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Erdaw Tachbele,1,2 Samuel Kyobe,3 Fred Ashaba Katabazi,3 Edgar Kigozi,3 Savannah Mwesigwa,3 Moses Joloba,3 Alebachew Messele,1 Wondwossen Amogne,2 Mengistu Legesse,1 Rembert Pieper,4 Gobena Ameni1 1Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia; 2College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia; 3College of Health Sciences, Makerere University, Kampala, Uganda; 4Janssen Biopharma, South San Francisco, CA, USACorrespondence: Erdaw Tachbele Tel +251 911642880Email erdawt@yahoo.comPurpose: This study was conducted to investigate the drug resistance mutations and genetic diversity of HIV-1 in ART experienced patients in South Omo, Ethiopia.Patients and Methods: A cross-sectional study conducted on 253 adult patients attending ART clinics for ≥ 6 months in South Omo. Samples with VL ≥ 1000 copies/mL were considered as virological failures (VF) and their reverse transcriptase gene codons 90– 234 were sequenced using Illumina MiSeq. MinVar was used for the identification of the subtypes and drug resistance mutations. Phylogenetic tree was constructed by neighbor-joining method using the maximum likelihood model.Results: The median duration of ART was 51 months and 18.6% (47/253) of the patients exhibited VF. Of 47 viraemic patients, the genome of 41 were sequenced and subtype C was dominant (87.8%) followed by recombinant subtype BC (4.9%), M-09-CPX (4.9) and BF1 (2.4%). Of 41 genotyped subjects, 85.4% (35/41) had at least one ADR mutation. Eighty-one percent (33/41) of viraemic patients harbored NRTI resistance mutations, and 48.8% (20/41) were positive for NNRTI resistance mutations, with 43.9% dual resistance mutations. Among NRTI resistance mutations, M184V (73.2%), K219Q (63.4%) and T215 (56.1%) complex were the most mutated positions, while the most common NNRTI resistance mutations were K103N (24.4%), K101E, P225H and V108I 7.5% each. Active tuberculosis (aOR=13, 95% CI= 3.46– 29.69), immunological failure (aOR=3.61, 95% CI=1.26– 10.39), opportunistic infections (aOR=8.39, 95% CI= 1.75– 40.19), and poor adherence were significantly associated with virological failure, while rural residence (aOR 2.37; 95% CI: 1.62– 9.10, P= 0.05), immunological failures (aOR 2.37; 95% CI: 1.62– 9.10, P= 0.05) and high viral load (aOR 16; 95% CI: 5.35 51.59, P < 0.001) were predictors of ADR mutation among the ART experienced and viraemic study subjects.Conclusion: The study revealed considerable prevalence of VF and ADR mutation with the associated risk indicators. Regular virological monitoring and drug resistance genotyping methods should be implemented for better ART treatment outcomes of the nation.Keywords: HIV-1, genetic diversity, acquired drug resistance, ART experienced, South Omo, Ethiopia

Phalkun Chheng,1,2 Mary Nsereko,2 LaShaunda L Malone,2 Brenda Okware,2 Sarah Zalwango,2 Moses Joloba,2,3 W Henry Boom,2 Ezekiel Mupere,1,2,4 Catherine M Stein1,2 On behalf of the Tuberculosis Research Unit 1Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA; 2Uganda-Case Western Reserve University Research Collaboration, 3Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda; 4Department of Pediatrics and Child Health, College of Health Sciences, Makerere University, Kampala, Uganda Purpose: To assess the prevalence of pulmonary tuberculosis among first-degree relative (FDR) contacts not living with tuberculosis (TB) cases. Methods: A cross-sectional analysis of household contacts living with an index TB case and FDR contacts living outside of households in Kampala, Uganda, is presented. Results: A total of 177 contacts (52 FDRs and 125 index household contacts) of 31 TB cases were examined. Compared with index household contacts, FDR contacts were older, more likely to be TB symptomatic (50% vs 33%), had a higher percentage of abnormal chest X-rays (19% vs 11%), sputum smear positive (15% vs 5%), and many similar epidemiologic risk factors, including HIV infection (13% vs 10%). Contact groups had similar pulmonary tuberculosis prevalence: 9.6% in FDR vs 10.4% in index household contacts and similar Mycobacterium tuberculosis infection: 62% in FDR vs 61% in index households. Conclusion: TB is common among FDR contacts. High TB prevalence justifies targeting FDRs during household contact investigations. Combining TB active-case finding among FDR contacts with household contact investigation in low-income setting is feasible. This should be part of national TB control program strategies for increasing TB case-detection rates and reducing community TB transmission and death. Keywords: prevalence of pulmonary tuberculosis, limited resource setting, contact tracing

