School of Biosecurity, Biotechnolgy and Laboratory Sciences (SBLS) Collection
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ItemEvaluation of the viral haemorrhagic fever surveillance system in Uganda (2020-2025): assessing system performance, critical gaps, and opportunities in strengthening surveillance(Makerere University, 2026)Background: Recurrent outbreaks of viral haemorrhagic fevers (VHFs) continue to threaten public health security in Uganda. Although investments have been made in surveillance and outbreak preparedness, the time required for case detection, notification, and response, along with incomplete multisectoral information sharing, continues to pose significant challenges. This study measured the effectiveness of the VHF surveillance system in some districts of Uganda between 2020 and 2025 and found the key gaps and opportunities for strengthening surveillance based on CDC evaluation attributes and WHO framework 7-1-7. Methods: A convergent parallel design was used, which involved a retrospective review of 640 suspected VHF case records from Mubende, Kyegegwa and Mbarara districts and ten key informant interviews. All indicators of the WHO 7-1-7 timeliness indicators, data completeness, laboratory turnaround time, and positive predictive value (PPV) were used to assess surveillance performance. Quantitative data were analysed in Stata 18, and Qualitative data in a thematic approach to identify gaps in human, animal and environmental health surveillance data flows. Results: There were 640 suspected VHF case records, 75.2% of which were recorded in Mubende. Full 7-1-7 compliance was achieved in 182 (28.4%) records. 62.8% (402) of the records were detected within seven days, 268 (42%) were notified within one day, and 318(49.7%) were initiated within seven days. Data completeness (90% or more of the essential fields completed) was found in 337 (52.7%) records, and 182 records (28.4%) were missing or had inconsistent critical dates. The median laboratory turnaround time was 5 days and 120/312 (38.5%) laboratory turnaround time of 3 days or less. The overall PPV of all suspected cases with definitive laboratory results was 20.6% (48/233). There were no significant differences found between districts on 7-1-7 indicators and data completeness. Qualitative results showed that the community detection was delayed, the One Health coordination was poor, the involvement of the wildlife sector was limited, and the interoperability of information systems on surveillance was poor. Conclusion: The performance of the VHF surveillance system was found to be different across the selected districts with notification being the lowest performing part of the 7-1-7 surveillance pathway. Enhancing community-based detection, notification, surveillance data quality, lab processes and systematic multi-sectoral sharing of information will be critical to enhance early warning and outbreak response.
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ItemSpatial-temporal patterns of rabies outbreaks in Uganda : a retrospective study 2018-2022(Makerere University, 2023)Rabies is a major global public health concern, with the majority of cases occurring in the developing countries of Asia and Africa. The disease is endemic in Uganda and has been ranked among the top-priority seven zoonotic diseases that impact public health in the country. Effective management of the disease in endemic countries has been greatly affected by the absence of reliable data. This study aims at determining the spatial-temporal patterns of rabies outbreaks in domestic animals (dogs, cats, goats, and cows) in Uganda. A retrospective study was carried out based on rabies reporting data from January 2018 to September 2022 as compiled by NADDEC. Descriptive statistical techniques were employed to calculate the prevalence of the disease. The temporal patterns of rabies were achieved by creating a line graph that depicted how rabies cases changed over time. QGIS software version 3.28 was used to explore the spatial patterns of the disease, enabling the visualization of the distribution of rabies cases across various districts in Uganda. ARMA (13,4) model was opted to predict rabies cases in Uganda from October 2022 to December 2023. A total of 2,081 rabies cases were reported in Uganda from January 2018 to September 2022. This represents 2.29% of the total number of animals (90,895) reported to be at risk. The predominant method of diagnosis used by veterinary technical staff was clinical manifestation; only 8 cases were laboratory confirmed. The year 2019 had the highest number of cases (29.56%), whereas 2020 had the lowest number of cases (7.11%). Of the reported cases, 23 (goats and cows) were slaughtered, 515 died, and 581(cats and dogs) were euthanized. Districts of Mukono, Tororo, Iganga, Kalangala, Busia, and Serere reported the highest number of cases (between 35 and 688) while Kiboga, Mityana, Sheema, Rubirizi, Moyo, and Pader reported the least cases. The most predominant method of rabies prevention was vaccination where total a of 39,735 animals were vaccinated. The model projected 89 cases of rabies between October and December 2022 and a total of 248 rabies cases in the year 2023, January was predicted to have the fewest cases while April had the highest. The main outbreak management methods used were culling, movement control, and awareness creation. The spatial-temporal patterns of rabies identified in this study indicate a heterogeneous distribution of the disease throughout the country. This, therefore, calls for appropriate planning and resource allocation by key actors to achieve the global target of “Zero rabies by 2030.”
