Browsing by Author "Kyobe, Samuel"
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Item The Collaborative African Genomics Network (CAfGEN): Applying Genomic technologies to probe host factors important to the progression of HIV and HIV-tuberculosis infection in sub-Saharan Africa [version 1; referees: awaiting peer review](AAS open research, 2018) Mboowa, Gerald; Mwesigwa, Savannah; Katagirya, Eric; Retshabile, Gaone; Mlotshwa, Busisiwe C.; Williams, Lesedi; Kekitiinwa, Adeodata; Kateete, David; Wampande, Eddie; Wayengera, Misaki; Nsangi Kintu, Betty; Kisitu, Grace P.; Kyobe, Samuel; Brown, Chester W.; Hanchard, Neil A.; Mardon, Graeme; Joloba, Moses; Anabwani, Gabriel; Pettitt, Ed; Tsimako-Johnstone, Masego; Kasvosve, Ishmael; Maplanka, Koketso; Mpoloka, Sununguko W.; Hlatshwayo, Makhosazana; Matshaba, MogomotsiThe Human Heredity and Health in Africa consortium (H3Africa) was conceived to facilitate the application of genomics technologies to improve health across Africa. Here, we describe how the Collaborative African Genomics Network (CAfGEN) of the H3Africa consortium is using genomics to probe host genetic factors important to the progression of HIV and HIV-tuberculosis (TB) coinfection in sub-Saharan Africa. Methods: CAfGEN is an H3Africa collaborative centre comprising expertise from the University of Botswana; Makerere University; Baylor College of vItem The collaborative African genomics network training program: a trainee perspective on training the next generation of African scientists(Genetics in Medicine, 2017) Mlotshwa, Busisiwe C.; Mwesigwa, Savannah; Mboowa, Gerald; Williams, Lesedi; Retshabile, Gaone; Kekitiinwa, Adeodata; Wayengera, Misaki; Kyobe, Samuel; Brown, Chester W.; Hanchard, Neil A.; Mardon, Graeme; Joloba, Moses; Anabwani, Gabriel; Mpoloka, Sununguko W.The Collaborative African Genomics Network (CAf- GEN) aims to establish sustainable genomics research programs in Botswana and Uganda through long-term training of PhD students from these countries at Baylor College of Medicine. Here, we present an overview of the CAfGEN PhD training program alongside trainees’ perspectives on their involvement. Background: Historically, collaborations between high-income countries (HICs) and low- and middle-income countries (LMICs), or North–South collaborations, have been criticized for the lack of a mutually beneficial distribution of resources and research findings, often undermining LMICs. CAfGEN plans to address this imbalance in the genomics field through a program of technology and expertise transfer to the participating LMICs. Methods: An overview of the training program is presented. Trainees from the CAfGEN project summarized their experiences, looking specifically at the training model, benefits of the program, challenges encountered relating to the cultural transition, and program outcomes after the first 2 years. Conclusion: Collaborative training programs like CAfGEN will not only help establish sustainable long-term research initiatives in LMICs but also foster stronger North–South and South–South networks. The CAfGEN model offers a framework for the development of training programs aimed at genomics education for those for whom genomics is not their “first language.”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 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 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 Antimicrobial Susceptibility Patterns of Bacteria from Milkmen and Cows with Clinical Mastitis in and around Kampala, Uganda(PloS one, 2013) Kateete, David Patrick; Kabugo, Usuf; Baluku, Hannington; Nyakarahuka, Luke; Kyobe, Samuel; Okee, Moses; Najjuka, Christine Florence; Joloba, Moses LutaakomeIdentification of pathogens associated with bovine mastitis is helpful in treatment and management decisions. However, such data from sub-Saharan Africa is scarce. Here we describe the distribution and antimicrobial susceptibility patterns of bacteria from cows with clinical mastitis in Kampala, Uganda. Due to high concern of zoonotic infections, isolates from milkmen are also described.Ninety seven milk samples from cows with clinical mastitis and 31 nasal swabs from milkmen were collected (one sample per cow/human). Fifty eight (60%) Gram-positive isolates namely Staphylococci (21), Enterococci (16), Streptococci (13), Lactococci (5), Micrococci (2) and Arcanobacteria (1) were detected in cows; only one grew Staphylococcus