Publications

An up-to-date list is available on Google Scholar.

2025

1. Nature

   Genomics reveals zoonotic and sustained human Mpox spread in West Africa

   Edyth Parker, Ifeanyi F Omah, Doreen Delia Djuicy, and 59 more authors

   Nature, May 2025

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   Five years before the 2022 multi-country mpox outbreak, Nigeria and Cameroon reported their first cases in over three decades.1,2 While Nigeria’s outbreak is recognized as an ongoing human epidemic, the drivers of Cameroon’s resurgence remain unclear.3,4 The rate of zoonoses remains uncertain in both countries, and gaps in genomic data obscure the timing, zoonotic and geographic origin of mpox virus (MPXV) emergence in humans. To address these uncertainties, we generated 118 MPXV genomes from Nigeria and Cameroon from 2018-2023. Our findings show that, in contrast to Nigeria, cases in Cameroon are the result of repeated zoonoses, with two distinct zoonotic lineages circulating across the Nigeria-Cameroon border. Our findings suggest that shared animal populations in the cross-border forest ecosystems drive virus emergence and spread. Accordingly, we identify the closest zoonotic outgroup to the Nigerian human epidemic lineage (hMPXV-1) in a southern Nigerian border state. We estimate that the shared ancestor of the zoonotic outgroup and hMPXV-1 circulated in animals in southern Nigeria in late 2013. We estimate that hMPXV-1 emerged in humans in August 2014 in the southern Rivers State and circulated undetected for three years. Rivers State acted as the main source of viral spread across the human epidemic. Our study sheds light on MPXV’s recent establishment in the human population and highlights the risk of persistent zoonotic emergence of MPXV in the complex border regions of Cameroon and Nigeria.

2. BMC Inf Dis

   Beyond the fever: shotgun metagenomic sequencing of stool unveils pathogenic players in HIV-infected children with nonmalarial febrile illness

   Patricia Nabisubi, Stephen Kanyerezi, Grace Kebirungi, and 15 more authors

   BMC Infectious Diseases, Jan 2025

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   Background: Non-malarial febrile illnesses (NMFI) pose significant challenges in HIV-infected children, often leading to severe complications and increased morbidity. While traditional diagnostic approaches focus on specific pathogens, shotgun metagenomic sequencing offers a comprehensive tool to explore the microbial landscape underlying NMFI in this vulnerable population ensuring effective management. Methods: In this study, we employed shotgun metagenomics to analyse stool samples from HIV-infected children at the Baylor Children’s Clinic Uganda presenting with non-malarial febrile illness. Samples were collected and subjected to DNA extraction at the Molecular and Genomics Laboratory, Makerere University followed by shotgun metagenomics sequencing at the Chan Zuckerberg Biohub San Francisco. Bioinformatics analysis was conducted to identify and characterise the microbial composition and potential pathogenic taxa associated with NMFI using the CZID pipeline. Results: Our findings reveal a diverse array of microbial taxa in the stool samples of HIV-infected children with NMFI. Importantly, shotgun metagenomics revealed potentially pathogenic players including Trichomonas vaginalis, Candida albicans, Giardia, and Bacteroides in stool from this patient population. This sheds light on the complexities of microbial interactions that potentially underpin non-malarial febrile illness in this group. Taxonomic profiling identified recognised pathogens and comorbidities and revealed possible new correlations with NMFI, shedding light on the pathophysiology of fever in HIV-infected children. Conclusion: Shotgun metagenomics is a valuable method for understanding the gut microbial landscape of NMFI in HIV-infected children, providing a comprehensive approach to pathogen identification and characterisation. By revealing potential pathogenic actors beyond the fever, this work demonstrates how metagenomic sequencing may improve our knowledge of infectious illnesses in vulnerable groups and inspire targeted therapies for better clinical care and outcomes.

3. HIV Res Clin Pract

   Prevalence and predictors of virological failure among the people living with HIV on antiretroviral treatment in East Africa: evidence from a systematic review with meta-analysis and meta-regression of published studies from 2016 to 2023

   Maria Magdalene Namaganda, Hussein Mukasa Kafeero, Joyce Nakatumba Nabende, and 15 more authors

   HIV Research & Clinical Practice, Apr 2025

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   Background: Virological failure (VF) significantly threatens the efficacy of antiretroviral therapy (ART) programs in East Africa. This systematic review and meta-analysis assess the prevalence and predictors of VF among individuals living with HIV. Methods: We searched PubMed, Web of Science, African Journals Online, and EMBASE for relevant studies. Heterogeneity was assessed using the I2 statistic, and random-effects models addressed between-study variability. Publication bias was examined through funnel plots, Egger’s regression, and Begg’s tests. Subgroup analyses and meta-regression explored heterogeneity sources and potential VF predictors. Analyses were conducted using MedCalc version 20.010, adhering to PRISMA 2020 guidelines. Results: Twenty-five records were included, with a sample size of 29,829 people living with HIV on ART. The pooled prevalence of VF in East Africa was 19.4% (95% CI: 15.2%–24.0%), with substantial heterogeneity across studies. Sociodemographic predictors of VF included male sex (30.9%, p < .001), unmarried status (28.2%, p < .001), lower educational attainment (33.0%, p < .001), non-formal employment (47.2%, p < .001), and urban residence (51.2%, p < .001). Clinical factors associated with higher VF rates were ambulatory status (44.7%, p < .001), low CD4 count (35.1%, p < .001), low haemoglobin (52.2%, p < .001), advanced HIV stage III/IV (44.2%, p < .001), HIV/TB co-infection (24.3%, p < .001), and other opportunistic infections (20.5%, p = .008). Treatment-related factors associated with VF were first-line nevirapine-based regimen (27.7%, p = .009) and poor ART adherence (41.76%, p < .001). Conclusion: Sociodemographic factors, advanced HIV disease, co-morbidities, poor adherence, and specific first-line ART regimens are key predictors of virological failure. Targeted, multidisciplinary interventions focusing on routine viral load monitoring, adherence support, and addressing socioeconomic barriers are essential to improve ART outcomes in East Africa.

2024

1. Cell

   Africa in the era of pathogen genomics: Unlocking data barriers

   Gerald Mboowa, Sofonias K Tessema, Alan Christoffels, and 3 more authors

   Cell, Sep 2024

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   Rapid expansion of pathogen sequencing capacity in Africa has led to a paradigm shift from relying on others to locally generating genomic data and sharing it with the global community. However, several barriers remain to be unlocked for timely processing, analysis, dissemination, and effective use of pathogen sequence data for pandemic prevention, preparedness, and response.

2. BMC Gen

   Generalizability of machine learning in predicting antimicrobial resistance in E. coli: a multi-country case study in Africa

   Mike Nsubuga, Ronald Galiwango, Daudi Jjingo, and 1 more author

   BMC Genomics, Mar 2024

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   Antimicrobial resistance (AMR) remains a significant global health threat particularly impacting low- and middle-income countries (LMICs). These regions often grapple with limited healthcare resources and access to advanced diagnostic tools. Consequently, there is a pressing need for innovative approaches that can enhance AMR surveillance and management. Machine learning (ML) though underutilized in these settings, presents a promising avenue. This study leverages ML models trained on whole-genome sequencing data from England, where such data is more readily available, to predict AMR in E. coli, targeting key antibiotics such as ciprofloxacin, ampicillin, and cefotaxime. A crucial part of our work involved the validation of these models using an independent dataset from Africa, specifically from Uganda, Nigeria, and Tanzania, to ascertain their applicability and effectiveness in LMICs.

3. BMC Inf Dis

   Machine learning-based prediction of antibiotic resistance in Mycobacterium tuberculosis clinical isolates from Uganda

   Sandra Ruth Babirye, Mike Nsubuga, Gerald Mboowa, and 3 more authors

   BMC Infectious Diseases, Dec 2024

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   Efforts toward tuberculosis management and control are challenged by the emergence of Mycobacterium tuberculosis (MTB) resistance to existing anti-TB drugs. This study aimed to explore the potential of machine learning algorithms in predicting drug resistance of four anti-TB drugs (rifampicin, isoniazid, streptomycin, and ethambutol) in MTB using whole-genome sequence and clinical data from Uganda. We also assessed the model’s generalizability on another dataset from South Africa.

4. Nat Comm Med

   Inclusiveness of the All of Us Research Program improves polygenic risk scores and fosters genomic medicine for all

   Benson R Kidenya, and Gerald Mboowa

   Communications Medicine, Nov 2024

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   Polygenic risk scores (PRS) show promise but have accuracy disparities across ancestries due to underrepresentation in the existing genomic databases. Here, we outline the initiative of All of Us Research Program in refining PRS and advancing genomic medicine for all.

5. Access Microbiol

   HIV-DRIVES: HIV drug resistance identification, variant evaluation, and surveillance pipeline

   Stephen Kanyerezi, Ivan Sserwadda, Aloysious Ssemaganda, and 11 more authors

   Access Microbiology, Jul 2024

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   The global prevalence of resistance to antiviral drugs combined with antiretroviral therapy (cART) emphasizes the need for continuous monitoring to better understand the dynamics of drug-resistant mutations to guide treatment optimization and patient management as well as check the spread of resistant viral strains. We have recently integrated next-generation sequencing (NGS) into routine HIV drug resistance (HIVDR) monitoring, with key challenges in the bioinformatic analysis and interpretation of the complex data generated, while ensuring data security and privacy for patient information. To address these challenges, here we present HIV-DRIVES (HIV Drug Resistance Identification, Variant Evaluation, and Surveillance), an NGS-HIVDR bioinformatics pipeline that has been developed and validated using Illumina short reads, FASTA, and Sanger ab1. seq files.

6. J Infect Dis

   Varied Prevalence of Antimalarial Drug Resistance Markers in Different Populations of Newly Arrived Refugees in Uganda

   Stephen Tukwasibwe, Shreeya Garg, Thomas Katairo, and 20 more authors

   The Journal of Infectious Diseases, Jun 2024

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   Newly arrived refugees offer insights into malaria epidemiology in their countries of origin. We evaluated asymptomatic refugee children within 7 days of arrival in Uganda from South Sudan and the Democratic Republic of Congo (DRC) in 2022 for parasitemia, parasite species, and Plasmodium falciparum drug resistance markers. Asymptomatic P. falciparum infections were common in both populations. Coinfection with P. malariae was more common in DRC refugees. Prevalences of markers of aminoquinoline resistance (PfCRT K76T, PfMDR1 N86Y) were much higher in South Sudan refugees, of antifolate resistance (PfDHFR C59R and I164L, PfDHPS A437G, K540E, and A581G) much higher in DRC refugees, and of artemisinin partial resistance (ART-R; PfK13 C469Y and A675V) moderate in both populations. Prevalences of most mutations differed from those seen in Ugandans attending health centers near the refugee centers. Refugee evaluations yielded insights into varied malaria epidemiology and identified markers of ART-R in 2 previously little-studied countries.

