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Background: Diagnosis of tuberculosis (TB) in children is challenging mainly due to the difficulty of obtaining respiratory specimen and lack of sensitive diagnostic tests. The objective of this study was to evaluate the diagnostic performance of Xpert MTB/RIF (Xpert here after) for the diagnosis of pulmonary TB (PTB) from stool specimen in children., Methods: A cross-sectional study was conducted among consecutively recruited children (less than 15 years old) with presumptive PTB at Jimma Medical Center, Ethiopia. One pulmonary specimen (expectorated sputum or gastric aspirate) was collected from each participant and tested for TB by Xpert and Lowenstein-Jensen (LJ) culture. In addition, one stool specimen per child was collected and tested by Xpert after a single step, centrifuge-free stool processing method adapted from KNCV TB Foundation. Diagnostic performance of Xpert was calculated with reference to LJ culture and to a composite reference standards (CRS) comprising of confirmed TB (positive by Xpert and/or culture) and unconfirmed TB (clinical diagnosis with improvement after anti-TB treatment)., Results: A total of 178 children were enrolled; 152 of whom had complete microbiological results. Overall, TB was diagnosed in 13.2% (20/152) of the children with presumptive TB. Of these, only ten had microbiologically confirmed TB (positive Xpert and/or culture) and the remaining ten were clinically diagnosed with positive response to anti-TB treatment and were classified as unconfirmed TB. Stool Xpert had sensitivity of 100% (95%CI: 66.4-100) and specificity of 99.3% (95%CI: 96.2-100) compared to culture; however, the sensitivity was decreased to 50% (95%CI: 27.2-72.8) when compared to CRS. The Xpert on gastric aspirate had sensitivity of 77.8% (95%CI: 40-97.2) compared to culture and 40% (95%CI: 19.1-64) compared to CRS., Conclusions: The sensitivity of Xpert for stool sample is comparable to that for gastric aspirate. Stool sample is a potential alternative to pulmonary specimen in the diagnosis of pulmonary TB in children using Xpert., Competing Interests: The authors have declared that no competing interests exist.

Background: Ethiopia is one of the high burden countries for extrapulmonary tuberculosis (EPTB); however, the prompt diagnosis of EPTB remains challenging. This study is aimed to evaluate the diagnostic performance of Xpert MTB/RIF and DetermineTM TB-LAM Ag (TB-LAM) for the prompt diagnosis of EPTB in Ethiopia., Methods: A total of 147 presumptive EPTB patients, including 23 HIV- positive participants were enrolled. Extra-pulmonary samples were collected from all presumptive EPTB cases and tested for Mycobacterium tuberculosis complex (MTBC) using fluorescent microscopy, Xpert MTB/RIF, and culture. Additionally, urine samples were also collected from 126 participants and were tested by DetermineTM TB-LAM Ag (Alere Inc, Waltham, USA). The Sensitivity and specificity of Xpert and TB- LAM tests were calculated by comparing with a composite reference standard (CRS), which comprises smear microscopy, culture and response to empirical anti-TB treatment., Results: Of 147 patients, 23 (15.6%) were confirmed EPTB cases (culture-positive), 14 (9.5%) were probable EPTB (clinically, radiologically or cytologically positive and received anti-TB treatment with good response), and 110 (74.8%) were classified as "non- TB" cases. Compared to the composite reference standard (CRS), the overall sensitivity and specificity of Xpert MTB/RIF were 43.2% and 100%, respectively with the highest sensitivity for Lymph node aspirate (85.7%) and lower sensitivity for pleural fluid (14.3%) and 100% specificity for all specimen types. The sensitivity and specificity of TB-LAM were 33.3% and 94.4% respectively with the highest sensitivity for HIV co-infected participants (83.3%). The sensitivity of the combination of Xpert MTB/RIF and TB-LAM tests regardless of HIV status was 61.1% whereas the sensitivity was improved to 83.3% for HIV-positive cases., Conclusion: TB-LAM alone has low sensitivity for EPTB diagnosis; however, the combination of TB-LAM and Xpert MTB/RIF improves the diagnosis of EPTB particularly for countries with high EPTB and HIV cases., Competing Interests: NO authors have competing interests.

