Comparison of the yield of two tuberculosis screening approaches among household contacts in a community setting of Silti Zone, Central Ethiopia: a prospective cohort study.

BACKGROUND: Household contacts of tuberculosis (TB) patients are at a greater risk of infection and developing TB as well. Despite recommendations to actively screen such high-risk groups for TB, it is poorly implemented in Ethiopia. A community-based household contact screening was conducted to compare the yield of two different screening approaches and to identify factors associated with TB occurrence. METHODS: Smear-positive pulmonary TB index cases from six health facilities in six districts of Silti Zone were identified and enrolled prospectively between September 2020 and December 2022. Trained healthcare workers conducted house visits to screen household contacts for TB. WHO (World Health Organization) recommended symptom-based screening algorithms were used. The yield of screening was compared between a two-time screening at study site I and a single baseline screening at study site II, which is the current programmatic approach. Generalized estimating equation was used to run multivariate logistic regression to identify factors associated with TB occurrence. RESULTS: A total of 387 index TB cases (193 at site I and 194 at site II) with 1,276 eligible contacts were included for analysis. The TB yield of repeat screening approach did not show a significant difference compared to a single screening (2.3% at site I vs. 1.1% at site II, p < 0.072). The number needed to screen was 44 and 87 for the repeat and single screening, respectively, indicating a high TB burden in both settings. The screening algorithm for patients with comorbidities of asthma and heart failure had a 100% sensitivity, 19.1% specificity and a positive predictive value of 5.6%. Cough [AOR: 10.9, 95%CI: 2.55,46.37], fatigue [AOR: 6.1, 95%CI: 1.76,21.29], daily duration of contact with index case [AOR: 4.6, 95%CI; 1.57,13.43] and age of index cases [AOR: 0.9, 95%CI; 0.91-0.99] were associated with the occurrence of TB among household contacts. CONCLUSION: Our study showed that the yield of TB was not significantly different between one-time screening and repeat screening. Although repeat screening has made an addition to case notification, it should be practiced only if resources permit. Cough, fatigue, duration of contact and age of index cases were factors associated with TB. Further studies are needed to establish the association between older age and the risk of transmitting TB.

Mechanisms of Bacterial Drug Resistance with Special Emphasis on Phenotypic and Molecular Characterization of Extended Spectrum Beta-lactamase.

Antibiotics are designed to effectively treat bacterial infections while minimizing harm to the human body. They work by targeting specific components of bacteria or by disrupting essential processes such as cell wall synthesis, membrane function, protein production, and metabolic pathways. However, the misuse and overuse of antibiotics have led to the emergence of drug resistance in humans, animals, and agriculture, contributing to the global spread of this problem. Drug resistance can be either innate or acquired, with acquired resistance involving changes in the bacterial chromosomes or transferable elements. Bacterial species employ various mechanisms of drug resistance, including modifying the antibiotic targets, inactivating the drug, reducing uptake or increasing efflux, overexpressing the target, utilizing alternative pathways, and forming biofilms. One significant concern in the realm of drug resistance revolves around the emergence and proliferation of extended-spectrum beta-lactamases (ESBLs), a gene that is found in most gram-negative bacteria, primarily carried by Escherichia coli and Klebsiella pneumoniae in healthcare settings. ESBL-mediated resistance poses challenges for diagnosis, treatment, infection control, and antibiotic stewardship. Accurate detection of ESBL genes is crucial, and phenotypic methods are commonly used for initial screening. However, these methods have limitations, and confirmatory molecular techniques such as PCR and DNA sequencing are employed to accurately identify ESBL genes. Despite the significant global concerns surrounding ESBLs, they have spread worldwide, mainly facilitated by healthcare settings, inappropriate antimicrobial use, and host susceptibility. Addressing this issue requires implementing comprehensive measures, including enhanced surveillance, strict infection control practices, antibiotic stewardship programs, rapid diagnostic methods, alternative therapies, public education initiatives, and research focused on developing new drugs. Furthermore, collaboration among the healthcare, public health, and research sectors is pivotal in effectively combating the escalating threat posed by ESBL-mediated resistance. Antibiotics have revolutionized medical care by effectively treating bacterial infections. However, the emergence of ESBL gene resistance poses a global challenge that requires an integrated approach to prevent a threatening future.

Capacity building for whole genome sequencing of Mycobacterium tuberculosis and bioinformatics in high TB burden countries.