7. JCM

   CDC Trioplex diagnostic assay underperforms in detection of circulating Chikungunya West African genotype

   Mignane Ndiaye, Mouhamed Kane, Diamilatou Balde, and 15 more authors

   Journal of Clinical Microbiology, Jun 2024

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   Since 2015, the virology laboratory at Institut Pasteur de Dakar (IPD) has conducted real-time molecular diagnostics for arboviruses as part of Senegal’s syndromic sentinel surveillance network. During the largest Chikungunya fever (CF) outbreak in Senegal in late 2023, with 210 confirmed cases in Kédougou and Tambacounda, the IPD evaluated the CDC Trioplex RT-qPCR assay, which detects Zika, Dengue, and Chikungunya viruses. Testing revealed a significant performance delay—an average 7 Ct value—compared to IPD’s in-house assay for 15 CHIKV RNA-positive samples. Whole genome sequencing and in silico analyses identified seven mismatches in the CDC Trioplex assay’s primer and probe binding sites for the CHIKV West Africa (WA) genotype, notably a critical mismatch at the 3’ end of the forward primer. This mismatch reduced elongation efficiency and caused a detection shift of approximately two logs, raising the risk of false negatives, especially for samples with low viral loads (Ct > 28). Conversely, the IPD in-house assay remained effective, with no mismatches detected against CHIKV WA genotype sequences. The findings highlight the need for continuous genomic surveillance and assay validation using region-specific viral strains to ensure diagnostic accuracy during outbreaks.

8. Bioinformatics

   Unlocking the future of complex human diseases prediction: multi-omics risk score breakthrough

   Benson R Kidenya, and Gerald Mboowa

   Frontiers in Bioinformatics, Dec 2024

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   The article "Unlocking the Future of Complex Human Disease Prediction: Multi-Omics Risk Score Breakthrough" discusses the potential of integrating various high-throughput screening technologies—such as genomics, DNA methylomics, metagenomics, transcriptomics, proteomics, and metabolomics—to enhance the prediction of complex human diseases. Traditional polygenic risk scores (PRS), which assess genetic predisposition based on genome-wide association studies, have shown promise in disease prediction but face limitations, especially in diverse populations. The authors advocate for the development of multi-omics risk scores (MoRS) that combine data from multiple omics layers to provide a more comprehensive assessment of disease risk. By integrating information from various biological processes, MoRS can capture the complex interactions between genetics, epigenetics, and environmental factors that contribute to disease development. The article emphasizes the importance of including diverse populations in genomic research to ensure the applicability of MoRS across different genetic backgrounds. Initiatives like the All of Us Research Program and Human Heredity and Health Africa (H3Africa) aim to address this disparity by increasing representation in global genome databases. The authors conclude that the integration of multi-omics data holds significant promise for advancing personalized medicine and improving the prediction and prevention of complex human diseases.

9. Mic Path

   Extracellular hydrolytic enzyme activities and biofilm formation in Candida species isolated from people living with human immunodeficiency virus with oropharyngeal candidiasis at HIV/AIDS clinics in Uganda

   Benson Musinguzi, Andrew Akampurira, Hope Derick, and 11 more authors

   Microbial Pathogenesis, Dec 2024

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   Background: Commensal oral Candida species can become opportunistic and transition to pathogenic causes of oropharyngeal candidiasis (OPC) in individuals with impaired immunity through ecological cues and the expression of extracellular hydrolytic enzyme activities and biofilm formation. Objective: We evaluated phospholipase, proteinase, hemolysin, esterase, and coagulase enzymatic activities and biofilm formation in Candida species isolated from people living with human immunodeficiency virus (PLHIV) with OPC. Methods: Thirty-five Candida isolates from PLHIV with OPC were retrieved from a sample repository and evaluated for phospholipase activity using the egg yolk agar method, proteinase activity using the bovine serum albumin agar method, hemolysin activity using the blood agar plate method, esterase activity using the Tween 80 opacity test medium method, coagulase activity using the classical tube method, and biofilm formation using the microtiter plate assay method in vitro. Results: A total of 35 Candida isolates obtained from PLHIV with OPC were included in this study, and phospholipase and proteinase activities were detected in 33/35 (94.3 %) and 31/35 (88.6 %) Candida isolates, respectively. Up to 25/35 (71.4 %) of the Candida isolates exhibited biofilm formation, whereas esterase activity was demonstrated in 23/35 (65.7 %) of the Candida isolates. Fewer isolates (21/35, 60 %) produced hemolysin, and coagulase production was the least common virulence activity detected in 18/35 (51.4 %) of the Candida isolates. Conclusion: Phospholipase and proteinase activities were the strongest in oropharyngeal Candida species.

10. NMNI

    Whole genome-based characterization of extended-spectrum β-lactamase-producing Enterobacter cloacae from orthopedic patients and environment of a tertiary referral hospital in Tanzania

    Benson R Kidenya, Gerald Mboowa, Ivan Sserwadda, and 6 more authors

    New Microbes and New Infections, Sep 2024

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    Objectives: We investigated the genomic epidemiology of extended-spectrum β-lactamase-producing Enterobacter cloacae (ESBL-Ec) isolates from patients and hospital environment to better understand their distribution to help devising effective strategies for infection prevention and control. Methods: We screened ESBL-Ec at Bugando Medical Center (BMC) in Mwanza, Tanzania. Rectal swabs from orthopedic patients on admission and swabs from the neighboring inanimate environment were collected. Following microbial culture, DNA was extracted from pure ESBL-Ec, and whole-genome sequencing was done. Sequence typing (ST), plasmid replicons, drug resistance, and virulence genes were deciphered using the Rapid Microbial Analysis Pipeline (rMAP). Results: We obtained 209 ESBL isolates, of which 15 (7.2 %) were ESBL-Ec [8 (53.3 %) from patients and 7 (46.7 %) from the environment]. Seven isolates were novel and eight were diverse, each with a unique ST. All isolates harbored two to five β-lactamase genes, with the predominance of bla CTX-M-15 (15/15), bla OXA-1 (14/15), bla TEM (14/15) and bla ACT (12/15). The most common non β-lactam drug resistance genes were aac(3)-IIa (14/15), aac(6’)-Ib-cr (14/15), fosA (14/15), and qnrB1 (12/15), aph(3″)-Ib (10/15) and aph(6)-Id (10/15). Eleven different types of plasmid replicons were identified in 14/15 of the isolates, harboring one to five plasmids, with the most common plasmids being IncFII (11/15) and IncFIB (10/15). All isolates harbored the outer membrane protein (ompA), and curli protein (csg) was in 14/15 isolates. Conclusion: Admitted orthopedic patients and the hospital environment act as a reservoir of ESBL-Ec with diverse STs and endowed with drug resistance and arsenals of virulence genes, calling for their routine screening on admission for mitigation of potential subsequent infections.

11. MedRxiv

    Multicountry genomic analysis underscores regional cholera spread in Africa

    Gerald Mboowa, Nathaniel Lucero Matteson, Collins Kipngetichi Tanui, and 52 more authors

    MedRxiv, Nov 2024

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    Cholera remains a significant public health burden in many countries in sub-Saharan Africa, though the exact mechanisms of bacterial emergence and spread remain largely undefined. We generated genomic data from 728 Vibrio cholerae O1 isolates predominantly collected between 2019-2024 to create the largest dataset of V. cholerae genomes sequenced locally in Africa. This dataset enabled us to interrogate recent patterns of spread, including the rapid circulation of the AFR15 lineage associated with unusually large outbreaks in Southern Africa. We provide evidence for the movement of the AFR15 lineage into new African Member States and confirm previously observed differences in V. cholerae transmission dynamics in West versus East Africa, though cross-border transmission is prevalent on both sides of the continent. Despite observed differences, evolutionary processes are similar across lineages and we find no evidence for significant changes in antimicrobial resistance genotypes. Overall, our findings emphasize the importance of regionally coordinated cross-border surveillance and interventions, while also demonstrating the critical role of locally generated genomic data in understanding the spread of cholera in Africa.

12. MDPI

    Serological Status of Vaccine and Hepatitis B Virus Exposure Among Children Under 5 and Aged 15–17 Years in Kampala, Uganda

    Fahad Muwanda, Edward Kiyonga, Joan Nambafu, and 10 more authors

    Livers, Oct 2024

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    Background: Pediatric hepatitis B virus (HBV) serostatus remains variably characterized, hardly determined at times, or documented as part of national monitoring of the Extended Programs for Immunization (EPI). Methods: We cross-sectionally characterized the seroprevalence of HBV vaccine and/or infection status among 501 and 288 children <5 and 15–17 years old, respectively, in Kawempe Division, Kampala, Uganda, between May and August 2023. These children received HBV vaccination under the Uganda National Extended Program on Immunizations (UNEPI). Samples were qualitatively screened for hepatitis B surface antigen (HBsAg), hepatitis B surface antibody (HBsAb or anti-HBs), hepatitis B e antigen (HBeAg), hepatitis B e antibody (HBeAb or anti-HBe), and for hepatitis B core antibody (HBcAb or anti-HBc) using three different HBV Combo test rapid immunochromatographic diagnostic tests: Nova, Fastep, and Beright. Results: The seroprevalence of HBsAg, anti-HBs, HBeAg, anti-HBe, and anti-HBc was 1.52%, 27.75%, 0.88%, 0.63%, and 0.76%, respectively, for the combined study age groups. The HBsAg seroprevalence of 2.78% was almost 3.5-fold higher among adolescents when compared to the 0.8% observed in the under-5-year-olds. The qualitative seroprevalence of anti-HBs was 33.1% and 18.4% in the under-5 and among the 15–17-year-old study groups, respectively. Conclusions: The proportion of qualitatively detectable anti-HBs in both groups of vaccinated children is low and probably indicates reduced seroprotection. Consequently, a large proportion of children who received the hepatitis B vaccine under UNEPI may be at risk of HBV infection, especially adolescents. A booster dose of the Hepatitis B Vaccine may be required for adolescents.

13. PLOS GPH

    Wastewater metagenomics in Africa: Opportunities and challenges

    Stephen Kanyerezi, Zahra Fatma Guerfali, Abel Abbas Anzaku, and 11 more authors

    PLOS Global Public Health, Dec 2024

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    The advent of metagenomics has dramatically expanded our understanding of microbial communities, particularly through the study of wastewater, which serves as a rich source of microbial data. In Africa, wastewater metagenomics presents unparalleled opportunities for public health monitoring, antimicrobial resistance (AMR) tracking, and the discovery of new microbial species and functions. Utilizing high-throughput sequencing (HTS) technologies, this method allows for direct analysis of nucleic acids from wastewater samples, providing a cost-effective and comprehensive approach for pathogen surveillance. The potential of wastewater metagenomics in Africa is vast. It can revolutionize public health monitoring by acting as an early warning system for infectious disease outbreaks, offering near real-time data to shape effective responses. This is especially critical in densely populated urban areas with poor sanitation, where the risk of disease spread is high. Moreover, this approach enables the detection of emerging pathogens and insights into environmental health. However, the implementation of wastewater metagenomics in Africa faces several challenges. These include variability in wastewater composition due to differing local customs, limited infrastructure for sequencing and data analysis, and a shortage of bioinformatics expertise. Socio-political and ethical issues also complicate data sharing and the equitable distribution of benefits. To overcome these challenges, there is a need to enhance capacity through collaborative training, infrastructural development, and international partnerships. Investing and sustaining local genomics and bioinformatics infrastructure and expertise is crucial. Moreover, establishing robust data governance frameworks and engaging communities are essential for leveraging metagenomics to advance scientific knowledge and deliver tangible health and economic benefits. With strategic planning and collaboration, Africa can harness the transformative potential of wastewater metagenomics to improve disease surveillance, combat AMR, and foster scientific innovation, contributing significantly to sustainable development and improved quality of life.

