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BackgroundUganda is one of the most biodiverse regions on the planet and a hotspot for virus emergence. In particular, the warm-humid lowlands favour tick population growth with the associated risk of tick-borne disease. The prevalent tick speciesRhipicephalus appendiculatus, R. evertsi evertsiandAmblyomma variegatumharbour a diverse range of viruses, from harmless to highly pathogenic. Notably, the orthonairoviruses cause human outbreaks of Crimean-Congo haemorrhagic fever (CCHF) regularly within the cattle corridor of Uganda, a region spanning from the south-west to the north-east of the country.MethodsIn the ArboViral Infection (AVI) study, the first to explore the virome of ticks in Uganda using next generation sequencing (NGS), we collected ticks from three geographically diverse areas and subjected these to target-enrichment (TE) NGS. Viral genomes were detected byde novoassembly, mapping and BLASTn.ResultsWe analyzed a total of 2,754 ticks collected from 31 livestock farms in the districts of Arua, Nakaseke and Lyantonde. These were combined into 219 pools by site of collection and tick species, includingR. appendiculatus, R. evertsi evertsi,A. variegatumandHyalomma rufipes. We detected partial or near-complete viral genomes in 163 tick pools; 110 (67%) of which were from Arua, 39 (24%) from Nakaseke and 12 (7%) from Lyantonde districts. 2 pools (2%) were from Arua/Lyantonde. These included 22 species of virus, representing 15 genera and 9 families, including theNairoviridae,Retroviridae,Orthomyxoviridae,Chuviridae,Rhabdoviridae,Phenuiviridae, Parvoviridae, PoxviridaeandFlaviviridae. There were 8 viral species known to be pathogens of humans or animals and 5 highly divergent genomes detected, representing novel virus species. A high abundance of orthonairoviruses was notable, including CCHFV, Dugbe virus and a novelOrthonairovirusspecies that we have named Macira virus.InterpretationTicks in Uganda are an important reservoir of diverse virus species, many of which remain uncharacterised and of unknown pathogenic potential.Author SummaryTicks are parasitic arachnids that may transmit a spectrum of viral diseases to humans and animals. Uganda is a hotspot for such tick-borne diseases. In this study, we sequenced ticks collected from three geographically diverse regions of Uganda using a semi-agnostic next- generation sequencing method in order to detect viruses from all known virus families. We collected and analyzed 2,754 ticks from 31 farms across the country. Within these ticks, we detected 22 species of virus from 15 genera and 9 viral families, including 8 animal or human pathogens and 5 new novel virus species. Notably, orthonairoviruses, including the highly pathogenic Crimean-Congo haemorrhagic fever virus, were highly prevalent in the ticks. The researchers suggest that ticks in Uganda serve as an important reservoir for diverse viruses, many of which have significant pathogenic potential. This information will inform public health efforts to prevent and control tick-borne diseases in Uganda and other similar regions.

Background The development of malaria vaccines is constrained by genetic polymorphisms exhibited by Plasmodium falciparum antigens. The project the age-dependent distribution of alleles or haplotypes of three P. falciparum malaria vaccine candidates, Circumsporozoite Protein (csp), Erythrocyte Binding Antigen 175 (eba-175) and Serine Repeat Antigen 5 (sera5) in a region of intense malaria transmission in Uganda. Methods A cross-sectional study was carried out between August and November 2009 in which 250 study participants were selected from a population of 600. Finger prick blood samples were collected after informed consent from participants below 5 years, 5–10 years, and above 10 years of age. Blood was used for microscopy, RDT and dried blood spots. Plasmodium falciparum DNA was extracted by chelex method. Alleles of sera5 and eba-175 were determined by polymerase chain reaction (PCR) amplification followed by resolution of products by agarose gel electrophoresis. Allele calling was done using gel photographs from ethiduim bromide stained gels. Haplotypes of csp were identified by sequencing 63 PCR products using the P. falciparum 7G8 laboratory strain sequence as a reference. The data were analysed using SPSS 16, EQX for windows and Chi-square test was used to calculate associations (P-values), Excel was used to generate graphs. The BioEdit and NCBI blast software programs were used to analyse the sequences from which csp haplotypes map was constructed. Results Eba-175 FCR3 (48/178) and CAMP (16/178) alleles were observed, the FCR3 (24/67) allele being predominant among children aged below 5 years old while the CAMP (12/67) allele was predominant among older participants. Sera5 alleles ORI (6/204) and ORII (103/204) were observed in the population, ORII was more prevalent and was significantly associated with age (P values csp diversity in the Th2/Th3 region. Out of 63 sequences, 16 conformed to the reference strain and one (1/16) was similar to a West African haplotype and the majority (14/16) of the haplotypes were unique to this study region. There was an age-dependent distribution of csp haplotypes with more haplotypes being harbored by children csp haplotype corresponding to 3D7 whose prototypical sequence is identical to the sequence of the leading malaria vaccine candidate RTS, S was not observed. Conclusion This data suggest that the eba-175 FCR3 allele, sera5 ORII allele, and csp haplotypes are targets of host immunity and under immune selection pressure in Apac District. These molecules could provide alternative malaria vaccine candidates as sub-unit vaccines.