BACKGROUND: Whole genome sequencing (WGS) is increasingly used for Mycobacterium tuberculosis (Mtb) research. Countries with the highest tuberculosis (TB) burden face important challenges to integrate WGS into surveillance and research. METHODS: We assessed the global status of Mtb WGS and developed a 3-week training course coupled with long-term mentoring and WGS infrastructure building. Training focused on genome sequencing, bioinformatics and development of a locally relevant WGS research project. The aim of the long-term mentoring was to support trainees in project implementation and funding acquisition. The focus of WGS infrastructure building was on the DNA extraction process and bioinformatics. FINDINGS: Compared to their TB burden, Asia and Africa are grossly underrepresented in Mtb WGS research. Challenges faced resulted in adaptations to the training, mentoring and infrastructure building. Out-of-date laptop hardware and operating systems were overcome by using online tools and a Galaxy WGS analysis pipeline. A case studies approach created a safe atmosphere for students to formulate and defend opinions. Because quality DNA extraction is paramount for WGS, a biosafety level 3 and general laboratory skill training session were added, use of commercial DNA extraction kits was introduced and a 2-week training in a highly equipped laboratory was combined with a 1-week training in the local setting. INTERPRETATION: By developing and sharing the components of and experiences with a sequencing and bioinformatics training program, we hope to stimulate capacity building programs for Mtb WGS and empower high-burden countries to play an important role in WGS-based TB surveillance and research.

New molecular tools for meningitis diagnostics in Ethiopia - a necessary step towards improving antimicrobial prescription.

BACKGROUND: Meningitis remains a top cause of premature death and loss of disability-adjusted life years in low-income countries. In resource-limited settings, proper laboratory diagnostics are often scarce and knowledge about national and local epidemiology is limited. Misdiagnosis, incorrect treatment and overuse of antibiotics are potential consequences, especially for viral meningitis. METHODS: A prospective study was conducted over three months in a teaching hospital in Ethiopia with limited laboratory resources. Cerebrospinal fluid (CSF) samples from patients with suspected meningitis were analysed using a multiplex PCR-based system (FilmArray, BioFire), in addition to basic routine testing with microscopy and culture. Clinical data, as well as information on treatment and outcome were collected. RESULTS: Two hundred and eighteen patients were included; 117 (54%) neonates (0-29 days), 63 (29%) paediatrics (1 month-15 years) and 38 (17%) adults (≥16 years). Of 218 CSF samples, 21 (10%) were PCR positive; 4% in neonates, 14% in paediatrics and 18% in adults. Virus was detected in 57% of the PCR positive samples, bacteria in 33% and fungi in 10%. All CSF samples that were PCR positive for a bacterial agent had a white cell count ≥75 cells/mm3 and/or turbid appearance. The majority (90%) of patients received more than one antibiotic for treatment of the meningitis episode. There was no difference in the mean number of different antibiotics received or in the cumulative number of days with antibiotic treatment between patients with a microorganism detected in CSF and those without. CONCLUSIONS: A rapid molecular diagnostic system was successfully implemented in an Ethiopian setting without previous experience of molecular diagnostics. Viral meningitis was diagnosed for the first time in routine clinical practice in Ethiopia, and viral agents were the most commonly detected microorganisms in CSF. This study illustrates the potential of rapid diagnostic tests for reducing antibiotic usage in suspected meningitis cases. However, the cost of consumables for the molecular diagnostic system used in this study limits its use in low-income countries.

Diagnostic performance of fluorescent light-emitting diode microscopy for tuberculous lymphadenitis in a high-burden setting.

OBJECTIVE: Diagnosis of tuberculous lymphadenitis using fine-needle aspiration cytology is a simple and safe but low-specificity method, whereas conventional smear microscopy has variable sensitivity due to low bacterial load. We evaluated the diagnostic performance of fluorescent light-emitting diode (LED) microscopy on routinely collected fine-needle aspirates from tuberculous lymphadenitis presumptive cases. METHODS: Fine-needle aspirates were collected from patients clinically suspected of having tuberculous lymphadenitis as part of routine diagnosis. Smear preparation was performed from the aspirate and processed for cytology, conventional Ziehl-Neelsen and LED microscopy. The remaining aspirate was processed for culture on Lowenstein-Jensen media. Capilia TB-Neo test was used to differentiate M. tuberculosis complex from non-tuberculous mycobacteria. RESULT: A total of 144 tuberculous lymphadenitis presumptive cases were included. 66.7% (96/144) were positive for M. tuberculosis complex on culture. Only one isolate was identified as non-tuberculous mycobacteria. The detection rates of Ziehl-Neelsen and LED microscopy were 18.8% (27/144) and 34% (49/144), respectively. As compared to culture, sensitivity was 25.0% [95% CI: 16.3-33.7] for Ziehl-Neelsen microscopy and 45.8% [95% CI: 35.9-55.8] for LED microscopy. The specificity was 93.8% [95% CI: 86.9-100] for Ziehl-Neelsen microscopy and 89.6% [95% CI: 80.9-98.2] for LED microscopy. LED microscopy showed a statistically significant increase in sensitivity and similar specificity compared to Ziehl-Neelsen microscopy. Mean reading time of positive slides was 2.62 min/slide for Ziehl-Neelsen and 1.60 min/slide for LED microscopy. Cytology showed sensitivity of 82.3% and specificity of 54.2%. LED microscopy detected TB bacilli in 33.3% of cases cytologically classified as suppurative abscess. CONCLUSION: The LED microscopy for tuberculous lymphadenitis had significantly higher sensitivity and shorter screening time than Ziehl-Neelsen microscopy. Use of LED microscopy among cases classified as suppurative abscess on fine-needle aspirate cytology improves evidence-based diagnosis of presumptive tuberculous lymphadenitis cases. Moreover, LED microscopy could be considered as an alternative approach in settings where fine-needle aspirate cytology is impractical.