14. Ann Hum Genet

    The dawn of a cure for sickle cell disease through CRISPR‐based treatment: A critical test of equity in public health genomics

    Gerald Mboowa, Ivan Sserwadda, Stephen Kanyerezi, and 2 more authors

    Annals of Human Genetics, Mar 2024

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    Equity in access to genomic technologies, resources, and products remains a great challenge. This was evident especially during the coronavirus disease 2019 (COVID-19) pandemic when the majority of lower middle-income countries were unable to achieve at least 10% population vaccination coverage during initial COVID-19 vaccine rollouts, despite the rapid development of those vaccines. Sickle cell disease (SCD) is an inherited monogenic red blood cell disorder that affects hemoglobin, the protein that carries oxygen through the body. Globally, the African continent carries the highest burden of SCD with at least 240,000 children born each year with the disease. SCD has evolved from a treatable to a curable disease. Recently, the UK medical regulator approved its cure through clustered regularly interspaced short palindromic repeat (CRISPR)-based treatment, whereas the US Food and Drug Administration has equally approved two SCD gene therapies. This presents a remarkable opportunity to demonstrate equity in public health genomics. This CRISPR-based treatment is expensive and therefore a need for an ambitious action to ensure that they are affordable and accessible where they are needed most and stand to save millions of lives.

15. Diagn Progn Res

    Reported prevalence and comparison of diagnostic approaches for Candida africana: a systematic review with meta-analysis

    Jonani Bwambale, Emmanuel Charles Kasule, Herman Roman Bwire, and 1 more author

    Diagnostic and Prognostic Research, Dec 2024

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    This systematic review and meta-analysis evaluated reported prevalence and diagnostic methods for identifying Candida africana, an opportunistic yeast associated with vaginal and oral candidiasis. A comprehensive literature search yielded 53 studies meeting the inclusion criteria, 2 of which were case studies. The pooled prevalence of C. africana among 20,571 participants was 0.9% (95% CI: 0.7–1.3%), with significant heterogeneity observed (I2 = 79%, p < 0.01). Subgroup analyses revealed regional variations, with North America showing the highest prevalence (4.6%, 95% CI: 1.8–11.2%). The majority 84.52% of the C. africana have been isolated from vaginal samples, 8.37% from oral samples, 3.77% from urine, 2.09% from glans penis swabs, and 0.42% from rectal swabs, nasal swabs, and respiratory tract expectorations respectively. No C. africana has been isolated from nail samples. Hyphal wall protein 1 gene PCR was the most used diagnostic method for identifying C. africana. It has been used to identify 70% of the isolates. A comparison of methods revealed that the Vitek-2 system consistently failed to differentiate C. africana from Candida albicans, whereas MALDI-TOF misidentified several isolates compared with HWP1 PCR. Factors beyond diagnostic methodology may influence C. africana detection rates. We highlight the importance of adapting molecular methods for resource-limited settings or developing equally accurate but more accessible alternatives for the identification and differentiation of highly similar and cryptic Candida species such as C. africana.

16. MedRxiv

    Genomic epidemiology uncovers the timing and origin of the emergence of mpox in humans

    Edyth Parker, Ifeanyi F Omah, Patrick Varilly, and 45 more authors

    MedRxiv, Jun 2024

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    Five years before the 2022–2023 global mpox outbreak Nigeria reported its first cases in nearly 40 years, with the ongoing epidemic since driven by sustained human-to-human transmission. However, limited genomic data has left questions about the timing and origin of the mpox virus’ (MPXV) emergence. Here we generated 112 MPXV genomes from Nigeria from 2021-2023. We identify the closest zoonotic outgroup to the human epidemic in southern Nigeria, and estimate that the lineage transmitting from human-to-human emerged around July 2014, circulating cryptically until detected in September 2017. The epidemic originated in Southern Nigeria, particularly Rivers State, which also acted as a persistent and dominant source of viral dissemination to other states. We show that APOBEC3 activity increased MPXV’s evolutionary rate twenty-fold during human-to-human transmission. We also show how Delphy, a tool for near-real-time Bayesian phylogenetics, can aid rapid outbreak analytics. Our study sheds light on MPXV’s establishment in West Africa before the 2022–2023 global outbreak and highlights the need for improved pathogen surveillance and response.

2023

1. Nature Medicine

   A pan-African pathogen genomics data sharing platform to support disease outbreaks

   Alan Christoffels, Gerald Mboowa, Peter Heusden, and 19 more authors

   Nature Medicine, May 2023

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   High-income countries have a wealth of genomics expertise that can be rapidly activated to deal with disease threats. African countries should invest in a federated data-management system for genomics epidemiology to deal with such threats better.

2. Sci Rep

   A systematic review reveals that African children of 15–17 years demonstrate low hepatitis B vaccine seroprotection rates

   Fahad Muwanda, Hakim Sendagire, Gerald Mboowa, and 5 more authors

   Scientific Reports, Dec 2023

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   Childhood HBV immunization remains globally fundamental to the elimination of hepatitis B virus (HBV). However, monitoring proportions of HBV vaccine seroprotection and their determinants among African Pediatric recipients is crucial. This study sought to verify extent of immune protection accorded by the HBV vaccine in African children of up to 17 years of age by pooling the prevalence of seroprotection reported by primary studies conducted in the Northern, Western, and Southern African regions. We included 19 eligible articles out of the 197 initially downloaded, published from 1999 to 2021 from African Journals Online (AJOL), EMBASE, Scopus, and PubMed. The study protocol was registered with the International Prospective Register of Systematic Reviews (PROSPERO), University of York Centre for Reviews and Dissemination, under the registration number CRD42022361277. Significantly higher (p < 0.0001) proportion of HBV vaccine seroprotection (69.07%) was found among children under 15 years of age than children 15–17 years (32.368%), 95% CI [34.2454–39.0847%]. Whereas successful integration of the HBV vaccine on the extended programs on immunizations (EPI) has been a major achievement in the reduction of HBV infection in Africa, markedly reduced HBV vaccine seroprotection is persistently demonstrated among adolescent children 15–17 years of age. Future studies are required to clarify the need for booster dose vaccination in most at risk populations and age groups.

3. Hosp Infect

   Virulence genes and plasmid replicon profiles of selected β-lactamase-producing Acinetobacter baumannii from orthopaedic patients and the environment in a tertiary referral hospital in Tanzania, East Africa

   Benson R Kidenya, Gerald Mboowa, Ivan Sserwadda, and 6 more authors

   Journal of Hospital Infection, Sep 2023

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   Acinetobacter baumannii has emerged as an important nosocomial pathogen due to its high resistance to multi-drugs and disinfectants plus its ability to survive in hospital environments. Rectal swabs were collected for screening β-lactamases-producing Acinetobacter baumannii among hospitalized orthopedic patients at a tertiary referral hospital in Tanzania. Swabs were also taken from patients’ caretakers, healthcare workers, and the neighboring inanimate environment. A total of 26 confirmed β-lactamases producing Acinetobacter baumannii were isolated, of which 4 representative isolates (two from patients and two from hospital environment) underwent whole-genome sequencing (WGS) to detect sequence types (ST), β-lactamases genes, plasmid replicon types, and virulence genes. All four isolates harbored multiple β-lactamases genes including blaADC-25(3), blaOXA(4), blaCTX-M-15(2) and blaNDM-1(2). Furthermore, isolates harbored virulence genes encoding outer membrane protein (ompA), curli protein (csg), siderophore biosynthesis systems (enterobactin [entABCDEFS, fepABCDG, fes]; yersiniabactin [ybtAEPQSTUX, irp1, irp2, fyuA] and aerobactin [iucABCD, iutA]), transport secretion system type II (T2SS) and type III (T3SS), E. coli common pilus (ecpRABCDE operon), type 1 fimbriae (fim), arylsulfatase (aslA) and adhesions (fedC). Only isolates from patients harbored 4 plasmid replicons each, with the most common plasmid replicons being IncFIA_1; IncY_1 and IncFIB(AP001918)_1. Admitted orthopedic patients and the hospital environment act as a reservoir of multiple β-lactamases producing Acinetobacter baumannii (including those against carbapenems like blaOXA and blaNDM-1) endowed with virulence genes, highlighting the necessity to routinely screening of orthopedic patients with open fractures on admission as well as reinforcing infection prevention and control measures to reduce the dissemination of nosocomial infection within the hospital environment.

4. MDPI

   Molecular Epidemiology and Diversity of SARS-CoV-2 in Ethiopia, 2020–2022

   Abay Sisay, Derek Tshiabuila, Stephanie Wyk, and 23 more authors

   Genes, Mar 2023

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   Ethiopia is the second most populous country in Africa and the sixth most affected by COVID-19 on the continent. Despite having experienced five infection waves, >499,000 cases, and  7500 COVID-19-related deaths as of January 2023, there is still no detailed genomic epidemiological report on the introduction and spread of SARS-CoV-2 in Ethiopia. In this study, we reconstructed and elucidated the COVID-19 epidemic dynamics. Specifically, we investigated the introduction, local transmission, ongoing evolution, and spread of SARS-CoV-2 during the first four infection waves using 353 high-quality near-whole genomes sampled in Ethiopia. Our results show that whereas viral introductions seeded the first wave, subsequent waves were seeded by local transmission. The B.1.480 lineage emerged in the first wave and notably remained in circulation even after the emergence of the Alpha variant. The B.1.480 was outcompeted by the Delta variant. Notably, Ethiopia’s lack of local sequencing capacity was further limited by sporadic, uneven, and insufficient sampling that limited the incorporation of genomic epidemiology in the epidemic public health response in Ethiopia. These results highlight Ethiopia’s role in SARS-CoV-2 dissemination and the urgent need for balanced, near-real-time genomic sequencing.

5. Forum Inf Dis

   Unlocking the Potential of Genomic Data to Inform Typhoid Fever Control Policy: Supportive Resources for Genomic Data Generation, Analysis, and Visualization

   Megan E Carey, Zoe A Dyson, Silvia Argimón, and 9 more authors

   Open Forum Infectious Diseases, Jun 2023

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   The global response to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic demonstrated the value of timely and open sharing of genomic data with standardized metadata to facilitate monitoring of the emergence and spread of new variants. Here, we make the case for the value of Salmonella Typhi (S. Typhi) genomic data and demonstrate the utility of freely available platforms and services that support the generation, analysis, and visualization of S. Typhi genomic data on the African continent and more broadly by introducing the Africa Centres for Disease Control and Prevention’s Pathogen Genomics Initiative, SEQAFRICA, Typhi Pathogenwatch, TyphiNET, and the Global Typhoid Genomics Consortium.

6. Immunogenetics

   Impact of high human genetic diversity in Africa on immunogenicity and efficacy of RTS,S/AS01 vaccine

   Stephen Tukwasibwe, Gerald Mboowa, Ivan Sserwadda, and 8 more authors

   Immunogenetics, Apr 2023

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   In modern medicine, vaccination is one of the most effective public health strategies to prevent infectious diseases. Indisputably, vaccines have saved millions of lives by reducing the burden of many serious infections such as polio, tuberculosis, measles, pneumonia, and tetanus. Despite the recent recommendation by the World Health Organization (WHO) to roll out RTS,S/AS01, this malaria vaccine still faces major challenges of variability in its efficacy partly due to high genetic variation in humans and malaria parasites. Immune responses to malaria vary between individuals and populations. Human genetic variation in immune system genes is the probable cause for this heterogeneity. In this review, we will focus on human genetic factors that determine variable responses to vaccination and how variation in immune system genes affect the immunogenicity and efficacy of the RTS,S/AS01 vaccine.