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., Competing Interests: The authors have declared that no competing interests exist.

Background: Drug-resistance in Mycobacterium tuberculosis complex remains a major health burden in human history and still is a major leading cause of death in developing countries including Ethiopia. Early detection of all forms of drug-resistant Tuberculosis(TB) is a key factor to reduce and contain the spread of these resistant strains., Methods: A health facility-based cross-sectional study was employed, based on demographic, clinical, and laboratory data collected from 204 patients with bacteriological confirmed TB. Sputum samples were analyzed using conventional TB culture and identification test followed by molecular species identification, and then phenotypic drug susceptibility tests. Data were entered using an excel spreadsheet and exported to SPSS version 20 for analysis. Descriptive analysis; frequencies, and proportions were computed., Results: Among the 204 sputum samples inoculated in culture media, Mycobacterium species were recovered from 165 specimens, with 160 Mycobacterium tuberculosis complex and five Non- Tuberculosis Mycobacterium(NTM) species. All Mycobacterium tuberculosis complex was found to be M. tuberculosis. Of the five NTM species, 2 M.fortuitum, 2 M.intracellulare, and 1 M.gordonae were identified. Among 160 species of M. tuberculosis isolates, 110(68.8%) were resistant to any of the anti-TB drugs. The resistance pattern was; INH (109, 68.1%), RIF (99, 61.9%), STM (73,45.6%), and EMB (32,20.0%). Mono-resistance was found for INH (7,4.3%) and STM (1,0.6%). Ninety-nine (61.9%) isolates become MDR, while resistance to any of the second-line anti-TB drugs was detected in 9 (5.6%) strains, with 8(5%) Pre-XDR and one (0.6%) XDR cases., Conclusion: Our findings highlight high frequencies of drug resistance to first and second-line anti-TB drugs.Determining the drug-resistance pattern of MTB is important for programmatic management of drug-resistant TB in Ethiopia. The circulating Pre-XDR and XDR case identified in the current study is alarming to the tuberculosis control program in the country., Competing Interests: The authors have declared that no competing interests exist.

Background: Tuberculous lymphadenitis (TBLN) diagnosis remains a challenge in resource limited countries like Ethiopia. Most diagnostic centers in Ethiopia use smear microscopy, but it has low sensitivity in detecting tubercle bacilli in fine needle aspiration (FNA) specimens. FNA cytology (FNAC) is another widely applicable diagnostic option but it has low specificity for diagnosing TBLN. In 2014, WHO recommended Xpert MTB/RIF assay to be used in detecting TB from FNA specimen by considering the diagnostic limitations of microscopy and cytology. In Ethiopia, there is limited data on Xpert MTB/RIF performance in detecting TBLN from FNA. Therefore, this study aimed to evaluate the diagnostic performance of Xpert MTB/RIF assay and non-molecular methods (cytology, microscopy and culture) for the diagnosis of TBLN., Methods: A cross-sectional study was conducted on 152 presumptive TBLN patients at St. Paul's Hospital Millennium Medical College (SPHMMC) from December 2015 to May 2016 in Addis Ababa, Ethiopia. FNA specimens were collected from each patient. Individual patient specimens were examined by microscopy (acid fast and auramine O staining), cytology, Xpert MTB/RIF and culture. Each specimen was directly inoculated and its sediment following decontamination procedure onto two duplicate Löwenstein-Jensen (LJ) media. Composite culture (specimen positive by direct or concentrated or both culturing methods) and composite method (positive by either one of the non-molecular methods) were taken as reference methods. The data was captured and analyzed using software packages SPSS version 20 (SPSS Inc, Chicago, Illinois, USA). Sensitivity, specificity, positive predictive value, and negative predictive value were calculated., Result: A total of 152 presumptive TBLN patients were enrolled in this study. Of these, 105(69%), 68(44.7%), 64(42%), 48(32%) and 33(22%) were positive for M. tuberculosis using composite method (positive by either one of the non-molecular method), composite culture, direct, and concentrated culture, respectively. TB positivity rate was 67.8%, 49.3%, 24.3%, and 14.5% using cytology, Xpert MTB/RIF, Auramine O (FM) microscopy, and Ziehl Nelson (ZN) microscopy, respectively. Using composite culture as reference, the sensitivity and specificity of Xpert MTB/RIF was 78% (95% CI: 73.7% to 82.3%) and 74% (95%CI: 69.4% to 78.6%), respectively. However, the sensitivity of Xpert MTB/RF improved from 78% to 92% using composite method as a reference. The high positivity rate observed in purulent (70%) followed by caseous (66.7%) type of aspirates by Xpert MTB/RIF., Conclusion: Xpert MTB/RIF assay has both considerable sensitivity and specificity; it may be employed for better diagnosis, management and treatment of presumptive TBLN patients., Competing Interests: The authors have declared that no competing interests exist.

