School of Biosecurity, Biotechnolgy and Laboratory Sciences (SBLS)

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Analyzing diagnostic infrastructure and capacity building needs for effective rabies control strategies in selected districts of Uganda

(Makerere University, 2024-11) Apio, Felister

Rabies remains a significant public health concern in Uganda, particularly in rural districts where the disease is often underreported and inadequately managed. This study aims to assess the management and control strategies of rabies in selected districts of Uganda, with a specific focus on evaluating the diagnostic infrastructure and identifying capacity-building needs within district veterinary laboratories. Through a comprehensive analysis involving 42 key informant interviews with veterinary practitioners, laboratory technologists and nurses; 8 focus group discussions with veterinary para-professionals and a direct observation of laboratory facilities, the findings reveal significant disparities in the availability and functionality of veterinary laboratories, with Masaka and Arua exhibiting relatively well-established facilities, while Kyegegwa lacks any veterinary laboratories entirely. Soroti has a partially functional laboratory. The study also identifies key challenges, including gaps in diagnostic capabilities, resource limitations, and the need for enhanced training programs elaborated by participants with quotes such as “Inadequate facilities…”, “Limited understanding of procedures..”, “Collecting samples is risky...”, “More training is needed..”. The study underscores the critical importance of strengthening diagnostic infrastructure and capacity building in district veterinary laboratories to improve rabies management and control efforts. The findings advocate for Implementing comprehensive on job training programs for veterinary personnel in all districts, with a focus on proper sample collection techniques, testing procedures, and improvement and maintenance of diagnostic equipment including creating awareness among the community and increasing their level of knowledge about rabies in order to increase reporting and improve the management of rabies.
Antibacterial activity and acute toxicity of herbs used in treatment of water borne diarrheal diseases in Butaleja District

(Makerere University, 2021-04) Ongodia, Raphael

Uganda is still negatively impacted by a huge burden of water borne diseases, the heaviest being diarrhoeal diseases. This may result in high morbidity and mortality rates if left unattended to. The study documented herbs used in Butaleja district to treat water borne diarrhoeal diseases and evaluated their antibacterial efficacy and safety. This was achieved by: conducting an ethnobotanical survey employing observation, focus group discussions, informal, field & in-depth interviews; Evaluating in vitro antibacterial activity for crude ethanol, petroleum ether and aqueous extracts of six preferred medicinal plants against selected bacteria species: Bacillus cereus, Staphylococcus aureus and Clostridium perfringens (gram positives) and Shigella dysenteriae, Salmonella typhi, Escherichia coli (gram negatives) using agar well diffusion, minimal inhibitory concentration (MIC) values determined using a microplate serial dilution technique and consequently minimum bactericidal concentration (MBC) values; Evaluating oral acute toxicity of three preferred plant extracts in BALB/c mice of 5-7 weeks using old Lorke’s method. Ethnobotanical data was summarized using descriptive statistics, antibacterial assay data analysed using one-way analysis of variance and then tukey tests, acute toxicity data was subjected to probit analysis to determine median lethal doses. Fifty-six plant species from 31 families were reported, most dominant family was Fabaceae with eight plant species, 40% were sourced from wild and home gardens, tree life forms (33%) were most dominant, most dominant plant parts were leaves (37%), most dominant mode of preparation was decoction (40.9%) and most frequently cited plants were Microglossa pyrifolia & Tamarindus indica with a 5% frequency of citation. The preferred plant species basing on informant consensus were Erythrina abyssinica, Zanthoxylum leprieurii, Hydnora abyssinica, Cryptolepis Sanguinolenta, Diospyros natalensis, Securidaca longipedunculata. Five out of six preferred plant species exhibited antibacterial activity in at least some extracts with variable potency with MIC values ranging from 0.039 mg/mL to 2.5 mg/mL whereas MBC values ranged from 0.313 mg/mL to 5.0 mg/mL of crude extract. All three most effective plant extracts showed LD50 values above 5000 mg/kg of body weight, therefore, exhibited safety margins so people may use them without any doubts though more studies are required to isolate active compounds. The best solvent people should use is alcohol because they extract out active ingredients best which can be used to provide leads for drug discovery and among the selected plant species, Cryptolepis sanguinolenta was most effective.
Antimicrobial knowledge among communities and sSusceptibility patterns of staphylococcus aureus isolated form wildlife-livestock-human Interface at Lake Mburo National Park, Western Uganda

(Makerere University, 2023-01-04) Matovu, Catherine

Antibiotic resistance has become a global public health concern because of the organisms causing infections are becoming resistant to most commonly prescribed antibiotic treatments, resulting in prolonged illness and greater risk of death. The knowledge of antimicrobial resistance is extremely vital to human, livestock and wildlife health. Such information can be relevant in understanding patterns of disease occurrences and prediction of emerging resistant bacteria strains. This cross-sectional study was aimed at assessing antimicrobial knowledge among host communities and susceptibility pattern of Staphylococcus aureus isolates from wildlife-livestock-human interface at Lake Mburo National Park. A total of 277 samples were collected from domestic animals (58), humans (159), and wild animals (60). Isolation and identification were done for the Staphylococcus aureus organism and antimicrobial susceptibility determined using the disc diffusion test. The results indicated that the prevalence of Staphylococcus aureus was 17 (6.1%). From all the eight antimicrobial drugs used Staphylococcus aureus was most susceptible to Gentamicin (100%), Ciprofloxacin (100%), Imipenem (100%), Chloramphenicol (100%), Trimethoprim (94.1%) and Ceftriaxone (94.1%) respectively. Tetracycline and Ampicillin were the most resistant drugs by the Staphylococcus aureus species at 10 (58.8%) and 2(11.7%) respectively. Almost all participants 109 (93.2%) did not know how antimicrobial resistance came about and (70.1%) did not know that it could affect treatment outcome. In conclusion, we observed 17 (6.1%) isolates of Staphylococcus aureus which were more susceptible to Gentamicin, Ciprofloxacin, Imipenem and Chloramphenicol followed by Trimethoprim and Ceftriaxone but showed resistance to Tetracycline and Ampicillin which are frequently used by the communities around the wildlife-livestock-human interface in western Uganda. Therefore, there is need for broader susceptibility studies not only focusing on Staphylococcus aureus but also other micro-organisms. Additionally, policy and laboratory based antimicrobial resistance surveillance should be encouraged through continued data sharing, large-scale collaboration, and coordination of all stakeholders to understand and manage the national AMR burden.
Antimicrobial profiles of E. coli, Salmonella and Campylobacter spp from raw and roasted chicken meat. A case of vending points along selected highways in Uganda

