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Daily cotrimoxazole (TMP/SXT) prophylaxis is part of the HIV treatment package for all new HIV-infected individuals in Uganda. Although this treatment has shown reduced morbidity and mortality in HIV, it remains controversial due to its contribution to developing antibiotic-resistant bacteria. Moreover, the effects of daily use of a broad-spectrum antibiotic on the gut microbiome remain unknown. To study the early effects, we analysed shotgun metagenome sequence data from stool samples of five newly HIV-infected individuals initiating TMP/SXT prophylaxis longitudinally for the first 30 days of treatment. Using shotgun metagenomics sequencing, we generated both taxonomic and functional profiles from each patient and compared gut microbial changes Pre- TMP/SXT and post-TMP/SXT on Day 5, Day 14, and Day 30. Daily TMP/SXT prophylaxis resulted in a shift characterised by an enrichment of Prevetollea and Ruminococcus genera members and the depletion of Lactococcus and Bacteroides genera members. Furthermore, these microbial shifts were associated with changes in the functional profile revealed by a differential abundance of pathways of amino acid metabolism, carbohydrate metabolism, and nucleotide biosynthesis linked to members of the Bacteroidaceae and Enterobacteriaceae families. TMP/SXT daily prophylaxis in HIV-infected individuals is associated with dramatic changes in microbial composition and functional profiles; however, other factors such as Age, Gender, HIV clinical stage, and ART regiment are at play. Further investigation is needed to examine the implication of these shifts on clinical management and outcomes among HIV patients., Competing Interests: Competing interests The authors declare that they have no competing interests.

Background: Antibiotic resistance (ABR) is a global challenge, and its control depends on robust evidence primarily derived from surveillance systems., Methods: We utilised a national surveillance data set to demonstrate how such evidence can be systematically generated. In doing so, we characterised the ABR profiles of priority clinical pathogens, identified associated factors, and drew inferences on antibiotic usage in Uganda., Results: Of the 12 262 samples collected between 2019-21, we analysed 9033 with complete metadata. ABR was steadily increasing at a rate of 0.5% per year, with a surge in 2021 and the highest and lowest levels of penicillin and carbapenems detected in the northern (odds ratio (OR) = 2.26; P < 0.001) and the northeast (OR = 0.28; P < 0.001) regions of Uganda respectively. ABR was commonly observed with Escherichia coli (OR = 1.18; P < 0.001) and Klebsiella pneumoniae (OR = 1.25; P < 0.001) among older and male patients (61-70 years old) (OR = 1.88; P = 0.005). Multi-drug resistance (MDR) and ABR were disproportionately higher among bloodstream infections than respiratory tract infections and urinary tract infections, often caused by Acinetobacter baumannii. Co-occurrence of ABR suggests that cephalosporins such as ceftriaxone are in high use all over Uganda., Conclusions: ABR is indeed a silent pandemic, and our results suggest it is increasing at 0.5% per year, with a notable surge in 2021 likely due to coronavirus disease 2019 (COVID-19). Of concern, ABR and MDR are mainly associated with bloodstream and surgical wound infections, with a gender and age dimension. However, it is encouraging that carbapenem resistance remains relatively low. Such evidence is critical for contextualising the implementation and evaluation of national action plans., Competing Interests: Disclosure of interest: The authors completed the ICMJE Disclosure of Interest Form (available upon request from the corresponding author) and disclose no relevant interests., (Copyright © 2024 by the Journal of Global Health. All rights reserved.)

Background: Antimicrobial resistance (AMR) poses a significant global health threat, particularly in low- and middle-income countries (LMICs). Self-treatment with antibiotics, the practice of using antibiotics without professional guidance, is often considered an important contributor to the emergence and spread of AMR., Method: This study investigated the drivers of self-treatment in three common types of agricultural communities in northern Tanzania. The research employed a comprehensive array of methods, including cross-sectional surveys (n = 790), interviews (n = 30) and observations (n = 178) targeting both antibiotic (human and animal) providers and users (patients and farmers). Qualitative interview data were analysed using a coding and association matrix, while descriptive analyses were performed on survey and observation data., Results: Self-treatment with antibiotics was highly prevalent in all communities. Between 41.0% (self-reported) and 60.3% (observed) of human antibiotics were obtained without a prescription and we observed that veterinary antibiotics were regularly purchased in retail shops without referral by a professional. Structural deficiencies in the healthcare system drove this practice: limited access to healthcare facilities, medication stockouts and prolonged waiting times were identified as key factors. The absence of safety nets like insurance schemes further contributed to self-medication. Retail shops offered a convenient and cost-effective alternative when antibiotics were inaccessible or unaffordable. Notably, informal networks comprising treatment vendors, friends or neighbours, as well as personal experiences played a crucial role in guiding individuals in their self-treatment decisions by providing advice on treatment choice and modalities., Conclusions: Addressing self-treatment requires a multi-faceted approach. Improving the availability and accessibility of antibiotics, enhancing healthcare services and involving retail vendors in antibiotic stewardship are essential. Structural issues like access to diagnostics and medicines must be tackled, alongside reducing barriers and incentivising individuals to use professional healthcare services. Training retail vendors to sell specific first-line antibiotics over the counter with guidance on appropriate usage should be considered. Such bottom-up interventions will enable sustainable promotion of responsible antibiotic use, mitigating AMR emergence and securing a healthier future for all., (© 2024. The Author(s).)

Introduction: The enteric microbiome and its possible modulation to improve feed conversion or vaccine efficacy is gaining more attention in pigs. Weaning pigs from their dam, along with many routine procedures, is stressful. A better understanding of the impact of this process on the microbiome may be important for improving pig production. The objective of this study was to develop a weaner pig cannulation model, thus allowing ileum content collection from the same pig over time for 16S rRNA sequencing under different porcine reproductive and respiratory syndrome virus (PRRSV) infection statuses., Methods: A total of 15 3-week-old pigs underwent abdominal surgery and were fitted with an ileum cannula, with ileum contents collected over time. In this pilot study, treatment groups included a NEG-CONTROL group (no vaccination, no PRRSV challenge), a POS-CONTROL group (no vaccination, challenged with PRRSV), a VAC-PRRSV group (vaccinated, challenged with PRRSV), a VAC-PRO-PRRSV group (vaccinated, supplemented with a probiotic, challenged with PRRSV), and a VAC-ANTI-PRRSV group (vaccinated, administered an antibiotic, challenged with PRRSV). We assessed the microbiome over time and measured anti-PRRSV serum antibodies, PRRSV load in serum and nasal samples, and the severity of lung lesions., Results: Vaccination was protective against PRRSV challenge, irrespective of other treatments. All vaccinated pigs mounted an immune response to PRRSV within 1 week after vaccination. A discernible impact of treatment on the diversity, structure, and taxonomic abundance of the enteric microbiome among the groups was not observed. Instead, significant influences on the ileum microbiome were observed in relation to time and treatment., Discussion: The cannulation model described in this pilot study has the potential to be useful in studying the impact of weaning, vaccination, disease challenge, and antimicrobial administration on the enteric microbiome and its impact on pig health and production. Remarkably, despite the cannulation procedures, all vaccinated pigs exhibited robust immune responses and remained protected against PRRSV challenge, as evidenced by the development of anti-PRRSV serum antibodies and viral shedding data., 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 Opriessnig, Halbur, Bayne, Rawal, Tong, Mou, Li, Zhang, Zhang and Muwonge.)

Animal movements are a major driver for the spread of Transboundary Animal Diseases (TADs). These movements link populations that would otherwise be isolated and hence create opportunities for susceptible and infected individuals to meet. We used social network analysis to describe the seasonal network structure of cattle movements in Uganda and unravel critical network features that identify districts or sub-regions for targeted risk-based surveillance and intervention. We constructed weighted, directed networks based on 2019 between-district cattle movements using official livestock mobility data; the purpose of the movement ('slaughter' vs. 'live trade') was used to subset the network and capture the risks more reliably. Our results show that cattle trade can result in local and long-distance disease spread in Uganda. Seasonal variability appears to impact the structure of the network, with high heterogeneity of node and edge activity identified throughout the seasons. These observations mean that the structure of the live trade network can be exploited to target influential district hubs within the cattle corridor and peripheral areas in the south and west, which would result in rapid network fragmentation, reducing the contact structure-related trade risks. Similar exploitable features were observed for the slaughter network, where cattle traffic serves mainly slaughter hubs close to urban centres along the cattle corridor. Critically, analyses that target the complex livestock supply value chain offer a unique framework for understanding and quantifying risks for TADs such as Foot-and-Mouth disease in a land-locked country like Uganda. These findings can be used to inform the development of risk-based surveillance strategies and decision making on resource allocation. For instance, vaccine deployment, biosecurity enforcement and capacity building for stakeholders at the local community and across animal health services with the potential to limit the socio-economic impact of outbreaks, or indeed reduce their frequency., (© 2023. The Author(s).)

