School of Biosecurity, Biotechnolgy and Laboratory Sciences (SBLS) Collection

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    HIV drug resistant mutations associated with virological failure among HIV-1 zero positive infants in Uganda after intensified adherence counseling
    (Makerere University, 2026) Muwabe, Faryad
    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.
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    Morphological, molecular and histopathological characterization of fungi isolated from formalin-fixed animal cadavers and possible sources of contamination from anatomy laboratory, COVAB, Makerere University
    (Makerere University, 2025) Naluzze, Joan
    Animal cadavers play a crucial role as a fundamental instructional resource in the training of anatomists and veterinary students. While formalin is known for its potent antimicrobial properties, certain fungi continue to grow in the presence of formalin. This study aimed at identifying the fungal species that grow on formalin-fixed animal cadavers and internal tissues of fixed cadavers using morphological molecular and histopathological techniques. In addition, the study identified potential environmental sources of contamination. Finally, this study also identified fungal taxa carrying the adhc and fdh genes associated with formalin degradation. The fungi isolated from formalin-fixed animal cadaver tanks, the environmental air from the store, and the embalming room floor, were characterized using PCR amplification and sequencing of the internal transcribed spacer (ITS) region, β-tubulin (Bt), adhc, and fdh genes, together with morphological characterization. The resulting sequences were analyzed using BLAST, and species identification was confirmed by comparison with representative sequences in GenBank. Formalin fixed tissues were processed in the histopathology laboratory and stained with Gridley’s stain. A total of ten fungal isolates belonging to three genera; Aspergillus, Penicillium, and Scedosporium were identified, with Aspergillus being the predominant genus (8/10). Seven isolates originated from the three formalin-fixed animal cadavers. No fungal growth was detected in the distilled water used to prepare the 10% formalin. Two isolates of A. flavus were obtained from the environmental air (store), and one Penicillium species was isolated from the embalming room floor. β-tubulin gene sequencing confirmed Aspergillus niger (isolate 2) and Aspergillus flavus var. flavus (isolate 9). The fdh gene was detected in two Aspergillus isolates whereas adhc formaldehyde-degrading gene was detected in four Aspergillus isolates. The Penicillium isolate contained both genes. Histopathological examination revealed fungal mycelia of Aspergillus in formalin-fixed tissues without accompanying inflammation, indicating post-fixation invasion. The detection of fungal species capable of degrading formaldehyde presents a potential veterinary public health concern. Similar studies should be carried out in other laboratories that use formalin fixed tissues to determine whether comparable contamination challenges exist.
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    The link between Acaricide usage and Oxytetracycline resistance genes in Anaplasma marginale infected cattle blood from selected farms in Kyenjojo, Kumi and Serere Districts
    (Makerere University, 2026) Kakuru, Mesearch
    The management of Bovine Anaplasmosis relies on vector control and chemotherapy. Following the rise of acaricide resistance in Uganda, there is an increase in TBDs incidence, resulting into over reliance on antimicrobials to treat infected animals. Oxytetracycline, being cheap, effective with minimal adverse effects, is mostly used in treating Anaplasmosis. This study was conducted on selected farms in Kyenjojo, Kumi and Serere districts, where resistance in Boophilus decoloratus had been previously reported. The study aimed at investigating otrA and otrB resistance genes in A. marginale infected cattle and access their association with acaricide usage. DNA was extracted from 316 cattle blood samples and screened for msp4 gene. A. marginale positive samples were screened for otrA and otrB using in house primers, and representative samples sequenced using Oxford Nanopore to confirm the PCR product. Six out of the Eight farmers (6/8) in Kyenjojo reported to have used more than one acaricide in the last six months. The proportion of A. marginale was 70% (140/200) and 35.3% (41/116) in Kyenjojo and Kumi/Serere farms respectively. The difference in the frequency of A. marginale between Kyenjojo and Kumi/Serere was statistically significant (P=<0.001). The general proportion of otrA and otrB among the 181 A. marginale infected cattle was 71.8% (130/180) and 47.8% (86/180) respectively. Among Kyenjojo sampled animals, otrA and otrB proportion was 68.6% and 44.3% respectively, while in Kumi & Serere animals, otrA and otrB proportion was 82.9% and 58.5% respectively. Multivariate regression revealed that Exotic breeds were 1.89 times more likely to have otrA compared to local breeds (OR=1.89, 95%CI=0.85-4.40, p=0.13). No acaricide usage factor had a significant relationship with otrA, despite the higher proportions of otrA observed among animals from farms that rotated acaricides due to presence of a new product on market (77.3%), randomly changed acaricides on observing resistance (75.2%) and those that sprayed every week (71.8%). Sequence analysis revealed a 50-55% similarity with sequences available in the database, with study sequences clustering together. This study reveals high proportions of OTC resistance genes in A. marginale infected cattle blood. Animals from farms with poor acaricide use practices had higher proportions of otrA. Larger studies involving more farms and culturing of A. marginale would provide stronger statistical power to define acaricide usage association with OTC resistance as well as assessing invitro anti-microbial resistance profiles.