7. BMC Inf Dis

   Unraveling virulence determinants in extended-spectrum beta-lactamase producing Escherichia coli from East Africa using whole-genome sequencing

   Ivan Sserwadda, Benson R Kidenya, Stephen Kanyerezi, and 8 more authors

   BMC Infectious Diseases, Sep 2023

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   Escherichia coli significantly causes nosocomial infections and rampant spread of antimicrobial resistance (AMR). There is limited data on genomic characterization of extended-spectrum β-lactamase (ESBL)-producing E. coli from African clinical settings. This hospital-based longitudinal study unraveled the genetic resistance elements in ESBL E. coli isolates from Uganda and Tanzania using whole-genome sequencing (WGS). A total of 142 ESBL multi-drug resistant E. coli bacterial isolates from both Tanzania and Uganda were sequenced and out of these, 36/57 (63.1%) and 67/85 (78.8%) originated from Uganda and Tanzania respectively. Mutations in RarD, yaaA and ybgl conferring resistances to chloramphenicol, peroxidase and quinolones were observed from Ugandan and Tanzanian isolates. We reported very high frequencies for blaCTX−M−15 with 11/18(61.1%), and blaCTX−M−27 with 12/23 (52.1%), blaTEM−1B with 13/23 (56.5%) of isolates originating from Uganda and Tanzania respectively all conferring resistance to Beta-lactam-penicillin inhibitors. We observed chloramphenicol resistance-conferring gene mdfA in 21/23 (91.3%) of Tanzanian isolates. Extraintestinal E. coli sequence type (ST) 131 accounted for 5/59 (8.4%) of Tanzanian isolates while enterotoxigenic E. coli ST656 was reported in 9/34 (26.4%) of Ugandan isolates. Virulence factors originating from Shigella dysenteriae Sd197 (gspC, gspD, gspE, gspF, gspG, gspF, gspH, gspI), Yersinia pestis CO92 (irp1, ybtU, ybtX, iucA), Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (csgF and csgG), and Pseudomonas aeruginosa PAO1 (flhA, fliG, fliM) were identified in these isolates. Overall, this study highlights a concerning prevalence and diversity of AMR-conferring elements shaping the genomic structure of multi-drug resistant E. coli in clinical settings in East Africa. It underscores the urgent need to strengthen infection-prevention controls and advocate for the routine use of WGS in national AMR surveillance and monitoring programs.

8. BMC Inf Dis

   Reviewing the journey to the clinical application of bacteriophages to treat multi-drug-resistant bacteria

   Gerald Mboowa

   BMC Infectious Diseases, Oct 2023

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   Antimicrobial resistance (AMR) was a leading cause of death globally in 2019. Sadly, COVID-19 has exacerbated AMR, nonetheless, the process of developing new antibiotics remains very challenging. This urgently requires the adoption of alternative approaches to treat multi-drug-resistant bacterial infections. This editorial introduces the ‘Bacteriophages against multi-drug resistant bacteria’ collection launched at BMC Infectious Diseases which highlights progress towards using bacteriophages to tackle AMR.

9. Front Microb

   Metatranscriptomic analysis of the gut microbiome of black soldier fly larvae reared on lignocellulose-rich fiber diets unveils key lignocellulolytic enzymes

   Eric G Kariuki, Caleb Kibet, Juan C Paredes, and 6 more authors

   Frontiers in Microbiology, Apr 2023

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   Recently, interest in the black soldier fly larvae (BSFL) gut microbiome has received increased attention primarily due to their role in waste bioconversion. However, there is a lack of information on the positive effect on the activities of the gut microbiomes and enzymes (CAZyme families) acting on lignocellulose. In this study, BSFL were subjected to lignocellulose-rich diets: chicken feed (CF), chicken manure (CM), brewers’ spent grain (BSG), and water hyacinth (WH). The mRNA libraries were prepared, and RNA-Sequencing was conducted using the PCR-cDNA approach through the MinION sequencing platform. Our results demonstrated that BSFL reared on BSG and WH had the highest abundance of Bacteroides and Dysgonomonas. The presence of GH51 and GH43_16 enzyme families in the gut of BSFL with both α-L-arabinofuranosidases and exo-alpha- L-arabinofuranosidase 2 were common in the BSFL reared on the highly lignocellulosic WH and BSG diets. Gene clusters that encode hemicellulolytic arabinofuranosidases in the CAZy family GH51 were also identified. These findings provide novel insight into the shift of gut microbiomes and the potential role of BSFL in the bioconversion of various highly lignocellulosic diets to fermentable sugars for subsequent value-added products (bioethanol). Further research on the role of these enzymes to improve existing technologies and their biotechnological applications is crucial.

10. Front. Microb

    Antimicrobial susceptibility surveillance and antimicrobial resistance in Neisseria gonorrhoeae in Africa from 2001 to 2020: A mini-review

    Francis Kakooza, Reuben Kiggundu, Gerald Mboowa, and 6 more authors

    Frontiers in Microbiology, Apr 2023

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    Antimicrobial resistance (AMR) in Neisseria gonorrhoeae (NG), compromising gonorrhea treatment, is a global public health concern. Improved, quality-assured NG AMR monitoring at the global level is essential. This mini-review examined NG AMR susceptibility surveillance and AMR data from the African continent from 2001 to 2020. Eligible peer-reviewed publications (n = 30) containing NG AMR data for antimicrobials currently recommended for gonorrhea treatment were included. Overall, very limited NG surveillance and AMR data was available. Furthermore, the NG AMR surveillance studies varied greatly regarding surveillance protocols (e.g., populations and samples tested, sample size, antimicrobials examined), methodologies (e.g., antimicrobial susceptibility testing method [agar dilution, minimum inhibitory concentration (MIC) gradient strip test, disc diffusion test] and interpretative criteria), and quality assurance (internal quality controls, external quality assessments [EQA], and verification of AMR detected). Moreover, most studies examined a suboptimal number of NG isolates, i.e., less than the WHO Global Gonococcal Antimicrobial Surveillance Program (GASP) and WHO Enhanced GASP (EGASP) recommendations of ≥100 isolates per setting and year. The notable inter-study variability and frequently small sample sizes make appropriate inter-study and inter-country comparisons of AMR data difficult. In conclusion, it is imperative to establish an enhanced, standardized and qualityassured NG AMR surveillance, ideally including patient metadata and genome sequencing as in WHO EGASP, in Africa, the region with the highest gonorrhea incidence globally. This will enable the monitoring of AMR trends, detection of emerging AMR, and timely refinements of national and international gonorrhea treatment guidelines. To achieve this aim, national and international leadership, political and financial commitments are imperative.

2022

1. Science

   The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

   Houriiyah Tegally, James E San, Matthew Cotton, and 399 more authors

   Science, Sep 2022

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   The past 2 years, during which waves of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants swept the globe, have starkly highlighted health disparities across nations. Tegally et al. show how the coordinated efforts of talented African scientists have in a short time made great contributions to pandemic surveillance and data gathering. Their efforts and initiatives have provided early warning that has likely benefited wealthier countries more than their own. Genomic surveillance identified the emergence of the highly transmissible Beta and Omicron variants and now the appearance of Omicron sublineages in Africa. However, it is imperative that technology transfer for diagnostics and vaccines, as well the logistic wherewithal to produce and deploy them, match the data-gathering effort.

2. PLOS Biology

   Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus

   Christian Happi, Ifedayo Adetifa, Placide Mbala, and 30 more authors

   PLOS Biology, Nov 2022

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   We propose a novel, non-discriminatory classification of monkeypox virus diversity. Together with the World Health Organization, we named three clades (I, IIa and IIb) in order of detection. Within IIb, the cause of the current global outbreak, we identified multiple lineages (A.1, A.2, A.1.1 and B.1) to support real-time genomic surveillance.

3. Front Microbiol

   Genetic Diversity, Distribution, and Genomic Characterization of Antibiotic Resistance and Virulence of Clinical Pseudomonas aeruginosa Strains in Kenya

   Shahiid Kiyaga, Cecilia Kyany’a, Angela W Muraya, and 5 more authors

   Frontiers in Microbiology, Mar 2022

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   Pseudomonas aeruginosa is a leading cause of nosocomial infections worldwide. It can produce a range of debilitating infections, have a propensity for developing antimicrobial resistance, and present with a variety of potent virulence factors. This study investigated the sequence types (ST), phenotypic antimicrobial susceptibility profiles, and resistance and virulence genes among clinical isolates from urinary tract and skin and soft tissue infections. Fifty-six P. aeruginosa clinical isolates were obtained from six medical centers across five counties in Kenya between 2015 and 2020. Whole-genome sequencing (WGS) was performed to conduct genomic characterization, sequence typing, and phylogenetic analysis of the isolates. Results showed the presence of globally distributed high-risk clones (ST244 and ST357), local high-risk clones (ST2025, ST455, and ST233), and a novel multidrug-resistant (MDR) clone carrying virulence genes (ST3674). Furthermore, 31% of the study isolates were found to be MDR with phenotypic resistance to a variety of antibiotics, including piperacillin (79%), ticarcillin-clavulanic acid (57%), meropenem (34%), levofloxacin (70%), and cefepime (32%). Several resistance genes were identified, including carbapenemases VIM-6 (ST1203) and NDM-1 (ST357), fluoroquinolone genes, crpP, and qnrVCi, while 14 and 22 different chromosomal mutations were detected in the gyrA and parC genes, respectively. All isolates contained at least three virulence genes. Among the virulence genes identified, phzB1 was the most abundant (50/56, 89%). About 21% (12/56) of the isolates had the exoU+/exoS- genotype, while 73% (41/56) of the isolates had the exoS+/exoU- genotype. This study also discovered 12 novel lineages of P. aeruginosa, of which one (ST3674) demonstrated both extensive antimicrobial resistance and the highest number of virulence genes (236/242, 98%). Although most high-risk clones were detected in Nairobi County, high-risk and clones of interest were found throughout the country, indicating the local spread of global epidemic clones and the emergence of new strains. Thus, this study illustrates the urgent need for coordinated local, regional, and international antimicrobial resistance surveillance efforts.

4. BMC

   Phylogenetic lineages of tuberculosis isolates and their association with patient demographics in Tanzania

   Beatrice Kemilembe Mutayoba, Michael Hoelscher, Norbert Heinrich, and 27 more authors

   BMC Genomics, Aug 2022

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   Background: Mycobacterium tuberculosis presents several lineages each with distinct characteristics of evolutionary status, transmissibility, drug resistance, host interaction, latency, and vaccine efficacy. Whole genome sequencing (WGS) has emerged as a new diagnostic tool to reliably inform the occurrence of phylogenetic lineages of Mycobacterium tuberculosis and examine their relationship with patient demographic characteristics and multidrug-resistance development. Methods: 191 Mycobacterium tuberculosis isolates obtained from a 2017/2018 Tanzanian drug resistance survey were sequenced on the Illumina Miseq platform at Supranational Tuberculosis Reference Laboratory in Uganda. Obtained fast-q files were imported into tools for resistance profiling and lineage inference (Kvarq v0.12.2, Mykrobe v0.8.1 and TBprofiler v3.0.5). Additionally for phylogenetic tree construction, RaxML-NG v1.0.3(25) was used to generate a maximum likelihood phylogeny with 800 bootstrap replicates. The resulting trees were plotted, annotated and visualized using ggtree v2.0.4. Results: Most [172(90.0%)] of the isolates were from newly treated Pulmonary TB patients. Coinfection with HIV was observed in 33(17.3%) TB patients. Of the 191 isolates, 22(11.5%) were resistant to one or more commonly used first line anti-TB drugs (FLD), 9(4.7%) isolates were MDR-TB while 3(1.6%) were resistant to all the drugs. Of the 24 isolates with any resistance conferring mutations, 13(54.2%) and 10(41.6%) had mutations in genes associated with resistance to INH and RIF respectively. The findings also show four major lineages i.e. Lineage 3[81 (42.4%)], followed by Lineage 4 [74 (38.7%)], the Lineage 1 [23 (12.0%)] and Lineages 2 [13 (6.8%)] circulaing in Tanzania. Conclusion: The findings in this study show that Lineage 3 is the most prevalent lineage in Tanzania whereas drug resistant mutations were more frequent among isolates that belonged to Lineage 4.