Digital contact tracing presents numerous advantages compared to manual contact tracing methods, especially in terms of enhanced speed and automation. Nevertheless, a lack of comprehensive evaluation regarding functionality, efficiency, benefits, and acceptance within communities remains. Here we primarily focus on the functionality of THEA-GS, an open-source digital contact tracing tool developed through consultation with stakeholders. Additionally, we provide insights from its implementation on a limited sample of haulage drivers in Uganda, serving as a representative case for a low- and middle-income country. THEA-GS comprises two primary components: (a) a smartphone application, and (b) a suite of server-programs responsible for data processing and analysis, including databases and a web-based interface featuring dashboards. In essence, the mobile application records the timestamped location of haulage drivers within the road network and identifies possible transmission hotspots by analyzing factors such as the duration of stops and the communities associated with them. The tool can be integrated with national infrastructure to compare drivers' diagnostic results and contact structure, thereby generating individual and community risk assessments relative to the road network. During the Omicron-variant wave of the COVID-19 pandemic, a total of 3,270 haulage drivers were enrolled between October 2021 and October 2022. Around 75% of these drivers utilized THEA-GS for approximately two months. Based on an analysis of 3,800 test results, which included 48 positive cases, 125 contacts, and 40 million time-stamped GPS points, THEA-GS shows a significant speed improvement, being approximately 90 times faster than MCT. For instance, the average time from sample collection to notifying a case and their contacts was approximately 70 and 80 min, respectively. The adoption of this tool encountered challenges, mainly due to drivers' awareness of its purpose and benefits for public health. THEA-GS is a place-based digital contact tracing tool specifically designed to assist National Public Health Institutions in managing infectious disease outbreaks involving the haulage industry as a high-risk group. While its utility, acceptance, and accuracy have not been fully evaluated, our preliminary tests conducted in Uganda indicate the tool's functionality is robust, but social acceptance and adoption are heavily reliant on establishing trust among users., Competing Interests: ES was employed by Bodastage Solutions. The remaining 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., (© 2023 Muwonge, Wee, Mugerwa, Nabunya, Mpyangu, Bronsvoort, Ssebaggala, Kiayias, Mwaka and Joloba.)

Introduction: Escherichia coli, Klebsiella pneumoniae and Enterobacter (EKE) are the leading cause of mortality and morbidity in neonates in Africa. The management of EKE infections remains challenging given the global emergence of carbapenem resistance in Gram-negative bacteria. This study aimed to investigate the source of EKE organisms for neonates in the maternity environment of a national referral hospital in Uganda, by examining the phenotypic and molecular characteristics of isolates from mothers, neonates, and maternity ward., Methods: From August 2015 to August 2016, we conducted a cross-sectional study of pregnant women admitted for elective surgical delivery at Mulago hospital in Kampala, Uganda; we sampled (nose, armpit, groin) 137 pregnant women and their newborns (n = 137), as well as health workers (n = 67) and inanimate objects (n = 70 -beds, ventilator tubes, sinks, toilets, door-handles) in the maternity ward. Samples (swabs) were cultured for growth of EKE bacteria and isolates phenotypically/molecularly investigated for antibiotic sensitivity, as well as β-lactamase and carbapenemase activity. To infer relationships among the EKE isolates, spatial cluster analysis of phenotypic and genotypic susceptibility characteristics was done using the Ridom server., Results: Gram-negative bacteria were isolated from 21 mothers (15%), 15 neonates (11%), 2 health workers (3%), and 13 inanimate objects (19%); a total of 131 Gram-negative isolates were identified of which 104 were EKE bacteria i.e., 23 (22%) E. coli, 50 (48%) K. pneumoniae, and 31 (30%) Enterobacter. Carbapenems were the most effective antibiotics as 89% (93/104) of the isolates were susceptible to meropenem; however, multidrug resistance was prevalent i.e., 61% (63/104). Furthermore, carbapenemase production and carbapenemase gene prevalence were low; 10% (10/104) and 6% (6/104), respectively. Extended spectrum β-lactamase (ESBL) production occurred in 37 (36%) isolates though 61 (59%) carried ESBL-encoding genes, mainly blaCTX-M (93%, 57/61) implying that blaCTX-M is the ideal gene for tracking ESBL-mediated resistance at Mulago. Additionally, spatial cluster analysis revealed isolates from mothers, new-borns, health workers, and environment with similar phenotypic/genotypic characteristics, suggesting transmission of multidrug-resistant EKE to new-borns., Conclusion: Our study shows evidence of transmission of drug resistant EKE bacteria in the maternity ward of Mulago hospital, and the dynamics in the ward are more likely to be responsible for transmission but not individual mother characteristics. The high prevalence of drug resistance genes highlights the need for more effective infection prevention/control measures and antimicrobial stewardship programs to reduce spread of drug-resistant bacteria in the hospital, and improve patient outcomes., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Mayanja et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

When studying the dynamics of a pathogen in a host population, one crucial question is whether it transitioned from an epidemic (i.e., the pathogen population and the number of infected hosts are increasing) to an endemic stable state (i.e., the pathogen population reached an equilibrium). For slow-growing and slow-evolving clonal pathogens such as Mycobacterium bovis , the causative agent of bovine (or animal) and zoonotic tuberculosis, it can be challenging to discriminate between these two states. This is a result of the combination of suboptimal detection tests so that the actual extent of the pathogen prevalence is often unknown, as well as of the low genetic diversity, which can hide the temporal signal provided by the accumulation of mutations in the bacterial DNA. In recent years, the increased availability, efficiency, and reliability of genomic reading techniques, such as whole-genome sequencing (WGS), have significantly increased the amount of information we can use to study infectious diseases, and therefore, it has improved the precision of epidemiological inferences for pathogens such as M. bovis . In this study, we use WGS to gain insights into the epidemiology of M. bovis in Cameroon, a developing country where the pathogen has been reported for decades. A total of 91 high-quality sequences were obtained from tissue samples collected in four abattoirs, 64 of which were with complete metadata. We combined these with environmental, demographic, ecological, and cattle movement data to generate inferences using phylodynamic models. Our findings suggest M. bovis in Cameroon is slowly expanding its epidemiological range over time; therefore, endemic stability is unlikely. This suggests that animal movement plays an important role in transmission. The simultaneous prevalence of M. bovis in co-located cattle and humans highlights the risk of such transmission being zoonotic. Therefore, using genomic tools as part of surveillance would vastly improve our understanding of disease ecology and control strategies., 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 © 2023 Rossi, Shih, Egbe, Motta, Duchatel, Kelly, Ndip, Sander, Tanya, Lycett, Bronsvoort and Muwonge.)

Foot-and-mouth disease (FMD) is one of the most important transboundary animal diseases affecting livestock and wildlife species worldwide. Sustained viral circulation, as evidenced by serological surveys and the recurrence of outbreaks, suggests endemic transmission cycles in some parts of Africa, Asia and the Middle East. This is the result of a complex process in which multiple serotypes, multi-host interactions and numerous socio-epidemiological factors converge to facilitate disease introduction, survival and spread. Spatial and spatio-temporal analyses have been increasingly used to explore the burden of the disease by identifying high-risk areas, analysing temporal trends and exploring the factors that contribute to the outbreaks. We systematically retrieved spatial and spatial-temporal studies on FMD outbreaks to summarize variations on their methodological approaches and identify the epidemiological factors associated with the outbreaks in endemic contexts. Fifty-one studies were included in the final review. A high proportion of papers described and visualized the outbreaks (72.5%) and 49.0% used one or more approaches to study their spatial, temporal and spatio-temporal aggregation. The epidemiological aspects commonly linked to FMD risk are broadly categorizable into themes such as (a) animal demographics and interactions, (b) spatial accessibility, (c) trade, (d) socio-economic and (e) environmental factors. The consistency of these themes across studies underlines the different pathways in which the virus is sustained in endemic areas, with the potential to exploit them to design tailored evidence based-control programmes for the local needs. There was limited data linking the socio-economics of communities and modelled FMD outbreaks, leaving a gap in the current knowledge. A thorough analysis of FMD outbreaks requires a systemic view as multiple epidemiological factors contribute to viral circulation and may improve the accuracy of disease mapping. Future studies should explore the links between socio-economic and epidemiological factors as a foundation for translating the identified opportunities into interventions to improve the outcomes of FMD surveillance and control initiatives in endemic contexts., (© 2022 The Authors. Transboundary and Emerging Diseases published by Wiley-VCH GmbH.)

Background: Dental caries is a multifactorial disease that affects many people. Even though microorganisms play a crucial role in causing dental caries, diagnosis is routinely macroscopic. In order to improve early detection especially in HIV patients who are disproportionately affected, there is need to reconcile the macroscopic and microscopic characteristics of dental caries. Therefore, the aim of this study was to characterize the oral microbiota profile along the decayed, missing, filled teeth (DMFT) index using amplicon sequencing data., Methods: Amplicon sequencing of the V6-V8 region of the 16S rRNA gene was done on DNA recovered from whole unstimulated saliva of 59 HIV positive and 29 HIV negative individuals. The microbial structure, composition and co-occurrence networks were characterized using QIIME-2, Phyloseq, Microbiome-1.9.2 and Metacoder in R., Results: We characterized the oral microbiota into 2,093 operational taxonomic units (OTUs), 21 phyla and 239 genera from 2.6 million high quality sequence reads. While oral microbiota did not cluster participants into distinct groups that track with the DMFT index, we observed the following: (a) The proportion of accessory microbiota was highest in the high DMFT category while the core size (∼50% of richness) remained relatively stable across all categories. (b) The abundance of core genera such as Stomatobaculum , Peptostreptococcus and Campylobacter was high at onset of dental caries, (c) A general difference in oral microbial biomass. (d) The onset of dental caries (low DMFT) was associated with significantly lower oral microbial entropy., Conclusions: Although oral microbial shifts along the DMFT index were not distinct, we demonstrated the potential utility of microbiota dynamics to characterize oral disease. Therefore, we propose a microbial framework using the DMFT index to better understand dental caries among HIV positive people in resource limited settings., 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., (© 2022 Kalanzi, Mayanja-Kizza, Nakanjako, Semitala, Mboowa, Mbabali, Kigozi, Katabazi, Sserwadda, Kateete, Achan, Sewankambo and Muwonge.)

