Browsing by Author "Ssengooba, Willy"
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Item Accuracy of different Xpert MTB/Rif implementation strategies in programmatic settings at the regional referral hospitals in Uganda: Evidence for country wide roll out(PLoS ONE, 2018) Muttamba, Winters; Ssengooba, Willy; Sekibira, Rogers; Kirenga, Bruce; Katamba, Achilles; Joloba, MosesXpert MTB/RIF assay is a highly sensitive test for TB diagnosis, but still costly to most lowincome countries. Several implementation strategies instead of frontline have been suggested; however with scarce data. We assessed accuracy of different Xpert MTB/RIF implementation strategies to inform national roll-out. Methods This was a cross-sectional study of 1,924 adult presumptive TB patients in five regional referral hospitals of Uganda. Two sputum samples were collected, one for fluorescent microscopy (FM) and Xpert MTB/RIF examined at the study site laboratories. The second sample was sent to the Uganda Supra National TB reference laboratory for culture using both Lowenstein Jensen (LJ) and liquid culture (MGIT). We compared the sensitivities of FM, Xpert MTB/RIF and the incremental sensitivity of Xpert MTB/RIF among patients negative on FM using LJ and/or MGIT as a reference standard. Results A total 1924 patients were enrolled of which 1596 (83%) patients had at least one laboratory result and 1083 respondents had a complete set of all the laboratory results. A total of 328 (30%) were TB positive on LJ and /or MGIT culture. The sensitivity of FM was n (%; 95% confidence interval) 246 (63.5%; 57.9±68.7) overall compared to 52 (55.4%; 44.1±66.3) among HIV positive individuals, while the sensitivity of Xpert MTB/RIF was 300 (76.2%; 71.7±80.7) and 69 (71.6%; 60.5±81.1) overall and among HIV positive individuals respectively. Overall incremental sensitivity of Xpert MTB/RIF was 60 (36.5%; 27.7±46.0) and 20 (41.7%; 25.5±59.2) among HIV positive individuals. Conclusion Xpert MTB/RIF has a higher sensitivity than FM both in general population and HIV positive population. Xpert MTB/RIF offers a significant increase in terms of diagnostic sensitivity even when it is deployed selectively i.e. among smear negative presumptive TB patients. Our results support frontline use of Xpert MTB/RIF assay in high HIV/TB prevalent countries. In settings with limited access, mechanisms to refer smear negative sputum samples to Xpert MTB/RIF hubs are recommended.Item Accuracy of the tuberculosis molecular bacterial load assay to diagnose and monitor response to anti-tuberculosis therapy: a longitudinal comparative study with standard-of-care smear microscopy, Xpert MTB/RIF Ultra, and culture in Uganda(Elsevier Ltd, 2024-03) Musisi, Emmanuel; Wamutu, Samuel; Ssengooba, Willy; Kasiinga, Sharifah; Sessolo, Abdulwahab; Sanyu, Ingvar; Kaswabuli, Sylvia; Zawedde, Josephine; Byanyima, Patrick; Kia, Praiscillia; Muwambi, William; Toskin, Divine Tracy; Kigozi, Edgar; Walbaum, Natasha; Dombay, Evelin; Legrady, Mate Bonifac; Ssemambo, Kizza David-Martin; Joloba, Moses; Kuchaka, Davis; Worodria, William; Huang, Laurence; Gillespie, Stephen H; Sabiiti, WilberAbstract In 2018, the tuberculosis molecular bacterial load assay (TB-MBLA), a ribosomal RNA-based test, was acknowledged by WHO as a molecular assay that could replace smear microscopy and culture for monitoring tuberculosis treatment response. In this study, we evaluated the accuracy of TB-MBLA for diagnosis and monitoring of treatment response in comparison with standard-of-care tests. For this longitudinal prospective study, patients aged 18 years or older with presumptive tuberculosis (coughing for at least 2 weeks, night sweats, and weight loss) were enrolled at China-Uganda Friendship Hospital Naguru (Kampala, Uganda). Participants were evaluated for tuberculosis by TB-MBLA in comparison with Xpert MTB/RIF Ultra (Xpert-Ultra) and smear microscopy, with Mycobacteria Growth Indicator Tube (MGIT) culture as a reference test. Participants who were positive on Xpert-Ultra were enrolled on a standard 6-month anti-tuberculosis regimen, and monitored for treatment response at weeks 2, 8, 17, and 26 after initiation of treatment and then 3 months after treatment. Between Nov 15, 2019, and June 15, 2022, 210 participants (median age 35 years [IQR 27–44]) were enrolled. 135 (64%) participants were male and 72 (34%) were HIV positive. The pretreatment diagnostic sensitivities of TB-MBLA and Xpert-Ultra were similar (both 99% [95% CI 95–100]) but the specificity was higher for TB-MBLA (90% [83–96]) than for Xpert-Ultra (78% [68–86]). Ten participants were Xpert-Ultra trace positive, eight (80%) of whom were negative by TB-MBLA and MGIT culture. Smear microscopy had lower diagnostic sensitivity (75% [65–83]) but higher specificity (98% [93–100]) than TB-MBLA and Xpert-Ultra. Among participants who were smear microscopy negative, the sensitivity of TB-MBLA was 96% (95 CI 80–100) and was 100% (95% CI 86–100) in those who were HIV positive. 