Drug resistance patterns of Mycobacterium tuberculosis complex and associated factors among retreatment cases around Jimma, Southwest Ethiopia.

BACKGROUND: Information on the pattern of drug resistant tuberculosis (TB) among re-treatment cases is crucial to develop appropriate control strategies. Therefore, we conducted this study to assess the drug resistance pattern of M. tuberculosis complex (MTBC) isolates and associated factors among re-treatment cases in Jimma area, Southwest Ethiopia. METHODS: Health facility-based cross-sectional study was conducted between March 2012 and April 2013 in Jimma area, Southwest Ethiopia. We included 79 re-treatment cases selected conveniently. Socio demographic and clinical data were collected using structured questionnaire. Sputum sample processing, mycobacterial culture, isolation and drug susceptibility testing (DST) were done at Mycobacteriology Research Centre (MRC) of Jimma University. All data were registered and entered in to SPSS version 20. Crude odds ratio (COR) and adjusted odds ratios (AOR) were calculated. P-values less than 0.05 were considered statistically significant. RESULTS: Seventy-nine re-treatment cases included in the study; 48 (60.8%) were males. Forty-seven (59.5%) study participants were from rural area with the mean age of 31.67 ± 10.02 SD. DST results were available for 70 MTBC isolates. Majority (58.6% (41/70)) isolates were resistant to at least one of the four first line drugs. The prevalence of multidrug-resistant TB (MDR-TB) was 31.4% (22/70). Place of residence (AOR = 3.44 (95 % CI: 1.12, 10.60), duration of illness (AOR = 3.00 (95 % CI: 1.17, 10.69) and frequency of prior TB therapy (AOR = 2.99, (95 % CI: 1.01, 8.86) were significant factors for any drug resistance. Moreover, history of treatment failure was found to be associated with MDR-TB (AOR = 3.43 (95 % CI: 1.14, 10.28). CONCLUSION: The overall prevalence of MDR-TB among re-treatment cases around Jimma was high. The rate of MDR-TB was higher in patients with the history of anti-TB treatment failure. Timely identification and referral of patients with the history of treatment failure for culture and DST need to be strengthened.

Bacteriological methods as add on tests to fine-needle aspiration cytology in diagnosis of tuberculous lymphadenitis: can they reduce the diagnostic dilemma?

BACKGROUND: The diagnostic accuracy of fine-needle aspiration (FNA) cytology for the diagnosis of tuberculous lymphadenitis (TBLN) is confounded by mimicking cytomorphologic disorders. The objective of this study was to determine whether supplementing FNA cytology with bacteriological methods improves the overall accuracy of TBLN diagnosis. METHODS: Two hundred presumptive TBLN cases were included in the study. FNA specimens were collected and examined for cytomorphologic changes, for acid-fast bacilli (AFB) by microscopy and for mycobacterial growth on culture. Culture was done using Lowenstein-Jensen (LJ) medium and mycobacteria growth indicator tube (BACTEC MGIT 960 TB detection system). Differentiation between M. tuberculosis complex (MTBc) and non-tuberculous mycobacteria (NTM) was done by using 500 µg/ml para-nitrobenzoic acid (PNB) susceptibility testing. RESULTS: Cytomorphology detected TBLN among 80% (160/200) of the presumptive cases. Culture results were available for 188 cases. Twelve samples were excluded due to contamination on both culture methods. Culture confirmed cases accounted for 78% (147/188) of which MTBc constituted 97.3% (143/147). Among presumptive cases, classified by FNA cytology as 'abscess', 11 were culture positive. Microscopy detected 31.3% (46/147) of culture confirmed mycobacterial lymphadenitis of which 11% (4/37) were diagnosed non-suggestive for tuberculosis (TB) by FNA cytology. Compared to culture (LJ & BACTEC MGIT 960) and AFB microscopy as composite gold standard, FNA cytology had a sensitivity of 88.4% and a specificity of 48.8%. The positive predictive value was 86.1% while the negative predictive value was 54.1%. The confirming power and the ROC curve area was 1.73 and 0.69, respectively. CONCLUSION: FNA cytology showed a relatively high sensitivity but a low specificity. Combining bacteriological methods with FNA cytology in an endemic region like Ethiopia improves the overall accuracy of the diagnosis of mycobacterial lymphadenitis, which in turn may lead to better patient management.

Discordance between genotypic and phenotypic methods for the detection of rifampicin and isoniazid resistant Mycobacterium tuberculosis and the correlation with patient treatment outcomes.

