Browsing by Author "Kigozi, Edgar"
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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 Biobanking: Strengthening Uganda’s Rapid Response to COVID-19 and Other Epidemics(Biopreservation and Biobanking, 2021) Kamulegeya, Rogers; Kateete, David Patrick; Bagaya, Bernard S.; Nasinghe, Emmanuel; Muttamba, Winters; Nsubuga, Gideon; Kigozi, Edgar; Ashaba Katabazi, Fred; Nakwagala, Fred; Kalungi, Sam; Byamugisha, Josaphat; Worodria, William; Magala, Rose; Kirenga, Bruce; Joloba, Moses L.SARS-CoV-2 is a fatal disease of global public health concern. Measures to reduce its spread critically depend on timely and accurate diagnosis of virus-infected individuals. Biobanks can have a pivotal role in elucidating disease etiology, translation, and advancing public health. In this article, we show how a biobank has been a critical resource in the rapid response to coronavirus disease of 2019 (COVID-19) in Uganda. Materials and Methods: The Integrated Biorepository of H3Africa Uganda established a COVID-19 biobank. Standard Operating Procedures for sample and data collection, sample processing, and storage were developed. An e-questionnaire data tool was used to collect sociodemographic factors. Samples were collected at 7-day intervals from patients, analyzed for key parameters, processed, annotated, characterized, and stored at appropriate temperatures. Results: Stored samples have been used in validation of 17 diagnostic kits, the Cepheid Xpert Xpress SARSCoV- 2 assay, as well as a sample pooling technique for mass screening and polymerase chain reaction assay validation. Kits that passed validation were deployed for mass screening boosting early detection, isolation, and treatment of COVID-19 cases. Also, 10 applications from researchers and biotech companies have been received and approved and 4 grants have been awarded Conclusion: The CoV-Bank has proven to be an invaluable resource in the fight against the COVID-19 pandemic in Uganda, as samples have been resources in the validation and development of COVID-19 diagnostic tools, which are important in tracing and isolation of infected cases to confront, delay, and stop the spread of the SARS-CoV-2 virus.Item Exome Sequencing Reveals a Putative Role for HLA-C*03:02 in Control of HIV-1 in African Pediatric Populations(Frontiers in Genetics, 2021) Kyobe, Samuel; Mwesigwa, Savannah; Kisitu, Grace P.; Farirai, John; Katagirya, Eric; Mirembe, Angella N.; Ketumile, Lesego; Wayengera, Misaki; Ashaba Katabazi, Fred; Kigozi, Edgar; Wampande, Edward M.; Retshabile, Gaone; Mlotshwa, Busisiwe C.; Williams, Lesedi; Morapedi, Koketso; Kasvosve, Ishmael; Kyosiimire-Lugemwa, Jacqueline; Nsangi, Betty; Tsimako-Johnstone, Masego; Brown, Chester W.; Joloba, Moses; Anabwani, Gabriel; Bhekumusa, Lukhele; Mpoloka, Sununguko W.; Mardon, Graeme; Matshaba, Mogomotsi; Kekitiinwa, Adeodata; Hanchard, Neil A.Human leucocyte antigen (HLA) class I molecules present endogenously processed antigens to T-cells and have been linked to differences in HIV-1 disease progression. HLA allelotypes show considerable geographical and inter-individual variation, as does the rate of progression of HIV-1 disease, with long-term non-progression (LTNP) of disease having most evidence of an underlying genetic contribution. However, most genetic analyses of LTNP have occurred in adults of European ancestry, limiting the potential transferability of observed associations to diverse populations who carry the burden of disease. This is particularly true of HIV-1 infected children. Here, using exome sequencing (ES) to infer HLA allelotypes, we determine associations with HIV- 1 LTNP in two diverse African pediatric populations. We performed a case-control association study of 394 LTNPs and 420 rapid progressors retrospectively identified from electronic medical records of pediatric HIV-1 populations in Uganda and Botswana. We utilized high-depth ES to perform high-resolution HLA allelotyping and