129 (61%) participants were identified as tuberculosis positive by Xpert-Ultra and these individuals were enrolled in the treatment group and monitored for treatment response. According to TB-MBLA, 19 of these patients cleared bacillary load to zero by week 2 of treatment and remained negative throughout the 6-month treatment follow-up. Positivity for tuberculosis decreased with treatment as measured by all tests, but the rate was slower with Xpert-Ultra. Consequently, 31 (33%) of 95 participants were still Xpert-Ultra positive at the end of treatment but were clinically well and negative on TB-MBLA and culture at 6 months of treatment. Two patients were still Xpert-Ultra positive with a further 3 months of post-treatment follow-up. The rate of conversion to negative of the DNA-based Xpert-Ultra was 3·3-times slower than that of the rRNA-based TB-MBLA. Consequently for the same patient, it would take 13 weeks and 52 weeks to reach complete tuberculosis negativity by TB-MBLA and Xpert-Ultra, respectively. Participants who were positive on smear microscopy at 8 weeks, who received an extra month of intensive treatment, had a similar TB-MBLA-measured bacillary load at 8 weeks to those who were smear microscopy negative. TB-MBLA has a similar performance to Xpert-Ultra for pretreatment diagnosis of tuberculosis, but is more accurate at detecting and characterising the response to treatment than Xpert-Ultra and standard-of-care smear microscopy. European and Developing Countries Clinical Trials Partnership, Makerere University Research and Innovation Fund, US National Institutes of Health.Item Airway microbiome signature accurately discriminates Mycobacterium tuberculosis infection status(Elsevier Inc, 2024-06) Kayongo, Alex; Ntayi, Moses Levi; Olweny, Geoffrey; Kyalo, Edward; Ndawula, Josephine; Ssengooba, Willy; Kigozi, Edgar; Kalyesubula, Robert; Munana, Richard; Namaganda, Jesca; Caroline, Musiime; Sekibira, Rogers; Bagaya, Bernard Sentalo; Kateete, David Patrick; Joloba, Moses Lutaakome; Jjingo, Daudi; Sande, Obondo James; Mayanja-Kizza, HarrietAbstract Mycobacterium tuberculosis remains one of the deadliest infectious agents globally. Amidst efforts to control TB, long treatment duration, drug toxicity, and resistance underscore the need for novel therapeutic strategies. Despite advances in understanding the interplay between microbiome and disease in humans, the specific role of the microbiome in predicting disease susceptibility and discriminating infection status in tuberculosis still needs to be fully investigated. We investigated the impact of M.tb infection and M.tb-specific IFNγ immune responses on airway microbiome diversity by performing TB GeneXpert and QuantiFERON-GOLD assays during the follow-up phase of a longitudinal HIV-Lung Microbiome cohort of individuals recruited from two large independent cohorts in rural Uganda. M.tb rather than IFNγ immune response mainly drove a significant reduction in airway microbiome diversity. A microbiome signature comprising Streptococcus, Neisseria, Fusobacterium, Prevotella, Schaalia, Actinomyces, Cutibacterium, Brevibacillus, Microbacterium, and Beijerinckiacea accurately discriminated active TB from Latent TB and M.tb-uninfected individuals. [Display omitted] •M.tb infection drives a significant reduction in airway microbiome diversity•M.tb-specific IFNg does not directly impact airway microbiome diversity•Airway microbiome signature discriminates active TB from LTBI and uninfected states•LTBI and M.tb-uninfected states display similar airway microbiome diversity Microbiology; Bacteriology; MicrobiomeItem Antimycobacterial Activity of the Extract and Isolated Compounds From the Stem Bark of Zanthoxylum leprieurii Guill. and Perr.(Natural Product Communications, 2021) Oloya, Benson; Namukobe, Jane; Heydenreich, Matthias; Ssengooba, Willy; Schmidt, Bernd; Byamukama, RobertZanthoxylum leprieurii Guill. and Perr. (Rutaceae) stem bark is used locally in Uganda for treating tuberculosis (TB) and cough-related infections. Lupeol (1), sesamin (2), trans-fagaramide (3), arnottianamide (4), (S)-marmesinin (5), and hesperidin (6) were isolated from the chloroform/methanol (1:1) extract of Z. leprieurii stem bark. Their structures were elucidated using spectroscopic techniques and by comparison with literature data. Furthermore, the extract and isolated compounds were subjected to antimycobacterial activity. The extract exhibited moderate activity against the susceptible (H37Rv) TB strain, but weak activity against the multidrug resistant (MDR)-TB strain with minimum inhibitory concentrations (MICs) of 586.0 and 1172.0 μg/mL, respectively. Compound 3 (trans-fagaramide) showed significant antimycobacterial activity against the susceptible (H37Rv) TB strain (MIC 6 μg/mL), but moderate activity against the MDR-TB strain (MIC 12.2 μg/mL). Compounds 2, 5, 6, and 1 showed moderate activitiesagainst the susceptible (H37Rv) strain (MIC 12.2-98.0 μg/mL) and moderate to weak activities against theMDR-TB strain (MIC24.4-195.0 μg/mL). This study reports for the first time the isolation of compounds 1 to 6 from the stem bark of Z leprieurii. trans-Fagaramide (3) may present a vital template in pursuit of novel and highly effective TB drugsItem Assessing a transmission network of Mycobacterium tuberculosis in an African city using single nucleotide polymorphism threshold analysis(MicrobiologyOpen, 2021) Yassine, Edriss; Galiwango, Ronald; Ssengooba, Willy; Ashaba, Fred; Joloba, Moses L.; Zalwango, Sarah; Whalen, Christopher C.; Quinn, FrederickTuberculosis (TB) is the leading cause of death in humans by a single infectious agent worldwide with approximately two billion humans latently infected with the bacterium Mycobacterium tuberculosis. Currently, the accepted method for controlling the disease is Tuberculosis Directly Observed Treatment Shortcourse (TB-DOTS). This program is not preventative and individuals may transmit disease before diagnosis, thus better understanding of disease transmission is