(Makerere University, 2022-03) Pimundu, Godfrey

Food-borne pathogens are an emerging threat in lieu of increased population growth and urbanization. Safety of ready-to-eat foods notably those on highways is questionable as several cases of gastro-intestinal issues have frequently been reported. Paucity of data on microbial safety of ready-to-eat foods hinders appropriate planning of strategies to alleviate food related illnesses. Therefore, this study aimed at determining the prevalence of E. coli, Salmonella and Campylobacter in raw and roasted chicken meat vended on major sites along the three major routes in Uganda. A field based cross sectional study was carried out to establish the prevalence and susceptibility to antibiotics of E. coli, Salmonella and Campylobacter in raw and roasted chicken meat vended on major sites along the three major routes in Uganda that is Namawojjolo (Kampala-Jinja highway), Lukaya (Kampala-Masaka highway) and Balikyejjusa (Kampala-Gulu highway). E. coli was the most common contaminant in both roasted and raw chicken meat (72.4%, 110/152); followed by Campylobacter, (26.3%, 40/152) and lastly Salmonella (5.9%, 9/152). In raw chicken meat E. coli was the most isolated bacteria with 92.9% (78/84), followed by Campylobacter with 47.6% (40/84) and Salmonella with 10.7% (9/84). Roasted chicken meat was contaminated with only E. coli 47.1% (32/68) but was free of Campylobacter and Salmonella. The latter were abundant in raw chicken meat. Antimicrobial resistance was observed towards Ampicillin, Tetracycline and Amoxicillin and Clavulanic acid by E. coli and Salmonella. Meanwhile Campylobacter was mainly resistant to Ceftriaxone and Ciprofloxacin. Generally, hygiene and sanitation of the sites and vendors was very poor; poor personal hygiene, dirty abattoir surfaces, dirty knives used and dirty working environment with the presence of stagnant dirty water observed in one of the sites. Therefore, there is need to conduct full scale sensitization and continuous education to chicken meat handlers along these routes on standard hygiene and sanitation practices. A study to follow up at the poultry farms that supply these chickens is also needed to determine if meat contamination and antimicrobial resistance are associated with farming practices that can facilitate mitigation strategies.
Antimicrobial resistance of staphylococcus aureus; knowledge, attitude, and practices on antibiotic use among farmers in Isingiro and Kamuli districts – Uganda

(Makerere University, 2022) Awke, Ilyas Abdi

Bacterial resistance to antibiotics is fast becoming a big challenge as resistance to multiple drugs is rising rapidly. The emergence of resistant Staphylococcus aureus worldwide is life-threatening for both the human and animal sectors. The antimicrobial resistance (AMR) is accompanied by high morbidity and mortality. The study was designed to determine the prevalence of AMR in S. aureus among humans and animals, and the knowledge, attitude, and practice of farmers in relation to AMR of S. aureus. This was a cross-sectional study whereby households in Isingiro and Kamuli districts which have cattle were selected and nasal swab samples were collected from both animals and humans (farmers) and taken to the laboratory for processing and analysis using microbial techniques. Questionnaires were administered to the selected farmers to assess their knowledge, attitude, and practices. A total of 147 farmers were interviewed, 71 (48.3%) from Isingiro district and 76 (51.7%) from Kamuli district between July and September 2020. Data analysis was done using STATA version 15.0 with results reported as frequencies and percentages. The majority of the respondents were males in both Isingiro (77.5%) and Kamuli (71.4%). Cattle in Kamuli, S. aureus was isolated from 10/76 (13.2%, 95% CI 9.9-27.1) of animal swab samples. Cattle from Isingiro, S. aureus was isolated from 8/71 (11.3%, 95% CI 5.7-21.1) of animal swab samples. There was 100% susceptibility to Ciprofloxacin and Gentamycin among animals in both Kamuli and Isingiro. In Kamuli highest resistance was to penicillin G 100% and Metronidazole 100%. In Isingiro, highest resistance was to; Penicillin-G 75%, Ampicillin 87.5%, and Metronidazole 100%. Farmers in Kamuli, S. aureus was isolated from 29/76 (38.2%, 95% CI 24.7-66.2) of human swab samples. Farmers in Isingiro, S. aureus was isolated from 18/71 (25.4%, 95% CI 16.5-36.9) of human swab samples. In Isingiro there was 100% susceptibility to Ciprofloxacin and Gentamycin among humans. High resistance was to Penicillin G 94.7%, Ampicillin 94.7%, and Metronidazole (100%). In Kamuli high resistance was to Penicillin G 92.3%, Ampicillin 88.5%, and Metronidazole 100%. Farmers in Isingiro have better knowledge and attitude about AMR compared to those in Kamuli and the practices also significantly varied among farmers in the two districts (P-value < 0.05). 64.8% of the farmers in Isingiro said that the withholding period to wait until selling or consuming is 5 days, while the majority (34.67%) in Kamuli said there is no withholding period to wait until selling or consuming animal products. Staphylococcus aureus is still a burden among farmers in Isingiro and Kamuli districts and it was more prevalent in Kitayundwa and Mbaale sub-counts compared to Balawoli and Ndiizi sub-counts respectively. There is a need for a massive public awareness campaign to improve national awareness of AMR.
Antimicrobial resistance profiles of Escerichia coli in different farming systems in Kamuli and Isingiro districts of Uganda