assessed evidence of association between HLA class I alleles and LTNP. Sixteen HLA alleles and haplotypes had significantly different frequencies between Uganda and Botswana, with allelic differences being more prominent in HLA-A compared to HLA-B and C allelotypes. Three HLA allelotypes showed association with LTNP, including a novel association in HLA-C (HLA-B 57:03, aOR 3.21, Pc = 0.0259; B 58:01, aOR 1.89, Pc = 0.033; C 03:02, aOR 4.74, Pc = 0.033). Together, these alleles convey an estimated population attributable risk (PAR) of non-progression of 16.5%. We also observed novel haplotype associations with HLA-B 57:03-C 07:01 (aOR 5.40, Pc = 0.025) and HLA-B 58:01- C 03:02 (aOR 4.88, Pc = 0.011) with a PAR of 9.8%, as well as a previously unreported independent additive effect and heterozygote advantage of HLA-C 03:02 with B 58:01 (aOR 4.15, Pc = 0.005) that appears to limit disease progression, despite weak LD (r2 = 0.18) between these alleles. These associations remained irrespective of gender or country. In one of the largest studies of HIV in Africa, we find evidence of a protective effect of canonical HLA-B alleles and a novel HLA-C association that appears to augment existing HIV-1 control alleles in pediatric populations. Our findings outline the value of using multi-ethnic populations in genetic studies and offer a novel HIV-1 association of relevance to ongoing vaccine studies.Item Frequency and patterns of second-line resistance conferring mutations among MDR-TB isolates resistant to a second-line drug from eSwatini, Somalia and Uganda (2014–2016)(BMC pulmonary medicine, 2019) Kateete, David Patrick; Kamulegeya, Rogers; Kigozi, Edgar; Katabazi, Fred Ashaba; Lukoye, Deus; Sebit, Sindani Ireneaus; Abdi, Hergeye; Arube, Peter; Kasule, George William; Musisi, Kenneth; Dlamini, Myalo Glen; Khumalo, Derrick; Joloba, Moses L.Pulmonary tuberculosis is a leading cause of morbidity and mortality in developing countries. Drug resistance, a huge problem in this contagious disease, is driven by point mutations in the Mycobacterium tuberculosis genome however, their frequencies vary geographically and this affects applicability of molecular diagnostics for rapid detection of resistance. Here, we report the frequency and patterns of mutations associated with resistance to second-line anti-TB drugs in multidrug-resistant (MDR) M. tuberculosis isolates from eSwatini, Somalia and Uganda that were resistant to a second-line anti-TB drug.The quinolone resistance determining region (QRDR) of gyrA/gyrB genes and the drug resistance associated fragment of rrs gene from 80 isolates were sequenced and investigated for presence of drug resistance mutations. Of the 80 isolates, 40 were MDR, of which 28 (70%) were resistant to a second-line anti-TB injectable drug, 18 (45%) were levofloxacin resistant while 12 (30%) were extensively drug resistant (XDR). The remaining 40 isolates were susceptible to anti-TB drugs. MIRU-VNTR analysis was performed for M/XDR isolates.We successfully sub-cultured 38 of the 40 M/XDR isolates. The gyrA resistance mutations (Gly88Ala/Cys/Ala, Ala90Val, Ser91Pro, Asp94Gly/Asn) and gyrB resistance mutations (Asp500His, Asn538Asp) were detected in 72.2% (13/18) and 22.2% (4/18) of the MDR and levofloxacin resistant isolates, respectively. Overall, drug resistance mutations in gyrA/gyrB QRDRs occurred in 77.8% (14/18) of the MDR and levofloxacin resistant isolates. Furthermore, drug resistance mutations a1401g and g1484 t in rrs occurred in 64.3% (18/28) of the MDR isolates resistant to a second-line anti-TB injectable drug. Drug resistance mutations were not detected in drug susceptible isolates.The frequency of resistance mutations to second-line anti-TB drugs in MDR-TB isolates resistant to second line anti-TB drugs from eSwatini, Somalia and Uganda is high, implying that rapid molecular tests are useful in detecting second-line anti-TB drug resistance in those countries. Relatedly, the frequency of fluoroquinolone resistance