essential. Using whole-genome sequencing and single nucleotide polymorphism analysis, we analyzed genomes of 145 M. tuberculosis clinical isolates from active TB cases from the Rubaga Division of Kampala, Uganda. We established that these isolates grouped into M. tuberculosis complex (MTBC) lineages 1, 2, 3, and 4, with the most isolates grouping into lineage 4. Possible transmission pairs containing ≤12 SNPs were identified in lineages 1, 3, and 4 with the prevailing transmission in lineages 3 and 4. Furthermore, investigating DNA codon changes as a result of specific SNPs in prominent virulence genes including plcA and plcB could indicate potentially important modifications in protein function. Incorporating this analysis with corresponding epidemiological data may provide a blueprint for the integration of public health interventions to decrease TB transmission in a region.Item Baseline Xpert MTB/RIF ct values predict sputum conversion during the intensive phase of anti-TB treatment in HIV infected patients in Kampala, Uganda: a retrospective study(BMC Infectious Diseases, 2021) Namugenyi, Juliet; Musaazi, Joseph; Katamba, Achilles; Kalyango, Joan; Sendaula, Emmanuel; Kambugu, Andrew; Fehr, Jan; Castelnouvo, Barbara; Manabe, Yukari C.; Ssengooba, Willy; Sekaggya-Wiltshire, ChristineIn resource-limited settings, sputum smear conversion is used to document treatment response. Many People living with HIV (PLHIV) are smear-negative at baseline. The Xpert MTB/RIF test can indirectly measure bacterial load through cycle threshold (ct) values. This study aimed to determine if baseline Xpert MTB/RIF could predict time to culture negativity in PLHIV with newly diagnosed TB. Methods: A subset of 138 PLHIV from the ‘SOUTH’ study on outcomes related to TB and antiretroviral drug concentrations were included. Bacterial load was estimated by Mycobacterium Growth Indicator Tubes (MGIT) culture time-to-positivity (TTP) and Lowenstein Jensen (LJ) colony counts. Changes in TTP and colony counts were analyzed with Poisson Generalised Estimating Equations (GEE) and multilevel ordered logistic regression models, respectively, while time to culture negativity analysed with Cox proportional hazard models. ROC curves were used to explore the accuracy of the ct value in predicting culture negativity. Results: A total of 81 patients (58.7%) were males, median age 34 (IQR 29 ̶ 40) years, median CD4 cell count of 180 (IQR 68 ̶345) cells/μL and 77.5% were ART naive. The median baseline ct value was 25.1 (IQR 21.0 ̶ 30.1). A unit Increase in the ct value was associated with a 5% (IRR = 1.05 95% CI 1.04 ̶ 1.06) and 3% (IRR = 1.03 95% CI 1.03 ̶ 1.04) increase in TTP at week 2 and 4 respectively. With LJ culture, a patient’s colony grade was reduced by 0.86 times (0R = 0.86 95% CI 0.74 ̶ 0.97) at week 2 and 0.84 times (OR = 0.84 95% CI 0.79 ̶ 0.95 P = 0.002) at week 4 for every unit increase in the baseline ct value. There was a 3% higher likelihood of earlier conversion to negativity for every unit increase in the ct value. A ct cut point ≥28 best predicted culture negativity at week 4 with a sensitivity of 91. 7% & specificity 53.7% while a cut point ≥23 best predicted culture negativity at week 8. Conclusion: Baseline Xpert MTB/RIF ct values predict sputum conversion in PLHIV on anti-TB treatment. Surrogate biomarkers for sputum conversion in PLHIV are still a research priority.Item Burden of tuberculosis disease among adolescents in a rural cohort in Eastern Uganda(BMC Infectious Diseases,, 2013) Waako, James; Verver, Suzanne; Wajja, Anne; Ssengooba, Willy; Joloba, Moses L; Colebunders, Robert; Musoke, Philippa; Mayanja-Kizza, HarrietBackground: The world health organization (WHO) declared tuberculosis (TB) a global emergency, mainly affecting people in sub-Saharan Africa. However there is little data about the burden of TB among adolescents. We estimated the prevalence and incidence of TB and assessed factors associated with TB among adolescents aged 12–18 years in a rural population in Uganda in order to prepare the site for phase III clinical trials with novel TB vaccines among adolescents. Methods: In a prospective cohort study, we recruited 5000 adolescents and followed them actively, every 6 months, for 1–2 years. Participants suspected of having TB were those who had any of; TB signs and symptoms, history of TB contact or a positive tuberculin skin test (TST) of ≥10 mm. Laboratory investigations included sputum smear microscopy and culture. Results: Of the 5000 participants, eight culture confirmed cases of TB were found at baseline: a prevalence of 160/100,000 (95% confidence interval (CI), 69–315). There were 13 incident TB cases detected in an average of 1.1 person years: an incidence of 235/100,000 person years (95% CI, 125–402). None of the confirmed TB cases were HIV infected. Predictors for prevalent TB disease were: a history of TB contact and a cough ≥ 2 weeks at baseline and being out of school, while the only predictor for incident TB was a positive TST during follow-up. Conclusion: The TB incidence among adolescents in this rural part of Uganda seemed too low for a phase III TB vaccine trial. However, the study site demonstrated capability to handle a large number of participants with minimal loss to follow-up and its suitability for future clinical trials. Improved contact tracing in TB program activities is likely to increase TB case detection among adolescents. Future studies should explore possible pockets of higher TB incidence in