Introduction: At the peak of Uganda's first wave of SARS-CoV-2 in May 2020, one in three COVID-19 cases was linked to the haulage sector. This triggered a mandatory requirement for a negative PCR test result at all ports of entry and exit, resulting in significant delays as haulage drivers had to wait for 24-48 hours for results, which severely crippled the regional supply chain.To support public health and economic recovery, we aim to develop and test a mobile phone-based digital contact tracing (DCT) tool that both augments conventional contact tracing and also increases its speed and efficiency., Methods and Analysis: To test the DCT tool, we will use a stratified sample of haulage driver journeys, stratified by route type (regional and local journeys).We will include at least 65% of the haulage driver journeys ~83 200 on the network through Uganda. This allows us to capture variations in user demographics and socioeconomic characteristics that could influence the use and adoption of the DCT tool. The developed DCT tool will include a mobile application and web interface to collate and intelligently process data, whose output will support decision-making, resource allocation and feed mathematical models that predict epidemic waves.The main expected result will be an open source-tested DCT tool tailored to haulage use in developing countries.This study will inform the safe deployment of DCT technologies needed for combatting pandemics in low-income countries., Ethics and Dissemination: This work has received ethics approval from the School of Public Health Higher Degrees, Research and Ethics Committee at Makerere University and The Uganda National Council for Science and Technology. This work will be disseminated through peer-reviewed publications, our websites https://project-thea.org/ and Github for the open source code https://github.com/project-thea/., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2022. Re-use permitted under CC BY. Published by BMJ.)

Despite sub-Saharan Africa (SSA) accounting for ~20% of the global cattle population, prevalence estimates and related risk factors of bovine tuberculosis (bTB) are still poorly described. The increased sensitivity of the IFN-γ assay and its practical benefits suggest the test could be useful to investigate bTB epidemiology in SSA. This study used a population-based sample to estimate bTB prevalence, identify risk factors and estimate the effective reproductive rate in Cameroonian cattle populations. A cross-sectional study was conducted in the North West Region (NWR) and the Vina Division (VIN) of Cameroon in 2013. A regional stratified sampling frame of pastoral cattle herds produced a sample of 1,448 cattle from 100 herds. In addition, a smaller cross-sectional study sampled 60 dairy cattle from 46 small-holder co-operative dairy farmers in the NWR. Collected blood samples were stimulated with bovine and avian purified protein derivatives, with extracted plasma screened using the IFN-γ enzyme-linked immunosorbent assay (Prionics Bovigam ® ). Design-adjusted population prevalences were estimated, and multivariable mixed-effects logistic regression models using Bayesian inference techniques identified the risk factors for IFN-γ positivity. Using the IFN-γ assay, the prevalence of bTB in the dairy cattle was 21.7% (95% CI: 11.2-32.2). The design-adjusted prevalence of bTB in cattle kept by pastoralists was 11.4% (95% CI: 7.6-17.0) in the NWR and 8.0% (95% CI: 4.7-13.0) in the VIN. A within-herd prevalence estimate for pastoralist cattle also supported that the NWR had higher prevalence herds than the VIN. Additionally, the estimates of the effective reproductive rate R t were 1.12 for the NWR and 1.06 for the VIN, suggesting different transmission rates within regional cattle populations in Cameroon. For pastoral cattle, an increased risk of IFN-γ assay positivity was associated with being male (OR = 1.89; 95% CI:1.15-3.09), increasing herd size (OR = 1.02; 95% CI:1.01-1.03), exposure to the bovine leucosis virus (OR = 2.45; 95% CI: 1.19-4.84) and paratuberculosis (OR = 9.01; 95% CI: 4.17-20.08). Decreased odds were associated with contacts at grazing, buffalo (OR = 0.20; 95% CI: 0.03-0.97) and increased contact with other herds [1-5 herds: OR = 0.16 (95% CI: 0.04-0.55); 6+ herds: OR = 0.18 (95% CI: 0.05-0.64)]. Few studies have used the IFN-γ assay to describe bTB epidemiology in SSA. This study highlights the endemic situation of bTB in Cameroon and potential public health risks from dairy herds. Further work is needed to understand the IFN-γ assay performance, particularly in the presence of co-infections, and how this information can be used to develop control strategies in the SSA contexts., 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 © 2022 Kelly, Gonzaléz Gordon, Egbe, Freeman, Mazeri, Ngwa, Tanya, Sander, Ndip, Muwonge, Morgan, Handel and Bronsvoort.)

The interferon-gamma (IFN-γ) assay and single comparative cervical skin test (SCITT) are used to estimate bovine tuberculosis (bTB) prevalence globally. Prevalence estimates of bTB, caused by Mycobacterium bovis , are poorly quantified in many Sub-Saharan African (SSA) cattle populations. Furthermore, antemortem diagnostic performance can vary at different stages of bTB pathogenesis and in different cattle populations. In this study, we aim to explore the level of agreement and disagreement between the IFN-γ assay and SCITT test, along with the drivers for disagreement, in a naturally infected African cattle population. In, 2013, a pastoral cattle population was sampled using a stratified clustered cross-sectional study in Cameroon. A total of 100 pastoral cattle herds in the North West Region (NWR) and the Vina Division (VIN) were sampled totalling 1,448 cattle. Individual animal data and herd-level data were collected, and animals were screened using both the IFN-γ assay and SCITT. Serological ELISAs were used to detect exposure to immunosuppressing co-infections. Agreement analyses were used to compare the performance between the two bTB diagnostic tests, and multivariable mixed-effects logistic regression models (MLR) were developed to investigate the two forms of IFN-γ assay and SCITT binary disagreement. Best agreement using the Cohen's κ statistic, between the SCITT (>2 mm) and the IFN-γ assay implied a 'fair-moderate' agreement for the NWR [κ = 0.42 (95%CI: 0.31-0.53)] and 'poor-moderate' for the VIN [κ = 0.33 (95% CI: 0.18-0.47)]. The main test disagreement was the animals testing positive on the IFN-γ assay and negative by the SCITT. From MLR modeling, adults (adults OR: 7.57; older adults OR = 7.21), females (OR = 0.50), bovine leucosis (OR = 2.30), and paratuberculosis positivity (OR = 6.54) were associated with IFN-γ-positive/SCITT-negative disagreement. Subsets to investigate diagnostic test disagreement for being SCITT-positive and IFN-γ-negative also identified that adults (adults OR = 15.74; older adults OR = 9.18) were associated with IFN-γ-negative/SCITT-positive disagreement. We demonstrate that individual or combined use of the IFN-γ assay and SCITT can lead to a large variation in bTB prevalence estimates. Considering that animal level factors were associated with disagreement between the IFN-γ assay and SCITT in this study, future work should further investigate their impact on diagnostic test performance to develop the approaches to improve SSA prevalence estimates., 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 © 2022 Kelly, Gonzaléz Gordon, Egbe, Freeman, Mazeri, Ngwa, Tanya, Sander, Ndip, Muwonge, Morgan, Handel and Bronsvoort.)

Information on microbiota dynamics in pulmonary tuberculosis (TB) in Africa is scarce. Here, we sequenced sputa from 120 treatment-naïve TB patients in Uganda, and investigated changes in microbiota of 30 patients with treatment-response follow-up samples. Overall, HIV-status and anti-TB treatment were associated with microbial structural and abundance changes. The predominant phyla were Bacteroidetes, Firmicutes, Proteobacteria, Fusobacteria and Actinobacteria, accounting for nearly 95% of the sputum microbiota composition; the predominant genera across time were Prevotella, Streptococcus, Veillonella, Haemophilus, Neisseria, Alloprevotella, Porphyromonas, Fusobacterium, Gemella, and Rothia. Treatment-response follow-up at month 2 was characterized by a reduction in abundance of Mycobacterium and Fretibacterium, and an increase in Ruminococcus and Peptococcus; month 5 was characterized by a reduction in Tannerella and Fusobacterium, and an increase in members of the family Neisseriaceae. The microbiota core comprised of 44 genera that were stable during treatment. Hierarchical clustering of this core's abundance distinctly separated baseline (month 0) samples from treatment follow-up samples (months 2/5). We also observed a reduction in microbial diversity with 9.1% (CI 6-14%) of the structural variation attributed to HIV-status and anti-TB treatment. Our findings show discernible microbiota signals associated with treatment with potential to inform anti-TB treatment response monitoring., (© 2021. The Author(s).)

Previous work identified that bacterial zoonoses (Brucella species, Coxiella burnetii and Leptospira hardjo) were present in Cameroonian pastoral cattle. To assess the characteristics of this zoonotic risk, we analyse seroprevalence of each pathogen and the associated management, herd and environmental factors in Cameroonian pastoral and dairy cattle. Cross-sectional samples included pastoralist herds in the Northwest Region (NWR n = 750) and Vina Division (VD n = 748) and small holder dairy herds in the NWR (n = 60). Exposure to Brucella spp., C. burnetii and L. hardjo were screened for using commercial ELISAs and population adjusted estimates made. In addition, individual, herd and ecological metadata were collected and used to identify risk factors associated with animal-level seropositivity. In the pastoral cattle, seroprevalence to Brucella spp. was relatively low but was higher in the NWR (4.2%, CI: 2.5%-7.0%) than the VD (1.1%: CI 0.5%-2.4%), while L. hardjo seroprevalence was much higher though similar in the NWR (30.7%, CI 26.3%-35.5%) and VD (35.9%, CI 31.3%-40.7%). No differences were noted in C. burnetii seroprevalence between the two study sites (NWR: 14.6%, CI 11.8%-18.0%. VD: 12.4%, 9.6%-15.9%). Compared to pastoral, dairy cattle had lower seroprevalences for L. hardjo (1.7%, CI: 0.0%-4.9%), C. burnetii (0.0%, CI 0.0%-6.0%) but similar for Brucella spp. (5.0%, CI 0.0%-10.6%). Increased odds of Brucella spp. seropositivity were associated with owning sheep or rearing sheep and fencing cattle in at night. Adult cattle had increased odds of being seropositive for both C. burnetii and L. hardjo. Additionally, exposure to C. burnetii was associated with local ecological conditions and L. hardjo was negatively associated with cattle undertaking transhumance. This work highlights that exposure to these 3 important production diseases and occupational zoonoses are widespread in Cameroonian cattle. Further work is required to understand transmission dynamics between humans and livestock to inform implementation of effective control measures., (© 2021 The Authors. Zoonoses and Public Health published by Wiley-VCH GmbH.)