(Makerere University, 2022-12-16) Nabirye, Dorah

Antimicrobial resistance (AMR) is a global crisis, as new forms of resistance emerge and are spreading quickly between continents. The problem of AMR is vast in developing countries, where the burden of infectious diseases is enormous. E. coli is commensal organism of the mammalian gut and is also a reservoir of AMR genes. Through horizontal gene transfer, E. coli exchanges genetic material especially of resistant genes making it a useful indicator of AMR. Additionally, it’s found everywhere which makes its monitoring especially in food producing animals possible.(Fearnley, 2022) Several pathogenic strains of E. coli are known to be resistant to a number of antibiotics. However, there is limited data on antimicrobial profiles of Escherichia coli isolates from Ugandan livestock and farmers. We, therefore, conducted this cross-sectional study to determine the prevalence of E. coli AMR among humans, cattle and the associated predisposing factors in agro-pastoral farming systems of Kamuli and Isingiro districts of Uganda, as both of these districts are located within the cattle corridor. A total of 284 fecal samples were collected from both animals and humans in the study areas, followed by bacterial isolation and antimicrobial susceptibility tests on nine antimicrobial drugs from (Oxoid; Basingstoke, in the United Kingdom) i.e ciprofloxacin (5μg), gentamycin (10 μg), tetracycline (30 μg), amoxicillin (25μg), vancomycin (30μg), ampicillin (10μg), erythromycin (15μg), metronidazole (10μg), and penicillin-g (10μg). Selected farmers who kept animals and drug shop owners were interviewed using a structured questionnaire in the kobo collect application to assess the associated predisposing factors of AMR. The collected data were analyzed using STATA. Bacterial isolation was performed on all fecal samples. From these, antimicrobial sensitivity tests were carried out on 119 viable E. coli isolates (62 (52.10%) were of animal origin while 57(47.9%) were human fecal samples). Overall, 96.98% of the E. coli isolates had developed resistance against at least one antimicrobial agent used in this study. Probably due to the high level of abuse of antimicrobial drugs among farmers. Generally, ciprofloxacin and gentamycin, were highly effective against E. coli isolates from both cattle and humans, whereas the isolates were resistant (100%) against vancomycin and metronidazole. Therefore, vancomycin and Metronidazole are not effective against E. coli isolates as shown by the 100% resistance to both drugs in both humans and cattle. I would recommend the use of ciprofloxacin and gentamicin as these had a high susceptibility. Rational use of antimicrobial products by all stakeholders should be practiced.
Antimicrobial resistance surveillance: a case study of escherichia coli isolates from selected chicken farms in Masaka City, Uganda

(Makerere University, 2023-09) Wakulira, Stephen Lubega

The increasing field reports of apparent antimicrobial resistance and resulting treatment failures in poultry farms, that were not supported by scientific evidence was the impetus for this study on chicken farms in Masaka City. The study recruited 50 chicken farms from which 280 samples were collected to investigate the antibiograms, genetic drivers and risk factors associated with development of antimicrobial resistance among E. coli. The E. coli isolates were subjected to a panel of six antibiotics including ampicillin (10μg), neomycin (30μg), Gentamycin (30μg); tetracycline (30μg), ciprofloxacin (30μg); and potentiated Sulphonamides [trimethoprim/sulfamethoxazole (1.25/ 23.75μg)]. The highest level of resistance was recorded against Tetracycline and Sulphonamides at 76% and 74%, respectively. The E. coli isolates demonstrated the highest susceptibility (96%) to gentamycin (CN). Conventional and multiplex PCRs were run on the E. coli isolates to screen for genes that code for Tetracycline (Tet M, O, & K) and Sulphonamide (Sul-1 & Sul-2) resistances respectively. All isolates were negative for the tetracycline resistance at genotypic level. Only three (3) and four (4) isolates were positive for the Sul 1 & 2 genes respectively. The prophylactic use of antibiotics as an intervention against disease occurrence was 2.02 times responsible for causation of AMR on chicken farms. To the contrary, farms where antibiotics were only prudently used during disease outbreaks had less chances of AMR occurrence. This association was significant at odds of 0.21 and a p-value of 0.002. Therefore, when used appropriately amidst outbreaks, antibiotics are protective against development of AMR on farms as opposed to other concoctions such as herbs. Furthermore, farms that kept < 500 chickens were 3.63 times more at risk of experiencing E. coli resistance compared to farms that had flocks of over 1000 chickens. At adjusted odds ratio of 3.63 and 95% confidence interval of 1.16 to 11.31, this association was statistically significant at p-value 0.027. In conclusion, the findings are indicative of a likely bigger challenge in Masaka city. Therefore, there is a need for regular AMU on-farm monitoring, use of available laboratory diagnostics in addition to further in-depth studies as regards AMR on chicken farms.
Antimicrobial susceptibility patterns of escherichia coli isolates from livestock and predisposing factors to antimicrobial resistance in Isingiro and Kamuli Districts, Uganda

(Makerere University, 2024-11) Oyirwoth, Osborn

Antimicrobial resistance (AMR) is a global health challenge to human and animal population. Increase in livestock population coupled with intensive husbandry practices has greatly resulted into increased utilization of antimicrobial products in the management of livestock diseases. This was a cross-sectional study conducted between August and November 2022 in 183 and 87 randomly selected livestock keeping households in Kamuli and Isingiro Districts respectively; to determine the antimicrobial susceptibility patterns of Escherichia coli isolates from livestock. Fresh fecal samples collected from rectum of each cattle, goats, and cloacal swab from chicken were placed in Stuart Transport medium and taken to College of Veterinary medicine, Animal Resources and Biosecurity public health laboratory for processing. Escherichia coli culture and isolation was done using chromocult selective media. This was followed by antimicrobial susceptibility testing (AST) by the Kirby Bauer disc diffusion method. A total of fecal samples was collected. However, 683 fecal samples were collected from which 572 E. coli isolates were obtained. These were 191 (33.1%) from cattle, 200 (35.0%) from goats and 181 (31.6%) from chicken. Only samples from which E. coli was isolated were subjected to AST. The study revealed that E. coli isolates exhibited variation in susceptibility with highest susceptibility 97.5% to kanamycin, and resistance 79.8% to tetracycline. Correct farmers’ knowledge of AMR, human sharing water sources with livestock and open field disposal of animal wastes and use of trained veterinarians were significant predictors of AMR. Evidence of the high prevalence of AMR documented here provides a baseline for the need of further surveillance and call for urgent implementation of mitigation strategies to combat this public health challenge in line with the Uganda AMR National action plan.
Antimicrobial susceptibility profile of klebsiella species associated with mastitis in cattle from Ssembabule District, Uganda