urban areas and among out of school youthItem Cardiovascular risk factors among people with drug-resistant tuberculosis in Uganda(BMC Cardiovascular Disorders, 2022) Baruch Baluku, Joseph; Nabwana, Martin; Nalunjogi, Joanitah; Muttamba, Winters; Mubangizi, Ivan; Nakiyingi, Lydia; Ssengooba, Willy; Olum, Ronald; Bongomin, Felix; Andia-Biraro, Irene; Worodria, WilliamTuberculosis (TB) and its risk factors are independently associated with cardiovascular disease (CVD). We determined the prevalence and associations of CVD risk factors among people with drug-resistant tuberculosis (DRTB) in Uganda. Methods In this cross-sectional study, we enrolled people with microbiologically confirmed DRTB at four treatment sites in Uganda between July to December 2021. The studied CVD risk factors were any history of cigarette smoking, diabetes mellitus (DM) hypertension, high body mass index (BMI), central obesity and dyslipidaemia. We used modified Poisson regression models with robust standard errors to determine factors independently associated with each of dyslipidaemia, hypertension, and central obesity. Results Among 212 participants, 118 (55.7%) had HIV. Overall, 196 (92.5%, 95% confidence interval (CI) 88.0-95.3) had ≥ 1 CVD risk factor. The prevalence; 95% CI of individual CVD risk factors was: dyslipidaemia (62.5%; 55.4–69.1), hypertension (40.6%; 33.8–47.9), central obesity (39.3%; 32.9–46.1), smoking (36.3%; 30.1–43.1), high BMI (8.0%; 5.0–12.8) and DM (6.5%; 3.7–11.1). Dyslipidaemia was associated with an increase in glycated haemoglobin (adjusted prevalence ratio (aPR) 1.14, 95%CI 1.06–1.22). Hypertension was associated with rural residence (aPR 1.89, 95% CI 1.14– 3.14) and previous history of smoking (aPR 0.46, 95% CI 0.21–0.98). Central obesity was associated with increasing age (aPR 1.02, 95%CI 1.00–1.03), and elevated diastolic blood pressure (aPR 1.03 95%CI 1.00–1.06). Conclusion There is a high prevalence of CVD risk factors among people with DRTB in Uganda, of which dyslipidaemia is the commonest. We recommend integrated services for identification and management of CVD risk factors in DRTB.Item Comparison of GeneXpert cycle threshold values with smear microscopy and culture as a measure of mycobacterial burden in five regional referral hospitals of Uganda- A cross-sectional study(PLoS ONE, 2019) Najjingo, Irene; Muttamba, Winters; Kirenga, Bruce J.; Nalunjogi, Joanitah; Bakesiima, Ritah; Olweny, Francis; Lusiba, Pastan; Katamba, Achilles; Joloba, Moses; Ssengooba, WillyDetermining mycobacterial burden is important in assessing severity of disease, evaluating infectiousness and predicting patient treatment outcomes. Mycobacterial burden assessed by smear microscopy grade and time to culture positivity is clearly interpretable by most physicians. GeneXpert (Xpert) has been recommended by WHO as a first line tuberculosis (TB) diagnostic test as an alternative to smear microscopy. Xpert gives cycle threshold (Ct) values as a potential measure for mycobacterial burden. For physicians to clearly interpret Ct values as measures of mycobacterial burden, this study compared the Xpert quantification capabilities with those of smear microscopy and culture. The study also determined a linear relationship between Xpert Ct values and MGIT culture time to positivity (MGIT-TTP) and associated factors. A cut off Ct value which best predicts smear positivity was also determined using the Receiver Operator Curve analysis method. Results Excluding missing results and rifampicin resistant TB cases, a moderately strong correlation of 0.55 between Xpert Ct value and smear grade was obtained. A weak correlation of 0.37 was obtained between Xpert Ct values and MGIT time to positivity while that between Xpert Ct values and LJ culture was 0.34. The Xpert Ct values were found to increase by 2.57 for every unit increase in days to positive and HIV status was significantly associated with this relationship. A cut off Ct value of 23.62 was found to best predict smear positivity regardless of HIV status. Conclusion Our study findings show that GeneXpert Ct values are comparable to smear microscopy as a measure of M. tuberculosis burden and can be used to replace smear microscopy. However, given the low correlation between Xpert Ct value and culture positivity, Xpert Ct values cannot replace culture as a measure of M. tuberculosis burden among TB patients.Item Discordance of the Repeat GeneXpert MTB/RIF Test for Rifampicin Resistance Detection Among Patients Initiating MDR-TB Treatment in Uganda(In Open forum infectious diseases, 2021) Ssengooba, Willy; Iragena, Jean de Dieu; Komakech, Kevin; Okello, Iginitius; Nalunjogi, Joanitah; Katagira, Winceslaus; Kimuli, Ivan; Adakun, Susan; Joloba, Moses L.; Torrea, Gabriela; Kirenga, Bruce J.The Global Laboratory Initiative (GLI) guidelines recommend repeat for GeneXpertMTB/RIF (XpertMTB/RIF) in patients with a low pretest probability of rifampicin resistance (RR). This was a cross-sectional study using results of sputum specimens collected from participants screened for the STREAM 2 trial. We recruited all patients with XpertMTB/RIF RR-TB detected who were referred for RR/multidrug-resistant (MDR) TB treatment initiation at Mulago National Referral Hospital, Kampala, between September 2017 and October 2019. At baseline, smear microscopy, repeat XpertMTB/RIF, Xpert Ultra, and MTBDRplus assays were done on sputum specimens. Culturebased drug susceptibility testing (DST) was performed on discordant specimens. We analyzed