Background: Accurate drug susceptibility testing (DST) of Mycobacterium tuberculosis (MTB) is essential for proper patient management. We investigated discordance between genotypic (Xpert MTB/RIF and MTBDRplus) and phenotypic (MGIT 960) methods for the detection of rifampicin (RIF) and isoniazid (INH) resistant MTB and its correlation with patient treatment outcomes in Jimma, Southwest Oromia, Ethiopia. Methods: A retrospective study was conducted on 57 stored MTB isolates with known Xpert RIF resistance status (45 RIF resistant and 12 RIF susceptible) at Jimma University Mycobacteriology Research Center from November 2, 2021, to December 28, 2022. We did MTBDRplus and phenotypic DST (using the Mycobacterial Growth Indicator Tube (MGIT) system). The Xpert and MTBDRplus results were compared using phenotypic DST as a reference standard method. The treatment outcome was determined as per national guideline. The discordance between the genotypic and phenotypic DST was calculated using GraphPad software. Results: Among the 57 MTB isolates, six (10.5 %) had discordant results between the two DST methods. Xpert yielded five discordant results for RIF when compared with phenotypic DST (kappa coefficient (κ) = 0.76, 95 % confidence interval 0.56-0.96). The MTBDRplus compared with phenotypic DST gave three discordant results for RIF (κ = 0.86, 95 % confidence interval 0.71-1.00) and three for INH (κ = 0.86, 95 % confidence interval 0.70-1.00). Compared with Xpert, MTBDRplus yielded lower discordance with phenotypic DST for RIF. Out of six patients with discordant results, three had unfavorable outcomes while the other three were cured. Of the three patients with unfavorable outcomes, only one patient has received an inappropriate treatment regimen. There was no correlation between unfavorable outcomes and incorrect treatment regimens due to discordant results (Χ2 = 0.404; P = 0.525). Conclusions: Discordance between genotypic and phenotypic DST for RIF or INH occurred in 10.5 % of isolates. Only one patient with discordant results has received an inappropriate treatment regimen, resulting in an unfavorable outcome. The impact of parallel use of rapid molecular assay with phenotypic DST on patient treatment outcomes requires further study.

Hierarchical Predictors of Mortality in Neonatal Sepsis at Jimma Medical Center, Ethiopia: A Case-Control Study.

Background: Neonatal sepsis made the neonatal period the most perilous time for child survival, and it continued to cause preventable mortalities worldwide. These mortalities stem from the interaction of several factors that have not been sufficiently studied and, in some cases, remain overlooked. Thus, the study aims to investigate the predictors of mortality that arise from the interaction of these factors and quantitatively determine their etiologic fraction. Methods: A case-control study with hierarchical data input was conducted at Jimma Medical Center (JMC) in Oromia, Ethiopia, spanning from May 2022 to July 2023. It employed logistic regression to calculate adjusted odds ratios (AORs) and their corresponding 95% confidence intervals (CI) at a significance level of p ≤ 0.05. The model adjusted odds ratios (ORs) for variables within each level and farther levels and presented an etiologic fraction (EF), indicating the proportion of neonatal mortality attributable to specific factors. Results: The analysis of 67 cases and 268 controls unveiled significant predictors of mortality in sepsis that emerged from distal, intermediate, and proximal levels. In the final model, thus, rural residence [AOR 3.1; 95% CI (1.5, 6.3), p ≤ 0.01], prolonged labor [AOR 4.5; 95% CI (2.2, 9.3), p ≤ 0.01], prematurity [AOR 3.9; 95% CI (1.9, 7.9), P ≤ 0.0], gram-negative bacteremia [AOR 3.8; 95% CI (1.9, 7.6); P ≤ 0.01], convulsion [AOR 3.2; 95% CI (1.6, 6.4); P ≤ 0.03], low birth weight [AOR 2.7; 95% CI (1.3, 5.4); P≤0.01], and delayed breastfeeding [AOR 2.5; 95% CI (1.2, 4.9); P ≤ 0.01] attributed a variable percentage of mortality. Conclusion: Factors emerging and interacting at distal (residence), intermediate (prolonged labor), and proximal (prematurity, birth weight, convulsion, bacterial etiology, and feeding) levels influence neonatal mortality in sepsis at JMC. Therefore, concurrently improving rural family characteristics, managing labor duration, strengthening diagnostic stewardship, and promoting essential newborn care can actively prevent and reduce these mortalities.

Bacterial pathogens in Xpert MTB/RIF Ultra-negative sputum samples of patients with presumptive tuberculosis in a high TB burden setting: a 16S rRNA analysis.

