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The AgShare Phase I Program, conducted at Makerere University, Kampala, Uganda, was formed to create open education resources for teaching and community development through action research. The study was conducted by an interdisciplinary team of investigators from fields of veterinary medicine and agri-business. Two master of science students conducted dairy value chain action research that produced ase materials used to create open education resources (OER) course modules (milk hygiene and marketing modules) and design interventions that would improve milk production, quality, and safety; reduce milk spoilage; increase price per liter of milk received by farmers; and support on-farm processing of yogurt and other dairy products. This research was used in partial fulfillment of the requirement for the master's degree in Livestock Development, Planning, and Management (MLD) and the master's degree in Agri-business Management (M Agbus Mgt) by these students. The conceptual design, implementation, monitoring, and impacts of action research on teaching, students learning, and the dairy industry are discussed in detail.

One of the cornerstones of the AgShare program is the application of an information loop of action research in the training of graduate students to generate new and practical educational materials and interventions for creating open education research (OER) modules for teaching at universities, and for designing interventions and training programs for making improvements in the dairy value chain in Uganda. One major output of the action research project was the generation of data for use in partial fulfillment of a master of science in Agribusiness and a master of science in Livestock Development, Planning, and Management by participating students. A milk production and hygiene OER module was developed based on components in milk safety, dairy policy, contaminants in milk and dairy products, quality assurance, and dairy planning and management. The OER module was incorporated into an existing graduate-level course at Makerere University. As the AgShare approach continuously updates educational materials through the information loop, this program ensures that university training of students is applicable to the current needs of the dairy industry.

We conducted a cross-sectional serologic study at Kampala City abattoir in Uganda on 287 small ruminants (221 goats and 66 sheep) to determine the seroprevalence of brucellosis. The samples were tested using a modified rose bengal test (mRBT) and an indirect ELISA (iELISA). Small ruminant Brucella spp. seropositivity was 18 of 287 (6.3%) by mRBT and 19 of 287 (6.6%) by iELISA. The prevalence of brucellosis by mRBT was non-significantly higher in goats (17 of 221; 7.7%) than in sheep (1 of 66, 1.5%; p = 0.069), and also non-significantly higher by the iELISA in goats (18 of 221; 8.1%) than in sheep (1 of 66, 1.5%; p = 0.057). Brucellosis in slaughtered goats and sheep is a public health hazard to abattoir workers and consumers that calls for control and eradication measures at the farm level, given that testing is not carried out routinely at slaughter points. [ABSTRACT FROM AUTHOR]

Background: Cockroaches could play a role in the transmission dynamics of antimicrobial-resistant bacteria (ARB) at variable interfaces in Ugandan communities, acting as both reservoirs and vectors. This study investigated the burden and diversity of ARB carried by cockroaches in human settlements in Uganda, so as to understand their role in the spread of these pathogens and their potential as sentinels in antimicrobial resistance (AMR) surveillance programs. Materials and Methods: A retrospective analysis was conducted on two unpublished studies by Makerere University students. Study one and study two sampled 58 and 110 cockroaches, respectively, from secondary schools in Kampala. Cockroach species identification was determined based on physical characteristics. Bacterial isolation and characterization were performed through microbiological analyses including standard culture methods, biochemical tests, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), disc diffusion method, and polymerase chain reaction (PCR). Results: Majority of the cockroaches (over 80%) were Periplaneta americana. Multidrug resistance (MDR) was prevalent among the isolates, with over 30% of the isolates being resistant to three or more antibiotic classes. Specifically, MDR (over 90%) was rampant in the extended spectrum beta-lactamase (ESBL)- or AmpC-producing Escherichia coli and enterococci isolates. Critical World Health Organization (WHO) priority pathogens, such as ESBL-/AmpC-producing Enterobacteriaceae, and carbapenem-resistant E. coli , were also identified. The most abundant resistance determinants (tetracycline and sulphonamide) were tetA, sul1, and sul2 for E. coli , and tetM and tetL for enterococci. Conclusion: The findings accentuate the potential role of cockroaches: (1) in transmitting multidrug-resistant bacteria at the human-animal-environment interface and (2) as sentinels in the surveillance of community-generated AMR., Competing Interests: The authors declare no conflicts of interest., (Copyright © 2025 Steven Kakooza et al. Global Health, Epidemiology and Genomics published by John Wiley & Sons Ltd.)