the prevalence and factors associated with discordance between initial and repeat XpertMTB/RIF RR and false XpertMTB/RIF RR. False XpertMTB/RIF RR was defined as no RR detected by any of Xpert Ultra, LPA, or culture DST (reference comparator).Item Evaluation of Cepheid’s Xpert MTB/RIF Test on Pleural Fluid in the Diagnosis of Pleural Tuberculosis in a High Prevalence HIV/TB Setting(PLoS ONE, 2014) Lusiba, John K.; Nakiyingi, Lydia; Kirenga, Bruce J.; Kiragga, Agnes; Lukande, Robert; Nsereko, Maria; Ssengooba, Willy; Katamba, Achilles; Worodria, William; Joloba, Moses L.; Mayanja-Kizza, HarrietDiagnosis of pleural tuberculosis (TB) using routinely available diagnostic methods is challenging due to the paucibacillary nature of the disease. Histopathology and pleural tissue TB culture involves an invasive procedure which requires expertise and appropriate equipment, both often unavailable in many health units. Xpert MTB/Rif test has been widely evaluated in sputum specimens but data on its performance in pleural TB is scarce. We evaluated the accuracy of Cepheid’s Xpert MTB/Rif test on pleural fluid in the diagnosis of pleural TB in Uganda. Methods: Consenting adult patients with exudative pleural effusions underwent pleural biopsy and the tissue obtained subjected to Lowenstein-Jensen and mycobacterial growth indicator tube MTB cultures and histopathology. Pleural fluid for Xpert MTB/Rif testing was also collected. Data on socio-demographic characteristics, clinical symptoms, HIV status and CD4 count were also collected. Sensitivity, specificity, positive and negative predictive values of Xpert MTB/Rif test on pleural fluid in pleural TB diagnosis were calculated using pleural tissue MTB culture and/or histopathology as the reference standard. Results: Of the 116 participants [female 50%, mean age 34 (SD 613], 87/116 (75%) had pleural TB confirmed on pleural tissue culture and/or histopathology. The Xpert MTB/Rif test identified 25 (28.7%) of the 87 confirmed pleural TB cases. The sensitivity and specificity of Xpert MTB/Rif test were 28.7% and 96.6% respectively while the positive and negative predictive values were 96.1% and 31.1% respectively. Conclusion: Xpert MTB/Rif test on pleural fluid does not accurately diagnose pleural TB and therefore cannot be used as an initial evaluation test in patients with suspected pleural TB. New, rapid and accurate tests for the diagnosis of pleural TB are still warranted.Item Evaluation Of The Xpert MTB/RIF Test For The Diagnosis Of Childhood Pulmonary Tuberculosis In Uganda: A Cross-Sectional Diagnostic Study(BMC infectious diseases, 2013) Sekadde, Moorine Penninah; Wobudeya, Eric; Joloba, Moses L.; Ssengooba, Willy; Kisembo, Harriet; Kitaka, Sabrina Bakeera; Musoke, PhilippaThe diagnosis of childhood tuberculosis remains a challenge worldwide. The Xpert MTB/RIF test, a rapid mycobacteria tuberculosis diagnostic tool, was recommended for use in children based on data from adult studies. We evaluated the performance of the Xpert MTB/RIF test for the diagnosis of childhood pulmonary tuberculosis using one induced sputum sample and described clinical characteristics associated with a positive Xpert MTB/RIF test. The sputum culture on both Lowenstein-Jensen (LJ) and Mycobacteria Growth Indicator Tube (MGIT) was the gold standard.We consecutively enrolled 250 Ugandan children aged 2 months to 12 years with suspected pulmonary tuberculosis between January 2011 and January 2012 into a cross-sectional diagnostic study at a tertiary care facility in Uganda.We excluded data from 15 children (13 contaminated culture and 2 indeterminate MTB/RIF test results) and analysed 235 records. The Xpert MTB/RIF test had a sensitivity of 79.4% (95% CI 63.2 - 89.7) and a specificity of 96.5% (95% CI 93 – 98.3). The Xpert MTB/RIF test identified 13 of the 14 (92.9%) smear positive-culture positive and 14 of the 20 (70%) smear negative -culture positive cases. The Xpert MTB/RIF identified twice as many cases as the smear microscopy (79.4% Vs 41.2%). Age > 5 years (OR 3.3, 95% CI 1.4 – 7.4, p value 0.005), a history of Tuberculosis (TB) contact (OR 2.4, 95% CI 1.1 – 5.2, p value 0.03), and a positive tuberculin skin test (OR 4.1, 95% CI 1.7 – 10, p value 0.02) was associated with a positive Xpert MTB/RIF test. The median time to TB detection was 49.5 days (IQR 38.4-61.2) for LJ, and 6 days (IQR 5 – 11.5) for MGIT culture and 2 hours for the Xpert MTB/RIF test.The Xpert MTB/RIF test on one sputum sample rapidly and correctly identified the majority of children with culture confirmed pulmonary tuberculosis with high specificity.Item Evaluation of the Xpert MTB/RIF test for the diagnosis of childhood pulmonary tuberculosis in Uganda: a cross-sectional diagnostic study(BioMed Central, 2013) Sekadde, Moorine Penninah; Wobudeya, Eric; Joloba, Moses L.; Ssengooba, Willy; Kisembo, Harriet; Musoke, Philippa; Bakeera-kitaka, SabrinaBackground: The diagnosis of childhood tuberculosis remains a challenge worldwide. The Xpert MTB/RIF test, a rapid mycobacteria tuberculosis diagnostic tool, was recommended for use in children based on data from adult studies. We evaluated the performance of the Xpert MTB/RIF test for the diagnosis of childhood pulmonary tuberculosis using one induced sputum sample and described clinical characteristics associated with a positive Xpert MTB/RIF test. The sputum culture on both Lowenstein-Jensen (LJ) and Mycobacteria Growth Indicator Tube (MGIT) was the gold standard. Methods: We consecutively