Background: The diagnoses of active smear negative PTB, remains difficult. As a result, treatment is often carried out empirically relaying on clinical criteria. The distribution and magnitude of smear negative PTB, smear negative MDR-TB and associated factors in the same day diagnosis strategy are not clearly known in the study area. Therefore, this study aimed to determine the prevalence of TB, MDR-TB and associated risk factors among presumptive smear negative pulmonary tuberculosis patients in Addis Ababa, Ethiopia., Methods: Analytic cross sectional study design was used. A total of 418 smear negative presumptive pulmonary TB patients were enrolled from selected health facilities since August 01, 2017 to January 5, 2018. Sputum samples were examined by Ziehl Neelsen microscopy, Xpert MTB/RIF assay and Culture. Drug susceptibility testing was performed by line probe assay and BACTEC MGIT 960 system. These laboratory tests were performed in Ethiopian Public Health Institute, National TB Reference Laboratory. Data was analyzed by SPSS Ver.20., Results: From the total of 418 enrolled patients, 27 (6.5%) were Xpert MTB/ RIF and 26 (6.4%) were culture confirmed smear negative PTB patients. The positivity rate among male and female was 10.2 and 3.5% (p = 0.005) respectively. From 26 culture positive isolates 3 (11.54%) were MDR TB; from MDR-TB confirmed isolates 2/23 (8.7%) were among new and 1/3 (33.3%) was among retreatment smear negative presumptive pulmonary TB patients. All Rifampicin resistant smear negative pulmonary TB isolates by Xpert MTB/ RIF assay were found to be MDR TB and 7/26 (26.9%) isolates were INH mono resistant. History of migration found to be a potential factor for developing smear negative pulmonary TB., Conclusion: In this study a significant proportion of smear negative pulmonary TB was diagnosed. Furthermore, a high smear negative multi drug resistant (MDR) TB and other mono drug resistant TB prevalence was confirmed. Due to the limitations of smear microscopy which is used as a primary diagnostic tool, these TB strains are missed to be diagnosed and transmission continues in the community.

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&#95;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., (© 2018 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.)

Background: In co-endemic areas, rate of intestinal parasites and tuberculosis (TB) co-infection thought to be high. However, there are limited studies on the epidemiology of this co-infection in Ethiopia. Therefore, the present study aimed to generate evidence on intestinal parasites co-infection rate and associated factors among pulmonary tuberculosis patients (PTB) and their household contacts in Addis Ababa, Ethiopia., Methods: Unmatched case-control study was conducted. Data were collected from 91 PTB patients (cases) and 89 household contacts (controls). Socio-demographic characteristics and associated factors were collected using structured questionnaire. Sputum, stool and blood specimens were collected, processed and examined for PTB, intestinal parasites and Human Immunodeficiency virus anti-body test, respectively. Data were entered and analyzed by Statistical Packages for Social Sciences (SPSS) Version 20. Descriptive statistics, Fisher's exact test, binary logistic regression, and odds ratio were used. P-value of < 0.05 was considered as statistically significant., Results: The infection rate of intestinal parasites based on one stool samples in PTB patients and controls was 22 and 9%, respectively. The difference was statistically significant (COR = 2.85;95% CI = 1.18-6.87). The most prevalent intestinal parasite in PTB patients was Gardia lamblia (8.8%, 8), followed equally by Ascaris lumbricoides, Haymenolopsis nana and Entamoeba histolytica/dispar (4.4%, 4). Co-infection in PTB patients was associated with body mass index (BMI) < 18.5 (AOR = 6.71;95% CI = 1.65-27.25) and dirty material in finger nails (AOR = 8.99;95% CI = 2.46-32.78). There was no variable associated with parasitic infections in controls in our analysis, which might be due to the low prevalence of intestinal parasites'., Conclusions: There was a statistical significant difference in the infection rate of intestinal parasites in PTB patients compared to healthy household contacts. The consequence of co-infection on developing an active disease, disease severity and treatment efficacy needs to be investigated in future.