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ItemAntibiotic susceptibility and selected toxin genes profiles among Bacillus cereus isolated from raw bovine milk from a milk collection center in Kawempe Division, Kampala District(Makerere University, 2023)Bacillus cereus causes food intoxication hence a burden to public health. Bacillus cereus is also among the top five foodborne pathogens, especially in starchy foods and raw cow milk. The pathogenicity of the B. cereus is associated with the potential to produce diarrheal and emetic toxins. The pathogen has been associated with clinical infections, whose management could be challenged by antimicrobial resistance. There is scanty information on the contamination levels of raw bovine milk with B. cereus, its toxigenic potential, and its susceptibility to antibiotics in Uganda. This study aimed to determine the proportion of raw bovine milk contaminated with B. cereus sold within Kawempe division, Kampala as well as its toxigenic potential and antibiotic susceptibility profiles. In the present study, 30 raw bovine milk samples were collected from a milk collection centre in the Kawempe division, Kampala . From the samples where growth occurred, five isolates were selected for further characterization. Isolates were identified and confirmed using gram-staining, citrate, catalase, oxidase and motility. Antibiotic susceptibility profiles were determined by the Kirby-Bauer technique, while multiplex real-time PCR allowed the detection of toxigenic genes (hblD, nheA, cytK 1 and ces). Of the 30 milk samples, eight (26.7%) were contaminated with B. cereus. All the 40 isolates that were selected for antibiotic sensitivity testing, exhibited susceptibility to gentamycin, tetracycline, chloramphenicol and ciprofloxacin, but all were resistant to ß-lactam products including Ampicillin and Penicillin. The hblD, nheA, cytK1 and ces were encountered in 82.5 % (33/40), 85 % (34/40), 0%, and 0% of the B. cereus isolates respectively. Contamination of milk with B. cereus and the presence of the diarrheal toxin genes, hblD and nheA, implies that there is a potential risk of associated food-borne illnesses, especially where raw bovine milk is consumed. The cytK1, a diarrheal toxin-encoding gene was absent. In this research, the ces was absent hence no potential for emesis. Thus, there is a need for wider surveillance of contamination of especially the raw bovine milk.