enrolled 250 Ugandan children aged 2 months to 12 years with suspected pulmonary tuberculosis between January 2011 and January 2012 into a cross-sectional diagnostic study at a tertiary care facility in Uganda. Results: We excluded data from 15 children (13 contaminated culture and 2 indeterminate MTB/RIF test results) and analysed 235 records. The Xpert MTB/RIF test had a sensitivity of 79.4% (95% CI 63.2 - 89.7) and a specificity of 96.5% (95% CI 93 – 98.3). The Xpert MTB/RIF test identified 13 of the 14 (92.9%) smear positive-culture positive and 14 of the 20 (70%) smear negative -culture positive cases. The Xpert MTB/RIF identified twice as many cases as the smear microscopy (79.4% Vs 41.2%). Age>5 years (OR 3.3, 95% CI 1.4 – 7.4, p value 0.005), a history of Tuberculosis (TB) contact (OR 2.4, 95% CI 1.1 – 5.2, p value 0.03), and a positive tuberculin skin test (OR 4.1, 95% CI 1.7 – 10, p value 0.02) was associated with a positive Xpert MTB/RIF test. The median time to TB detection was 49.5 days (IQR 38.4-61.2) for LJ, and 6 days (IQR 5 – 11.5) for MGIT culture and 2 hours for the Xpert MTB/RIF test.Item Feasibility Of Establishing A Biosafety Level 3 Tuberculosis Culture Laboratory Of Acceptable Quality Standards In A Resource-Limited Setting: An Experience From Uganda(Health research policy and systems, 2015) Ssengooba, Willy; Gelderbloem, Sebastian J.; Mboowa, Gerald; Wajja, Anne; Namaganda, Carolyn; Musoke, Philippa; Kizza, Harriet Mayanja; Joloba, Moses LutaakomeDespite the recent innovations in tuberculosis (TB) and multi-drug resistant TB (MDR-TB) diagnosis, culture remains vital for difficult-to-diagnose patients, baseline and end-point determination for novel vaccines and drug trials. Herein, we share our experience of establishing a BSL-3 culture facility in Uganda as well as 3-years performance indicators and post-TB vaccine trials (pioneer) and funding experience of sustaining such a facility.Between September 2008 and April 2009, the laboratory was set-up with financial support from external partners. After an initial procedure validation phase in parallel with the National TB Reference Laboratory (NTRL) and legal approvals, the laboratory registered for external quality assessment (EQA) from the NTRL, WHO, National Health Laboratories Services (NHLS), and the College of American Pathologists (CAP). The laboratory also instituted a functional quality management system (QMS). Pioneer funding ended in 2012 and the laboratory remained in self-sustainability mode.The laboratory achieved internationally acceptable standards in both structural and biosafety requirements. Of the 14 patient samples analyzed in the procedural validation phase, agreement for all tests with NTRL was 90% (P <0.01). It started full operations in October 2009 performing smear microscopy, culture, identification, and drug susceptibility testing (DST). The annual culture workload was 7,636, 10,242, and 2,712 inoculations for the years 2010, 2011, and 2012, respectively. Other performance indicators of TB culture laboratories were also monitored. Scores from EQA panels included smear microscopy >80% in all years from NTRL, CAP, and NHLS, and culture was 100% for CAP panels and above regional average scores for all years with NHLS. Quarterly DST scores from WHO-EQA ranged from 78% to 100% in 2010, 80% to 100% in 2011, and 90 to 100% in 2012.From our experience, it is feasible to set-up a BSL-3 TB culture laboratory with acceptable quality performance standards in resource-limited countries. With the demonstrated quality of work, the laboratory attracted more research groups and post-pioneer funding, which helped to ensure sustainability. The high skilled experts in this research laboratory also continue to provide an excellent resource for the needed national discussion of the laboratory and quality management systems.Item Health seeking behavior among individuals presenting with chronic cough at referral hospitals in Uganda; Missed opportunity for early tuberculosis diagnosis(PLoS ONE, 2019) Muttamba, Winters; Ssengooba, Willy; Kirenga, Bruce; Sekibira, Rogers; Walusimbi, Simon; Katamba, Achilles; Joloba, MosesTuberculosis (TB) is the 9th leading cause of death from a single infectious agent. Patients live in a complex health care system with both formal and informal providers, and it is important that a TB diagnosis is not missed at the first interaction with the health care system. In this study, we highlight the health seeking behavior of patients and missed opportunities for early TB diagnosis for which interventions could be instituted to ensure early TB diagnosis and prompt TB treatment initiation. Methods This study was nested in a cross-sectional study that assessed the accuracy of different Xpert MTB/Rif implementation strategies in programmatic settings at the referral hospitals in Uganda. We documented the symptom profile of presumptive TB patients and assessed the health seeking behavior of those with chronic cough by calculating proportion of patients that visited each type of health facility and further calculated the odds of being TB positive given the type of health facility initially visited for consultation. Results A total of 1,863 presumptive TB patients were enrolled of which 979 (54.5%) were male, and 1795 (99.9%) had chronic cough. A total of 1352 (75.4%) had previously sought care for chronic cough, with 805 (59.6%) seeking care from a public health facility followed by private health facility (289; 21.4%). Up to 182 (13.5%) patients