BackgroundThe World Health Organization (WHO) has endorsed the next-generation Xpert MTB/RIF Ultra (Ultra) cartridge, and Uganda is currently transitioning from the older generation Xpert MTB/RIF (Xpert) cartridge to Ultra as the initial diagnostic test for pulmonary tuberculosis (TB). We assessed the diagnostic accuracy of Ultra for pulmonary TB among adults in Kampala, Uganda.MethodsWe sampled adults referred for Xpert testing at two hospitals and a health center over a 12-month period. We enrolled adults with positive Xpert and a random 1:1 sample with negative Xpert results. Expectorated sputum was collected for Ultra, and for solid and liquid culture testing for Xpert-negative patients. We measured sensitivity and specificity of Ultra overall and by HIV status, prior history of TB, and hospitalization, in reference to Xpert and culture results. We also assessed how classification of results in the new "trace" category affects Ultra accuracy.ResultsAmong 698 participants included, 211 (30%) were HIV-positive and 336 (48%) had TB. The sensitivity of Ultra was 90.5% (95% CI 86.8-93.4) and specificity was 98.1% (95% CI 96.1-99.2). There were no significant differences in sensitivity and specificity by HIV status, prior history of TB or hospitalization. Xpert and Ultra results were concordant in 670 (96%) participants, with Ultra having a small reduction in specificity (difference 1.9, 95% CI 0.2 to 3.6, p=0.01). When "trace" results were considered positive for all patients, sensitivity increased by 2.1% (95% CI 0.3 to 3.9, p=0.01) without a significant reduction in specificity (- 0.8, 95% CI - 0.3 to 2.0, p=0.08).ConclusionsAfter 1 year of implementation, Ultra had similar performance to Xpert. Considering "trace" results to be positive in all patients increased case detection without significant loss of specificity. Longitudinal studies are needed to compare the benefit of greater diagnoses to the cost of overtreatment.

The performance of urine Xpert MTB/RIF Ultra (Xpert Ultra) for pulmonary TB diagnosis is unknown. HIV-positive and HIV-negative adults were enrolled at two health facilities in Kampala, Uganda. We compared the accuracy of urine Xpert Ultra and Determine TB-LAM in reference to sputum-based testing (positive Xpert MTB/RIF or culture), and assessed incremental yield. Urine Xpert Ultra had low sensitivity (17.2%, 95% CI 12.3-23.2) but high specificity (98.1%, 95% CI 94.4-99.6). Sensitivity reached 50.0% (95% CI 28.2-71.8) among HIV-positive patients with CD4

ObjectiveTo assess the feasibility of a streamlined strategy for improving tuberculosis (TB) diagnostic evaluation and treatment initiation among patients with presumed TB.DesignSingle-arm interventional pilot study at five primary care health centers of a streamlined, SIngle-saMPLE (SIMPLE) TB diagnostic evaluation strategy: 1) examination of two smear results from a single spot sputum specimen using light-emitting diode fluorescence microscopy, and 2) daily transportation of smear-negative sputum samples to Xpert® MTB/RIF testing sites.ResultsOf 1212 adults who underwent sputum testing for TB, 99.6% had two smears examined from the spot sputum specimen. Sputum was transported for Xpert testing within 1 clinic day for 83% (907/1091) of the smear-negative patients. Of 157 (13%) patients with bacteriologically positive TB, 116 (74%) were identified using sputum smear microscopy and 41 (26%) using Xpert testing of smear-negative samples. Anti-tuberculosis treatment was initiated in 142 (90%) patients with bacteriologically positive TB, with a median time to treatment of 1 day for smear-positive patients and 6 days for smear-negative, Xpert-positive patients.ConclusionThe SIMPLE TB strategy led to successful incorporation of Xpert testing and rapid treatment initiation in the majority of patients with bacteriologically confirmed TB in a resource-limited setting.

BackgroundImplementation of new tuberculosis (TB) diagnostic strategies in resource-constrained settings is challenging. We measured the impact of solid and liquid mycobacterial cultures on treatment practices for patients undergoing TB evaluation in Kampala, Uganda.MethodsWe enrolled consecutive smear-negative, human immunodeficiency virus positive adults with cough of ⩾2 weeks from September 2009 to April 2010. Laboratory technicians performed mycobacterial cultures on solid and liquid media. We compared empiric treatment decisions with solid and liquid culture in terms of diagnostic yield and time to results, and assessed impact on patient management.ResultsOf 200 patients enrolled, 26 (13%) had culture-confirmed TB: 22 (85%) on solid culture alone, 2 (8%) on liquid culture alone, and 2 (8%) on both solid and liquid culture. Thirty-four patients received empiric anti-tuberculosis treatment, but only 10 (29%) were culture-positive. Median time to a positive result on solid culture was 92 days (interquartile range [IQR] 69-148) compared to 106 days (IQR 66-157) for liquid culture. No patients initiated treatment following a positive result on liquid culture.ConclusionThe introduction of mycobacterial culture did not influence care for patients undergoing evaluation for TB in Kampala, Uganda. Attention to contextual factors surrounding implementation is needed to ensure the effective introduction of new testing strategies in low-income countries.