Antibiotic resistance and its mechanisms have been known for over six decades, but global efforts to characterize its routine drivers have only gained momentum in the recent past. Drivers of clinical and community resistance go beyond just clinical practice, which is why one-health approaches offer the most realistic option for controlling antibiotic resistance. It is noteworthy that the emergence of resistance occurs naturally in the environment, but akin to climate change, the current accelerated emergence and spread bears hallmarks of anthropomorphic influence. If left unchecked, this can undo the medical and agricultural advancements of the last century. The WHO recommends that nations develop, adopt, and implement strategies that track the changing trends in antibiotic resistance levels to tackle this problem. This article examines efforts and progress in developing and implementing a human health antimicrobial resistance surveillance strategy in Uganda. We do so within the context of the National Action Plan for tackling antimicrobial resistance (AMR-NAP) launched in 2018. We discuss the technical milestones and progress in implementing surveillance of GLASS priority pathogens under this framework. The preliminary output of the framework examines the performance and compares AMR and AMU surveillance data to explain observed trends. We conclude that Uganda is making progress in developing and implementing a functional AMR surveillance strategy for human health.

Universal access to healthcare, including quality medicines, is a fundamental human right but is still out of reach for many in low- and middle-income countries (LMICs). An existing framework capturing variability of access to healthcare in low-resource settings includes the 5 dimensions: availability, accessibility, affordability, adequacy, and acceptability. This framework encompasses key components, including health infrastructure and means to access it as well as service organisation, costs, and factors that influence users' satisfaction. However, in reality, the effectiveness of accessed healthcare is measured by the likelihood of a positive outcome. We therefore propose an expansion of this framework to include an additional dimension, "aspects of quality," incorporating quality, which critically influences the ability of the accessed services to generate optimal health outcomes. Within this framework, we explore literature from East Africa likely relevant to a range of LMIC contexts, mainly focusing on the provision of widely used antimicrobials such as antimalarials and antibiotics. We argue that major inadequacies exist across all 6 dimensions of access and quality of drugs and their provision. While the global focus is on curbing excessive antimicrobial use to tackle the antimicrobial resistance (AMR) crisis, major constraints around access shape patients' health-seeking decisions leading to potentially problematic practices that might exacerbate the AMR problem. We advocate for a holistic approach to tackling these inadequacies, encompassing all dimensions of access and quality of healthcare in order to improve health outcomes while simultaneously counteracting the AMR crisis., Competing Interests: The authors have declared that no competing interests exist.

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.)

Background: Clinical intervention during bacterial infections in farm animals such as pigs commonly includes the use of antimicrobials. With the rise of antimicrobial resistance and the attempts to reduce the use of antibiotics in food animals, effective alternatives are urgently needed to reduce or even remove pathogens and disease risks. Improving clinical outcomes and overall pig health by using probiotics appears attractive. However, reliable data sets on the efficacy of probiotics are scarce. The obligate intracellular bacterium Lawsonia intracellularis is widespread in pigs and associated with severe enteropathy, mainly in the ileum, commonly resulting in substantial reduction in weight gain. The impact of three in-feed probiotics and a commercial live L. intracellularis vaccine was compared in a pig challenge model. Probiotic treatment was associated with reduced L. intracellularis fecal shedding and reduced gut lesions. Here, the bacterial microbiota of the ileum of these pigs was characterized with 16S rRNA gene sequencing and was subsequently analyzed with bioinformatics tools., Results: The greatest microbial richness was observed in the probiotic treated group T03-LAW, which accounted for 87% of richness observed in the study. Treatment had a significant impact on both the microbiota structure and taxonomic profile in the ileum, explaining between 26 and 36% of the structural variation, with the strongest association in the T03-LAW group. Overall, the largest changes were observed for the pigs treated with in-feed Bacillus pumilus; the microbiota of these pigs had the greatest diversity and highest richness. We also observed depleted and enriched core microbiota amongst the groups; however, there was no correlation with clinical characteristics. The results suggest that an increased diversity of the ileal microbiota is associated with a reduction in shedding, i.e. a unit increase in Shannon diversity index resulted in 2.8 log reduction in shedding., Conclusions: Probiotic supplementation of a base feed ration increased ileum microbiota diversity leading to a mitigation of the effects of a pathogenic L. intracellularis challenge. An even and diverse microbiota community benefits pigs infected with L. intracellularis, however, investigations are needed to determine if this is also true for other pathogens. The study unambiguously demonstrates the usefulness of probiotic supplementation in reducing the impact of enteric pathogens and pathogen shedding rates in food animals without the use of antimicrobials.

Bovine Tuberculosis (bTB) caused by Mycobacterium bovis is a livestock disease of global economic and public health importance. There are currently no effective vaccines available for livestock and so control relies on animal level surveillance and pasteurization of dairy products. A new alternative control approach is to exploit the genetic variability of the host; recent studies have demonstrated that breeding European taurine cattle, such as Holsteins for increased resistance to bTB is feasible. The utility of such an approach is still unknown for African cattle populations. This study aims to assess genetic variation in bTB resistance and the underlying genomic architecture of cattle in Cameroon. We conducted a cross-sectional study of 2,346 slaughter cattle in Cameroon. Retropharyngeal lymph node samples were collected and cultured on Lowenstein Jensen media and the BACTEC MGIT 960 system, and M. bovis was identified using the Hain® Genotype kits. A total of 153 cattle were positive for M. bovis and were archived along with a random selection of negative samples. In this study, we genotyped archived samples from 212 cattle. Their genomic diversity was characterized using PCA, hierarchical clustering and admixture analysis. We assessed genetic variation in bTB resistance using heritability analysis and compared quantitative trait loci. Previous research on this study population have shown that Fulani cattle are more susceptible to bTB than mixed breeds. However, here we show that these apparent phenotypic differences in breeds are not reflected by clear genomic differences. At the genetic level, both the Fulani and mixed cattle show similar patterns of admixture with evidence of both taurine and indicine ancestry. There was little European taurine introgression within the studied population. Hierarchical clustering showed clusters of cattle that differed in their susceptibility to bTB. Our findings allude to bTB resistance being polygenic in nature. This study highlights the potential for genetic control of bTB in Africa and the need for further research into the genetics of bTB resistance within African cattle populations., (Copyright © 2020 Callaby, Kelly, Mazeri, Egbe, Benedictus, Clark, Doeschl-Wilson, Bronsvoort, Salavati and Muwonge.)

Group antimicrobial administration is used to control disease in livestock, but we have little insight into how this impacts antimicrobial resistance (AMR) gene dynamics. Here, a longitudinal study was carried out during a single production cycle on a commercial pig unit with high historic and current antimicrobial usage. Quantitative PCR, 16S rRNA gene metabarcoding and shotgun metagenomic sequencing were used to track faecal AMR gene abundance and diversity and microbiome alpha diversity. Shotgun metagenomic sequencing identified 144 AMR genes in total, with higher AMR gene diversity present in young pigs compared to dry sows. Irrespective of in-feed antibiotic treatment or changes in microbiome diversity, mean AMR gene copy number was consistently high, with some AMR genes present at copy numbers comparable to the bacterial 16S rRNA gene. In conclusion, AMR gene prevalence and abundance were not influenced by antibiotic use, either during the production cycle or following whole-herd medication. The high levels of certain genes indicate they are widely disseminated throughout the microbial population, potentially aiding stability. Despite the high and relatively stable levels of resistance genes against the main antimicrobials used, these compounds continue to control production limiting diseases on this unit.

A cross-sectional study was carried out between November 2015 and January 2016 to determine the seroprevalence of Brucella antibodies in cattle raised under communal, fenced farms and tethering systems and the associated factors. Seven hundred twenty-eight bovine sera were collected and tested with rose Bengal test as a screening test and the indirect enzyme-linked immunosorbent assay as a confirmatory test. Animal- and herd-level data were collected and binary logistic regression was used to assess the potential risk factors. True animal- and herd-level prevalence was highest in the fenced farms (4.5% (95%CI, 2.3-6.9) and 19.5% (95%CI, 8.2-32.7) respectively). The risks for natural brucellosis infection were sharing water with wild animals (OR = 0.21, 95%CI, 0.104-0.83), herd size (medium: OR = 0.089, 95%CI 0.017-0.449; large: OR = 0.024, 95%CI 0.003-0.203), fenced farms (OR = 3.7, 95% CI, 1.7-7.9), sex (OR = 0.03, 95%CI, 0.01-0.079), and lactation (OR = 0.013, 95%CI, 0.004-0.049). Changes in rangeland tenure and the shift towards intensive cattle production have influenced brucellosis epidemiology. Future studies should aim at identifying the infecting Brucellae and examining the role of wildlife in brucellosis epidemiology.

Background: In this study, we focused on three zoonotic brucellosis risk groups; abattoir workers, febrile cases at Wau hospital and cattle herders, in Bahr el Ghazal region, South Sudan. Competitive c-ELISA was used to detect anti- Brucella antibodies in 725 individuals between December 2015 and May 2016. In addition, questionnaire metadata, focus group discussions and key informant interviews were used to characterize the epidemiology of zoonotic brucellosis in this region. Results: Overall, we estimate 27.2 % (95% CI = 23.9-30.6) brucellosis sero-prevalence; 32.1% (95% CI = 26.2-38.4), 23.0% (95% CI = 19.1-27.4) and 34.6% (95% CI = 24.4-46.3) among abattoir workers, febrile cases, and herders, respectively. Marital status (Single, OR = 0.58, 95%CI: 0.36-0.91, P = 0.02) and ethnicity (Kerash OR = 6.01, 95%CI: 1.97-21.10, P = 0.003 and Balanda, OR = 3.78, 95%CI: 1.42-12.02, P = 0.01) were associated with brucellosis. While gender and ethnicity were important factors for general awareness of zoonotic diseases. Highly ranked occupations at risk included veterinarian, butchers and milk handlers. We also identified covariate patterns for clinical diagnostics and public health interventions. Conclusion: We report the highest sero-prevalence of zoonotic brucellosis in three risk groups in the East African region. All this is not only occurring in a population with limited awareness that brucellosis is a zoonotic disease but also where one in nine health workers tested was sero-positive. We identified social demographic associations with brucellosis, however, the qualitative analysis suggests these are more complex and nuanced. Therefore, future studies could benefit from the use of the mixed methods approach to add extensiveness and depth to our understanding of zoonotic disease drivers, in order to implement mitigating measures such as cattle vaccination.