visited a drug store for chronic cough. Patients whose first contact was a private health facility were more likely to have a positive GeneXpert test (adjOR 1.4, 95% CI: 1.0–1.9; p = 0.047). Conclusions Chronic cough is a main symptom for many of the presumptive TB patients presenting at referral hospitals, with several patients having to visit the health system more than once before a TB diagnosis is made. This suggests the need for patients to be thoroughly evaluated at first interface with the health care system to ensure prompt diagnosis and treatment initiation. Improved TB diagnosis possibly with the GeneXpert test, at first contact with the health care system has potential to increase TB case finding and break the transmission cycle in the community.Item High Incidence Of Pulmonary Tuberculosis In Children Admitted With Severe Pneumonia In Uganda(BMC pediatrics, 2013) Nantongo, Josephine M.; Wobudeya, Eric; Mupere, Ezekiel; Joloba, Moses; Ssengooba, Willy; Kisembo, Harriet N.; Lubega, Irene R.; Musoke, Philippa M.A high prevalence of tuberculosis (TB) in children presenting with severe pneumonia has previously been reported in South Africa. However, little is known about TB among children with pneumonia in Uganda and other resource limited countries. Moreover, TB is associated with high morbidity and mortality among such children. We conducted this study to establish the burden of pulmonary TB in children admitted with severe pneumonia in our setting.A cross-sectional study was conducted at Mulago, a National Referral and teaching hospital in Uganda. Hospitalised children 2 months to 12 years of age with severe pneumonia based on WHO case definition were enrolledfrom February to June 2011. Children with a previous TB diagnosis or receiving anti-TB treatment were excluded. Each child was screened for TB using Tuberculin skin test, Chest X-ray, induced sputum samples and blood culture for mycobacterium. Sputum smears were examined using fluorescent microscopy, and cultured on both Lowenstein Jensen media (LJ) and Mycobacterial Growth Indicator Tubes (MGIT).Of the 270 children with severe pneumonia who were recruited over a 5-month period in 2011, the incidence ratio of pulmonary TB in children admitted with severe pneumonia was 18.9% (95% CI 14.6 – 23.9). The proportion of culture confirmed PTB was 6.3% (95% CI 3.8 – 9.7). Age group under 1 year and 1 to 5 years (OR 2.8 (95% CI 1.7 – 7.4) and OR 2.4 (95% CI 1.05 – 5.9) respectively) were more likely to be associated with pulmonary TB compared to those children over 5 years of age. A history of TB smear positive contact was associated with pulmonary TB (OR 3.0 (95% CI 1.3–6.5).We found a high burden of pulmonary TB in children admitted with severe pneumonia. These data highlight the need for TB screening in children admitted with severe pneumonia so as to improve TB case finding and child survival.Item Incremental Yield of Serial Sputum Cultures for Diagnosis of Tuberculosis among HIV Infected Smear Negative Pulmonary TB Suspects in Kampala, Uganda(PLoS One, 2012) Ssengooba, Willy; Kiwanuka, Noah; Kateete, David P.; Katamba, Achilles; Joloba, Moses L.Sputum culture is the gold standard for diagnosis of pulmonary tuberculosis (PTB). Although mostly used for research, culture is recommended by the World Health Organization for TB diagnosis among HIV infected smear negative PTB suspects. Even then, the number of sputum samples required remains unspecified. Here, we determined the Incremental Yield (IY) and number of samples required to diagnose an additional PTB case upon second and third serial sputum culture. Methods/Findings: This was a cross sectional study done between January and March 2011. Serial sputum samples were provided by participants within two days and cultured using Lowenstein Jensen (LJ) and Mycobacteria Growth Indicator Tube (MGIT) methods. A PTB case was defined as a positive culture on either one or both methods. The IY from the second and third serial cultures was determined and the reciprocal of the product of the fractions of IY provided the number of samples required for an additional PTB case. Of the 170 smear negative PTB suspects, 62 (36.5%) met the case definition. The IY of the second sample culture was 12.7%, 23.6% and 12.6% and for the third sample culture was 6.8%, 7.5% and 7.3% with LJ, MGIT and LJ or MGIT, respectively. The number of samples required for an additional PTB case and 95% CI upon the second sample culture were 29.9 (16.6, 156.5), 11.3 (7.6, 21.9) and 20.8 (12.5, 62.7); while for the third sample culture were 55.6 (26.4, 500.4), 35.7 (19.0, 313.8) and 36.1 (19.1, 330.9) by LJ, MGIT and LJ or MGIT respectively. Conclusions/Significance: Among HIV infected smear negative PTB suspects in Kampala, 93% of PTB cases are diagnosed upon the second serial sputum culture. The number of cultures needed to diagnose an additional PTB case, ranges from 11–30 and 35–56 by the second and third sputum samples, respectively.Item Molecular Epidemiology, Drug Susceptibility and Economic Aspects of Tuberculosis in Mubende District, Uganda(PLoS ONE, 2013) Muwonge, Adrian; Malama, Sydney; Johansen, Tone B.; Kankya, Clovice; Biffa, Demelash; Ssengooba, Willy; Godfroid, Jacques; Djønne, Berit; Skjerve, EysteinTuberculosis (TB) remains a global public health problem whose effects have major impact in developing countries like Uganda. This study aimed at investigating genotypic characteristics and drug resistance profiles of Mycobacterium tuberculosis