Jeremiah Seni,1 Inyasi Lawrence Akaro,2,3 Baraka Mkinze,2,3 Zengo Kashinje,1 Modest Benard,1 Gerald Mboowa,4 Dickson Aruhomukama,4 Ivan Sserwadda,4 Moses L Joloba,4 Stephen E Mshana,1 Benson R Kidenya5 1Department of Microbiology and Immunology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, Mwanza, Tanzania; 2Department of Surgery, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, Mwanza, Tanzania; 3Department of Orthopaedic Surgery, Bugando Medical Centre, Mwanza, Tanzania; 4Department of Immunology and Molecular Biology, Makerere University College of Health Sciences, Kampala, Uganda; 5Department of Biochemistry and Molecular Biology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, Mwanza, TanzaniaCorrespondence: Jeremiah SeniDepartment of Microbiology and Immunology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, P.O. Box 1464, Bugando, Mwanza, TanzaniaTel: +255 784 593000Email senijj80@gmail.comBackground: The dual burden of road traffic accidents and antimicrobial resistance in orthopaedic infections is challenging already strained health-care systems. Limited information exists in Tanzania on antimicrobial resistance surveillance to delineate the potential sources of multi-drug-resistant bacteria for specific mitigation strategies among orthopaedic patients.Methods: A longitudinal study was conducted at Bugando Medical Centre in Mwanza city between January and May 2020. It involved the collection of rectal swabs/stools, hand swabs, and environmental sampling to identify extended-spectrum beta-lactamase (ESBL)-producing gram-negative bacteria. Participants’ data were collected using a structured questionnaire and analysed to determine factors associated with ESBL colonization among index orthopaedic patients and correlates with other ESBL sources using OR (95% CI) and a cut-off p-value of ≤ 0.05.Results: We found that 47.2% (125/265) of index patients, 77.8% (14/18) of neighbouring patients, 8.3% (2/24) of health-care workers, 72.2% (13/18) of non-medical caregivers, and 31.4% (27/86) of samples taken from the hospital environment had ESBL producers. Escherichia coli and Klebsiella spp. predominated among participants and Acinetobacter spp. predominated in the environmental samples. Patients with open fractures had increased odds of being colonized with ESBL producers [OR (95% CI): 2.08 (1.16– 3.75); p=0.015]. The floor below patients’ beds was commonly contaminated; however, the odds of environmental contamination decreased on the third round of sampling [OR (95% CI: 0.16 (0.04– 0.67); p=0.012], apparently as a result of parallel infection prevention and control responsive measures against coronavirus disease 2019 (COVID-19).Conclusion: We found a high occurrence of ESBL colonization among participants and in the environmentat this tertiary hospital. The importance of routine ESBL surveillance among orthopaedic patients with open fractures on admission and strengthened decontamination of health-care premises is reiterated.Keywords: ESBL colonization, orthopaedic patients, Mwanza, Tanzania

Rationale: Mycobacterium tuberculosis is transmitted by infectious aerosols, but assessing infectiousness currently relies on sputum microscopy that does not accurately predict the variability in transmission.Objectives: To evaluate the feasibility of collecting cough aerosols and the risk factors for infectious aerosol production from patients with pulmonary tuberculosis (TB) in a resource-limited setting.Methods: We enrolled subjects with suspected TB in Kampala, Uganda and collected clinical, radiographic, and microbiological data in addition to cough aerosol cultures. A subset of 38 subjects was studied on 2 or 3 consecutive days to assess reproducibility.Measurements and Main Results: M. tuberculosis was cultured from cough aerosols of 28 of 101 (27.7%; 95% confidence interval [CI], 19.9-37.1%) subjects with culture-confirmed TB, with a median 16 aerosol cfu (range, 1-701) in 10 minutes of coughing. Nearly all (96.4%) cultivable particles were 0.65 to 4.7 μm in size. Positive aerosol cultures were associated with higher Karnofsky performance scores (P = 0.016), higher sputum acid-fast bacilli smear microscopy grades (P = 0.007), lower days to positive in liquid culture (P = 0.004), stronger cough (P = 0.016), and fewer days on TB treatment (P = 0.047). In multivariable analyses, cough aerosol cultures were associated with a salivary/mucosalivary (compared with purulent/mucopurulent) appearance of sputum (odds ratio, 4.42; 95% CI, 1.23-21.43) and low days to positive (per 1-d decrease; odds ratio, 1.17; 95% CI, 1.07-1.33). The within-test (kappa, 0.81; 95% CI, 0.68-0.94) and interday test (kappa, 0.62; 95% CI, 0.43-0.82) reproducibility were high.Conclusions: A minority of patients with TB (28%) produced culturable cough aerosols. Collection of cough aerosol cultures is feasible and reproducible in a resource-limited setting. [ABSTRACT FROM AUTHOR]