mutations in gyrB/QRDR is high relative to global estimates, and they occurred independently of gyrA/QRDR mutations implying that their absence in panels of molecular tests for detecting fluoroquinolone resistance may yield false negative results in our setting.Item Genetic Diversity and Acquired Drug Resistance Mutations Detected by Deep Sequencing in Virologic Failures among Antiretroviral Treatment Experienced Human Immunodeficiency Virus-1 Patients in a Pastoralist Region of Ethiopia(Infection and Drug Resistance, 2021) Tachbele, Erdaw; Kyobe, Samuel; Ashaba Katabazi, Fred; Kigozi, Edgar; Mwesigwa, Savannah; Joloba, Moses; Messele, Alebachew; Amogne, Wondwossen; Legesse, Mengistu; Pieper, Rembert; Ameni, GobenaThis 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.Item Operationalization of COVID-19 Rapid Diagnosis Using Xpert® Xpress SARS CoV-2 Assay in Resource-Limited Settings: Early Implementation Lessons From Uganda(Research Square, 2021) Nsawotebba, Andrew; Ibanda, Ivan; Ssentalo Bagaya, Bernard; Nyombi, Abdunoor; Kagirita, Atek; Tugumisirize, Didas; Mujuni, Dennis; Majwala, Robert Kaos; Ocen, Francis; Kabugo, Joel; Adam, Isa; Wekiya, Enock; Munduku, Benoni; Linda, Lillian; Kalyesubula-Kibuuka, Simon; Okiira, Christopher; Kigozi, Edgar; Ogwok, Patrick; Lutakoome Joloba, Moses; Nabadda, Susan; Ssengooba, WillyThe novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) that causes COVID-19 disease is a global challenge. Several countries have adopted testing, isolation, and tracing strategy towards the control of the COVID-19 pandemic, but access to rapid and accurate testing is still a global challenge. The conventional PCR – based assay is the most commonly used test yet it has huge costs, infrastructural, and procurement logistical challenges. The Xpert® Xpress SARS-CoV-2 test is an automated in – vitro diagnostic test for the qualitative detection of nucleic acid from SARS-CoV-2 within a turnaround time of 60 minutes on the widely used GeneXpert Dx Instrument Systems. Here we document the best practices and challenges encountered with the operationalization of Xpert® Xpress SARS-CoV-2 testing in a resource-limited setting. Materials and Methods: The Xpert® Xpress SARS-CoV-2 implementation followed an operational work plan that included; Laboratory COVID-19 policy and planning, situational analysis of the Laboratory network, country Xpert® Xpress SARS-CoV-2 assay verification, and rollout at Mutukula Port Health Laboratory. The Laboratory strategy was based on a set of six objectives; conducting infrastructural modifications, building a strong COVID-19 testing capacity, developing robust Laboratory Quality and Information Management Systems, establishing a Bio-risk management and Bio-banking capacity.Item Pertussis Prevalence and Its Determinants among Children with Persistent Cough in Urban Uganda(PLoS ONE, 2015) Kayina, Vincent; Kyobe, Samuel; Katabazi, Fred A.; Kigozi, Edgar; Okee, Moses; Odongkara, Beatrice; Babikako, Harriet M.; Whalen, Christopher C.; Joloba, Moses L.; Musoke, Philippa M.; Mupere, EzekielWe determined prevalence of pertussis infection and its associated host and environmental factors to generate information that would guide strategies for disease control. Methods In a cross-sectional study, 449 children aged 3 months to 12 years with persistent cough lasting 14 days were enrolled and evaluated for pertussis using DNA polymerase chain reaction (PCR) and ELISA serology tests. Results Pertussis prevalence was 67 (15% (95% Confidence Interval (CI): 12–18)) and 81 (20% (95% CI: 16–24)) by PCR and ELISA, respectively among 449 participating children. The prevalence was highest in children with >59 months of age despite high vaccination coverage of 94% in this age group. Study demographic and clinical characteristics were similar between pertussis and non-pertussis cases. Of the 449 children, 133 (30%) had a coughing household member and 316 (70%) did not. Among 133 children that had a coughing