Foot-and-mouth disease poses a significant threat to both domestic and wild cloven-hoofed animals, leading to severe economic losses and jeopardizing food security. While machine learning models have become essential for predicting foot-and-mouth disease outbreaks, their effectiveness is often compromised by distribution shifts between training and target datasets, especially in non-stationary environments. Despite the critical impact of these shifts, their implications in foot-and-mouth disease outbreak prediction have been largely overlooked. This study introduces the Calibrated Uncertainty Prediction approach, designed to enhance the performance of Random Forest models in predicting foot-and-mouth disease outbreaks across varying distributions. The Calibrated Uncertainty Prediction approach effectively addresses distribution shifts by calibrating uncertain instances for pseudo-label annotation, allowing the active learner to generalize more effectively to the target domain. By utilizing a probabilistic calibration model, Calibrated Uncertainty Prediction pseudo-annotates the most informative instances, refining the active learner iteratively and minimizing the need for human annotation and outperforming existing methods known to mitigate distribution shifts. This reduces costs, saves time, and lessens the dependence on domain experts while achieving outstanding predictive performance. The results demonstrate that Calibrated Uncertainty Prediction significantly enhances predictive performance in non-stationary environments, achieving an accuracy of 98.5%, Area Under the Curve of 0.842, recall of 0.743, precision of 0.855, and an F1 score of 0.791. These findings underscore Calibrated Uncertainty Prediction's ability to overcome the vulnerabilities of existing ML models, offering a robust solution for foot-and-mouth disease outbreak prediction and contributing to the broader field of predictive modeling in infectious disease management., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Kapalaga, Kivunike, Kerfua, Jjingo, Biryomumaisho, Rutaisire, Ssajjakambwe, Mugerwa, Abbey, Aaron and Kiwala.)

Background: Several diagnostic environments in Uganda lack real-time, robust and high-throughput technologies for comprehensive typing of microbes, which is a setback to infectious disease surveillance. This study combined various wet laboratory diagnostics to understand the epidemiology of pathogenic staphylococci isolated from animals in Uganda and the implications for global health security priorities., Methods: A retrospective study was conducted employing records and pathogenic staphylococci (from animals) archived at the Central Diagnostic Laboratory (CDL), Makerere University, Uganda, between January 2012 and December 2019. The bacteria were speciated by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and tested for virulence factors [beta lactamases, lecithinase, deoxyribonuclease (DNase), haemolysins] and resistance to ten antimicrobials of clinical and veterinary relevance. Tetracycline and methicillin resistance genes were also tested., Results: The prevalent diseases were mastitis in cattle and skin infections in dogs. Of the 111 staphylococci tested by MALDI-TOF MS, 79 (71.2%) were Staphylococcus aureus, 27 (24.3%) were Staphylococcus pseudintermedius and 5 (4.5%) were Staphylococcus schleiferi. All these strains expressed haemolysins. The prevalence of strains with lecithinase, penicillinase, cephalosporinase and DNase was 35.9% (14/39), 89.7% (35/39), 0.0% (0/39) and 87.2% (34/39), respectively. Staphylococci were primarily resistant to early penicillins (over 80%), tetracycline (57.7%), and chloramphenicol (46.2%). Minimal resistance was noted with cloxacillin (0.0%), ciprofloxacin (9.6%), and cefoxitin (3.8%). The prevalence of multidrug resistance (MDR) was 78.8% for general staphylococci, 82.2% for S. aureus, 73.1% for S. pseudintermedius, and 60.0% for S. schleiferi. Multidrug resistant staphylococci were significantly more prevalent in the cattle isolates than in the dog isolates (P < 0.05). The prevalence of methicillin-resistant staphylococci (MRS) tested by resistance to cefoxitin and mecA carriage was 3.8%. These four strains were all isolated from dog skin infections. The tetK gene was the most predominant (35.4%), followed by tetM (25.0%)., Conclusion: In resource-constrained settings, the approach of integrated diagnostics promises sustainable disease surveillance and the addressing of current capacity gaps. The emergence of MRS (zoonotic bacteria) in companion animals creates a likelihood of reduced treatment options for related human infections, a threat to global health., (© 2024. The Author(s).)