Objective/background: The nature and frequency of mutations in rifampicin (RIF) and isoniazid (INH) resistant Mycobacterium tuberculosis isolates vary considerably according to geographic locations. However, information regarding specific mutational patterns in Ethiopia remains limited., Methods: A cross-sectional prospective study was carried out among confirmed pulmonary tuberculosis cases in Southwest Ethiopia. Mutations associated with RIF and INH resistances were studied using GenoType MTBDRplus line probe assay in 112 M. tuberculosis isolates. Culture (MGIT960) and identification tests were performed at the Mycobacteriology Research Center of Jimma University, Jimma, Ethiopia., Results: Mutations conferring resistance to INH, RIF, and multidrug resistance were detected in 36.6% (41/112), 30.4% (34/112), and 27.7% (31/112) of M. tuberculosis isolates respectively. Among 34 RIF-resistant isolates, 82.4% (28/34) had rpoB gene mutations at S531L, 2.9% (1/34) at H526D, and 14.7% (5/34) had mutations only at wild type probes. Of 41 INH-resistant strains, 87.8% (36/41) had mutations in the katG gene at Ser315Thr1 and 9.8% (4/41) had mutations in the inhA gene at C15T. Mutations in inhA promoter region were strongly associated with INH monoresistance., Conclusion: A high rate of drug resistance was commonly observed among failure cases. The most frequent gene mutations associated with the resistance to INH and RIF were observed in the codon 315 of the katG gene and codon 531 of the rpoB gene, respectively. Further studies on mutations in different geographic regions using DNA sequencing techniques are warranted to improve the kit by including more specific mutation probes in the kit., (Copyright © 2016 Asian-African Society for Mycobacteriology. Published by Elsevier Ltd. All rights reserved.)

Objective/background: The GeneXpert MTB/RIF assay (Xpert) was endorsed as the initial diagnostic tool in people suspected of human immunodeficiency virus-associated or drug-resistant tuberculosis (TB). However, information regarding the performance of Xpert for diagnosing smear-negative TB in high burden settings remains limited. We evaluated the diagnostic accuracy of Xpert and the impact of bleach concentration on the performance of Xpert using smear-negative sputum samples from human immunodeficiency virus-negative patients., Methods: One spot and one morning smear-negative sputum samples per patient were examined using Xpert and culture at the Mycobacteriology Research Center of Jimma University, Ethiopia. The sputum culture on both Löwenstein-Jensen and/or Mycobacteria Growth Indicator Tube was the gold-standard., Results: Of 185 smear-negative presumptive pulmonary TB cases, 19 (10.3%) had culture-proven TB. The sensitivity of Xpert on spot and morning sputum was similar (63.2%). Testing two specimens per patient insignificantly increased the sensitivity of Xpert. Bleach concentration and pelleting improved the sensitivity of Xpert over unprocessed sputum in paired samples (73.8% vs. 63.2%) without affecting the specificity (95%). Bleach concentration and pelleting allowed an additional seven cases of TB (missed on the first and second direct Xperts) to be detected, five of which were from culture-negative cases., Conclusion: Testing of a single sputum sample by Xpert can reach reasonable sensitivity and results would be available on the same day, avoiding loss of patients and treatment delay. The sensitivity of Xpert was improved after bleach concentration and pelleting, although its added value needs further study on a larger scale., (Copyright © 2016 Asian-African Society for Mycobacteriology. Published by Elsevier Ltd. All rights reserved.)