household member, sex of child, sharing bed with a coughing household member and having a coughing individual in the neighborhood were factors associated with pertussis. Children that had shared a bed with a coughing household individual had seven-fold likelihood of having pertussis compared to children that did not (odds ratio (OR) 7.16 (95% CI: 1.24– 41.44)). Among the 316 children that did not have a coughing household member, age <23 months, having or contact with a coughing individual in neighborhood, a residence with one room, and having a caretaker with >40 years of age were the factors associated with pertussis. Age <23months was three times more likely to be associated with pertussis compared to age 24–59 months (OR 2.97 (95% CI: 1.07–8.28)). Conclusion Findings suggest high prevalence of pertussis among children with persistent cough at a health facility and it was marked in children >59 months of age, suggesting the possibility of waning immunity. The factors associated with pertussis varied by presence or absence of a coughing household member.Item Prevalence and determinants of virological failure among adult antiretroviral treatment experienced HIV-1 patients in South Omo, Ethiopia(Ethiopian Journal of Health Development, 2022) Tachbele, Erdaw; Kyobe, Samuel; Ashaba, Fred; Kigozi, Edgar; Mwesigwa, Savannah; Joloba, Moses; Amogne, Wondwossen; Legesse, Mengistu; Peiper, Rembert; Ameni, GobenaVirological failure (VF) is a challenge which hinders the success of the antiretroviral treatment (ART) program. Although viral load is the preferred method used to detect and confirm treatment failure, research into its prevalence and determinants is limited. Objective: This study was conducted to determine the prevalence of virological failure and its determinants among HIV-1 infected adults, who experienced first line ART in South Omo, Ethiopia. Methods: A cross-sectional study was conducted on patients attending ART clinics at Jinka Zonal hospital and four rural health centers found in South Omo. A total of 253 adult patients who were on ART for ≥ 6 months were recruited sequentially from January 2015- December 2016. In addition to the socio-demographic and clinical data, 10 ml of blood was collected for the CD4+ T cell count and the viral load measurements. CD4+T cell count was conducted using the FACS Caliber flow cytometer and the viral load was estimated using a quantitative real time reverse transcriptase polymerase chain reaction (qRT-PCR). Samples with a VL ≥1000 copies/mL were considered as virological failure. Logistic regression analysis was used to identify correlates of virological failure. Results: The median duration of ART was 51 months. About 61% of the participants were females with a mean age of 33.5 years. Majority of the participants (70%) were taking the tenofovir (TDF) based ART, while 30% were taking a zidovudine (AZT) based regimen. Majority (71.9%) of the participants started ART in WHO III/IV stage, with a median base line CD4 count of 239 cell/μL. More than 40% of the participants reported poor ART adherence, and 11% had immunological failure. From a total of 253 patients, 206(81.4 %) [95%CI: 76.7-86.2] had viral suppression, while 47 (18.6%) [95%CI: 13.8-23.3] had virological failure with a mean viral load of 185,506 copies/mL (95%CI: 39083-408100). None of the virological failures were switched to second line ART. According to the multivariate logistic analysis, 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 VF among the study participants. Conclusion: The study revealed a considerable prevalence of virological failures with the associated risk indicators. Based on the results and the difficulty faced, of being unable to place patients who were treatment resistant in second line ART, indicates that immunological and clinical criteria are poor biomarkers of drug switching. Hence, regular virological monitoring should be implemented for better ART treatment outcomes in individuals who are HIV positive.