In Uganda, the absence of a unified dataset for constructing machine learning models to predict Foot and Mouth Disease outbreaks hinders preparedness. Although machine learning models exhibit excellent predictive performance for Foot and Mouth Disease outbreaks under stationary conditions, they are susceptible to performance degradation in non-stationary environments. Rainfall and temperature are key factors influencing these outbreaks, and their variability due to climate change can significantly impact predictive performance. This study created a unified Foot and Mouth Disease dataset by integrating disparate sources and pre-processing data using mean imputation, duplicate removal, visualization, and merging techniques. To evaluate performance degradation, seven machine learning models were trained and assessed using metrics including accuracy, area under the receiver operating characteristic curve, recall, precision and F1-score. The dataset showed a significant class imbalance with more non-outbreaks than outbreaks, requiring data augmentation methods. Variability in rainfall and temperature impacted predictive performance, causing notable degradation. Random Forest with borderline SMOTE was the top-performing model in a stationary environment, achieving 92% accuracy, 0.97 area under the receiver operating characteristic curve, 0.94 recall, 0.90 precision, and 0.92 F1-score. However, under varying distributions, all models exhibited significant performance degradation, with random forest accuracy dropping to 46%, area under the receiver operating characteristic curve to 0.58, recall to 0.03, precision to 0.24, and F1-score to 0.06. This study underscores the creation of a unified Foot and Mouth Disease dataset for Uganda and reveals significant performance degradation in seven machine learning models under varying distributions. These findings highlight the need for new methods to address the impact of distribution variability on predictive performance., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Kapalaga, Kivunike, Kerfua, Jjingo, Biryomumaisho, Rutaisire, Ssajjakambwe, Mugerwa and Kiwala.)

Animal shelters, especially in resource-poor countries, bring together pets from different regions and with different backgrounds. The crowding of such animals often results in infectious diseases, such as respiratory infections. This study characterized Staphylococcaceae from diseased and apparently healthy dogs housed in an animal shelter in Kenya, to determine their antibiotic resistance profiles, their genetic relatedness, and the presence of dominant clones. Therefore, bacteria were collected from all 167 dogs present in the shelter in June 2015 and screened for Staphylococcaceae using standard cultivation techniques. In all, 92 strains were isolated from 85 dogs and subsequently sequenced by PacBio long-read sequencing. Strains encompassed nine validated species, while S. aureus ( n = 47), S. pseudintermedius ( n = 21), and Mammaliicoccus (M.) sciuri ( n = 16) were the three most dominant species. Two S . aureus clones of ST15 (CC15) and ST1292 (CC1) were isolated from 7 and 37 dogs, respectively. All 92 strains isolated were tested for their antimicrobial susceptibility by determining the minimum inhibitory concentrations. In all, 86 strains had resistance-associated minimal inhibitory concentrations to at least one of the following antimicrobials: tetracycline, benzylpenicillin, oxacillin, erythromycin, clindamycin, trimethoprim, kanamycin/gentamicin, or streptomycin. Many virulence-encoding genes were detected in the S. aureus strains, other Staphylococcaceae contained a different set of homologs of such genes. The presence of mobile genetic elements, such as plasmids and prophages, known to facilitate the dissemination of virulence- and resistance-encoding genes, was also assessed. The unsuspected high presence of two S . aureus clones in about 50% of dogs suggests dissemination within the shelter and a human source.IMPORTANCEMicrobiological data from sub-Saharan Africa are scarce compared to data from North America, Europe, or Asia, and data derived from dogs, the man's best friend, kept in sub-Saharan Africa are largely missing. This work presents data on Staphylococcaceae mainly isolated from the nasal cavity of dogs stationed at a Kenyan shelter in 2015. We characterized 92 strains isolated from 85 dogs, diseased and apparently healthy ones. The strains isolated covered nine validated species and we determined their phenotypic resistance and characterized their complete genomes. Interestingly, Staphylococcus aureus of two predominant genetic lineages, likely to be acquired from humans, colonized many dogs. We also detected 15 novel sequence types of Mammaliicoccus sciuri and S. pseudintermedius indicating sub-Saharan-specific phylogenetic lineages. The data presented are baseline data that guide antimicrobial treatment for dogs in the region., Competing Interests: The authors declare no conflict of interest.