aureus. Furthermore, 24 (25%) coliforms namely Escherichia coli (12), Klebsiella oxytoca (5), Proteus vulgaris (2), Serratia (2), Citrobacter (1), Cedecea (1) and Leclercia (1) were identified. From humans, 24 Gram-positive bacteria grew, of which 11 were Staphylococci (35%) including four Staphylococcus aureus. Upon susceptibility testing, methicillin-resistant coagulase-negative staphylococci (CoNS) were prevalent; 57%, 12/21 in cows and 64%, 7/11 in humans. However, methicillin-resistant Staphylococcus aureus was not detected. Furthermore, methicillin and vancomycin resistant CoNS were detected in cows (Staphylococcus hominis, Staphylococcus lugdunensis) and humans (Staphylococcus scuiri). Also, vancomycin and daptomycin resistant Enterococci (Enterococcus faecalis and Enterococcus faecium, respectively) were detected in cows. Coliforms were less resistant with three pan-susceptible isolates. However, multidrug resistant Klebsiella, Proteus, Serratia, Cedecea, and Citrobacter were detected. Lastly, similar species grew from human and bovine samples but on genotyping, the isolates were found to be different. Interestingly, human and bovine Staphylococcus aureus were genetically similar (spa-CC435, spa-type t645 corresponding to ST121) but with different susceptibility patterns.CoNS, Enterococci, Streptococci, and Escherichia coli are the predominant pathogens associated with clinical bovine-mastitis in Kampala, Uganda. Multidrug resistant bacteria are also prevalent. While similar species occurred in humans and cows, transmission was not detected.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.Item Rhomboids of Mycobacteria: Characterization Using an aarA Mutant of Providencia stuartii and Gene Deletion in Mycobacterium smegmatis(Plos One, 2012) Kateete, David Patrick; Katabazi, Fred Ashaba; Okeng, Alfred; Okee, Moses; Musinguzi, Conrad; Asiimwe, Benon Byamugisha; Kyobe, Samuel; Asiimwe, Jeniffer; Boom, W. Henry; Joloba, Moses LutaakomeRhomboids are ubiquitous proteins with unknown roles in mycobacteria. However, bioinformatics suggested putative roles in DNA replication pathways and metabolite transport. Here, mycobacterial rhomboid-encoding genes were characterized; first, using the Providencia stuartii null-rhomboid mutant and then deleted from Mycobacterium smegmatis for additional insight in mycobacteria.Using in silico analysis we identified in M. tuberculosis genome the genes encoding two putative rhomboid proteins; Rv0110 (referred to as “rhomboid protease 1”) and Rv1337 (“rhomboid protease 2”). Genes encoding orthologs of these proteins are widely represented in all mycobacterial species. When transformed into P. stuartii null-rhomboid mutant (ΔaarA), genes encoding mycobacterial orthologs of “rhomboid protease 2” fully restored AarA activity (AarA is the rhomboid protein of P. stuartii). However, most genes encoding mycobacterial “rhomboid protease 1” orthologs did not. Furthermore, upon gene deletion in M. smegmatis, the ΔMSMEG_4904 single mutant (which lost the gene encoding MSMEG_4904, orthologous to Rv1337, “rhomboid protease 2”) formed the least biofilms and was also more susceptible to ciprofloxacin and novobiocin, antimicrobials that inhibit DNA gyrase. However, the ΔMSMEG_5036 single mutant (which lost the gene encoding MSMEG_5036, orthologous to Rv0110, “rhomboid protease 1”) was not as susceptible. Surprisingly, the double rhomboid mutant ΔMSMEG_4904–ΔMSMEG_5036 (which lost genes encoding both homologs) was also not as susceptible suggesting compensatory effects following deletion of both rhomboid-encoding genes. Indeed, transforming the double mutant with a plasmid encoding MSMEG_5036 produced phenotypes of the ΔMSMEG_4904 single mutant (i.e. susceptibility to ciprofloxacin and novobiocin).Mycobacterial rhomboid-encoding genes exhibit differences in complementing aarA whereby it's only genes encoding “rhomboid protease 2” orthologs that fully restore AarA activity. Additionally, gene deletion data suggests inhibition of DNA gyrase by MSMEG_4904; however, the ameliorated effect in the double mutant suggests occurrence of compensatory mechanisms following deletion of genes encoding both rhomboids.Item Unmapped exome reads implicate a role for Anelloviridae in childhood HIV-1 long-term non-progression(NPJ Genomic Medicine, 2021) Mwesigwa, Savannah; Williams, Lesedi; Retshabile, Gaone; Katagirya, Eric; Mboowa, Gerald; Mlotshwa, Busisiwe; Kyobe, Samuel; Kateete, David