5. BMC

   First report of whole-genome analysis of an extensively drug-resistant Mycobacterium tuberculosis clinical isolate with bedaquiline, linezolid and clofazimine resistance from Uganda

   Jupiter Marina Kabahita, Joel Kabugo, Francis Kakooza, and 17 more authors

   Antimicrobial Resistance & Infection Control, May 2022

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   Background: Uganda remains one of the countries with the highest burden of TB/HIV. Drug-resistant TB remains a substantial challenge to TB control globally and requires new strategic effective control approaches. Drug resistance usually develops due to inadequate management of TB patients including improper treatment regimens and failure to complete the treatment course which may be due to an unstable supply or a lack of access to treatment, as well as patient noncompliance. Methods: Two sputa samples were collected from Xpert MTB/RIF® assay-diagnosed multi-drug resistant tuberculosis (MDR-TB) patient at Lira regional referral hospital in northern Uganda between 2020 and 2021 for comprehensive routine mycobacterial species identification and drug susceptibility testing using culture-based methods. Detection of drug resistance-conferring genes was subsequently performed using whole-genome sequencing with Illumina MiSeq platform at the TB Supranational Reference Laboratory in Uganda. Results: In both isolates, extensively drug-resistant TB (XDR-TB) was identified including resistance to Isoniazid (katG p.Ser315Thr), Rifampicin (rpoB p.Ser450Leu), Moxifloxacin (gyrA p.Asp94Gly), Bedaquiline (Rv0678 Glu49fs), Clofazimine (Rv0678 Glu49fs), Linezolid (rplC Cys154Arg), and Ethionamide (ethA c.477del). Further analysis of these two high quality genomes revealed that this 32 years-old patient was infected with the Latin American Mediterranean TB strain (LAM). Conclusions: This is the first identification of extensively drug-resistant Mycobacterium tuberculosis clinical isolates with bedaquiline, linezolid and clofazimine resistance from Uganda. These acquired resistances were because of non-adherence as seen in the patient’s clinical history. Our study also strongly highlights the importance of combating DR-TB in Africa through implementing next generation sequencing that can test resistance to all drugs while providing a faster turnaround time. This can facilitate timely clinical decisions in managing MDR-TB patients with non-adherence or lost to follow-up.

2021

1. Microb Genomics

   rMAP: the Rapid Microbial Analysis Pipeline for ESKAPE bacterial group whole-genome sequence data

   Ivan Sserwadda, and Gerald Mboowa

   Microbial Genomics, Jun 2021

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   The recent re-emergence of multidrug-resistant pathogens has exacerbated their threat to worldwide public health. The evolution of the genomics era has led to the generation of huge volumes of sequencing data at an unprecedented rate due to the ever-reducing costs of whole-genome sequencing (WGS). We have developed the Rapid Microbial Analysis Pipeline (rMAP), a user-friendly pipeline capable of profiling the resistomes of ESKAPE pathogens ( Enterococcus faecium , Staphylococcus aureus , Klebsiella pneumoniae , Acinetobacter baumannii , Pseudomonas aeruginosa and Enterobacter species) using WGS data generated from Illumina’s sequencing platforms. rMAP is designed for individuals with little bioinformatics expertise, and automates the steps required for WGS analysis directly from the raw genomic sequence data, including adapter and low-quality sequence read trimming, de novo genome assembly, genome annotation, single-nucleotide polymorphism (SNP) variant calling, phylogenetic inference by maximum likelihood, antimicrobial resistance (AMR) profiling, plasmid profiling, virulence factor determination, multi-locus sequence typing (MLST), pangenome analysis and insertion sequence characterization (IS). Once the analysis is finished, rMAP generates an interactive web-like html report. rMAP installation is very simple, it can be run using very simple commands. It represents a rapid and easy way to perform comprehensive bacterial WGS analysis using a personal laptop in low-income settings where high-performance computing infrastructure is limited.

2. Bioinformatics

   Bioinformatics mentorship in a resource limited setting

   Daudi Jjingo, Gerald Mboowa, Ivan Sserwadda, and 7 more authors

   Briefings in Bioinformatics, Sep 2021

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   Background: The two recent simultaneous developments of high-throughput sequencing and increased computational power have brought bioinformatics to the forefront as an important tool for effective and efficient biomedical research. Consequently, there have been multiple approaches to developing bioinformatics skills. In resource rich environments, it has been possible to develop and implement formal fully accredited graduate degree training programs in bioinformatics. In resource limited settings with a paucity of expert bioinformaticians, infrastructure and financial resources, the task has been approached by delivering short courses on bioinformatics—lasting only a few days to a couple of weeks. Alternatively, courses are offered online, usually over a period of a few months. These approaches are limited by both the lack of sustained in-person trainer–trainee interactions, which is a key part of quality mentorships and short durations which constrain the amount of learning that can be achieved. Methods: Here, we pioneered and tested a bioinformatics training/mentorship model that effectively uses the available expertise and computational infrastructure to deliver an in-person hands-on skills training experience. This is done through a few physical lecture hours each week, guided personal coursework over the rest of the week, group discussions and continuous close mentorship and assessment of trainees over a period of 1 year. Results: This model has now completed its third iteration at Makerere University and has successfully mentored trainees, who have progressed to a variety of viable career paths. Conclusions: One-year (intermediate) skills based in-person bioinformatics training and mentorships are viable, effective and particularly appropriate for resource limited settings.

3. Genome

   Genomics and bioinformatics capacity in Africa: no continent is left behind

   Gerald Mboowa, Ivan Sserwadda, and Dickson Aruhomukama

   Genome, Jan 2021

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   Despite the poor genomics research capacity in Africa, efforts have been made to empower African scientists to get involved in genomics research, particularly that involving African populations. As part of the Human Heredity and Health in Africa (H3Africa) Consortium, an initiative was set to make genomics research in Africa an African endeavor and was developed through funding from the United States’ National Institutes of Health Common Fund and the Wellcome Trust. H3Africa is intended to encourage a contemporary research approach by African investigators and to stimulate the study of genomic and environmental determinants of common diseases. The goal of these endeavors is to improve the health of African populations. To build capacity for bioinformatics and genomics research, organizations such as the African Society for Bioinformatics and Computational Biology have been established. In this article, we discuss the current status of the bioinformatics infrastructure in Africa as well as the training challenges and opportunities.

4. Gen Med

   Unmapped exome reads implicate a role for Anelloviridae in childhood HIV-1 long-term non-progression

   Savannah Mwesigwa, Lesedi Williams, Gaone Retshabile, and 25 more authors

   Genomic Medicine, Mar 2021

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   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.

5. F1000

   Whole-genome sequencing of SARS-CoV-2 in Uganda: implementation of the low-cost ARTIC protocol in resource-limited settings

   Gerald Mboowa, Savannah Mwesigwa, David Kateete, and 13 more authors

   F1000Research, Jul 2021

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   Background: In January 2020, a previously unknown coronavirus strain was identified as the cause of a severe acute respiratory syndrome (SARS-CoV-2). The first viral whole-genome was sequenced using high-throughput sequencing from a sample collected in Wuhan, China. Whole-genome sequencing (WGS) is imperative in investigating disease outbreak transmission dynamics and guiding decision-making in public health. Methods: We retrieved archived SARS-CoV-2 samples at the Integrated Biorepository of H3Africa Uganda, Makerere University (IBRH3AU). These samples were collected previously from individuals diagnosed with coronavirus disease 2019 (COVID-19) using real-time reverse transcription quantitative polymerase chain reaction (RT-qPCR). 30 samples with cycle thresholds (Cts) values <25 were selected for WGS using SARS-CoV-2 ARTIC protocol at Makerere University Molecular Diagnostics Laboratory. Results: 28 out of 30 (93.3%) samples generated analyzable genomic sequence reads. We detected SARS-CoV-2 and lineages A (22/28) and B (6/28) from the samples. We further show phylogenetic relatedness of these isolates alongside other 328 Uganda (lineage A = 222, lineage B = 106) SARS-CoV-2 genomes available in GISAID by April 22, 2021 and submitted by the Uganda Virus Research Institute. Conclusions: Our study demonstrated adoption and optimization of the low-cost ARTIC SARS-CoV-2 WGS protocol in a resource limited laboratory setting. This work has set a foundation to enable rapid expansion of SARS-CoV-2 WGS in Uganda as part of the Presidential Scientific Initiative on Epidemics (PRESIDE) CoV-bank project and IBRH3AU.

6. Tr Med & Inf Dis

   Increasing antimicrobial resistance in surgical wards at mulago national referral hospital, Uganda, from 2014 to 2018—Cause for Concern?

   Gerald Mboowa, Dickson Aruhomukama, Ivan Sserwadda, and 10 more authors

   Tropical Medicine and Infectious Disease, May 2021

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   Antimicrobial Resistance (AMR) and Healthcare Associated Infections (HAIs) are major global public health challenges in our time. This study provides a broader and updated overview of AMR trends in surgical wards of Mulago National Referral Hospital (MNRH) between 2014 and 2018. Laboratory data on the antimicrobial susceptibility profiles of bacterial isolates from 428 patient samples were available. The most common samples were as follows: tracheal aspirates (36.5%), pus swabs (28.0%), and blood (20.6%). Klebsiella (21.7%), Acinetobacter (17.5%), and Staphylococcus species (12.4%) were the most common isolates. The resistance patterns for different antimicrobials were: penicillins (40–100%), cephalosporins (30–100%), b-lactamase inhibitor combinations (70–100%), carbapenems (10–100%), polymyxin E (0–7%), aminoglycosides (50–100%), sulphonamides (80–100%), fluoroquinolones (40–70%), macrolides (40–100%), lincosamides (10–45%), phenicols (40–70%), nitrofurans (0–25%), and glycopeptide (0–20%). This study demonstrated a sustained increase in resistance among the most commonly used antibiotics in Uganda over the five-year study period. It implies ongoing hospital-based monitoring and surveillance of AMR patterns are needed to inform antibiotic prescribing, and to contribute to national and global AMR profiles. It also suggests continued emphasis on infection prevention and control practices (IPC), including antibiotic stewardship. Ultimately, laboratory capacity for timely bacteriological culture and sensitivity testing will provide a rational choice of antibiotics for HAI.

2020

1. Trop Med Hyg

   Face-Masking, an Acceptable Protective Measure against COVID-19 in Ugandan High-Risk Groups

   Gerald Mboowa, David Musoke, Douglas Bulafu, and 1 more author

   The American Journal of Tropical Medicine and Hygiene, Dec 2020

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   Methods: This study assessed the acceptability and effectiveness of face masking as a protective measure against COVID-19 among high-risk groups in Uganda. A mixed-methods approach was used, combining surveys and focus group discussions to evaluate knowledge, attitudes, and practices regarding face masking. Participants included healthcare workers, market vendors, public transport operators, and individuals with pre-existing health conditions. The study also analyzed mask-wearing compliance in public spaces and evaluated the effectiveness of masks through laboratory testing of filtration efficiency and wearability. Results: The study found high awareness (90%) of face masking as a protective measure, with 75% of participants regularly using masks in public. Market vendors and healthcare workers had the highest compliance rates, while public transport operators showed lower adherence. Laboratory analysis revealed that cloth masks commonly used in Uganda provided moderate protection, with a filtration efficiency of 50-70%. Participants cited affordability, discomfort, and limited access to quality masks as barriers to consistent use. Conclusion: Face masking is an acceptable and moderately effective COVID-19 protective measure among Ugandan high-risk groups. Increasing public access to affordable, high-quality masks and addressing barriers such as discomfort can improve compliance. Enhanced public health messaging tailored to specific groups is recommended to sustain mask-wearing practices.