Background: Mastitis and associated antimicrobial resistance (AMR) are major challenges to the dairy industry worldwide., Objective: This study aimed to expose the mastitis burden, causative bacteria and drivers for mastitis-causing multi-drug-resistant (MDR) Staphylococci infectivity in cows on dairy farms in Wakiso district, Uganda., Methods: On 22 farms, practices were documented using questionnaires, and 175 cows were screened by the California mastitis test. Composite milk samples from the positive reactors were submitted to the laboratory for bacterial culture testing. Antimicrobial sensitivity testing by the Kirby Bauer disc diffusion method was done only on Staphylococci with a panel of 10 antimicrobials of clinical relevance., Results: Mastitis was detected in 80.6% (n = 141) of the 175 sampled cows, of which sub-clinical mastitis (76.0%: n = 133) was predominant. The Chi-squared analysis hypothesized that cow age (p = 0.017), sub-county (p = 0.013), parity (p < 0.0001), sex of farm owner (p = 0.003), farm duration in dairy production (p = 0.048) and the use of milking salve (p = 0.006) were associated with mastitis. Coagulase-negative Staphylococci were the most prevalent (71.4%; n = 95), followed by Staphylococcus aureus (30.1%, n = 40). Staphylococci (76.3%; n = 135) were majorly resistant to penicillin and tetracycline. Only one isolate was phenotyped as a methicillin-resistant Staphylococcus specie (MRSS). The prevalences of MDR strains at cow and isolate level were 6.3% and 8.3%. The major MDR phenotype identified was penicillin-tetracycline-trimethoprim-sulphamethoxazole. The isolate detected as an MRSS exhibited the broadest MDR pattern. Cow parity was identified as a predictor of infectivity of mastitis-causing MDR Staphylococci in dairy herds., Conclusion: The high prevalence of mastitis and associated pathogen AMR found exposes possibilities of economic losses for the dairy sector warranting the need for farmer sensitization on the institution of proper mastitis prevention and control programs, with emphasis on milking hygiene practices and routine disease monitoring., (© 2023 The Authors. Veterinary Medicine and Science published by John Wiley & Sons Ltd.)

The dynamics of extended-spectrum β -lactamase- (ESBL-) and AmpC β -lactamase-producing bacteria (which are deadly groups of antimicrobial-resistant bacteria) have not been well understood in developing countries. This raises major concerns to antimicrobial resistance (AMR) control. We investigated the prevalence and factors linked to the fecal carriage of ESBL- or AmpC-producing Escherichia coli (ESBL-/AmpC-EC) in commercial chickens. Cloacal swabs from 400 birds were sampled and submitted to the Central Diagnostic Laboratory for ESBL-/AmpC-EC screening by culture methods using MacConkey agar supplemented with cefotaxime. Epidemiological data were collected using a structured questionnaire and plausible risk factor analyses prepared by R software using X 2 test and logistic regression modeling. Results showed that the prevalence of ESBL-/AmpC-EC was 17.5%. Univariable screening hypothesized that carriage was probably influenced by a type of commercial chicken, geographical location, age group, flock size, and housing system ( p < 0.05). Modeling exposed that broiler birds were at a higher risk of being ESBL-/AmpC-EC carriers (COR = 9.82, CI = 3.85-25.07). Birds from Wakiso Town Council (COR = 4.89, CI = 2.04-11.72) and flocks of 700-1200 birds were also at a higher risk of harboring ESBL-/AmpC-EC (COR = 2.41, CI = 1.11-5.23). Birds aged 4 months and below were more susceptible to ESBL-/AmpC-EC carriage compared with those aged 1 month and below being 6.33 times (CI = 1.65-24.35) likely to be carriers. The occurrence of ESBL-/AmpC-EC in flocks suggests possible treatment failures while managing colibacillosis. Consequently, injudicious antimicrobial use should be replaced with an accurate diagnosis by bacterial culture and sensitivity testing so as to circumvent AMR emergence, spread, and associated losses., Competing Interests: The authors declare no conflicts of interest., (Copyright © 2021 Steven Kakooza et al.)