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ItemMathematical modeling and simulation of malaria vector propagation : a tool for evaluation of novel control tools(Makerere University, 2026)Background: Malaria transmission is sustained by highly adaptable Anopheles mosquitoes that persist across dry seasons and rebound in large numbers when the rains return. Despite major progress in vector control, knowledge gaps remain regarding the survival mechanisms that sustain mosquito populations during dry seasons. This study investigated the evolutionary and ecological mechanisms enabling such persistence and spread. It contributes critical insights for evaluating the effectiveness and sustainability of current and emerging vector control tools, including gene drive technologies. Methods: To investigate the dry season persistence mechanisms of malaria mosquitoes, existing studies on survival strategies were critically evaluated to identify strengths, weaknesses, and knowledge gaps. A novel population genetic modeling framework was developed to estimate the proportion of aestivating adults, mosquitoes typically difficult to sample due to unknown habitats, and was initially applied to the Anopheles coluzzii dataset from Mali. This model was subsequently extended to jointly estimate both aestivation and long-distance migration and then applied to temporal genetic data from Eastern Uganda. Additionally, to assess the potential impact of novel vector control strategies such as gene drive, the population genetic structure and demographic history of Anopheles gambiae and Anopheles arabiensis were characterized using amplicon sequencing data collected from three island and three mainland sites in Uganda. Results: Malaria mosquito populations persist through the dry season and rapidly rebound at the onset of the rainy season via four key mechanisms: aestivation, local refugia, local migration, and long-distance migration. Application of the developed population genetic model to temporal data from Mali successfully estimated the proportion of aestivating adults. When extended to incorporate both aestivation and long-distance migration and applied to temporal data from Eastern Uganda, the model revealed that the Sahelian region exhibits stronger seasonality compared to Eastern Uganda. Furthermore, genomic analysis of amplicon sequencing data from island and mainland sites in Uganda showed pronounced spatial population structure, with island populations showing greater genetic differentiation not only from mainland populations but also among individual island sites. This strong within-island differentiation highlights their potential suitability for contained gene drive field trials. Conclusion: This study aimed to determine the role of seasonal and evolutionary dynamics in mosquito survival by demonstrating that population genetics models can effectively estimate proportions of aestivating mosquitoes typically difficult to sample in the field. Moreover, this modelling framework is adaptable to quantify the relative contributions of multiple mosquito survival mechanisms within diverse ecological contexts. These insights are critical for optimizing the design of field trials for novel vector control strategies, such as gene drive, by elucidating population connectivity and seasonal persistence patterns. Additionally, the findings contribute to improved insecticide resistance management by illuminating how seasonal dynamics and vector life-history strategies influence the strength of selection and the spread of adaptive alleles, thereby supporting the responsible and sustainable deployment of genetic control technologies.
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ItemHIV drug resistant mutations associated with virological failure among HIV-1 zero positive infants in Uganda after intensified adherence counseling(Makerere University, 2026)Paediatric HIV treatment is setback by poor adherence and emerging drug resistance. This longitudinal cohort study assessed the impact of intensified adherence counselling (IAC) on viral suppression and the development of HIV drug resistance mutations in HIV-positive infants receiving antiretroviral therapy (ART). 100 HIV-positive infants (aged 4–12 months) with unsuppressed viral loads (>1000 copies/mL) were enrolled at the Joint Clinical Research Centre (JCRC), Uganda. Mother-infant pairs received IAC for a period of three months. After three months, re-evaluation was conducted, during which HIV viral load was measured using the Abbott assay and adherence was assessed using the pill-count method. Infants with persistent viremia were subjected to drug resistance testing using next-generation sequencing using a MiSeq from which the resulting FASTA files were downloaded from Hydra and submitted to the Stanford University HIV Drug Resistance Database (Version 9.8). The output, provided as a Comma-Separated Values (CSV) file, included classified mutations, mixtures, corresponding scores, susceptibility status, and other relevant parameters. A tabular summary of these findings was then generated to facilitate interpretation and further analysis. Intensified Adherence Counselling (IAC) in mother–infant pairs prompted better results in viral suppression despite changes in adherence, with viral loads continually decreasing after IAC compared to before IAC. HIV drug resistance mutations showed changes in both NRTI and NNRTI profiles. The common NRTI mutation M184V/I reduced slightly post-IAC (43.5% to 40.2%), while increase in TAM-associated mutations (K219, K70, D67) suggested ongoing selective pressure from thymidine-based regimens. NNRTI resistance showed an overall decline, with major mutations such as K103N and Y181C decreasing significantly after IAC, with the disappearance of variants like E138Q and G190S, confirming improved viral suppression and reduced propagation of resistant quasispecies. Mixture mutation analysis showed reductions in NRTI (M184, K219) and NNRTI (V179, V108, Y181, V106) variants, further indicating suppression of resistant viral populations. Emergence and persistence of mutations such as E138A, K238, P225H reflects ongoing viral suppression under treatment pressure. Overall, IAC contributed to improved viral control and reductions in several resistance-associated variants, though there is a continued need for vigilant resistance monitoring and optimized ART regimens.