In patients with presumptive tuberculosis (TB) in whom the diagnosis of TB was excluded, understanding the bacterial etiology of lower respiratory tract infections (LRTIs) is important for optimal patient management. A secondary analysis was performed on a cohort of 250 hospitalized patients with symptoms of TB. Bacterial DNA was extracted from sputum samples for Illumina 16S rRNA sequencing to identify bacterial species based on amplicon sequence variant level. The bacterial pathogen most likely to be responsible for the patients' LRTI could only be identified in a minority (6.0%, 13/215) of cases based on 16S rRNA amplicon sequencing: Mycoplasma pneumoniae (n = 7), Bordetella pertussis (n = 2), Acinetobacter baumanii (n = 2), and Pseudomonas aeruginosa (n = 2). Other putative pathogens were present in similar proportions of Xpert Ultra-positive and Xpert Ultra-negative sputum samples. The presence of Streptococcus (pseudo)pneumoniae appeared to increase the odds of radiological abnormalities (aOR 2.5, 95% CI 1.12-6.16) and the presence of S. (pseudo)pneumoniae (aOR 5.31, 95% CI 1.29-26.6) and Moraxella catarrhalis/nonliquefaciens (aOR 12.1, 95% CI 2.67-72.8) increased the odds of 6-month mortality, suggesting that these pathogens might have clinical relevance. M. pneumoniae, B. pertussis, and A. baumanii appeared to be the possible causes of TB-like symptoms. S. (pseudo)pneumoniae and M. catarrhalis/nonliquefaciens also appeared of clinical relevance based on 16S rRNA amplicon sequencing. Further research using tools with higher discriminatory power than 16S rRNA sequencing is required to develop optimal diagnostic and treatment strategies for this population.IMPORTANCEThe objective of this study was to identify possible bacterial lower respiratory tract infection (LRTI) pathogens in hospitalized patients who were initially suspected to have TB but later tested negative using the Xpert Ultra test. Although 16S rRNA was able to identify some less common or difficult-to-culture pathogens such as Mycoplasma pneumoniae and Bordetella pertussis, one of the main findings of the study is that, in contrast to what we had hypothesized, 16S rRNA is not a method that can be used to assist in the management of patients with presumptive TB having a negative Xpert Ultra test. Even though this could be considered a negative finding, we believe it is an important finding to report as it highlights the need for further research using different approaches.

Resistance to pyrazinamide in Mycobacterium tuberculosis complex isolates from previously treated tuberculosis cases in Southwestern Oromia, Ethiopia.

Objective: Pyrazinamide (PZA) susceptibility testing is important to develop evidence-based algorithms for case management. We aimed to assess the prevalence of PZA-resistance and its impact on treatment outcomes in previously treated tuberculosis (TB) cases in southwestern Oromia, Ethiopia. Methods: A Phenotypic Drug Susceptibility Testing (DST) of PZA with BACTEC MGIT 960 was conducted at the Mycobacteriology Research Center of Jimma University (MRC-JU) from June to November 2021 on sixty-six Mycobacterium tuberculosis complex (MTBC) isolates from previously treated TB cases. SPSS software package version 21 was used. The differences in the proportion of PZA resistance between the groups were compared using the chi squared test. Logistic regression was used to identify the association between PZA resistance and treatment outcomes. Results: Among 66 MTBC isolates (49 rifampicin-resistant and 17 rifampicin-sensitive) included in this study, 31.8 % were resistant to PZA. The proportion of PZA resistance was almost three times higher in previously treated TB cases with rifampicin resistance than in rifampicin-sensitive patients (38.8 % vs. 11.8 %, p = 0.039). An unfavorable treatment outcome was documented for 23 % (15/65) of the participants. Patients with PZA resistance were almost four times more likely to have an unfavorable treatment outcome than patients with PZA sensitive (aOR 4.2, 95 % CI: 1.13-15.3). Conclusions: The prevalence of PZA resistance was high compared to the pooled PZA resistance estimated worldwide. The majority of TB cases with PZA resistance had an unfavorable treatment outcome. PZA susceptibility testing should be included in the multidrug-resistant TB diagnostic algorithm to improve management of these patients.

Evaluation of the 2007 WHO guideline to diagnose smear negative tuberculosis in an urban hospital in Ethiopia.

BACKGROUND: The 2007 World Health Organization (WHO) guideline to diagnose smear-negative tuberculosis (TB) in HIV-prevalent settings was mainly based on expert advice and therefore requires evaluation in real life situations. METHODS: In 2009, this guideline was introduced at the ALERT hospital in Ethiopia. From October 2009 to January 2011, the accuracy of the guideline was evaluated using Mycobacterium tuberculosis culture positivity as reference standard in HIV positive TB suspects. RESULTS: A total of 459 TB suspects were enrolled during the study period; 336 (73.2%) were HIV positive. Acid fast bacilli sputum smear microscopy was done for 74.7% (251/336) HIV positive TB suspects; 94.4% (237/251) were smear negative. A chest X-ray was performed in 92.8% (220/237) and a Mycobacterium tuberculosis culture in 63.7% (151/237). The median TB diagnostic delay for smear negative cases was 3 days (interquartile range 3-4 days). Of the 75 patients diagnosed with smear negative pulmonary TB, 89. 4% (67/75) were diagnosed by chest X-ray, 9.4% (7/75) by culture and 1.3% (1/75) by clinical suspicion only. In 147 smear negative TB suspects Mycobacterium tuberculosis culture and chest X-ray results were available. Among these 147 patients, the sensitivity of the chest X-ray to diagnose smear negative TB in HIV-positive TB suspects was 53.3% (95% CI: 26.7-78.7); the specificity 67.4% (95% CI: 58.7-75.3). CONCLUSION: The 2007 WHO diagnostic algorithm for the diagnosis of smear negative TB is likely to reduce the diagnostic delay and therefore decrease morbidity and mortality of TB in a HIV prevalent settings like Ethiopia.