(Makerere University, 2022-12-30) Asiimwe, Ismail

Mastitis is one of the major burdens affecting the dairy sector lowering both the quality and quantity of milk. In an attempt to manage or prevent mastitis, farmers have resorted to frequent and irrational use of antimicrobial drugs that have resulted in the development of resistance to some of the frequently used antimicrobials. This study aimed to establish the prevalence of Klebsiella spp. in mastitis cases and the antimicrobial susceptibility profile of the isolates. A total of 224 lactating cows in selected herds were examined for both clinical and subclinical mastitis. Screening for subclinical mastitis was done using the California Mastitis Test (CMT) while that of clinical mastitis was through clinical examination. Milk from CMT positive cases were taken to the laboratory for bacteriological analysis. Klebsiella spp. were isolated and then identified by morphological and biochemical tests. The antimicrobial susceptibility patterns of Klebsiella isolates were determined using Kirby-Bauer disc diffusion method. The prevalence of subclinical mastitis in the 224 cows screened was 47.39% and that of Klebsiella spp. was 39.1%. Almost all the Klebsiella isolates (95.56%) were resistant to Erythromycin, while most of the isolates (84.44%) were sensitive to Gentamycin. The isolates exhibited variable susceptibility to Ceftriaxone, Cotrimoxazole, Meropenem, Tetracycline, Ceftazidime, Cefepime and imipenem; and over four isolates demonstrated multiple drug resistance. Among Gram-negative bacteria, Klebsiella spp. potentially causes bovine mastitis and exhibited resistance to some of the commonly used antimicrobials in livestock and dairy production systems. There was high prevalence of Klebsiella spp. isolated from milk samples of bovine mastitis cases, with highest resistance demonstrated against antimicrobial classes of Macrolide followed by third generation Cephalosporin and then Tetracyclines. Highest susceptibility was exhibited for aminoglycoside followed by carbapenems. Farmers are encouraged to regularly screen their lactating cows for mastitis so that the infected are given early treatment. Then veterinary practitioners are required to conduct antimicrobial susceptibility testing to guide the choice of drug for appropriate treatment.
Antimicrobial use in pig production and its associated risk factors in Wakiso District, Uganda

(Makerere University, 2023-11) Musiitwa, Rogers

The high use of antimicrobials in food animals such as pigs raises concerns about food safety, security, trade and market access for livestock and livestock products. The study determined the prevalence of antimicrobial use in pig production and its associated risk factors in Wakiso district, Uganda. A cross-sectional study was conducted in Wakiso district, Uganda between August and October 2022. It involved the use of mixed methods design to collect both qualitative and quantitative data from pig farmers and veterinary workers. The quantitative data was collected from 409 households in Kakiri, Kyengera, and Kasanje Town Council, Wakiso district. Three Key Informant Interviews and three Focus Group Discussions were conducted with the veterinary workers and pig farmers respectively. Quantitative data was analysed using STATA 14 and qualitative data analysed thematically using NVIVO 12 pro software. The majority of the respondents were females (65.3%) with at least 91.7% of the respondents had completed the primary level of education. Out of the surveyed households, 94.1% (385/409) had used antimicrobials in pig production in the past six months to the time of study. Most of the respondents (94.8%) who used antimicrobials obtained them from veterinary workers or pharmacies. The common antimicrobials used by pig farmers were; Sulphonamides, tetracyclines, penicillin and streptomycin, gentamicin, and amoxicillin. Qualitative results showed that pig farmers were also using extra label drugs such as Paracetamol, Antiretroviral drugs, and Ampicillin in pig production. Vaccination of pigs (6.9 odds ratio), farmers’ knowledge on antimicrobials and antimicrobial use (3.2 odds ratio), and people freely accessing the pig farms (2.6 odds ratio) were all associated with high antimicrobial use in pig production in Wakiso district. Qualitative results also emphasized that farmers with high knowledge on antimicrobials were more likely to use antimicrobials in pig production than their counterparts. The study found a high use of antimicrobials in pig production among the study households of Wakiso district. Therefore, there is a need for farmers to improve the biosecurity measures on their farms to reduce the risks of diseases and thus reduce the need for antimicrobials. Sensitization should also be done to create a positive attitude among farmers to use antimicrobials only when necessary.
Antiretroviral resistance mutation profiles among drug regimens and HIV-1 Subtypes in Uganda

(Makerere University, 2019-05) Ayitewala, Alisen

Antiretroviral drug resistance is highly considered as a key limiting factor in HIV management because of its varying impact across drug regimens and HIV-1 subtypes. In Uganda, there is a paucity of data on how this factor scores among the different drug regimens and HIV-1 subtypes. The purpose of this study was to determine mutation profile differences between first-line drug regimens; Tenofovir/Lamivudine/Efavirenz (TDF/3TC/EFV) & Zidovudine/Lamivudine/Efavirenz (AZT/3TC/EFV) and HIV-1 subtypes; A and D in Uganda. The study also investigated the potential usage of Rilpivirine and Etravirine in patients who failed treatment on Efavirenz. A retrospective study was done on 199 archived plasma samples which were collected from patients who had virological treatment failure between 2006 and 2017 at five (5) sites of Joint Clinical Research Center, Uganda. Sequencing of the Reverse Transcriptase gene from codon 1-300 was done and drug resistance reports were generated from Stanford University HIV database. A Chi-square test was used to determine the association between drug resistance mutation (DRM)s and drug regimens or HIV-1 subtypes. The prevalence of DRMs was 83.4% in treatment failure patients. M184V/I (67.3%), K219/Q/E (22.6%) and K65R (21.1%) as the most prevalent among nucleoside reverse transcriptase inhibitor (NRTI) mutations. K103N (50.8 %) and G190A/S/E/G (29.1 %) as the most prevalent among non-nucleoside reverse transcriptase inhibitor (NNRTI) mutations. No significant difference (P=0.367) was found between AZT/3TC/EFV and TDF/3TC/EFV in the acquisition of overall DRMs. However, within the NRTI class, mutations K65R (p=0.00005), K70E/G/Q/T/N/S (P=0.004) and L74V/I (P=0.003) appeared more frequently in the TDF/3TC/EFV. On the other hand, mutations L210W (P=0.002), K70R (P=0.005), T215Y (P=0.022) were more in AZT/3TC/EFV. No significant difference (P=0.336) was found for overall DRMs across HIV-1 subtypes A and D. Among the patients who had resistance to EFV, 37 (23.6%) were susceptible to newer NNRTIs. It was concluded that resistance mutation profiles do not differ between AZT/3TC/EFV and TDF/3TC/EFV, therefore the choice of drug regimen should be based on other factors other than resistance profiles. However, individual mutations that confer resistance to particular drugs should be considered at treatment failure. The study also concluded that having either HIV-1 subtype A or D is not associated with acquisition of DRMs, therefore HIV diversity should not determine the choice of treatment. It was further concluded that Rilpivirine and Etravirine had minimal benefits for patients who failed on Efavirenz, therefore they should not to be considered as options for second line treatment in the national guidelines.
Assessing the aetiology of measles disease and measles-like illness in Uganda