P.; Mujjwiga Wampande, Eddie; Wayengera, Misaki; Wata Mpoloka, Sununguko; Mirembe, Angella N.; Kasvosve, Ishmael; Morapedi, Koketso; Kisitu, Grace P.; Kekitiinwa, Adeodata R.; Anabwani, Gabriel; Joloba, Moses L.; Matovu, Enock; Mulindwa, Julius; Noyes, Harry; Botha, Gerrit; Brown, Chester W.; Mardon, Graeme; Matshaba, Mogomotsi; Hanchard, Neil A.Human immunodeficiency virus (HIV) infection remains a significant public health burden globally. The role of viral co-infection in the rate of progression of HIV infection has been suggested but not empirically tested, particularly among children. We extracted and classified 42 viral species from whole-exome sequencing (WES) data of 813 HIV-infected children in Botswana and Uganda categorised as either long-term non-progressors (LTNPs) or rapid progressors (RPs). The Ugandan participants had a higher viral community diversity index compared to Batswana (p = 4.6 × 10−13), and viral sequences were more frequently detected among LTNPs than RPs (24% vs 16%; p = 0.008; OR, 1.9; 95% CI, 1.6–2.3), with Anelloviridae showing strong association with LTNP status (p = 3 × 10−4; q = 0.004, OR, 3.99; 95% CI, 1.74–10.25). This trend was still evident when stratified by country, sex, and sequencing platform, and after a logistic regression analysis adjusting for age, sex, country, and the sequencing platform (p = 0.02; q = 0.03; OR, 7.3; 95% CI, 1.6–40.5). Torque teno virus (TTV), which made up 95% of the Anelloviridae reads, has been associated with reduced immune activation. We identify an association between viral co-infection and prolonged AIDs-free survival status that may have utility as a biomarker of LTNP and could provide mechanistic insights to HIV progression in children, demonstrating the added value of interrogating off-target WES reads in cohort studies.Item Whole-Exome Sequencing Reveals Uncaptured Variation and Distinct Ancestry in the Southern African Population of Botswana(The American Journal of Human Genetics, 2018) Retshabile, Gaone; Mlotshwa, Busisiwe C.; Williams, Lesedi; Mwesigwa, Savannah; Mboowa, Gerald; Huang, Zhuoyi; Rustagi, Navin; Swaminathan, Shanker; Katagirya, Eric; Kyobe, Samuel; Wayengera, Misaki; Kisitu, Grace P.; Kateete, David P.; Wampande, Eddie M.; Maplanka, Koketso; Kasvosve, Ishmael; Pettitt, Edward D.; Matshaba, Mogomotsi; Nsangi, Betty; Marape, Marape; Tsimako-Johnstone, Masego; Brown, Chester W.; Yu, Fuli; Kekitiinwa, Adeodata; Joloba, Moses; Mpoloka, Sununguko W.; Mardon, Graeme; Anabwani, Gabriel; Hanchard, Neil A.Large-scale, population-based genomic studies have provided a context for modern medical genetics. Among such studies, however, African populations have remained relatively underrepresented. The breadth of genetic diversity across the African continent argues for an exploration of local genomic context to facilitate burgeoning disease mapping studies in Africa.We sought to characterize genetic variation and to assess population substructure within a cohort of HIV-positive children from Botswana—a Southern African country that is regionally underrepresented in genomic databases. Using whole-exome sequencing data from 164 Batswana and comparisons with 150 similarly sequenced HIV-positive Ugandan children, we found that 13%–25% of variation observed among Batswana was not captured by public databases. Uncaptured variants were significantly enriched (p ¼ 2.2 3 10 16) for coding variants with minor allele frequencies between 1% and 5% and included predicted-damaging non-synonymous variants. Among variants found in public databases, corresponding allele frequencies varied widely, with Botswana having significantly higher allele frequencies among rare (<1%) pathogenic and damaging variants. Batswana clustered with other Southern African populations, but distinctly from 1000 Genomes African populations, and had limited evidence for admixture with extra-continental ancestries. We also observed a surprising lack of genetic substructure in Botswana, despite multiple tribal ethnicities and language groups, alongside a higher degree of relatedness than purported founder populations from the 1000 Genomes project. Our observations reveal a complex, but distinct, ancestral history and genomic architecture among Batswana and suggest that disease mapping within similar Southern African populations will require a deeper repository of genetic variation and allelic dependencies than presently exists.