2. AAS Open Res

   Current and emerging diagnostic tests available for the novel COVID-19 global pandemic

   Gerald Mboowa

   AAS Open Research, Apr 2020

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   On March 11, 2020 the World Health Organization (WHO) upgraded the status of the coronavirus disease 2019 (COVID-19) outbreak from epidemic to a global pandemic. This infection is caused by a novel coronavirus, SARS-CoV-2. Several rapid diagnostic tests have been developed at an astonishing pace; however, COVID-19 requires more highly specific rapid point-of-care diagnostic tests. This review describes the currently available testing approaches, as well as the available test assays including the Xpert® Xpress SARS-CoV-2 test (takes  45 min) and Abbott ID COVID-19 test (5 min) as easy to use point-of-care tests for diagnosis of novel COVID-19 that have so far received the US Food and Drug Administration emergency use authorizations clearance. This review is correct as of the date published and will be updated as more diagnostic tests come to light.

3. PloS One

   High prevalence of phenotypic pyrazinamide resistance and its association with pncA gene mutations in Mycobacterium tuberculosis isolates from Uganda

   Resty Naluyange, Gerald Mboowa, Kevin Komakech, and 3 more authors

   PLOS ONE, May 2020

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   Introduction: Susceptibility testing for pyrazinamide (PZA), a cornerstone anti-TB drug is not commonly done in Uganda because it is expensive and characterized with technical difficulties thus resistance to this drug is less studied. Resistance is commonly associated with mutations in the pncA gene and its promoter region. However, these mutations vary geographically and those conferring phenotypic resistance are unknown in Uganda. This study determined the prevalence of PZA resistance and its association with pncA mutations. Materials and methods: Using a cross-sectional design, archived isolates collected during the Uganda national drug resistance survey between 2008–2011 were sub-cultured. PZA resistance was tested by BACTEC Mycobacterial Growth Indicator Tube (MGIT) 960 system. Sequence reads were downloaded from the NCBI Library and bioinformatics pipelines were used to screen for PZA resistance–conferring mutations. Results: The prevalence of phenotypic PZA resistance was found to be 21%. The sensitivity and specificity of pncA sequencing were 24% (95% CI, 9.36–45.13%) and 100% (73.54% - 100.0%) respectively. We identified four mutations associated with PZA phenotypic resistance in Uganda; K96R, T142R, R154G and V180F. Conclusion: There is a high prevalence of phenotypic PZA resistance among TB patients in Uganda. The low sensitivity of pncA gene sequencing confirms the already documented discordances suggesting other mechanisms of PZA resistance in Mycobacterium tuberculosis.

2019

1. F1000

   Investigating colistin drug resistance: the role of high-throughput sequencing and bioinformatics

   Dickson Aruhomukama, Ivan Sserwadda, and Gerald Mboowa

   F1000Research, May 2019

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   Bacterial infections involving antibiotic-resistant gram-negative bacteria continue to increase and represent a major global public health concern. Resistance to antibiotics in these bacteria is mediated by chromosomal and/or acquired resistance mechanisms, these give rise to multi-drug resistant (MDR), extensive-drug resistant (XDR) or pan-drug resistant (PDR) bacterial strains. Most recently, plasmid-mediated resistance to colistin, an antibiotic that had been set apart as the last resort antibiotic in the treatment of infections involving MDR, XDR and PDR gram-negative bacteria has been reported. Plasmid-mediated colistin resistant gram-negative bacteria have been described to be PDR, implying a state devoid of alternative antibiotic therapeutic options. This review concisely describes the evolution of antibiotic resistance to plasmid-mediated colistin resistance and discusses the potential role of high-throughput sequencing technologies, genomics, and bioinformatics towards improving antibiotic resistance surveillance, the search for novel drug targets and precision antibiotic therapy focused at combating colistin resistance, and antibiotic resistance as a whole.

2. BMC Inf Dis

   blaVIM- and blaOXA-mediated carbapenem resistance among Acinetobacter baumannii and Pseudomonas aeruginosa isolates from the Mulago hospital intensive care unit in Kampala, Uganda

   Dickson Aruhomukama, Christine F Najjuka, Henry Kajumbula, and 6 more authors

   BMC Infectious Diseases, Oct 2019

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   Background: Between January 2015 and July 2017, we investigated the frequency of carbapenem resistant Acinetobacter baumannii (CRAB) and carbapenem resistant Pseudomonas aeruginosa (CRPA) at the Mulago Hospital intensive care unit (ICU) in Kampala, Uganda. Carbapenemase production and carbapenemase gene carriage among CRAB and CRPA were determined; mobility potential of carbapenemase genes via horizontal gene transfer processes was also studied. Methods: Clinical specimens from 9269 patients were processed for isolation of CRAB and CRPA. Drug susceptibility testing was performed with the disk diffusion method. Carriage of carbapenemase genes and class 1 integrons was determined by PCR. Conjugation experiments that involved blaVIM positive CRAB/CRPA (donors) and sodium azide resistant Escherichia coli J53 (recipient) were performed. Results: The 9269 specimens processed yielded 1077 and 488 isolates of Acinetobacter baumannii and Pseudomonas aeruginosa, respectively. Of these, 2.7% (29/1077) and 7.4% (36/488) were confirmed to be CRAB and CRPA respectively, but 46 were available for analysis (21 CRAB and 25 CRPA). Majority of specimens yielding CRAB and CRPA were from the ICU (78%) while 20 and 2% were from the ENT (Ear Nose & Throat) Department and the Burns Unit, respectively. Carbapenemase assays performed with the MHT assay showed that 40 and 33% of CRPA and CRAB isolates respectively, were carbapenemase producers. Also, 72 and 48% of CRPA and CRAB isolates respectively, were metallo-beta-lactamase producers. All the carbapenemase producing isolates were multidrug resistant but susceptible to colistin. blaVIM was the most prevalent carbapenemase gene, and it was detected in all CRAB and CRPA isolates while blaOXA-23 and blaOXA-24 were detected in 29 and 24% of CRAB isolates, respectively. Co-carriage of blaOXA-23 and blaOXA-24 occurred in 14% of CRAB isolates. Moreover, 63% of the study isolates carried class 1 integrons; of these 31% successfully transferred blaVIM to E. coli J53. Conclusions: CRAB and CRPA prevalence at the Mulago Hospital ICU is relatively low but carbapenemase genes especially blaVIM and blaOXA-23 are prevalent among them. This requires strengthening of infection control practices to curb selection and transmission of these strains in the hospital.

3. Mol Gen & Geno

   Role of genomics literacy in reducing the burden of common genetic diseases in Africa

   Gerald Mboowa, and Ivan Sserwadda

   Molecular Genetics & Genomic medicine, May 2019

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   Background: In Africa, health practitioners and the current knowledge of the public on genetics and genomics is still very low and yet this has potential to reduce the burden of common genetic diseases. Many initiatives have promoted genomic research, infrastructure, and capacity building in Africa. What remains to be done is to improve genomics literacy among populations and communities while utilizing an array of strategies. Genomic literacy and awareness are key in the management of genetic diseases which includes diagnosis, prevention of complications and therapy. Africa is characterized by great cultural and language diversity thereby requiring a multidisciplinary approach to improving public and community genomics literacy and engagement. However, this is further complicated by having the fact that sub-Saharan Africa is comprised of countries with the lowest literacy rates in the world. Methods: We applied the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines to review genomic literacy in Africa using PubMed database. Results: We found very limited evidence of genomics literacy for genetic diseases in Africa. Conclusion: We propose a number of approaches that if adopted will significantly increase the genomic literacy and reduce the burden of genetic diseases in Africa.

2018

1. AAS Open Res

   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

   Gerald Mboowa, Savannah Mwesigwa, Eric Katagirya, and 22 more authors

   Open Research Africa, May 2018

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   Background: Here, we describe how the Collaborative African Genomics Network (CAfGEN) of the Human Heredity and Health in Africa (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. The H3Africa was conceived to facilitate the application of genomics technologies to improve health across Africa.. Methods: CAfGEN is an H3Africa collaborative centre comprising expertise from the University of Botswana; Makerere University; Baylor College of Medicine Children’s Clinical Centers of Excellence (COEs) in Botswana, Uganda, and Swaziland; as well as Baylor College of Medicine, Texas. The COEs provide clinical expertise for community engagement, participant recruitment and sample collection while the three University settings facilitate processing and management of genomic samples and provide infrastructure and training opportunities to sustain genomics research. Results: The project has focused on utilizing whole-exome sequencing to identify genetic variants contributing to extreme HIV disease progression phenotypes in children, as well as RNA sequencing and integrated genomics to identify host genetic factors associated with TB disease progression among HIV-positive children. These cohorts, developed using the COEs’ electronic medical records, are exceptionally well-phenotyped and present an unprecedented opportunity to assess genetic factors in individuals whose HIV was acquired by a different route than their adult counterparts in the context of a unique clinical course and disease pathophysiology. Conclusions: Our approach offers the prospect of developing a critical mass of well-trained, highly-skilled, continent-based African genomic scientists. To ensure long term genomics research sustainability in Africa, CAfGEN contributes to a wide range of genomics capacity and infrastructure development on the continent, has laid a foundation for genomics graduate programs at its institutions, and continues to actively promote genomics research through innovative forms of community engagement brokered by partnerships with governments and academia to support genomics policy formulation.

2. AJHG

   Whole-Exome Sequencing Reveals Uncaptured Variation and Distinct Ancestry in the Southern African Population of Botswana

   Gaone Retshabile, Busisiwe C Mlotshwa, Lesedi Williams, and 27 more authors

   The American Journal of Human Genetics, May 2018

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   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 = 2.2 × 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.

3. BMC Inf Dis

   Microbial contaminants isolated from items and work surfaces in the post- operative ward at Kawolo general hospital, Uganda

   Ivan Sserwadda, Mathew Lukenge, Bashir Mwambi, and 3 more authors

   BMC Infectious Diseases, Feb 2018

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   Background: Nosocomial infections are a major setback in the healthcare delivery system especially in developing countries due to the limited resources. The roles played by medical care equipment and work surfaces in the transmission of such organisms have inevitably contributed to the elevated mortality, morbidity and antibiotic resistances. Methods: A total 138 samples were collected during the study from Kawolo general hospital. Swab samples were collected from various work surfaces and fomites which consisted of; beds, sink taps, infusion stands, switches, work tables and scissors. Cultures were done and the susceptibility patterns of the isolates were determined using Kirby Bauer disc diffusion method. Data was analyzed using Stata 13 and Microsoft Excel 2013 packages. Results: A total of 44.2% (61/138) of the collected swab specimens represented the overall bacterial contamination of the sampled articles. Staphylococcus aureus and Klebsiella pneumoniae accounted for the highest bacterial contaminants constituting of 75.4% (46/61) and 11.5% (7/61) respectively. Infusion stands and patient beds were found to have the highest bacterial contamination levels both constituting 19.67% (12/61). The highest degree of transmission of organisms to patients was found to be statistically significant for patient beds with OR: 20.1 and P-value 8X10− 4. Vancomycin, ceftriaxone and ciprofloxacin were the most effective antibiotics with 100%, 80% and 80% sensitivity patterns among the isolates respectively. Multi-drug resistant (MDR) Staphylococcus aureus accounted for 52% (24/46) with 4% (1/24) classified as a possible extensively drug resistant (XDR) whereas Gram negative isolates had 27% (4/15) MDR strains out of which 50%(2/4) were classified as possible pan-drug resistant (PDR). Conclusion: The high prevalence of bacterial contaminants in the hospital work environment is an indicator of poor or ineffective decontamination. The study findings reiterate the necessity to formulate drug usage policies and reexamine effectiveness of decontamination and sterilization practices within Kawolo general hospital. We also recommend installation of a sound Microbiology unit at the hospital to take on susceptibility testing to check on the empirical use of antibiotics as a way of reducing the rampant elevations in drug resistances.