(Makerere University, 2024-12) Namuwulya, Prossy

Globally, measles is estimated to cause 140,000 deaths annually. Measles and measles-like illness (MLI) remain a significant cause of morbidity and mortality in children in sub-Saharan Africa including Uganda. Understanding the occurrence of measles outbreaks is of importance as well as elucidating the causes of measles like illnesses among the measles negative individuals. Methods. Ministry of Health measles surveillance data between 2010 and 2023 was analysed. Additionally, measles IgG/avidity assays, measles B3 and Edmonston A neutralisation assays were used to assess the impact of vaccination. Positive samples were sequenced using measles virus-specific genotype B3 amplicon primers that targeted the full-length measles genome using the MinION platform. Metagenomic next generation sequencing and the illumina platform were used to identify viruses associated with MLI in patient samples that had tested negative for measles between 2010 and 2020. Of the 21,453 individuals from the UNEPI surveillance data with laboratory IgM results between 2010 and 2023, 3181 (15%) tested positive while 15,783 (74%) tested negative, and the other 2489 (11%) had no conclusive results. Of the IgM positives, 2660 (84%; with evidence 323 (12%) and without evidence 2337(88%)) were vaccinated while 521 (16%) were not vaccinated. The likelihood of a positive measles IgM test among measles-suspects was significantly lower in vaccinated versus unvaccinated individuals (p<0.0001). There was a strong correlation between the serum neutralizing antibodies against the measles A Edmonston vaccine strain and B3 strain (Pearson correlation coefficient 0.88; p<0.0001). Measles whole genome sequencing indicated minimal nucleotide changes in the B3 genotype circulating in Uganda over a decade. Using metagenomic next-generation sequencing, 133 viruses including rubella, parvovirus and saffold virus among others were identified in 271 samples. The study highlights the ongoing problem of endemic measles infection in Uganda. Our data confirm the effectiveness of measles vaccination in the Ugandan population and support the need to enhance the vaccination coverage of the recently rolled out second MCV2 to prevent significant morbidity and mortality in the country. The measles whole genome sequencing identified 2 clades of highly conserved measles genotype B3. Several MLI viruses were identified using NGS including measles and rubella viruses that were missed using the routine serological diagnostical diagnostic assay. As two dose vaccination is rolled out, vaccine effectiveness should be monitored in the Ugandan population. Mortality data will be very helpful in determining whether one dose is protective against death. Development and optimization of new diagnostic assays which can accurately and timely detect measles like illness viruses.
Assessing the performance of TB-HIV activities at Masaka Regional Referral Hospital, 2012-2014

(Makerere University, 2021-02) Kisakye, Juliet

The TB-HIV co-infection burden globally, at regional level and locally, remains a health challenge that requires strong diagnosis, treatment and integrated support. A retrospective study was carried out at Masaka Regional Referral Hospital to assess the performance of integrated TB-HIV activities between 2012 and 2014. Data were obtained from review of 1885 patients’ records and key informant interviews with 06 TB unit and 06 laboratory staff members at Masaka regional referral hospital. The percentage of TB patients who were co-infected with HIV was found to be high at 56.7% with the trends of test results showing minimum decrease over years from 2012 to 2014. As compared to WHO set targets, the average proportions of HIV testing rate among TB patients, and provision of Cotrimoxazole Preventive Therapy (CPT) were found to be very good with average recordings of 95.39% and 97.22% respectively. However, the average coverage of Anti Retro-viral Therapy (ART) among TB-HIV patients was poor at 45.90%. HIV-positive patients who were found to be free of TB disease were referred to Uganda Cares for IPT and ART. The laboratory at MRRH was found to be strengthened to improve TB case detection and offer uninterrupted services. However, the hospital had low staffing levels, received insufficient personal protective equipment, and faced congestion in the TB wards in addition to untimely delivery of laboratory supplies and delays in servicing/repair of equipment. The observed performance in terms of HIV testing and provision of CPT to TB patients was attributed to availability of qualified personnel, trainings, and laboratory equipment as well as support from NGOs like TASO, and good working environment. On the other hand, poor access to ART was mainly found to be due to poor health seeking behavior. The performance was found to be depictive of positive progress towards the World Health Organisation’s “End TB Strategy”.
Assessment of health laboratories in handling epidemics of public health importance in Kampala District

(Makerere University, 2011) Kabasa, William M.

Background: Scanty information is available on the extent to which health laboratories in Uganda are involved in managing disease epidemics. According to Central Public Health laboratories report, laboratories in health facilities, including health centers in urban areas with high population densities have a special role in reducing risks, containing emergencies and responding to outbreaks. Moreover health facilities that are affected or exposed to risks, emergencies or outbreaks and are unprepared may pose additional or more serious risks to the communities they serve. This study assessed the level of preparedness of health laboratories in handling epidemics of public health importance in Kampala District. Method: A standardized, semi-structured questionnaire was used to collect information from (30) private health facilities and eight (8) public health center threes (HC3s) making a total of thirty eight (38) laboratories. The collected data was coded and analysed using a Stastical Package for Social Scientists (SPSS). Results: Seven core capacities were analysed where on staffing, laboratory based staff such as microbiologists, laboratory technologists, laboratory technicians and microscopists were 10.0%, 10.4%, 11.1%, and 10.4% , while staffs who got training for any specific disease outbreak of concern were highest in public health labs at 60% and lowest in private labs at 45.2% and those who never trained were highest in private at 52.4% and lowest in public labs at 30%.; Parasitology and serology scored highest at 74.1 %, in the tests performed while mycology scored the lowest at 1.9 %. Biosafety level 2 (BSL2) was more commonly used at 50% while BSL 3 was least used at 9.3%, moreover 25.9 % of respondents implemented Biosafety measures. Handling of disease outbreaks was more in private laboratories at 27.5% and lowest in public labs at 20%. As regards to equipment servicing, 60 % was found to be in public labs while private labs had 58.1%. Results referrals, with reference labs, was lowest in private labs at 83.7% while highest in public labs at 90%. Conclusion: This study suggests that laboratory requirements for management of disease outbreaks were the same for both private and public health units. The status of health laboratories in general laboratory safety management and good laboratory practices were inadequate. EQA practices in the study showed that results for laboratory disease diagnosis in the surveyed health units were accurate and reliable.
Assessment of human and veterinary drug shop sellers’ practices and awareness of antimicrobial resistance : a cross section study in Jinja, Uganda