The role of AFB microscopy training in improving the performance of laboratory professionals: analysis of pre and post training evaluation scores.

BACKGROUND: Tuberculosis (TB) remains major cause of morbidity and mortality due to any one of infectious agent worldwide. In low income countries, Ziehl-Neelsen sputum smear microscopy is the only cost-effective tool for diagnosis and monitoring of patients on treatment. In order to have efficient AFB microscopy centers, it is imperative to have continuous refresher training for laboratory professionals and strong External Quality Assessment (EQA) system). However, very little data exists as to the effect of in-service training on performance of laboratory personnel in Ethiopia.The objective of this study was to investigate the role of AFB microscopy refresher training on the performance of laboratory professionals. METHODS: A cross-sectional retrospective study was conducted to appraise theoretical and practical performance of laboratory professionals before and after AFB microscopy training. Theoretical assessment was based on standard questions while practical assessment was based on smear reading of 10 standard slides. Data on eight rounds of a five days training at Adama regional laboratory on AFB microscopy in 2009 was obtained and analyzed using SPSS 16.0 statistical software. RESULT: The pre-training mean score of the theoretical knowledge and practical skills were 61.8% and 75.7%, respectively. The post training mean scores were 84.2% and 89.2% for theoretical knowledge and practical skills, respectively. The increase in mean score of both theoretical and practical assessment was statistically significant (p < 0.0001). Post training mean score of theoretical knowledge was higher among diploma holders trainees than the BSc degree counter parts (p = 0.001). The mean scores on practice before and after training was dependent on participation in previous AFB microscopy trainings (p < 0.0001). Proportions of trainees with both major and minor errors were found to decrease after they were trained. Trainees who have had previous training were found to commit less errors than those who were not participated in previous training (p < 0.0001). CONCLUSION: Training has improved theoretical and practical performance of laboratory professionals. Pre-placement and continuous training irrespective of lab professionals qualification and service year and sustainable EQA are highly recommended to ensure quality of AFB microscopy service.

High non-compliance rate among presumptive tuberculosis cases referred from peripheral health facilities in silti district of Southern Ethiopia: a mixed methods study.

BACKGROUND: For presumptive Tuberculosis (TB) case referral to be effective, most of the referred cases need to present themselves to health facilities for assessment and testing. Otherwise, cases of TB could be missed, and these cases are at an increased risk of delayed diagnosis, complications and death. Further, their care incurs significantly higher costs. This study assessed referral compliance as well as factors attributable to compliance/non-compliance to referral of presumptive TB cases in Silti district, Southern Ethiopia. METHOD: We applied a mixed design involving both quantitative and qualitative methods. A randomly selected sample of 384 presumptive TB cases referred between January, 2014 and July 2021 were included in this study from the records of 12 health posts. Purposefully selected presumptive TB cases and Health Extension Workers were also interviewed to get in-depth information on the reasons for compliance and non-compliance to referral. STATA version 14 was employed to model the data using logistic regression. Qualitative data were analyzed using thematic content analysis. RESULTS: Of the 384 referred presumptive TB cases, close to 49% did not present themselves to the referral facilities. About 66% (n = 249) of the referred cases were women, and 62% (n = 119) of those who complied to referral were women. In multivariate analysis, cough [AOR = 3.4, 95%CI: 1.54-7.32], and chest pain [AOR = 2.7, 95%CI: 1.45-5.05] were independent predictors of compliance to referral. Nearly 5.5% (n = 21) of TB cases of all types were identified. The qualitative data analysis revealed that severe disease symptoms, HEW's recommendations, and social issues as reasons improving compliance while personal and social factors, financial problems, lack of awareness about TB and transportation were reasons impeding compliance to referral. CONCLUSION: Our study showed a high level of non-compliance to referral among referred presumptive TB cases. We also found that more women were referred and also complied with the referral. Strengthening community awareness about the disease symptoms and the existence of free treatment, addressing misconceptions about TB, supporting the elderly and disabled, and checkup house visits after referral could improve compliance to referral.

Epidemiologic features of neonatal sepsis and its COVID-19 associated temporal patterns in Jimma Medical Center, Ethiopia: A Joinpoint regression analysis.