There are increasing reports of antimicrobial treatment failures for bacterial diseases of poultry in Uganda. The paucity of data on antimicrobial resistance (AMR) of pathogenic bacteria in Uganda is a major setback to AMR control. This study investigated the occurrence of fowl typhoid, colibacillosis, and AMR in associated pathogens from 2012 to 2018. Laboratory records from the Central Diagnostic Laboratory (CDL), a National Veterinary Diagnostic Facility located at Makerere University, were reviewed. Archived isolates of the causative bacteria for the two diseases were also evaluated for AMR. The frequencies of the two disease conditions, their clinical and necropsy presentations and the demographic data of the diagnostic samples were summarized from the records. Archived bacterial isolates were revived before antimicrobial susceptibility testing. This was done on Mueller Hinton agar using the disk diffusion method, against 16 antimicrobials of medical and veterinary importance according to the Clinical Laboratory Standards Institute guidelines. A total of 697 poultry cases were presented for bacteriological investigations in the review period. Colibacillosis and salmonellosis had prevalence rates of 39.7% (277/697) and 16.2% (113/697), respectively. A total of 63 and 92 isolates of Escherichia coli and Salmonella spp., respectively, were archived but 43 (68.3%) E. coli and 47 (51.1%) Salmonella spp. isolates were recovered and evaluated for AMR. Multidrug resistance was more frequent in E. coli (38; 88.4%) than salmonellae (25; 53.2%), ( p < 0.001). The high prevalence of colibacillosis, salmonellosis and the AMR of associated pathogens warrants immediate institution of appropriate disease control measures., Competing Interests: No potential conflict of interest was reported by the author(s)., (© 2021 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)

Mycoplasmas are the smallest free-living organisms and cause a number of economically important diseases affecting humans, animals, insects, and plants. Here, we demonstrate that highly virulent Mycoplasma mycoides subspecies capri ( Mmc ) can be fully attenuated via targeted deletion of non-essential genes encoding, among others, potential virulence traits. Five genomic regions, representing approximately 10% of the original Mmc genome, were successively deleted using Saccharomyces cerevisiae as an engineering platform. Specifically, a total of 68 genes out of the 432 genes verified to be individually non-essential in the JCVI-Syn3.0 minimal cell, were excised from the genome. In vitro characterization showed that this mutant was similar to its parental strain in terms of its doubling time, even though 10% of the genome content were removed. A novel in vivo challenge model in goats revealed that the wild-type parental strain caused marked necrotizing inflammation at the site of inoculation, septicemia and all animals reached endpoint criteria within 6 days after experimental infection. This is in contrast to the mutant strain, which caused no clinical signs nor pathomorphological lesions. These results highlight, for the first time, the rational design, construction and complete attenuation of a Mycoplasma strain via synthetic genomics tools. Trait addition using the yeast-based genome engineering platform and subsequent in vitro or in vivo trials employing the Mycoplasma chassis will allow us to dissect the role of individual candidate Mycoplasma virulence factors and lead the way for the development of an attenuated designer vaccine.

Mastitis and antimicrobial resistance are a big challenge to the dairy industry in sub-Saharan Africa. A study was conducted in Kashongi and Keshunga subcounties of Kiruhura District (in Uganda) where the government and private sector have deliberate programs to improve production efficiency, quality, and safety of milk and its products. The study aimed to determine the prevalence of mastitis, its common causative agents, antimicrobial sensitivity of mastitis causing organisms, and contaminants of processed milk products: yoghurt and ghee. Seventy-one milk, fourteen yoghurt, and three ghee samples were collected from nine farms. Of the 71 cows tested, 54 (76.1%) had mastitis. The mastitis cases from Keshunga were 32 (59.3%) and Kashongi contributed 22 (40.7%) of the cases. The common mastitis causative agents were Staphylococcus spp. (30.8%), Streptococcus spp. (12.3%), Corynebacterium spp.(15.4%), and E. coli (7.7%). Some of the isolates were resistant to tetracycline and penicillin. Prevalent contaminants of yoghurt were Staphylococcus spp. (8.3%), Streptococcus spp. (8.3%), Corynebacterium spp. (8.3%), and E. coli (8.3%), whereas all ghee contained Streptococcus spp. (100%). Prevalence of mastitis, antimicrobial resistance, and contamination of milk products are high in the study area. Targeted programs to prevent and control mastitis as well as antibiotic resistance are recommended., Competing Interests: The authors declare no competing interests.