Background: Brucellosis is an infectious zoonotic disease and is common especially among pastoral communities in most low and middle-income countries. The aim of this study was to determine sero-prevalence, and risk factors of Brucella infection among Slaughterhouse workers, in Bahr el Ghazal region, South Sudan., Methods: A cross sectional study was conducted among Slaughterhouse workers in Bahr el Ghazal region, South Sudan from December 2015 to May 2016. A pre-tested questionnaire was used in data collection. Each randomly selected participant was interviewed and a venous blood sample collected. The blood samples were screened for Brucellosis infection using Rose Bengal Plate Test (RBPT) and confirmed using Competitive Enzyme link Immuno Sorbet Assay (c-ELISA). Data was analyzed using Stata version 13 at 95% level of confidence., Results: A total of 234 Slaughterhouse workers were screen for Brucella infection. Overall, a third, 32.1% (75/234) of the participants were sero-positive for brucellosis. The prevalence of brucellosis was higher, 17.1% (40/234) in Wau state compared to other states. There was high prevalence among males, 28.6% (67/234) compared to females 3.4% (8/234). The mean age of study participants was 34.4 ± 9.6 years. A high proportion, 12.8% (30/234) of participants with confirmed brucellosis infection were 31-40 years of age. Brucellosis prevalence was high among butchers, 14.5% (34/234), and meat handlers, 9.0% (21/234)., Conclusions: Brucellosis is common among animal slaughterhouse workers in Bahr el Ghazal region, South Sudan. There is need for public awareness campaigns and educational programs to help sensitize communities on Brucella infection.

Typhoid fever affects 21 million people globally, 1% of whom succumb to the disease. The social, economic and public health consequences of this disease disproportionately affect people in Africa and Asia. In order to design context specific prevention strategies, we need to holistically characterise outbreaks in these settings. In this study, we used retrospective data (2013-2016) at national and district level to characterise temporal and spatial dynamics of Typhoid fever outbreaks using time series and spatial analysis. We then selected cases matched with controls to investigate household socio-economic drivers using a conditional logistic regression model, and also developed a Typhoid fever outbreak-forecasting framework. The incidence rate of Typhoid fever at national and district level was ~ 160 and 60 cases per 100,000 persons per year, respectively, predominantly in urban areas. In Kasese district, Bwera sub-county registered the highest incidence rate, followed by Kisinga, Kitholhu and Nyakiyumbu sub-counties. The male-female case ratio at district level was at 1.68 and outbreaks occurred between the 20th and 40th week (May and October) each year following by seven weeks of precipitation. Our forecasting framework predicted outbreaks better at the district level rather than national. We identified a temporal window associated with Typhoid fever outbreaks in Kasese district, which is preceded by precipitation, flooding and displacement of people. We also observed that areas with high incidence of Typhoid fever also had high environmental contamination with limited water treatment. Taken together with the forecasting framework, this knowledge can inform the development of specific control and preparedness strategies at district and national level., Competing Interests: The authors have declared that no competing interests exist.

Bovine tuberculosis (BTB) is a disease of animal and public health importance in developing countries. In rural Ethiopia, there is potential for a shift in the epidemiologic of this disease driven by transformation of dairy industry. This includes gradual change from the traditional mixed crop-livestock husbandry practice to a semi-intensification system. It is therefore, essential to document the prevalence and risk factors of BTB to continuously update the designing and implementation of control and prevention strategies. Here, we present findings of a cross-sectional study on the prevalence and associated risk factors of BTB among cattle reared under mixed crop-livestock farming system in Tigray region, Ethiopia. A multistage purposive sampling approach was used to select districts, villages, herds and individual cattle. A total of 1,357 cattle from 310 herds were examined for BTB infection using a comparative intradermal tuberculin skin test (CIDT). Questionnaires were used to gather data on herd structure and herd management practices. A multilevel logistic mixed effect model was used to determine risk factors after accounting for clustering effect at three levels (village, herd and individual animal). Overall prevalence of BTB was 4.3% (95% CI = 3.4-5.6), with the highest prevalence recorded in Alamata district (5.6%) and lowest in Korem (1.6%). Multilevel logistic mixed effect model analysis identified exotic breed (OR = 3, p = 0.014), closed barn (OR = 2.6, p = 0.018), large herd size (OR = 2.6, p = 0.05) and purchase of cattle (OR = 2.1, p = 0.027) as important risk factors for BTB. Taken together, these findings suggest that the current dairy development program centred on the introduction of exotic and or crossed animals could have contributed to changing epidemiological situations of BTB in the study area., (© 2018 Blackwell Verlag GmbH.)

Bovine tuberculosis (bTB), caused by Mycobacterium bovis , remains a major livestock and public health problem in both high and low-income countries. With the current absence of an effective vaccine, control in cattle populations is reliant on regular testing and removal of positive animals. However, surveillance and control are hampered by imperfect diagnostic tests that have poorly described properties in naturally infected populations. Recent research in cattle co-infected with the temperate liver fluke, Fasciola hepatica , has raised concerns about the performance of the intradermal skin test in high fluke incidence areas. Further, recent studies of parasitic co-infections have demonstrated their impact on Th1 and Th2 responses, concurrent disease pathology and susceptibility to mycobacterial infections. Here we report for the first time the association of co-infection with the tropical liver fluke, Fasciola gigantica , with the presence of bTB-like lesions and the IFN-γ response in naturally infected African cattle. After adjusting for age and sex we observed a complex interaction between fluke status and breed. Fulani cattle had a higher risk of having bTB-like lesions than the mixed breed group. The risk of bTB-like lesions increased in the mixed breed group if they had concurrent evidence of fluke pathology but was less clear in the coinfected Fulani breed. Further, we observed a slight decline in the IFN-γ levels in fluke infected animals. Finally we explored factors associated with IFN-γ false negative results compared to the presence of bTB-like lesions. Fulani cattle had a higher risk of having a false negative result compared to the mixed breed group. Further, the mixed breed cattle had an increased risk of being false negative if also co-infected with fluke. Interesting, as with the risk of bTB-like lesions, this association was less clear in the Fulani cattle with weak evidence of a slight decrease in risk of having a false negative test result when fluke pathology positive. This interesting interaction where different breeds appear to have different responses to co-infections is intriguing but further work is needed to confirm and understand more clearly the possible confounding effects of different other co-infections not measured here, breed, management or exposure risks.

Brucellosis is a zoonotic disease of public health importance; its prevalence varies globally. In low-income countries, brucellosis is an endemic and neglected disease affecting both animals and humans. This study was intended to establish brucellosis sero-prevalence among patients attending Wau hospital, South Sudan. Across sectional study, was done among randomly selected patients attending Wau hospital. Data was collected using questionnaires and laboratory investigations. Rose Bengal plate Test (RBPT), Serum agglutination test (SAT) and Competitive Enzyme Linked Immuno Sorbent Assay (c-ELISA) was used in the analysis of blood samples serially starting with RBPT which is more sensitive and least specific then SAT. c-ELISA test which is most specific and less sensitive compared to RBPT and SAT was then used to confirm presence of Brucella antibodies in the samples. A total of 416 participants out of 1664 were enrolled to this study. The majority of participants were between 7-to-76 years of age with mean age of 30.72 (SD+/- 12.83). The sero-positivity of patient's blood samples for brucellosis using c-ELISA was 23.3% (97/416) among patients presenting to Wau hospital. Socio-demographic characteristics, occupation, clinical signs of disease and types of animals reared by animal owners showed no significant correlation with occurrence of sero-positivity among patient's blood samples for brucellosis. While ethnicity (Nilotic), knowledge of zoonotic disease, and consumption of animal urine were statistically significant (p<0.05). The study found a high prevalence of brucellosis among febrile patients attending Wau hospital general outpatient clinic. There is need for co-ordination and collaboration between veterinary and health sectors of government to help prevent and control brucellosis in the region., Competing Interests: The authors have declared that no competing interests exist.

Background: Brucellosis is a worldwide recognized bacterial zoonotic disease. There is currently no information on bovine brucellosis sero-prevalence in South Sudan regardless of the economic, social and public health impact on populations. Therefore, for the first time in 33 years, we report the sero-prevalence of brucellosis in cattle and their herders. Furthermore, we characterize the drivers associated with the disease at the human-animal interface in Bahr el Ghazal region, South Sudan., Methods: A total of 893 and 87 animal and human sera respectively were examined between December 2015 and May 2016. Rose Bengal Plate Test (RBPT) and Competitive Enzyme Linked Immuno Sorbent Assay (c-ELISA) were used in parallel to detect anti-Brucella antibodies. Questionnaires were administered to collect relevant metadata used for the association analysis in R version 3.2.3. Odds Ratio (OR) and Confidence Intervals (CI) were determined., Results: Overall bovine brucellosis prevalence was 31% (95%CI = 28.0-34.2), with the highest 63% (95%CI = 53-70) and lowest 10% (95%CI = 4.5-20.1) prevalence estimates in Wau and Gogrial states respectively. The bovine sero-prevalence was approximately equally distributed among the male 30.4% (26.9-34.2) and the females 32.5% (26.8-38.7). Poor body condition (OR = 0.22; 95%CI = 0.07-0.54) and larger herd sizes (OR = 0.05; 95%CI = 0.008-0.173) were protective factors for brucellosis, while the opposite was true for the second (OR = 1.70; 95%CI = 1.08-2.67) and third (OR = 2.5; 95%CI = 1.46-4.47) lactation stage. The overall brucellosis sero-prevalence in herders was estimated at 33.3% (23.9-44.3)., Conclusion: We report a high prevalence of anti-Brucella antibodies in cattle and their herders in Bahr el Ghazal, indicating an enzootic status in the cattle population being an important source of infection for humans. This represents a genuine public health challenge. Therefore, there is need to raise awareness and build capacity and infrastructure in this fragile state to underwrite future public health strategies for brucellosis., Competing Interests: The authors have declared that no competing interests exist.