BACKGROUND: Neonatal sepsis remains a leading cause of morbidity and mortality in neonates across all regions, including Africa. Compared to developed and some developing countries, there are relatively few epidemiological trends for neonatal sepsis and associated patterns with COVID-19 in Ethiopia. We modeled an epidemiological trend and pattern to aid in the monitoring of changes in neonatal sepsis. METHODS: Retrospective data were collected from all admissions to the Neonatal Intensive Care Unit (NICU) in Ethiopia at Jimma Medical Center between May 2019 and April 2022. We analyzed the monthly neonatal sepsis incidence, mortality, and case-fatality rates using STATA software. Finally, we modeled a monthly time series of neonatal sepsis incidence trends and patterns associated with the COVID-19-impacted period using Joinpoint software. For all analyses, a P value of 0.05 was considered statistically significant at the 95% confidence interval (CI). RESULTS: In the 36 months, 6796 cases were admitted to the NICU, with a 9.5% (95% CI: 9.1, 10.0) incidence rate of neonatal sepsis. The overall admission mortality rate was 16.5% (95% CI: 13.6, 19.8), while sepsis-attributed mortality was 7.1% (95% CI: 5.8, 8.5). The data showed an unstable decreasing trend for three Joinpoints (August 2020, December 2020, and August 2021). Notably, a decrease in the incidence trend was observed from May 2019 to August 2020 (MPC, -4.1; 95% CI: -7.6, -0.5; P = 0.03), followed by a sharp increase (MPC, 23.7; 95% CI: -13.8, 77.7; P = 0.24) from August 2020 to December 2020. From December 2020 to August 2021, there was again a decreasing trend (MPC, -13.8; 95% CI: -23.3, -3.5; P = 0.01), followed by a slight increase from August 2021 to April 2022 (MPC, 4.2; 95% CI: -8.4, 18.6; P = 0.52). Finally, the study revealed an association between patterns of neonatal sepsis incidence trends and COVID-19, with a Joinpoint jump model comparability ratio (CR = 0.43) between pre- and COVID-19-impacted periods. CONCLUSIONS: Neonatal sepsis was prevalent at Jimma Medical Center, but it was on an unstably declining trend. The current results suggest a potential temporal association between the intensity of COVID-19 containment measures and a change in the incidence trend and patterns of neonatal sepsis. However, the quantified contribution of a particular containment measure requires further investigation.

Genomic transmission clusters and circulating lineages of Mycobacterium tuberculosis among refugees residing in refugee camps in Ethiopia.

BACKGROUND: Understanding the transmission dynamics of Mycobacterium tuberculosis (Mtb) could benefit the design of tuberculosis (TB) prevention and control strategies for refugee populations. Whole Genome Sequencing (WGS) has not yet been used to document the Mtb transmission dynamics among refugees in Ethiopia. We applied WGS to accurately identify transmission clusters and Mtb lineages among TB cases in refugee camps in Ethiopia. METHOD AND DESIGN: We conducted a cross-sectional study of 610 refugees in refugee camps in Ethiopia presenting with symptoms of TB. WGS data of 67 isolates was analyzed using the Maximum Accessible Genome for Mtb Analysis (MAGMA) pipeline; iTol and FigTree were used to visualize phylogenetic trees, lineages, and the presence of transmission clusters. RESULTS: Mtb culture-positive refugees originated from South Sudan (52/67, 77.6%), Somalia (9/67, 13.4%). Eritrea (4/67, 6%), and Sudan (2/67, 3%). The majority (52, 77.6%) of the isolates belonged to Mtb lineage (L) 3, and one L9 was identified from a Somalian refugee. The vast majority (82%) of the isolates were pan-susceptible Mtb, and none were multi-drug-resistant (MDR)-TB. Based on the 5-single nucleotide polymorphisms cutoff, we identified eight potential transmission clusters containing 23.9% of the isolates. Contact investigation confirmed epidemiological links with either family or social interaction within the refugee camps or with neighboring refugee camps. CONCLUSION: Four lineages (L1, L3, L4, and L9) were identified, with the majority of strains being L3, reflecting the Mtb L3 dominance in South Sudan, where the majority of refugees originated from. Recent transmission among refugees was relatively low (24%), likely due to the short study period. The improved understanding of the Mtb transmission dynamics using WGS in refugee camps could assist in designing effective TB control programs for refugees.

Prevalence of pulmonary TB and spoligotype pattern of Mycobacterium tuberculosis among TB suspects in a rural community in Southwest Ethiopia.