(Makerere University, 2021-03) Namala, Allen

Antimicrobial resistance (AMR) is a global problem whereby it can affect any person regardless of age, sex, location among other factors. It occurs naturally, although the misuse of antibiotics in humans, animals and environment accelerate the process. Therefore, this study was done to determine relationship of practices of antimicrobial used with awareness of antimicrobial resistance among human and veterinary drug shop sellers in Jinja district. Snow balling method was used for sampling drug shops of both human and veterinary drugs to identify the respondents. All drug shop sellers in the sub counties of Jinja were considered to participate in the study on consent. 444questionnaires were administered and mystery shopper done on all the participating drug shop sellers. Data was analyzed using descriptive analysis and logistic regression to determine the relationship of practices of antimicrobial use with awareness of AMR by human and veterinary drug shop sellers in Jinja district. In Jinja district 97.7% (434/444) were human drug shops and only 2.3% (6/444) were Veterinary drug shops. Demographic characteristics of drug shop sellers revealed that 60% were full time employees and 85% had attained tertiary level of education. Logistic regression was done to determine the prescription predictors of AMR awareness within the study population and none of the prescription practices had association with the awareness (P>0.05) of AMR by drug shop sellers. Univariate logistic regression analysis was performed to determine the dispensing predictors with awareness of AMR in Jinja district and only four dispensing practices of drugs with p-vale of <2.0 were then entered in a multivariate logistic regression model and only “Sale of half dose to those who cannot afford” (OR=1.82, 95%CI: 1.01-3.27, P=0.046) had a significant association with awareness of AMR by the drug sellers. Among selected factors known to influence the sale of antibiotic drugs only proximity to the source of supply (OR =1.82, 95% CI: 1.01-3.28) had an association with the awareness AMR. This study revealed that the there was no association with most of the drug shop sellers’ practices with awareness of AMR and generally the practices were found to be improper. Therefore, the regulatory bodies should enforce improvement of prescription and dispensing practices amongst drug shop sellers since they are the custodians of the drugs.
Associations between plasmodium falciparum aminoquinoline resistance genotypes and clinical presentations of malaria in Ugandan children, A case control study of Jinja District and the neighbouring Busoga Sub-Region Districts

(Makerere University, 2023-01) Cuu, Gloria

Plasmodium falciparum resistance mutations to aminoquinoline antimalarials are selected by prior drug use and may alter parasite fitness yet their associations with clinical malaria presentations are uncertain. Retrospectively, genotypes in samples were assessed from a case control study of determinants of severe malaria in Ugandan children aged 4 months to 10 years. 274 severe malaria cases matched by age and geographical location to 275 uncomplicated malaria and 179 asymptomatic aparasitemic controls. Target age groupings were 4 to 12 months, 1 to 3 years, 3 to 5 years, and 5 to 10 years. Adult caregivers of children with only severe or uncomplicated malaria detailed all medicines received during the acute illness. Genomic DNA was extracted from dried blood spots by using Chelex method. The PfCRT and PfMDR-1 alleles of interest were determined using a ligase detection reaction-fluorescent microsphere assay, with minor modifications, including nested PCR amplification of templates. Data was analyzed with STATA (version 14). Descriptive statistics were reported as proportions and medians with interquartile ranges. Chi-square test and the Wilcoxon signed rank test were used for categorical and continuous data, respectively. Associations between the polymorphisms and malaria outcomes were assessed by cross-tabulations with chi-square tests. Prevalence of mutations of interest was 67.2% (431) for PfCRT K76T, 8.4% (58) for PfMDR-1 N86Y, 71.4% (513) for PfMDR-1 Y184F, and 14.6% (96) for PfMDR-1 D1246Y. Compared to asymptomatic controls, the odds of mutant PfCRT 76T were lower for uncomplicated (odds ratio 0.42 (95% CI 0.24-0.72); p<0.001) or severe (0.56 (0.32-0.97); p=0.031) malaria; the odds of mutant PfMDR-1 86Y were lower for uncomplicated (0.33 (0.16-0.65); p<0.001) or severe (0.21 (0.09-0.45); p<0.001) malaria; and the odds of mutant PfMDR-1 1246Y were higher for uncomplicated (1.83 (0.90-3.98); p=0.076) or severe (2.06 (1.01-4.55); p=0.033) malaria. The odds of mutant PfMDR-1 184F were lower in severe compared to asymptomatic (0.59 (0.37-0.92); p=0.016) or uncomplicated (0.61 (0.41-0.90); p=0.009) malaria. Overall, the PfCRT 76T and PfMDR-1 86Y mutations were associated with decreased risk of symptomatic malaria, PfMDR-1 1246Y was associated with increased risk of symptomatic malaria, and PfMDR-1 184F with decreased risk of severe malaria. These results offer insights into parasite genotypes in children with different malaria clinical presentations.
Bacterial contamination of milk and antimicrobial resistance profiles of selected pathogens in Kiboga District