isolated from suspected TB patients. Furthermore, risk factors and economic burdens that could affect the current control strategies were studied. Methods: TB suspected patients were examined in a cross-sectional study at the Mubende regional referral hospital between February and July 2011. A questionnaire was administered to each patient to obtain information associated with TB prevalence. Isolates of M. tuberculosis recovered during sampling were examined for drug resistance to first line anti-TB drugs using the BACTEC-MGIT960TMsystem. All isolates were further characterized using deletion analysis, spoligotyping and MIRU-VNTR analysis. Data were analyzed using different software; MIRU-VNTR plus, SITVITWEB, BioNumerics and multivariable regression models. Results: M. tuberculosis was isolated from 74 out of 344 patients, 48 of these were co-infected with HIV. Results from the questionnaire showed that previously treated TB, co-infection with HIV, cigarette smoking, and overcrowding were risk factors associated with TB, while high medical related transport bills were identified as an economic burden. Out of the 67 isolates that gave interpretable results, 23 different spoligopatterns were detected, nine of which were novel patterns. T2 with the sub types Uganda-I and Uganda-II was the most predominant lineage detected. Antibiotic resistance was detected in 19% and multidrug resistance was detected in 3% of the isolates. Conclusion: The study detected M. tuberculosis from 21% of examined TB patients, 62% of whom were also HIV positive. There is a heterogeneous pool of genotypes that circulate in this area, with the T2 lineage being the most predominant. High medical related transport bills and drug resistance could undermine the usefulness of the current TB strategic interventions.Item Molecular investigation of multiple strain infections in patients with tuberculosis in Mubende district, Uganda(Infection, Genetics and Evolution, 2013) Muwonge, Adrian; Kankya, Clovice; Olea-Popelka, Francisco; Biffa, Demelash; Ssengooba, Willy; Berit, Djønne; Skjerve, Eystein; Johansen, Tone B.Multiple strain tuberculosis (TB) infections are now an acceptable facet of tuberculosis epidemiology. Identification of patients infected with more than one strain gives an insight in disease dynamics at individual and population level. This study therefore aimed at identifying multiple strain infections among TB infected patients. Furthermore, to determine factors associated with multiple strain infections in Mubende district of Uganda. A total of 72 Mycobacterium tuberculosis isolates from patients at Mubende regional referral hospital were characterized using 15 loci MIRU-VNTR, Spoligotyping and deletion analysis. Genotypic and epidemiological data were analyzed using MIRU-VNTR plus, Bionumerics software version 6.1 and an exact logistic regression model respectively. Eight (11.1%) of the 72 patients had mixed TB infections. Five were exclusively pulmonary mixed infections while three had both pulmonary and extra-pulmonary infections (Compartmentalized TB infections). Unlike previous studies that have linked this phenomenon to Beijing strains, multiple strains in this study belonged to T2-Uganda, X2 and T1 lineages. Two of the pulmonary mixed infections were resistant to rifampicin or isoniazid. All except one were HIV positive, newly diagnosed cases and urban residents of Mubende district. The study revealed that one in nine urban dwelling, HIV/TB co-infected patient were infected with more than one M. tuberculosis strains. The molecular findings give indications of a vital component of the disease dynamics that is most likely under looked at clinical level.Item Mycobacteriophages Exhibit Antibiofilm Activity at High Multiplicities of Infection(2022) Ssengooba, Willy; Kamya, Deus; Nakavuma, Jesca; Achan, Beatrice; Semanda, JosephBiofilm formation has been shown to be a very effective survival mechanism used by many bacteria pathogens, including Mycobacterium tuberculosis (Mtb). However, unlike other bacteria, mycobacterial biofilms tend to be very rich in lipids, and this accords them much more resilience than their carbohydratebased counterparts’. Mycobacteriophage therapy, as an up-and-coming technology, is envisaged to revolutionize the treatment of tuberculosis (TB), particularly involving antibiotic-resistant Mtb. Antibiofilm activity, therefore, is a highly sought-after characteristic of mycobacteriophages intended for therapeutic use. Here we investigated the in-vitro activity of a three-phage cocktail against biofilms of forty-six clinically isolated Mtb using the MBEC biofilm device. We demonstrate that multiplicity of infection and the age of the biofilms are significant determinants of phage antibiofilm activity. Furthermore, based on our host range data, we hypothesize that mycobacteriophages might have a preference for Mtb hosts from pulmonary infection sites compared to those from extrapulmonary sites. If accurate, this finding could have profound implications for both diagnostic and therapeutic applications of mycobacteriophages. Overall, our findings demonstrate the antibiofilm potential of mycobacteriophages and continue to endorse mycobacteriophage therapy as a treatment alternative to our failing antibiotic arsenal. We recommend further investigations to; understand the basis of the observed host preference in mycobacteriophages, evaluate combinatorial therapy of phages and antibiotics, and screen the phages for undesirable genes.