Mycobacterium bovis (M.bovis) is the main causative agent for bovine tuberculosis (BTB) and can also be the cause of zoonotic tuberculosis in humans. In view of its zoonotic nature, slaughterhouse surveillance, potentially resulting in total or partial condemnation of the carcasses and organs, is conducted routinely. Spoligotyping, VNTR profiling, and whole genome sequencing (WGS) of M. bovis isolated from tissues with tuberculosis-like lesions collected from 14 cattle at Eritrea's largest slaughterhouse in the capital Asmara, were conducted.The 14 M. bovis isolates were classified into three different spoligotype patterns (SB0120, SB0134 and SB0948) and six VNTR profiles. WGS results matched those of the conventional genotyping methods and further discriminated the six VNTR profiles into 14 strains. Furthermore, phylogenetic analysis of the M. bovis isolates suggests two independent introductions of BTB into Eritrea possibly evolving from a common ancestral strain in Europe.This molecular study revealed the most important strains of M. bovis in Eritrea and their (dis)similarities with the strains generally present in East Africa and Europe, as well as potential routes of introduction of M. bovis. Though the sample size is small, the current study provides important information as well as platform for future in-depth molecular studies on isolates from both the dairy and the traditional livestock sectors in Eritrea and the region. This study provides information onthe origin of some of the M. bovis strains in Eritrea, its genetic diversity, evolution and patterns of spread between dairy herds. Such information is essential in the development and implementation of future BTB control strategy for Eritrea.

Background: The non-tuberculous mycobacteria include those mycobacterium species that are not members of the Mycobacterium tuberculosis complex, the causative agent of pulmonary tuberculosis and Mycobacterium leprae. In Zambia, Non-tuberculous Mycobacteria are gaining recognition as pathogens of public health significance. However, there is scanty information on the isolation and speciation of these organisms for better patient management, consequently reducing the burden of these infections. Given the above information, the thrust of this study was to isolate and characterize NTM from humans and water in Namwala district of Zambia., Method: This was a cross-sectional study were 153 individuals with suspected TB were sampled from four health facilities in Namwala district, sputum samples were also collected. Additionally, 149 water samples were collected from different water drinking sources such as Tap water, Borehole water, rivers, wells and streams. Standard TB culture methods were employed to isolate Non-tuberculous Mycobacteria and later 16S-23S internal transcribed spacer region Sequencing was employed to characterize NTM., Results: Seven (7, 4.6%) NTM species were identified from humans with M. arupense (3, 42.9%) being the most common organism, while twenty three (23, 15.4%) NTM were identified from water with the common species being Mycobacterium gordonae (5, 21.7%). Mycobacterium avium and Mycobacterium fortuitum were both identified from human and water samples., Conclusion: This study has shown the isolation of NTM species from humans and water. The isolation of NTM from drinking water sources could signify a public health risk to humans.

Knowledge, attitude, and practice (KAP) studies guide the implementation of public health interventions (PHIs), and they are important tools for political persuasion. The design and implementation of PHIs assumes a linear KAP relationship, i.e., an awareness campaign results in the desirable societal behavioral change. However, there is no robust framework for testing this relationship before and after PHIs. Here, we use qualitative and quantitative data on pesticide usage to test this linear relationship, identify associated context specific factors as well as assemble a framework that could be used to guide and evaluate PHIs. We used data from a cross-sectional mixed methods study on pesticide usage. Quantitative data were collected using a structured questionnaire from 167 households representing 1,002 individuals. Qualitative data were collected from key informants and focus group discussions. Quantitative and qualitative data analysis was done in R 3.2.0 as well as qualitative thematic analysis, respectively. Our framework shows that a KAP linear relationship only existed for households with a low knowledge score, suggesting that an awareness campaign would only be effective for ~37% of the households. Context specific socioeconomic factors explain why this relationship does not hold for households with high knowledge scores. These findings are essential for developing targeted cost-effective and sustainable interventions on pesticide usage and other PHIs with context specific modifications.

Background: Non-typhoidal Salmonella (NTS) are among the leading global foodborne pathogens and a significant public health threat. Their occurrence in animal reservoirs and their susceptibilities to commonly used antimicrobials are poorly understood in developing countries. The aim of this study was to estimate the prevalence, determine antimicrobial susceptibility and identify risk factors associated with NTS presence in laying hen farms in Uganda through a cross-sectional study., Results: Pooled faecal samples were collected from 237 laying hen farms and these were analysed for NTS following standard laboratory procedures. In total, 49 farms (20.7%; 95% Confidence interval (CI): 15.6-25.6%) were positive for NTS presence. Altogether, ten Salmonella serotypes were identified among the confirmed 78 isolates, and the predominant serotypes were Salmonella Newport (30.8%), S. Hadar (14.1%), S. Aberdeen (12.8%), S. Heidelberg (12.8%), and S. Bolton (12.8%). Phenotypic antimicrobial resistance was detected in 45(57.7%) of the isolates and the highest resistance was against ciprofloxacin (50.0%) followed by sulphonamides (26.9%) and sulphamethoxazole/trimethoprim (7.7%). Resistance was significantly associated with sampled districts (p = 0.034). Resistance to three or more drugs, multi-drug resistance (MDR) was detected in 12 (15.4%) of the isolates, 9 (75%) of these were from Wakiso district. A multivariable logistic model identified large farm size (OR = 7.0; 95% CI: 2.5-19.8) and the presence of other animal species on the farm (OR = 5.9; 95% CI: 2.1-16.1) as risk factors for NTS prevalence on farms. Having a separate house for birds newly brought to the farms was found to be protective (OR = 0,4; 95% CI: 0.2-0.8)., Conclusion: This study has highlighted a high prevalence and diversity of NTS species in laying hen farms in Uganda and identified associated risk factors. In addition, it has demonstrated high levels of antimicrobial resistance in isolates of NTS. This could be because of overuse or misuse of antimicrobials in poultry production. Also importantly, the insights provided in this study justifies a strong case for strengthening One Health practices and this will contribute to the development of NTS control strategies at local, national and international levels.

Background: The aim of this study was to estimate the prevalence of gross pathology suggestive of bovine tuberculosis (TB-like lesions) and evaluate animal's characteristics associated with the risk of having bovine TB-like lesions among cattle slaughtered in Mubende district in the Uganda cattle corridor., Method: We conducted a cross sectional study in which 1,576 slaughtered cattle in Mubende district municipal abattoir underwent post-mortem inspection between August 2013 and January 2014. The presence of bovine TB-like lesions in addition to the animal's sex, age, breed, and sub-county of origin prior to slaughter were recorded. Associations between the presence of bovine TB-like lesions and animal's age, sex, breed, and sub-county of origin prior to slaughter were initially analysed using a univariable approach with the chi-square test, and subsequently with a multivariable logistic regression model to assess the combined impact of these animal characteristics with the risk of having a bovine TB-like lesion. Additionally, and as a secondary objective, tissue samples were collected from all carcases that had a bovine TB-like lesion and were processed using standard Mycobacterium culture and identification methods. The culture and acid fast positive samples were tested using Capilia TB-neo® assay to identify Mycobacterium tuberculosis complex (MTC)., Results: Of 1,576 carcasses inspected, 9.7% (153/1,576) had bovine TB-like lesions from which Mycobacterium spp and Mycobacterium Tuberculosis Complex (MTC) were isolated in 13 (8.4%) and 12 (7.8%) respectively. Bovine TB-like lesions were more likely to be found in females (OR = 1.49, OR 95% CI: 1.06-2.13) and in older cattle (OR = 2.5, 95% CI: 1.64-3.7). When compared to Ankole cattle, Cross breed (OR = 6.5, OR 95% CI: 3.37-12.7) and Zebu cattle (OR = 2.57, 95% CI: 1.78-3.72) had higher odds of having bovine TB-like lesions. Animals from Kasanda (OR = 2.5, 95% CI: 1.52-4.17) were more likely to have bovine TB-like lesions than cattle from Kasambya., Conclusions: The findings of study reveals that approximately one in ten slaughtered cattle presents with gross pathology suggestive of bovine TB in Mubende district in the Uganda cattle corridor district, however, we isolated MTC in only 8.4% of these bovine TB-like lesions. Therefore, there is a need to understand the cause of all the other bovine TB-like lesions in order to safe guard diagnostic integrity of meat inspection in Uganda.

Mycobacterium tuberculosis is recognised as the primary cause of human tuberculosis worldwide. However, substantial evidence suggests that the burden of Mycobacterium bovis, the cause of bovine tuberculosis, might be underestimated in human beings as the cause of zoonotic tuberculosis. In 2013, results from a systematic review and meta-analysis of global zoonotic tuberculosis showed that the same challenges and concerns expressed 15 years ago remain valid. These challenges faced by people with zoonotic tuberculosis might not be proportional to the scientific attention and resources allocated in recent years to other diseases. The burden of zoonotic tuberculosis in people needs important reassessment, especially in areas where bovine tuberculosis is endemic and where people live in conditions that favour direct contact with infected animals or animal products. As countries move towards detecting the 3 million tuberculosis cases estimated to be missed annually, and in view of WHO's end TB strategy endorsed by the health authorities of WHO Member States in 2014 to achieve a world free of tuberculosis by 2035, we call on all tuberculosis stakeholders to act to accurately diagnose and treat tuberculosis caused by M bovis in human beings., (Copyright © 2017 World Health Organization. Published by Elsevier Ltd/Inc/BV. All rights reserved. Published by Elsevier Ltd.. All rights reserved.)