(Makerere University, 2018) Mayanja, Raymond

Milk when not properly handled during transportation and storage, favors growth of several microorganisms. Many factors exist in the cattle corridor of Uganda that suggest bacteria contamination of milk during transport to collection centres is an issue. A study was carried out to determine the bacteria contamination of milk along the transportation chain in Kiboga district using total plate counts (TPC) and characterize some of the isolated pathogenic bacteria using drug resistance/susceptibility patterns and molecular typing for resistance against vancomycin. Milk samples from 50 farms were collected at the farm and the same milk followed upto the collection centres and again collected. Bacteria contamination of raw milk was enumerated by TPC. The mean TPC was 6.16 X 106 cfu/ml in the farms and 6.62 X 107 cfu/ml in the collection centres with a minimum of 0 in the farms and 2300 cfu/ml in the collection centres. The maximum TCP was 48.6 X 106 cfu/ml in the farms and 1 X 109 cfu/ml in the collection centres. Generally, higher milk contamination was observed at the collection centres than in the farms (p = 0.000). Bacteria with the wide drug resistance patterns were Klebshiela spp and E.coli whereas those with the narrow resistance patterns were Staphylococcus aureus and Streptococcus spp. Pen G was the most inefficient drug with the following resistance patterns: Staphylococcus aureus 48%, CNS 91%, Klebsiella 96%, E.coli 100% and Streptococcus ssp 15%. The most effective drug was Ciprofloxacin with a susceptibility pattern among isolates as follows: Staphylococcus aureus 96%, CNS 61%, Klebsiella 100% and Streptococcus ssp 62%. The Van A gene associated with vancomycin resistance was detected in one Staphylococcus aureus isolate. No Van B gene was identified amongst the 15 vancomycin resistant isolates screened suggesting presence of other genetic markers for vancomycin resistance. In conclusion the bacteria contamination of milk in Kiboga district deteriorated during transportation due to the increase in bacterial load.
Bacterial pathogens associated with febrile conditions and their antimicrobial sensitivity pattern in children from Mbale hospital, Uganda

(Makerere University, 2021-02) Okite, Augustine

Bacterial pathogens constitute a significant public health problem and are important cause of morbidity and mortality in febrile patients. The study was to determine the antimicrobial sensitivity pattern of bacterial pathogens associated with fever in children in Mbale Hospital. This cross-sectional study involved 227 children, was conducted from January to April 2017. Children with fever were selected; whole blood was obtained for preparing blood slides and bacterial cultures. Antibiotic susceptibility testing was done on pure culture isolates employing disc-diffusion method for the commonly used antibiotics. The data were analyzed by using SPSS version 21 and the results were summarized as tables and graphs. Out of 227 children, 121 (53.3%) and 106 (46.7%) were females and males, respectively. 184 (81.1%) were children age group of ≤5. The median age (IQR) was 6 (1-12). The prevalence of malaria infection due to P. falciparum was 79 (34.8%). 121 female 45(19.8%) and 34(15.0%) male children had malaria, while overall 27 (11.9%) samples had bacterial growth, culture positives results for females and males were 10 (4.4%) and 17 (7.5%), respectively. Bacteremia was highest among age group ≤5 21 (77.8%) and 66 (83.5%) of them had P. falciparum. The predominant bacteria isolated were Staphylococcus aureus 18 (56%), Streptococcus pneumoniae 6 (19%), Pseudomonas spp 6 (19%) and Enterobacter aerogenes 2 (6%) The gram positive and gram negative bacteria constituted 24 (75%) and 8 (25%) of the culture isolates; respectively. both single microorganisms 22 (81.5%) and polymicrobial agents 5(18.5%) were isolated and Co-infections between malaria and bacteria were observed in 3.8% (n=79) patients. The isolates showed high rates of resistance to most antibiotics tested. Staphylococcus aureus was the most common pathogen isolated. Further extensive studies to identify the sensitivity pattern and practicing the rationale use of antibiotics are recommended. Key words: Antibiotics; Antibiotics sensitivity testing, Bacteria, Bacterial growth, Malaria, P. falciparum Co-infection.
Bat ecology and social epidemiology of filoviruses in Uganda