BACKGROUND: In Ethiopia where there is no strong surveillance system and state of the art diagnostic facilities are limited, the real burden of tuberculosis (TB) is not well known. We conducted a community based survey to estimate the prevalence of pulmonary TB and spoligotype pattern of the Mycobacterium tuberculosis isolates in Southwest Ethiopia. METHODS: A total of 30040 adults in 10882 households were screened for pulmonary TB in Gilgel Gibe field research centre in Southwest Ethiopia. A total of 482 TB suspects were identified and smear microscopy and culture was done for 428 TB suspects. Counseling and testing for HIV/AIDS was done for all TB suspects. Spoligotyping was done to characterize the Mycobacterium tuberculosis isolates. RESULTS: Majority of the TB suspects were females (60.7%) and non-literates (83.6%). Using smear microscopy, a total of 5 new and 4 old cases of pulmonary TB cases were identified making the prevalence of TB 30 per 100,000. However, using the culture method, we identified 17 new cases with a prevalence of 76.1 per 100,000. There were 4.3 undiagnosed pulmonary TB cases for every TB case who was diagnosed through the passive case detection mechanism in the health facility. Eleven isolates (64.7%) belonged to the six previously known spoligotypes: T, Haarlem and Central-Asian (CAS). Six new spoligotype patterns of Mycobacterium tuberculosis, not present in the international database (SpolDB4) were identified. None of the rural residents was HIV infected and only 5 (5.5%) of the urban TB suspects were positive for HIV. CONCLUSION: The prevalence of TB in the rural community of Southwest Ethiopia is low. There are large numbers of undiagnosed TB cases in the community. However, the number of sputum smear-positive cases was very low and therefore the risk of transmitting the infection to others may be limited. Active case finding through health extension workers in the community can improve the low case detection rate in Ethiopia. A large scale study on the genotyping of Mycobacterium tuberculosis in Ethiopia is crucial to understand transmission dynamics, identification of drug resistant strains and design preventive strategies.

Tuberculosis lymphadenitis in Southwest Ethiopia: a community based cross-sectional study.

BACKGROUND: In Ethiopia where there is no strong surveillance system and diagnostic facilities are limited, the real burden of tuberculosis (TB) lymphadenitis is not well known. Therefore, we conducted a study to estimate the prevalence of TB lymphadenitis in Southwest Ethiopia. METHODS: A community based cross-sectional study was conducted from February to March 2009 in the Gilgel Gibe field research area. A total of 30,040 individuals 15 years or older in 10,882 households were screened for TB lymphadenitis. Any individual 15 years or older with lumps in the neck, armpits or groin up on interview were considered TB lymphadenitis suspect. The diagnosis of TB lymphadenitis was established when acid fast bacilli (AFB) smear microscopy of fine needle aspiration (FNA) sample, culture or cytology suggested TB. HIV counseling and testing was offered to all TB lymphadenitis suspects. Descriptive and bivariate analysis was done using SPSS version 15. RESULTS: Complete data were available for 27,597 individuals. A total of 87 TB lymphadenitis suspects were identified. Most of the TB lymphadenitis suspects were females (72.4%). Sixteen cases of TB lymphadenitis were confirmed. The prevalence of TB lymphadenitis was thus 58.0 per 100,000 people (16/27,597) (95% CI 35.7-94.2). Individuals who had a contact history with chronic coughers (OR 5.58, 95% CI 1.23-25.43) were more likely to have TB lymphadenitis. Lymph nodes with caseous FNA were more likely to be positive for TB lymphadenitis (OR 5.46, 95% CI 1.69-17.61). CONCLUSION: The prevalence of TB lymphadenitis in Gilgel Gibe is similar with the WHO estimates for Ethiopia. Screening of TB lymphadenitis particularly for family members who have contact with chronic coughers is recommended. Health extension workers could be trained to screen and refer TB lymphadenitis suspects using simple methods.

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.

Traditional medicinal plants used in the treatment of tuberculosis in Ethiopia: A systematic review.

Background: Majority of people in Ethiopia heavily rely on traditional medicinal plants to treat a number of diseases including tuberculosis (TB). However, there has been lack of comprehensive evidences on taxonomic distribution of medicinal plant species, methods of preparation of remedies from these plants and how the remedies are administered. This systematic review is designed to examine and synthesize available evidences focusing on medicinal plants that have been used for TB treatment in Ethiopia. Methods: Research findings related to ethno-botanical and pharmacological approaches of TB remedies were retrieved from databases. Electronic libraries of Ethiopian Universities and relevant church-based religious books were also reviewed as additional sources. Evidences are searched and organized in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guideline. Result: From a total of 68 research documents that reported use of plants for treatment of TB 98 plants species belonging to 82 genera and 49 families were identified. The most frequently reported plant species belonged to family Lamiaceae (n = 8), Euphorbiaceae (n = 7), Cucurbitaceae (n = 6) and Fabaceae (n = 6). Croton macrostachyus, Allium sativum, and Myrsine Africana were the most often mentioned anti-TB medicinal plants. Shrubs (35.7%) and trees (29.6%) were reported as dominant growth forms while plant roots (31.6%) and leaves (28.6%) were frequently used plant parts for the preparations of the treatment. The most favored administration route was oral (59.1%). About 87% of the preparations were made from fresh plant materials. No experimental/clinical evidence was presented for 79.6%(78/98) of the reported plants to support their anti-mycobacterial activities. Conclusion: In Ethiopia, the number of herbal remedies is enormous and their use for TB treatment is a common practice. However, majority of them are not yet backed up by evidence generated through scientific experimentation and this warrants further experimental and clinical validations. Moreover, the efficacy, toxicity and safety tests should be initiated and this would help in the rapid identification of new anti-TB regimens, and possibly it would lead to developing more effective new plant-based drugs. This systematic review will serve as a reference for the selection of plants for developing new anti-TB regimens.