Over the last two decades, the pig population in Africa has grown rapidly, reflecting the increased adoption of pig production as an important economic activity. Of all species, pigs are likely to constitute a greater share of the growth in the livestock subsector. However, constraints such as respiratory infectious diseases cause significant economic losses to the pig industry worldwide. Compared to industrialized countries, the occurrence and impacts of respiratory diseases on pig production in Africa is under-documented. Hence, knowledge on prevalence and incidence of economically important swine respiratory pathogens in pigs in Africa is necessary to guide interventions for prevention and control. The purpose of this review was to document the current status of research on five important respiratory pathogens of swine in Africa to inform future research and interventions. The pathogens included were porcine reproductive and respiratory syndrome virus (PPRSv), porcine circovirus 2 (PCV2), Mycoplasma hyopneumoniae (M. hyopneumoniae), Actinobacillus pleuropneumoniae (APP) and swine influenza A viruses (IAV). For this review, published articles were obtained using Harzing’s Publish or Perish software tool from GoogleScholar. Articles were also sourced from PubMed, ScienceDirect, FAO and OIE websites. The terms used for the search were Africa, swine or porcine, respiratory pathogens, M. hyopneumoniae, APP, PCV2, PPRSv, IAV, prevention and control. In all, 146 articles found were considered relevant, and upon further screening, only 85 articles were retained for the review. The search was limited to studies published from 2000 to 2019. Of all the studies that documented occurrence of the five respiratory pathogens, most were on IAV (48.4%, n = 15), followed by PCV2 (25.8%, n = 8), PPRSv (19.4%, n = 6), while only one study (3.2%, n = 1) reported APP and M. hyopneumoniae. This review highlights knowledge and information gaps on epidemiologic aspects as well as economic impacts of the various pathogens reported in swine in Africa, which calls for further studies.

Background A cross sectional study was conducted to determine genotypes of porcine reproductive and respiratory syndrome virus (PRRSv) isolated from slaughtered pigs in Lira district, northern Uganda. The study was conducted from March to September 2019 in three selected slaughter slabs. Pigs brought for slaughter were randomly sampled. At necropsy, lungs were extracted from the thoracic cavity and examined for pneumonic lesions. Seventy-three (73) pigs with gross lung lesions were sampled, from which one hundred and one (101) tissue samples were taken. A real-time reverse transcriptase PCR (RT-qPCR) was used to characterize PRRSv genotypes. Results A total of 20 samples tested positive for PRRSv. The respective prevalence of PRRSv type 1 and type 2 were 24.65% (n = 18) and 2.73% (n = 2) respectively. Of the pigs sampled (n = 73), only two pigs, 2.73% (n = 2) tested positive to both strains. The likelihood of PRRSv detection decreased with pig age, but increased with gross pneumonic pathology. Conclusions This study demonstrated dual circulation of both genotypes in northern Uganda. The association between PRRSv and lung pathology suggests that it may be an important cause of lung disease in pigs in Uganda and hence loss of production. This calls for further investigations on potential economic impacts of PRRSv on pig productivity. These findings contribute to discussions about the need of surveillance and possible vaccination strategies against PRRSv in Uganda.