The major histocompatibility complex (MHC) region contains many genes that are key regulators of both innate and adaptive immunity including the polymorphic MHCI and MHCII genes. Consequently, the characterisation of the repertoire of MHC genes is critical to understanding the variation that determines the nature of immune responses. Our current knowledge of the bovine MHCI repertoire is limited with only the Holstein-Friesian breed having been studied in any depth. Traditional methods of MHCI genotyping are of low resolution and laborious and this has been a major impediment to a more comprehensive analysis of the MHCI repertoire of other cattle breeds. Next-generation sequencing (NGS) technologies have been used to enable high throughput and much higher resolution MHCI typing in a number of species. In this study we have developed a MiSeq platform approach and requisite bioinformatics pipeline to facilitate typing of bovine MHCI repertoires. The method was validated initially on a cohort of Holstein-Friesian animals and then demonstrated to enable characterisation of MHCI repertoires in African cattle breeds, for which there was limited or no available data. During the course of these studies we identified >140 novel classical MHCI genes and defined 62 novel MHCI haplotypes, dramatically expanding the known bovine MHCI repertoire.

Background: Control of bovine tuberculosis (bTB) and zoonotic tuberculosis (zTB) has relied upon surveillance and slaughter of infected cattle, milk pasteurisation and public health education. In Cameroon, like many other sub-Saharan African countries, there is limited understanding of current cattle husbandry or milk processing practices or livestock keepers awareness of bTB. This paper describes husbandry and milk processing practices within different Cameroonian cattle keeping communities and bTB awareness in comparison to other infectious diseases., Study Design: A population based cross-sectional sample of herdsmen and a questionnaire were used to gather data from pastoralists and dairy farmers in the North West Region and Vina Division of Cameroon., Results: Pastoralists were predominately male Fulanis who had kept cattle for over a decade. Dairy farmers were non-Fulani and nearly half were female. Pastoralists went on transhumance with their cattle and came into contact with other herds and potential wildlife reservoirs of bTB. Dairy farmers housed their cattle and had little contact with other herds or wildlife. Pastoralists were aware of bTB and other infectious diseases such as foot-and-mouth disease and fasciolosis. These pastoralists were also able to identify clinical signs of these diseases. A similar proportion of dairy farmers were aware of bTB but fewer were aware of foot-and-mouth and fasciolosis. In general, dairy farmers were unable to identify any clinical signs for any of these diseases. Importantly most pastoralists and dairy farmers were unaware that bTB could be transmitted to people by consuming milk., Conclusions: Current cattle husbandry practices make the control of bTB in cattle challenging especially in mobile pastoralist herds. Routine test and slaughter control in dairy herds would be tractable but would have profound impact on dairy farmer livelihoods. Prevention of transmission in milk offers the best approach for human risk mitigation in Cameroon but requires strategies that improved risk awareness amongst producers and consumers.

Mycobacterium tuberculosis, the causative agent of tuberculosis in humans, is considered primarily a human pathogen. It has, however, been reported in a wide range of domestic and wild animals, often living in close prolonged contact with humans. Sputum samples in which acid fast bacteria were detected in smears were collected from patients at three health facilities in Namwala district, Zambia. Samples from cattle presenting gross lesions compatible with bovine tuberculosis were collected at a local abattoir in the same district. Isolated mycobacteria were identified and genotyped using classical molecular methods. From a total of 33 isolates of M. tuberculosis detected (30 from humans and 3 from cattle), two cattle isolates shared the same spoligotype and MIRU-VNTR pattern with a human patient. This study has for the first time documented the isolation of M. tuberculosis from cattle in Zambia and provides molecular evidence of an epidemiological link between M. tuberculosis isolates from humans and cattle in Namwala district. A possible spill back of M. tuberculosis to humans cannot be excluded and therefore further studies documenting to what extent M. tuberculosis is shed in cattle milk are needed. This finding further suggests that veterinary public health measures to control human TB, should also take into account the bovine reservoir.

Background: This study compared TB diagnostic tools and estimated levels of misdiagnosis in a resource-limited setting. Furthermore, we estimated the diagnostic utility of three-TB-associated predictors in an algorithm with and without Direct Ziehl-Neelsen (DZM)., Materials and Methods: Data was obtained from a cross-sectional study in 2011 conducted at Mubende regional referral hospital in Uganda. An individual was included if they presented with a two weeks persistent cough and or lymphadenitis/abscess. 344 samples were analyzed on DZM in Mubende and compared to duplicates analyzed on direct fluorescent microscopy (DFM), growth on solid and liquid media at Makerere University. Clinical variables from a questionnaire and DZM were used to predict TB status in multivariable logistic and Cox proportional hazard models, while optimization and visualization was done with receiver operating characteristics curve and algorithm-charts in Stata, R and Lucid-Charts respectively., Results: DZM had a sensitivity and specificity of 36.4% (95% CI = 24.9-49.1) and 97.1%(95% CI = 94.4-98.7) compared to DFM which had a sensitivity and specificity of 80.3%(95% CI = 68.7-89.1) and 97.1%(95% CI = 94.4-98.7) respectively. DZM false negative results were associated with patient's HIV status, tobacco smoking and extra-pulmonary tuberculosis. One of the false negative cases was infected with multi drug resistant TB (MDR). The three-predictor screening algorithm with and without DZM classified 50% and 33% of the true cases respectively, while the adjusted algorithm with DZM classified 78% of the true cases., Conclusion: The study supports the concern that using DZM alone risks missing majority of TB cases, in this case we found nearly 60%, of who one was an MDR case. Although adopting DFM would reduce this proportion to 19%, the use of a three-predictor screening algorithm together with DZM was almost as good as DFM alone. It's utility is whoever subject to HIV screening all TB suspects.

Bovine tuberculosis (BTB) remains a major threat to animal and human health, and obstructs international and inter-regional livestock trade in Ethiopia. Many aspects of epidemiology of BTB and its causative agent, Mycobacterium bovis (M. bovis) are not well known. Aims of the study were to elucidate molecular characteristics of M. bovis strains using MLVA typing method. Further aim was to determine infection pressure associated with occurrence of multiple genotypes in individual infected cattle. Data and samples were collected in the period July 2006-January 2007 in cattle slaughtered at five representative abattoirs across the country. Molecular investigation of the isolates was carried out using multilocus variable-number tandem-repeat analysis (MLVA) of 28 variable numbers of tandem repeat (VNTR) loci, and the results were compared to spoligotyping. This study is believed to contribute to the knowledge of molecular genetics and epidemiology of M. bovis in Ethiopia and elsewhere with similar BTB epidemic situation and livestock production settings. Four-hundred and six tissue samples from 337 carcasses revealing gross pathologic lesions compatible with BTB were collected from five abattoirs. Fifty-eight isolates obtained from cultured samples were subjected to region of difference (RD) analysis and MLVA typing. RD confirmed all isolates as being M. bovis. MLVA revealed a high heterogeneity of M. bovis (19 genotypes) and the discriminatory power of MLVA was higher than for spoligotyping (Hunter-Gaston Diversity Index (HGDI) 0.92 vs. 0.82). Adoption of the nine VNTR loci with ⩾3 alleles provided good differentiation between the isolates. However, differentiation was optimized when MLVA was combined with spoligotyping (HGDI=0.99). MLVA confirmed infections with multiple genotypes in 38.5% (10/26) of individual animals. In conclusion, the usefulness of MLVA for genotyping M. bovis in high prevalence settings was demonstrated. BTB in Ethiopia is caused by heterogeneous populations of M. bovis and individual carcasses were often infected with different genotypes, indicating a high infection pressure perhaps related to the absence of protective immunity conferred by infection., (Copyright © 2014 Elsevier B.V. All rights reserved.)

Background: Members of the Mycobacterium avium complex (MAC) cause disease in both human and animals. Their ubiquitous nature makes them both successful microbes and difficult to source track. The precise characterization of MAC species is a fundamental step in epidemiological studies and evaluating of possible reservoirs. This study aimed at identifying and characterizing Mycobacterium avium subsp. hominissuis isolated from human, slaughter cattle and pigs in various parts of the Uganda cattle corridor (UCC) at two temporal points using variable number of tandem repeat (VNTR) analysis., Methods: A total of 46 M. avium isolates; 31 from 997 pigs, 12 from 43 humans biopsies and three from 61 cattle lesions were identified to subspecies level using IS1245 and IS901 PCR, thereafter characterized using VNTR. Twelve loci from two previously described VNTR methods were used and molecular results were analyzed and interpreted using Bionumerics 6.1., Principal Findings: 37 of the isolates were identified as M. avium subsp. hominissuis and four as M. avium subsp. avium, while five could not be differentiated, possibly due to mixed infection. There was distinct clustering that coincides with the temporal and spatial differences of the isolates. The isolates from humans and cattle in the North Eastern parts of the UCC shared identical VNTR genotypes. The panel of loci gave an overall discriminatory power of 0.88. Some loci were absent in several isolates, probably reflecting differences in isolates from Uganda/Africa compared to isolates previously analyzed by these methods in Europe and Asia., Conclusions: The findings indicate a molecular difference between M. avium subsp. hominissuis isolates from pigs in Mubende and cattle and human in the rest of the UCC. Although human and cattle shared VNTR genotypes in the North Eastern parts of the UCC, it is most likely a reflection of a shared environmental source., (Copyright © 2013 Elsevier B.V. All rights reserved.)