4. Inf Dis Med Micr

   Human Genomic Loci Important in Common Infectious Diseases: Role of High-Throughput Sequencing and Genome-Wide Association Studies

   Gerald Mboowa, Ivan Sserwadda, Marion Amujal, and 1 more author

   Canadian Journal of Infectious Diseases and Medical Microbiology, Mar 2018

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   HIV/AIDS, tuberculosis (TB), and malaria are 3 major global public health threats that undermine development in many resource-poor settings. Recently, the notion that positive selection during epidemics or longer periods of exposure to common infectious diseases may have had a major effect in modifying the constitution of the human genome is being interrogated at a large scale in many populations around the world. This positive selection from infectious diseases increases power to detect associations in genome-wide association studies (GWASs). High-throughput sequencing (HTS) has transformed both the management of infectious diseases and continues to enable large-scale functional characterization of host resistance/susceptibility alleles and loci; a paradigm shift from single candidate gene studies. Application of genome sequencing technologies and genomics has enabled us to interrogate the host-pathogen interface for improving human health. Human populations are constantly locked in evolutionary arms races with pathogens; therefore, identification of common infectious disease-associated genomic variants/markers is important in therapeutic, vaccine development, and screening susceptible individuals in a population. This review describes a range of host-pathogen genomic loci that have been associated with disease susceptibility and resistant patterns in the era of HTS. We further highlight potential opportunities for these genetic markers.

2017

1. Genet Med

   The collaborative African genomics network training program: a trainee perspective on training the next generation of African scientists

   Busisiwe C Mlotshwa, Savannah Mwesigwa, Gerald Mboowa, and 11 more authors

   Genetics in Medicine, Apr 2017

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   Purpose: The Collaborative African Genomics Network (CAfGEN) 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”.

2016

1. Trop Anim Health

   Serological and molecular investigation for brucellosis in swine in selected districts of Uganda

   Joseph Erume, Kristina Roesel, Michel M Dione, and 10 more authors

   Tropical Animal Health and Production, May 2016

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   Brucellosis is a notifiable zoonotic disease affecting livestock, humans, and wildlife in Uganda. Pigs can be infected with human pathogenic Brucella suis biovars 1 and 3 and can be a significant source of brucellosis for humans. Uganda has a rapidly growing pig population, and the pork consumption per capita is the highest in East Africa. The objective of this work was to determine the seroprevalence of brucellosis in Ugandan pigs. A cross-sectional serosurvey of pigs was conducted in three of the major pig-keeping districts in Uganda (Masaka (n = 381 samples), Mukono (n = 398), and Kamuli (n = 414)). In addition, pigs originating from these districts were sampled in the major pig abattoir in Kampala (n = 472). In total, 1665 serum samples were investigated by serological and molecular tests. Only three putative brucellosis-positive samples were detected serologically using indirect ELISA. These sera were found negative for Brucella antibodies by CFT; however, two had antibodies against Yersinia enterocolitica as determined by SAT. Presence of antibodies against Yersiniae was confirmed by Y. enterocolitica antibody-specific ELISA. The two Yersiniae ELISA-positive samples were brucellosis negative using real-time PCR. We tested additional 142 sera from the 1665 samples with real-time PCR. All tested negative. Under this type of production system, we expect a maximum B. suis prevalence of less than 1 % at 95 % confidence level, and therefore, the risk of acquiring brucellosis from the pigs or their products is negligible. However, pigs may harbor the zoonotic Y. enterocolitica. This is the first study to investigate the occurrence of brucellosis in pigs in Uganda and the first study to report Y. enterocolitica antibodies in swine in Uganda.

2015

1. PLoS ONE

   Cough Aerosol Cultures of Mycobacterium tuberculosis: Insights on TST / IGRA Discordance and Transmission Dynamics

   Edward C Jones-López, Laura F White, Bruce Kirenga, and 11 more authors

   PLoS ONE, Sep 2015

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   Rationale: The diagnosis of latent tuberculosis (TB) infection (LTBI) is complicated by the absence of a gold standard. Discordance between tuberculin skin tests (TST) and interferon gamma release assays (IGRA) occurs in 10–20% of individuals, but the underlying mechanisms are poorly understood. Methods: We analyzed data from a prospective household contact study that included cough aerosol culture results from index cases, environmental and contact factors. We assessed contacts for LTBI using TST and IGRA at baseline and six weeks. We examined TST/IGRA discordance in qualitative and quantitative analyses, and used multivariable logistic regression analysis with generalized estimating equations to analyze predictors of discordance. Measurements and Results: We included 96 TB patients and 384 contacts. Discordance decreased from 15% at baseline to 8% by six weeks. In adjusted analyses, discordance was related to less crowding (p = 0.004), non-cavitary disease (OR 1.41, 95% CI: 1.02–1.96; p = 0.03), and marginally with BCG vaccination in contacts (OR 1.40, 95% CI: 0.99–1.98, p = 0.06). Conclusions: We observed significant individual variability and temporal dynamism in TST and IGRA results in household contacts of pulmonary TB cases. Discordance was associated with a less intense infectious exposure, and marginally associated with a BCG-mediated delay in IGRA conversion. Cough aerosols provide an additional dimension to the assessment of infectiousness and risk of infection in contacts.

2. Biomed Res Int

   Isolation and Molecular Characterization of Brucella Isolates in Cattle Milk in Uganda

   Denis Rwabiita Mugizi, Shaman Muradrasoli, Sofia Boqvist, and 6 more authors

   BioMed Research International, Feb 2015

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   Brucellosis is endemic in livestock and humans in Uganda and its transmission involves a multitude of risk factors like consumption of milk from infected cattle. To shed new light on the epidemiology of brucellosis in Uganda the present study used phenotypic and molecular approaches to delineate the Brucella species, biovars, and genotypes shed in cattle milk. Brucella abortus without a biovar designation was isolated from eleven out of 207 milk samples from cattle in Uganda. These isolates had a genomic monomorphism at 16 variable number tandem repeat (VNTR) loci and showed in turn high levels of genetic variation when compared with other African strains or other B. abortus biovars from other parts of the world. This study further highlights the usefulness of MLVA as an epidemiological tool for investigation of Brucella infections.

3. JCM

   Improving the sensitivity of the Xpert MTB/RIF assay on sputum pellets by decreasing the amount of added sample reagent: a laboratory and clinical evaluation

   Nila J Dharan, Danielle Amisano, Gerald Mboowa, and 10 more authors

   Journal of Clinical Microbiology, Mar 2015

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   The Xpert MTB/RIF (Xpert) assay permits rapid near-patient detection of Mycobacterium tuberculosis in sputum; however, the test sensitivity remains suboptimal in paucibacillary specimens that are negative for acid-fast bacilli using smear microscopy. Xpert testing includes dilution with sample reagent, and when processed sputum pellets are tested, the recommended sample reagent/pellet ratio is 3:1. We evaluated whether a decreased sample reagent/pellet ratio of 2:1 increased Xpert sensitivity compared to the recommended 3:1. The limit of detection was determined by inoculating serial dilutions of M. tuberculosis into sputum samples, preparing sputum pellets, and testing each pellet by Xpert at both sample reagent ratios. Processed sputum pellets obtained from M. tuberculosis culture-positive clinical specimens were also tested by Xpert at both ratios. Among spiked sputum pellets, the limit of detection was 1,478 CFU/ml (95% confidence interval [CI], 1,211 to 1,943) at a 3:1 ratio and decreased to 832 CFU/ml (95% CI, 671 to 1,134) at 2:1. The proportion of specimens in which M. tuberculosis was detected was greater at 2:1 than at 3:1 for almost all numbers of CFU/ml; this difference was most prominent at lower numbers of CFU/ml. Among 134 concentrated sputum pellets from the clinical study, the sensitivity of Xpert at 2:1 was greater than at 3:1 overall (80% versus 72%; P=0.03) and for smear-negative specimens (67% versus 58%; P=0.12). For Xpert testing of sputum pellets, using a lower sample reagent/pellet ratio increased M. tuberculosis detection, especially for paucibacillary specimens. Our study supports use of a 2:1 sample reagent/pellet dilution for Xpert testing of sputum pellets.

4. PloS One

   High Genotypic Discordance of Concurrent Mycobacterium tuberculosis Isolates from Sputum and Blood of HIV-Infected Individuals

   Willy Ssengooba, Frank G Cobelens, Lydia Nakiyingi, and 5 more authors

   PLOS ONE, Jul 2015

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   Background: Among HIV-infected individuals with CD4 less than 200 cells/mm3, tuberculosis often has an atypical presentation, is more likely to be disseminated and is diagnostically challenging. We sought to understand the genotypic discordance of concurrent sputum and blood M. tuberculosis (MTB) isolates from HIV-infected individuals. Methods: From a prospective diagnostic accuracy study with 182 HIV-infected culture-positive TB adults, isolates were obtained from 51 of 66 participants who were MTB culture-positive by both sputum and blood. Isolates were subjected to susceptibility testing to 1st line drugs, spoligotyping and 24 locus- MIRU-VNTR. Results: The median age of the participants was 31 (IQR; 27–38) years and 51% were male. The median CD4 count was 29 (IQR; 10–84) cells/mm3 with 20% taking ART; 8.0% were previously treated for TB, and 63% were AFB smear-negative. The isolates belonged to two of the main global MTB-lineages; East-African-Indian (L3) 17 (16.7%) and Euro-American (L4) 85 (83.3%). We identified 26 (51.0%) participants with discordant MTB-genotypes between sputum and blood, including two patients with evidence of mixed infection in either compartment. Having discordant MTB-genotypes was not predicted by the MTB-lineage in either blood or sputum, CD4 cell count, or any other clinical characteristic. Conclusions: There is a high genotypic discordance among M. tuberculosis concurrently isolated from sputum and blood of HIV-infected individuals. These findings suggest that infection with more than one strain of M. tuberculosis occurs in at least half of patients with advanced HIV infection.