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    Molecular characterization of multidrug resistant acinetobacter baumanii from patients at selected tertiary health care institutions in Uganda
    (Makerere University, 2026) Kabatesi, Hope Octavia
    Acinetobacter baumannii is a gram-negative non-motile bacterium known to be an opportunistic pathogen. It is responsible for health care and community- acquired infections causing a range of infections including skin and soft tissue, urinary tract infections, bacteremia, ventilator associated pneumonia, etc. Mortality rates for A. baumannii infections have been reported at over 60% and the pathogenesis of the bacterium is attributed to its various virulent factors like the outer membrane protein, capsule formation and biofilm formation etc. There is a major rise in the number of multidrug resistant strains of A. baumannii with many being extended drug resistant and pan-drug resistant. A total of 13 A. baumannii isolates were retrieved for this study from three tertiary healthcare facilities in Uganda; Kiruddu National Referral Hospital, Bwera general hospital and Bombo General Military Hospital. Kirby-Bauer disc diffusion test was performed to confirm the MDR status of the isolates following CLSI guidelines and was followed with whole genome sequencing (WGS) for genotypic characterization of the resistant determinants and virulent genes. All the isolates were 100% resistant to ceftazidime, ceftriaxone, piperacillin/tazobactam, cotrimoxazole, cefotaxime, cefepime and ciprofloxacin while 92% of the isolates were resistant to meropenem and 84.6% resistant to amikacin and gentamicin. WGS revealed various AMR determinants and virulent genes among the isolates. Fifteen virulent genes i.e. OmpA, AdeFGH efflux pump, bap, Csupili, PNAG, phospholipase C and D, LPS, acinetobactin, heme utilization gene, abal/abaR, bfmR/bfms, PbpG which were present in all isolates and katA gene which was only present in ST2 isolates and PilE only present in isolate MUWRP11105 of ST52 were revealed. Multiple AMR determinants including blaOXA -23 like genes, blaOXA- 51 genes, gyrA, parC, blaNDM-1 etc. Pasteur multi-locus sequence typing (MLST) reveled 4 sequence types; ST1, ST2, ST52 and ST2589 with 46.1%, 38.4%, 7.6% and 7.6% isolates belonging respectively. Two international high-risk clone IC 1 and IC 2 were revealed to be circulating among the three healthcare facilities.
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    Antimicrobial resistance, molecular epidemiology and farmer dynamics associated with salmonella infections in indigenous poultry in North Central Nigeria
    (Makerere University, 2025) Sati, Nancy Milton
    Salmonella serovars are globally known to cause diseases in animals and humans. This study sought to evaluate farmers’ perceptions and practices about Salmonella infections, identify and characterize the serovars circulating in indigenous poultry and their drinking water sources in North Central Nigeria. aimed at having targeted control measures. A total of 1,208 samples comprising of poultry faeces (n=1,108) and water (n=100) from 15 markets were collected and processed using ISO 6579:2002 protocols. Using the disk diffusion method, thirteen antimicrobials were used in antimicrobial susceptibility testing. Whole genome sequencing, traditional and molecular serotyping methods were used to characterize the isolates. Across 54 villages in North Central Nigeria, 419 farmer interviews were conducted using a structured e-questionnaire and data was analysed and associations were made between variables. About 6.5% (78/1,208) of the samples were positive for Salmonella, with 60.3% (47/78) susceptibility to all the antimicrobials used and 14.1% (11/78) being multi-drug-resistant phenotypes. Serotyping and whole genome sequencing carried out on 56.4% (44/78) of the isolates identified 23 serovars and 21 antimicrobial resistance genes. Multilocus sequence typing using 7 housekeeping gene loci identified 12 novel sequence types. Cluster analysis from 3255 loci using INNUENDO cgMLST showed close relatedness among isolates from different sources in the same location. Farmer interviews revealed 89.3% (p-value =0.001) of farmers were not aware of Salmonella infections in poultry while 94.5%, (p-value= 0.01) were unaware that Salmonella infections are zoonotic. This study has revealed diverse, pansusceptible and rare Salmonella serovars in indigenous poultry and the water they drink, highlighted farmers’ low awareness of Salmonella, and identified AMR genes, novel sequence types, and genetic relatedness among the isolates. This study calls for improved surveillance and farmer education regarding Salmonella infections so as to enhance poultry health and productivity, as well as reduce public health threats.