Tuberculosis remains a major public health problem in Zambia. While human to human transmission of Mycobacterium tuberculosis is of major importance in driving the tuberculosis epidemic, the impact of Mycobacterium bovis transmission from infected cattle is largely unknown. This cross-sectional study aimed at molecular characterization of M. bovis in humans and cattle. A total of 100 human sputum samples and 67 bovine tissues were collected and analyzed for the presence of mycobacteria. Of 65 human samples that harbored acid fast bacteria (AFB), 55 isolates were obtained of which 34 were identified as M. tuberculosis and 2 as M. bovis. AFB-positive bovine samples (n = 67) yielded 47 mycobacterial isolates among which 25 were identified as M. bovis and no M. tuberculosis was found. Among the M. bovis isolates, spoligotyping revealed a high homogeneity in genotypes circulating in Namwala district. Human and cattle isolates shared identical MIRU-VNTR genotypes, suggesting that transmission between the two hosts may occur. Therefore, this study has documented zoonotic TB in human patients in Namwala district of Zambia. However, further molecular epidemiological studies in the study area are recommended.

Multiple strain tuberculosis (TB) infections are now an acceptable facet of tuberculosis epidemiology. Identification of patients infected with more than one strain gives an insight in disease dynamics at individual and population level. This study therefore aimed at identifying multiple strain infections among TB infected patients. Furthermore, to determine factors associated with multiple strain infections in Mubende district of Uganda. A total of 72 Mycobacterium tuberculosis isolates from patients at Mubende regional referral hospital were characterized using 15 loci MIRU-VNTR, Spoligotyping and deletion analysis. Genotypic and epidemiological data were analyzed using MIRU-VNTR plus, Bionumerics software version 6.1 and an exact logistic regression model respectively. Eight (11.1%) of the 72 patients had mixed TB infections. Five were exclusively pulmonary mixed infections while three had both pulmonary and extra-pulmonary infections (Compartmentalized TB infections). Unlike previous studies that have linked this phenomenon to Beijing strains, multiple strains in this study belonged to T2-Uganda, X2 and T1 lineages. Two of the pulmonary mixed infections were resistant to rifampicin or isoniazid. All except one were HIV positive, newly diagnosed cases and urban residents of Mubende district. The study revealed that one in nine urban dwelling, HIV/TB co-infected patient were infected with more than one M. tuberculosis strains. The molecular findings give indications of a vital component of the disease dynamics that is most likely under looked at clinical level., (Copyright © 2013 Elsevier B.V. All rights reserved.)

Background: Tuberculosis (TB) remains a global public health problem whose effects have major impact in developing countries like Uganda. This study aimed at investigating genotypic characteristics and drug resistance profiles of Mycobacterium tuberculosis isolated from suspected TB patients. Furthermore, risk factors and economic burdens that could affect the current control strategies were studied., Methods: TB suspected patients were examined in a cross-sectional study at the Mubende regional referral hospital between February and July 2011. A questionnaire was administered to each patient to obtain information associated with TB prevalence. Isolates of M. tuberculosis recovered during sampling were examined for drug resistance to first line anti-TB drugs using the BACTEC-MGIT960(TM) system. All isolates were further characterized using deletion analysis, spoligotyping and MIRU-VNTR analysis. Data were analyzed using different software; MIRU-VNTR plus, SITVITWEB, BioNumerics and multivariable regression models., Results: M. tuberculosis was isolated from 74 out of 344 patients, 48 of these were co-infected with HIV. Results from the questionnaire showed that previously treated TB, co-infection with HIV, cigarette smoking, and overcrowding were risk factors associated with TB, while high medical related transport bills were identified as an economic burden. Out of the 67 isolates that gave interpretable results, 23 different spoligopatterns were detected, nine of which were novel patterns. T2 with the sub types Uganda-I and Uganda-II was the most predominant lineage detected. Antibiotic resistance was detected in 19% and multidrug resistance was detected in 3% of the isolates., Conclusion: The study detected M. tuberculosis from 21% of examined TB patients, 62% of whom were also HIV positive. There is a heterogeneous pool of genotypes that circulate in this area, with the T2 lineage being the most predominant. High medical related transport bills and drug resistance could undermine the usefulness of the current TB strategic interventions.

Owing to frequent reports of suspected outbreaks and the presence of reservoir hosts and vectors (warthogs, bushpigs and O. moubata ticks), African swine fever (ASF) is believed to be an endemic disease in Uganda. There have, however, been very few studies carried out to confirm its existence in Uganda. This study was carried out to describe the prevalence of ASF based on pathologic lesions and analysis of serum samples from slaughtered pigs during a suspected outbreak in the Mubende district of Uganda. The study was based on visits to 22 slaughterhouses where individual pigs were randomly selected for a detailed ante-mortem and post-mortem inspections. Sera were also collected for laboratory analysis. A total of 997 pigs (53.7% male and 46.3% female) were examined for lesions suggestive of ASF and sero-positivity of sera for ASF antibodies. The sera were tested using enzyme-linked immunosorbent assay (ELISA) and positive samples were further confirmed with an immunoblot assay. The results showed that 3.8% (38/997) of the pigs examined had clinical signs and post-mortem lesions suggestive of ASF. Two of 997 (0.2%) sera analysed were positive for ASF antibodies. Of the sub-counties investigated, Bagezza (12%) and Kiyuni (11%) had the highest prevalence of lesions suggestive of ASF based on ante- and post-mortem examination results, while Mubende town council (1.7%) had the lowest. This study found a low number of pigs (3.8%) with lesions suggestive of ASF at slaughter and an even lower number of pigs (0.2%) that were seropositive at slaughter, however a significantly higher number of pigs were slaughtered during the outbreak as a strategy for farmers to avoid losses associated with mortality.

Background: Bovine tuberculosis (TB) caused by Mycobacterium bovis is primarily a disease of ruminants, particularly cattle (Bos primigenius) and buffalo (Syncerus caffer), and is endemic in most developing countries. To date, studies done in Uganda have documented the prevalence of M. bovis in cattle, humans and wild life, in addition to non-tuberculous mycobacteria in pigs. Pigs are increasingly becoming an important component of the livestock sector and share the human ecosystem in rural Uganda. It is therefore of public health interest that they are not a source of human infections. As a follow up to previously published findings on mycobacteria in pigs, this study was aimed at investigating the occurrence and molecular characteristics of M. bovis detected in slaughter pigs in Mubende district, Uganda. One hundred fifty mesenteric lymph nodes with lesions suggestive of mycobacterial infections were collected from approximately one thousand slaughtered pigs in Mubende district over a period of five months. The isolation and identification of M. bovis was done using conventional mycobacteriological methods. Mycobacteria belonging to the Mycobacterium tuberculosis complex (MTC) were identified to species level using deletion analysis. Molecular typing was done using Spoligotyping and MIRU-VNTR analysis. Molecular data were analysed and interpreted using MIRU-VNTR plus, SpolDB4.0 and the Mycobacterium bovis spoligo database., Results: Of the examined animals, one boar and two sows from Madudu Sub County were infected with M. bovis which presented as lesions of a deep yellow colour and a grit-like texture in the mesenteric lymph nodes. This represents 2% (3/150) of the lymph nodes where lesions suggestive of mycobacterial infections were detected. Molecular analysis revealed that the isolates from the infected pigs showed identical MIRU-VNTR profile and spoligotype (SB1469)., Conclusions: This is the first study documenting the occurrence of M. bovis in slaughter pigs in Uganda, revealing that one in fifty slaughter pigs with suspected lesions in mesenteric lymph nodes were infected. Molecular analysis revealed that the isolates were identical, showing a spoligotype previously reported from humans and cattle in the north eastern part of the Uganda cattle corridor. This finding is of public health importance, therefore there is a need for close cooperation between medical and veterinary professionals in designing and implementing control and prevention measures that safeguard the public from this potential source of zoonotic TB in Uganda.

Background: The importance of infections caused by non-tuberculous mycobacteria (NTM) in animals and humans has gained considerable recognition during the past few years. In the developed world, where pig production is extensively practiced, studies on mycobacterial infections and related control strategies have received increasing attention. The infections are reported to be caused by a wide spectrum of NTM. Unfortunately, these infections have been less recognized in sub-Saharan Africa owing to lack of awareness and systematic studies. In this study we aimed at isolating and identifying species of mycobacteria involved in causing infections in slaughter pigs in Mubende district of Uganda. Furthermore we wanted to identify factors associated with infection prevalence in the study area., Methods: A total of 363 lymph nodes were collected and cultured for the presence of mycobacteria. Isolates were identified by 16S rDNA gene sequencing. A questionnaire survey was administered to identify production related factors associated with infection prevalence. Data were assembled and analysed using descriptive statistics and mixed effects logistic regression analysis., Results: Mycobacteria were detected in 39 % (143/363) of the examined lymph nodes, 63 % (59/93) of lymph nodes with gross lesions typical of mycobacteriosis and 31% (84/270) of lymph nodes with no visible lesions. Nineteen per cent of the isolated mycobacteria were identified as Mycobacterium (M) avium, of these 78% and 22% were M. avium sub sp. Hominissuis and avium respectively. Other mycobacterial species included M. senuense (16%), M. terrae (7%) and M. asiaticum (6%). This study found free range systems (OR = 3.0; P = 0.034) and use of water from valley dams (OR = 2.0; P = 0.049) as factors associated with high prevalence of mycobacteria in slaughter pigs., Conclusions: This study demonstrated a high prevalence of NTM infections among slaughter pigs in Mubende district of Uganda. M. avium was the most prevalent of all NTM isolated and identified. Free range system of pig management and valley dam water were the most significant factors associated with NTM prevalence in Mubende district. These findings could be of a major public health concern given that it is in a predominantly pork consuming population with 18% HIV/AIDS prevalence. Therefore, stringent post-mortem inspection at the slaughter houses is of paramount importance to reduce human exposure.