to rifampicin. Detailed study at population level is recommended to monitor its trend.

Tuberculous Lymphadenitis in Ethiopia Predominantly Caused by Strains Belonging to the Delhi/CAS Lineage and Newly Identified Ethiopian Clades of the Mycobacterium tuberculosis Complex

Background

Recently, newly defined clades of Mycobacterium tuberculosis complex (MTBC) strains, namely Ethiopia 1–3 and Ethiopia H37Rv-like strains, and other clades associated with pulmonary TB (PTB) were identified in Ethiopia. In this study, we investigated whether these new strain types exhibit an increased ability to cause TB lymphadenitis (TBLN) and raised the question, if particular MTBC strains derived from TBLN patients in northern Ethiopia are genetically adapted to their local hosts and/or to the TBLN.

Methods

Genotyping of 196 MTBC strains isolated from TBLN patients was performed by spoligotyping and 24-loci mycobacterial interspersed repetitive unit-variable number of tandem repeats (MIRU-VNTR) typing. A statistical analysis was carried out to see possible associations between patient characteristics and phylogenetic MTBC strain classification.

Results

Among 196 isolates, the majority of strains belonged to the Delhi/CAS (38.8%) lineage, followed by Ethiopia 1 (9.7%), Ethiopia 3 (8.7%), Ethiopia H37RV-like (8.2%), Ethiopia 2 and Haarlem (7.7% each), URAL (3.6%), Uganda l and LAM (2% each), S-type (1.5%), X-type (1%), and 0.5% isolates of TUR, EAI, and Beijing genotype, respectively. Overall, 15 strains (7.7%) could not be allocated to a previously described phylogenetic lineage. The distribution of MTBC lineages is similar to that found in studies of PTB samples. The cluster rate (35%) in this study is significantly lower (P = 0.035) compared to 45% in the study of PTB in northwestern Ethiopia.

Conclusion

In the studied area, lymph node samples are dominated by Dehli/CAS genotype strains and strains of largely not yet defined clades based on MIRU-VNTR 24-loci nomenclature. We found no indication that strains of particular genotypes are specifically associated with TBLN. However, a detailed analysis of specific genetic variants of the locally contained Ethiopian clades by whole genome sequencing may reveal new insights into the host-pathogen co-evolution and specific features that are related to the local host immune system.