(Makerere University, 2025) Ninsiima, Lesley Rose

Introduction: Filoviruses pose significant threats to both human and animal populations in Africa, particularly in Uganda, which ranks among the most affected by Ebola and Marburg virus outbreaks. These viruses are closely linked to bats, especially those in the Pteropodidae family. The 2022 outbreak of Sudan virus (Orthoebolavirus sudanense) in Uganda, reported 164 cases and 55 confirmed deaths before containment which underscores the ongoing risk of pathogen outbreak and spillover in the region. This is coupled with the prevailing traditional knowledge and systems with varying norms and beliefs that increase the bat-human interaction. The social epidemiological and ecological role of bats living in locales such as caves remains complex and largely unknown. Therefore, this study aimed to assess the relationship aspects of bat ecology and social epidemiology of filoviruses in central and western, Uganda. Materials and Methods: The study utilized a mixed methods approach to comprehensively assess bat ecology and social epidemiology of filoviruses in Uganda. This study utilized various methods including systematic review, quantitative surveys, participatory epidemiology, qualitative methods; focus group discussion (FGDs), key informant interviews (KIIs), and in-depth interviews (IDIs), bat fecal sample collection, respective laboratory-based techniques and mathematical modeling. The investigation consisted of five sub-studies each representing a study objective: Study 1: This was a systematic review adhering to PRISMA-P guidelines, examining relevant studies regarding bat ecological and behavioural factors as well as human actions that increase susceptibility to bat-borne pathogens. Data from published articles in different databases and grey literature were qualitatively analyzed, with key findings processed for reflexive thematic analysis in Excel to create themes. The themes generated were combined with Z-scores in R software for statistical analysis to create a Principal Component Analysis (PCA), cluster dendrogram and Pearson correlation for the variables within each theme. Study 2: To achieve this, the study utilized a mixed-methods approach involving surveys (n = 384) and FGDs with participants residing near bat caves in Bundibugyo district (western Uganda). Quantitively, the study assessed the knowledge aspects, perception and risk factors associated with bat exposure among persons living near bat roosting sites and analysed using descriptive statistics. Proportional piling through ranking was done using 10 FGDs (6–8 participants for each group) to explore community perceptions of activities associated with bat exposure and risk of bat-borne disease transmission. Study 3: This study was carried out in western Uganda i.e. Mubende and Kassanda districts which were known to have had Ebola cases. Qualitative data was collected through FGDs; n=4, IDIs; n=12, KIIs; n=12, and participatory landscape mapping to explore perceived drivers of the Ebola virus disease outbreak in the study areas. Thematic analysis using a deductive approach guided by social ecological model and epidemiological model in NVivo 12 pro software. Study 4: This study aimed to investigate the presence of filoviruses and characteristics of Kasokero (Masaka district, central region) and python caves (Rubirizi district, western region). To achieve this, 115 environmental bat fecal swab samples were collected and analysed using nested Reverse Transcriptase Polymerase Chain Reaction (RT-PCR). Additionally, the ecological characteristics were assessed through observation checklists. Study 5: This study developed and analyzed a stochastic model considering the bat-human-environment interface to assess the impacts on disease outbreak extinction and persistence. Using a multitype branching process, the model assessed transmission dynamics involving bats, humans, and environmental contamination. Parameters were based on existing data, incorporating bat excretions and human exposure behaviors. Numerical simulations of both deterministic and stochastic models depicted a major outbreak and persistence of the virus. Results: Study 1: Five key themes i.e. pathogen spillover from bats to humans, anthropogenic influences, pathways to spillover, seasonal and climate variability, and drivers of bat abundance and viral dynamics were identified related to bat and human leading to pathogen spillover. Among these, influence of anthropogenic activities and seasonal changes had a more significant role on transmission dynamics. The PCA highlighted strong correlations between bat abundance, viral dynamics, and environmental factors. Study 2: In total, 214/384 respondents (55.7%) had a history of bat exposure. Increased exposure to bats was associated with being male (OR = 1.6; 95% CI: 1.0, 2.4), staying in urban areas (OR=1.9; 95% CI: 1.2, 3.1), hunting (OR = 10.9; 95% CI: 1.4 to 87.6), and positive perception to bat guano being safe as fertiliser (OR= 2.5; 95% CI: 1.0, 5.9) and hunting was ranked as the major risk factor. Based on the provided data, the adjusted odds ratio of 0.7 for the good measures (95%CI: 0.4, 1.1), suggests a potential protective effect on the risk of bat exposure. Study 3: Five themes were identified as perceived drivers of Ebola virus outbreaks: (1) Individual factors (knowledge of EVD and fear from deaths of suspected cases); (2) Interpersonal factors (ecological, anthropogenic, environmental, and cultural sources of spillover); (3) Community impact (economic loss and lack of government support for survivors); (4) Organizational challenges (delayed lab results, inadequate reporting systems, and poor surveillance); and (5) Policy recommendations (One Health approach and ongoing public sensitization). Study 4: The study compared Kasokero and Python Caves, both home to fruit bats (Rousettus aegyptiacus). Python cave, with its larger colony size and water sources, supports greater bat populations. Kasokero cave features cultural practices at its entrance. No active viral shedding was revealed at the time of sampling despite the presence of large bat colonies. Despite verified RNA quality, the findings indicate a maximum filovirus prevalence of less than 0.02 at a 95% confidence level. Study 5: Through a multitype branching process approximation, it was demonstrated that both bats and humans can significantly increase the likelihood of disease outbreaks persisting. Managing environmental contamination alone is inadequate for controlling viral transmission without addressing infected hosts. The findings emphasize the need for a One Health approach, involving collaboration across public health, veterinary, wildlife, and environmental sectors, applicable to Marburg virus control. Conclusion: This thesis investigated the complex interactions between bats, humans, and the environment in Uganda regarding filovirus transmission. Through five studies, it highlights that spillover risks driven by human activities, viral dynamics, ecological and environmental factors, cultural norms, and seasonal changes along with bat exposure from hunting, gender roles, and geographical location, are crucial to transmission dynamics. The findings highlight that spillover is not solely due to ecological and environmental factors but is intensified by human behavior and socio- cultural practices, such as hunting, farming, and bat consumption, which increase bat-human interactions and amplify transmission. Understanding the ecology of bats alongside the associated social epidemiological dynamics is important for designing filovirus preparedness plans as well as heightening prevention and control of related outbreaks.
Biosecurity assessment of commercial chicken farms for highly pathogenic avian influenza infection in Wakiso District, Central Uganda

(Makerere University, 2022-12-14) Bayo, Maliyamungu Richard

This study assessed the biosecurity level of commercial chicken farms for highly pathogenic avian influenza infection in Uganda with a case study of Wakiso district in the central region of Uganda. A cross-sectional study method that involved both qualitative and quantitative survey approaches was used. A total of 110 commercial chicken farms were sampled using non-probability, purposeful, and snowball sampling techniques. The biosecurity scoring system developed and used consisted of two categories: internal and external biosecurity, each with four sub-categories. The minimum score of "0" represented the total absence of any biosecurity measure on the commercial chicken farm, whereas the maximum score of "100" meant full application of all investigated biosecurity measures. All statistical analysis was performed using SPSS 22 (IBM). The overall mean biosecurity score of the commercial chicken farms was 61.9. The commercial chicken farms scored better for internal biosecurity (mean score of 66.9) than external biosecurity (mean score of 55.7). There was variation in the mean biosecurity score for the different commercial chicken farms, ranging from 37 to 90 for internal biosecurity and 26–79 for external biosecurity. Within the category of external biosecurity, the sub-category "other livestock and animals" had the highest mean score (74.9), while the sub-category with the lowest mean score was related to biosecurity procedures for "Traffic on and off farm" (43.6). Within the category of internal biosecurity, the subcategory "House cleaning and disinfection" had the highest mean score (75.7). The mean overall biosecurity scores for commercial chicken farms varied further due to differences in bird populations between farms. The farms with 50-200 (n = 1796, mean score 31.7), 201–500 (n = 12175, mean score 50), 501–1000 (n = 35561, mean score 60), 1001–2000 (n = 34503, mean score 81), and >2001 (n = 3521, mean score 84.5). The poultry management system, the experience of the farmers, and the education level of the farm owners and managers had a significant influence on the biosecurity levels of the commercial chicken farms. The most significant risk factors observed in commercial chicken farms that could lead to HPAI infection were related to husbandry practices such as not vaccinating the chickens against HPAI, allowing poultry dealers free entry into the farm, allowing egg crates into farms without disinfection, and trading crates. It was therefore recommended that MAAIF strengthen farmer information through poultry biosecurity trainings, enforce chicken farm inspections to encourage farmers to practice best biosecurity practices, and build the capacity of poultry farmers to encourage them to develop biosecurity plans, which will ensure that all three separate but often blended sets of actions and overlapping components of biosecurity, namely bio-exclusion, bio-containment, and bio-management, are practiced to elicit biosecurity.

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