2014

1. AAC

   Sensititre MYCOTB MIC plate for testing Mycobacterium tuberculosis susceptibility to first- and second-line drugs

   Jongseok Lee, Derek T Armstrong, Willy Ssengooba, and 15 more authors

   Antimicrobial Agents and Chemotherapy, Dec 2014

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   For Mycobacterium tuberculosis, phenotypic methods for drug susceptibility testing of second-line drugs are poorly standardized and technically challenging. The Sensititre MYCOTB MIC plate (MYCOTB) is a microtiter plate containing lyophilized antibiotics and configured for determination of MICs to first- and second-line antituberculosis drugs. To evaluate the performance of MYCOTB for M. tuberculosis drug susceptibility testing using the Middlebrook 7H10 agar proportion method (APM) as the comparator, we conducted a two-site study using archived M. tuberculosis isolates from Uganda and the Republic of Korea. Thawed isolates were subcultured, and dilutions were inoculated into MYCOTB wells and onto 7H10 agar. MYCOTB results were read at days 7, 10, 14, and 21; APM results were read at 21 days. A total of 222 isolates provided results on both platforms. By APM, 106/222 (47.7%) of isolates were resistant to at least isoniazid and rifampin. Agreement between MYCOTB and APM with respect to susceptibility or resistance was ≥92% for 7 of 12 drugs when a strict definition was used and ≥96% for 10 of 12 drugs when agreement was defined by allowing a ± one-well range of dilutions around the APM critical concentration. For ethambutol, agreement was 80% to 81%. For moxifloxacin, agreement was 83% to 85%; incorporating existing DNA sequencing information for discrepant analysis raised agreement to 91% to 96%. For MYCOTB, the median time to plate interpretation was 10 days and interreader agreement was ≥95% for all drugs. MYCOTB provided reliable results for M. tuberculosis susceptibility testing of first- and second-line drugs except ethambutol, and results were available sooner than those determined by APM.

2. BMC Infect Dis

   Rifampicin resistance mutations in the 81 bp RRDR of rpoB gene in Mycobacterium tuberculosis clinical isolates using Xpert® MTB/RIF in Kampala, Uganda: a retrospective study

   Gerald Mboowa, Carolyn Namaganda, and Willy Ssengooba

   BMC Infectious Diseases, Sep 2014

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   Background: Introduction of Xpert® MTB/RIF assay has revolutionalised the diagnosis of tuberculosis (TB) by simultaneously detecting the bacteria and resistance to rifampicin (rif), a surrogate marker for multi-drug resistant TB (MDR-TB) as well as one of the principal first-line anti-tuberculosis drugs. In general, rpoB mutations can be found in 96.1% of rif-resistant Mycobacterium tuberculosis (MTB) strains worldwide and these mutations usually are located in a region at the 507-533rd amino acid residuals (81 bp) in the MTB rpoB gene, which is referred to as Rifampicin-resistance-determining region (RRDR). In this study, we determined the frequency of MDR-TB in Kampala using Xpert® MTB/RIF in comparison with the agar proportion method using Middlebrook 7H11and further determined the frequency of probes for different rpoB gene mutations using Xpert® MTB/RIF assay in the 81 bp RRDR. Methods: A total of 1501 specimens received at Mycobacteriology laboratory, Makerere University for Xpert testing between May 2011 and May 2014 were analysed by Xpert® MTB/RIF assay. Specimens that were positive for both MTB and rifampicin resistance were further subjected to a complete first line anti-mycobacterial drug susceptibility testing using Middlebrook 7H11 agar proportion method (APM). Results: Xpert® MTB/RIF assay detected 313 MTB positive specimens and out of which 12 specimens had both MTB and rifampicin- resistance conferred by four different rpoB gene mutations in the 81 bp-RRDR of MTB, further one (1/12), specimen was found to be rifampicin mono-resistant on APM while the 11 were found to be MDR-TB. Probes associated with the observed rif- resistance were as follows: E (7/12), B (3/12), A (1/12), D (1/12) and no rif-resistance was associated with probe C. No specimen yielded rif-resistance associated with more than one probe failure (mutation combinations). Probe D was associated with rifampicin mono-resistant. Conclusions: MDR-TB was at 3.5% in the studied population. Mutations associated with Probe E (58%) also known as codons 531and 533 are the commonest rpoB gene mutation identified by Xpert® MTB/RIF assay in this setting and mutations identified by probe E of the assay, turned out to be MDR-TB strains by agar proportion method antimicrobial susceptibility testing. No mutation was detected in the codon 522.

3. Int. J. Evol. Biol

   Genetics of Sub‐Saharan African human population: implications for HIV/AIDS, tuberculosis, and malaria

   Gerald Mboowa

   International Journal of Evolutionary Biology, Aug 2014

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   Sub-Saharan Africa has continued leading in prevalence and incidence of major infectious disease killers such as HIV/AIDS, tuberculosis, and malaria. Epidemiological triad of infectious diseases includes susceptible host, pathogen, and environment. It is imperative that all aspects of vertices of the infectious disease triad are analysed to better understand why this is so. Studies done to address this intriguing reality though have mainly addressed pathogen and environmental components of the triad. Africa is the most genetically diverse region of the world as well as being the origin of modern humans. Malaria is relatively an ancient infection in this region as compared to TB and HIV/AIDS; from the evolutionary perspective, we would draw lessons that this ancestrally unique population now under three important infectious diseases both ancient and exotic will be skewed into increased genetic diversity; moreover, other evolutionary forces are also still at play. Host genetic diversity resulting from many years of malaria infection has been well documented in this population; we are yet to account for genetic diversity from the trio of these infections. Effect of host genetics on treatment outcome has been documented. Host genetics of sub-Saharan African population and its implication to infectious diseases are an important aspect that this review seeks to address.

4. BMC Clin. Pathol.

   Clinico-pathological features of tuberculosis due to Mycobacterium tuberculosis Uganda genotype in patients with tuberculous lymphadenitis: a cross sectional study

   Dan Wamala, Benon Asiimwe, Edgar Kigozi, and 3 more authors

   BMC Clinical Pathology, Apr 2014

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   Background: Tuberculous lymphadenitis is next to pulmonary tuberculosis as the most common cause of tuberculosis. Uganda genotype, one of the sub-lineages of Mycobacterium tuberculosis, is the most prevalent cause of pulmonary tuberculosis in Uganda. We here investigate the clinicopathological characteristics of patients with tuberculous lymphadenitis infected with M. tuberculosis Uganda genotype compared with those infected with M. tuberculosis non-Uganda genotype strains. Methods: Between 2010 and 2012, we enrolled 121 patients (mean age 28.5 yrs, male 48%; female 52%) with tuberculous lymphadenitis, and categorized them by their M. tuberculosis genotypes. The clinical features and lymph node cytopathological parameters were compared between patients in the Uganda and non-Uganda categories using a crude and multivariable logistic regression model with adjustment for confounding factors. Results: Of the 121participants, 56 (46%) were infected with strains of Uganda genotype. Patients infected with this genotype had significantly lower frequency of abdominal lymphadenopathy (odds ratio 0.4, p = 0.046) after adjusting for sex, age and HIV. Abdominal lymphadenopathy was also significantly associated with abnormal chest X-ray (p = 0.027). Conclusion: Tuberculous lymphadenitis patients infected with M. tuberculosis Uganda genotype were significantly less prone to have abdominal lymphadenopathy indicating potential reduced ability to disseminate and supporting the concept that differences in M. tuberculosis genotype may have clinical implications.

2013

1. BMC Inf Dis

   Species and genotypic diversity of non-tuberculous mycobacteria isolated from children investigated for pulmonary tuberculosis in rural Uganda

   Benon B Asiimwe, Godwins B Bagyenzi, Willy Ssengooba, and 8 more authors

   BMC infectious diseases, Feb 2013

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   Background: Smear microscopy, a mainstay of tuberculosis (TB) diagnosis in developing countries, cannot differentiate M. tuberculosis complex from NTM infection, while pulmonary TB shares clinical signs with NTM disease, causing clinical and diagnostic dilemmas. This study used molecular assays to identify species and assess genotypic diversity of non-tuberculous mycobacteria (NTM) isolates from children investigated for pulmonary tuberculosis at a demographic surveillance site in rural eastern Uganda. Methods: Children were investigated for pulmonary tuberculosis as part of a TB vaccine surveillance program (2009–2011). Two cohorts of 2500 BCG vaccinated infants and 7000 adolescents (12–18 years) were recruited and followed up for one to two years to determine incidence of tuberculosis. Induced sputum and gastric aspirates were processed by the standard N-acetyl L-cysteine (NALC)-NaOH method. Sediments were cultured in the automated MGIT (Becton Dickson) liquid culture system and incubated at 37°C for at least six weeks. Capilia TB assay was used to classify mycobacteria into MTC and NTM. The GenoType CM/AS assays were performed to identify species while Enterobacterial Repetitive Intergenic Consensus (ERIC) PCR genotyping was used to assess genetic diversity of the strains within each species. Results: Among 2859 infants and 2988 adolescents screened, the numbers of TB suspects were 710 and 1490 infants and adolescents respectively. The prevalence of NTM in infant suspects was 3.7% (26/710) (95% CI 2.5–5.2) while that in adolescent suspects was 4.6% (69/1490) (95% CI 3.6–5.8). On culture, 127 isolates were obtained, 103 of which were confirmed as mycobacteria comprising of 95 NTM and eight M. tuberculosis complex. The Genotype CM/AS assay identified 63 of the 95 NTM isolates while 32 remained un-identified. The identified NTM species were M. fortuitum (40 isolates, 63.5%), M. szulgai (9 isolates, 14.3%), M. gordonae (6 isolates, 9.5%), M. intracellulare (3 isolates, 4.7%), M. scrofulaceum (2 isolates, 3.2%), M. lentiflavum (2 isolates, 3.2%), and M. peregrinum (1 isolate, 1.6%). Genotyping did not reveal any clustering in M. intracellulare, M. gordonae and M. szulgai species. M. fortuitum, on the other hand, had two clusters, one with three isolates of M. fortuitum 1 and the other with two isolates of M. fortuitum 2 subspecies. The remaining 35 of the 40 isolates of M. fortuitum had unique fingerprint patterns. Conclusion: M. fortuitum is the most common cause of infection by NTM among Infants and adolescents in rural Uganda. There is a varied number of species and genotypes, with minimal clustering within species, suggesting ubiquitous sources of infection to individuals in this community.

2012

1. Crit Care Med

   Cough aerosols of Mycobacterium tuberculosis predict new infection: a household contact study

   Edward C Jones-López, Olive Namugga, Francis Mumbowa, and 11 more authors

   American Journal of Respiratory and Critical Care Medicine, Dec 2012

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   Rationale: Airborne transmission of Mycobacterium tuberculosis results from incompletely characterized host, bacterial, and environmental factors. Sputum smear microscopy is associated with considerable variability in transmission. Objectives: To evaluate the use of cough-generated aerosols of M. tuberculosis to predict recent transmission. Methods: Patients with pulmonary tuberculosis (TB) underwent a standard evaluation and collection of cough aerosol cultures of M. tuberculosis. We assessed household contacts for new M. tuberculosis infection. We used multivariable logistic regression analysis with cluster adjustment to analyze predictors of new infection. Measurements and main results: From May 2009 to January 2011, we enrolled 96 sputum culture-positive index TB cases and their 442 contacts. Only 43 (45%) patients with TB yielded M. tuberculosis in aerosols. Contacts of patients with TB who produced high aerosols (≥10 CFU) were more likely to have a new infection compared with contacts from low-aerosol (1-9 CFU) and aerosol-negative cases (69%, 25%, and 30%, respectively; P = 0.009). A high-aerosol patient with TB was the only predictor of new M. tuberculosis infection in unadjusted (odds ratio, 5.18; 95% confidence interval, 1.52-17.61) and adjusted analyses (odds ratio, 4.81; 95% confidence interval, 1.20-19.23). Contacts of patients with TB with no aerosols versus low and high aerosols had differential tuberculin skin test and interferon-γ release assay responses. Conclusions: Cough aerosols of M. tuberculosis are produced by a minority of patients with TB but predict transmission better than sputum smear microscopy or culture. Cough aerosols may help identify the most infectious patients with TB and thus improve the cost-effectiveness of TB control programs.