Background: A cross-sectional study was conducted in three selected slaughter slabs in Lira district Uganda in 2019 to (i) determine prevalence and severity of pneumonia and (ii) establish associations between lung pneumonic lesions and serologic status to key respiratory pathogens in slaughter pigs. Blood samples were collected from pigs at antemortem from which sera were prepared. Using enzyme-linked immunosorbent (ELISA) assays, sera were screened for antibodies against Mycoplasma hyopneumoniae (M. hyo), Actinobacillus pleuropneumoniae (App), porcine reproductive and respiratory syndrome virus (PRRSv) and porcine circovirus type 2 (PCV2). At post-mortem, lungs were scored for possible pneumonic lesions and the type of pneumonia as previously described. Pneumonia types were grossly characterized as catarrhal purulent bronchopneumonia (CPBP), pleuropneumonia (PLP) and pleuritis as previously described. Metastrongylus spp infection was determined by examining lungs for gross presence or absence of helminths as previously described. T-tests were used to compute prevalence of pneumonia. Chi-square tests were used to compare the percentage of lungs positive or negative to CPBP, PLP and pleuritis. Ordinal logistic regression model was used to evaluate the odds of multiple pneumonia forms, with serostatus for different pathogens and Metastrongylus spp. infection as predictors. Results: One hundred and sixty seven (n=167) lungs were examined for pneumonic lesions. The prevalences of CPBP, PLP and pleuritis were 29.9% (95% CI 22.9-36.9), 74.2% (95% CI 67.5-80.9) and 17.3% (95% CI 22.4-36.3), respectively. The odds of multiple pneumonia forms increased in pigs with multiple pathogens and concurrent Metastrongylus spp. infestation (ORs 2.6, p=0.01 and 2.5, p=0.003, respectively), reaffirming synergistic effects of coinfections in the induction of lesions. Conclusions: This study revealed a high prevalence and severity of pneumonic lesions in slaughter pigs. It provides baseline information, undeniable evidence on the magnitude of pneumonia and justifies future studies on its potential economic impacts in Ugandan pigs.

Background A cross sectional study was conducted to detect and characterize species of porcine reproductive and respiratory syndrome virus (PRRSv) identified from slaughtered pigs in Lira district, northern Uganda. The study was conducted from March to September 2019 in three selected slaughter slabs. Pigs brought for slaughter were randomly sampled. At necropsy, lungs were extracted from the thoracic cavity and examined for pneumonic lesions. Seventy-three (73) pigs with gross lung lesions were sampled, from which one hundred and one (101) tissue samples were taken. A real-time reverse transcriptase PCR (RT-qPCR) was used to characterize PRRSv species. Results A total of 20 samples tested positive for PRRSv. The respective prevalence of PRRSv type 1 and type 2 were 24.65% (n = 18) and 2.73% (n = 2) respectively. Of the pigs sampled (n = 73), only two pigs, 2.73% (n = 2) tested positive to both species. The likelihood of PRRSv detection decreased with pig age, but increased with gross pneumonic pathology. Conclusions This study demonstrated dual circulation of both species in northern Uganda. The association between PRRSv and lung pathology suggests that it may be an important cause of lung disease in pigs in Uganda and hence loss of production. This calls for further investigations on potential economic impacts of PRRSv on pig productivity. These findings contribute to discussions about the need of surveillance and possible vaccination strategies against PRRSv in Uganda.

Post-weaning diarrhea (PWD) and edema disease (ED), caused by enterotoxigenic and Shiga toxin producing Escherichia coli (ETEC and STEC) strains, are important diseases of newly weaned piglets worldwide. The objective of this study is to develop a passive immunization strategy to protect piglets against PWD and ED using recombinant Lactococcus lactis added to piglet diet at weaning. The Variable Heavy chain domains of Heavy chain antibodies (VHHs) or Nanobodies (Nbs), directed against the fimbrial adhesins FaeG (F4 fimbriae) and FedF (F18 fimbriae) of E. coli were cloned and expressed on the surface of L. lactis. In vitro, the recombinant L. lactis strains agglutinated and inhibited adhesion of cognate F4 or F18 fimbriae expressing E. coli to pig villous preparation. In vivo, the anti-F4 L. lactis protected weaned piglets against a challenge with an F4-positive ETEC strain. Piglets supplemented with oral anti-F4 L. lactis showed reduced fecal E. coli shedding. We concluded that the surface expressed Nanobodies on L. lactis neutralized the adhesins of targeted E. coli and abrogated gut colonization, the first step in disease pathogenesis. As a proof of concept, we demonstrated the potential of passive immunization with recombinant L. lactis as a viable alternative to antibiotic prophylaxis in preventing piglet-post-weaning diarrhea.

ObjectiveTo assess the knowledge, attitude and practices (KAP) of animal and human health professionals towards rabies management and also to establish the level of relationship between KAP.MethodsA cross-sectional study was conducted between December 2012 and March 2013 among 147 randomly selected animal and human health professionals in Mbale District. Of these, only 16 were animal health professionals. Quantitative data was obtained using a semi-structured questionnaire while qualitative data was obtained from 4 Focus Group Discussions (FGDs) and 2 Key Informant (KI) interviews. Quantitative data was entered into EpiInfo version 3.5.1 and proportions computed while qualitative data was summarised into themes and sub-themes resulting from content analysis of interview scripts.FindingsOf all the respondents, only 44% (65/147) had sufficient knowledge about rabies while 25% (37/147) had positive attitude towards rabies management. A half of the respondents (50%, 73/147) had limited good practices. Respondents knowledgeable about rabies were more likely to have positive attitude towards rabies management (OR = 3.65; 95% CI: 1.60–8.3) while respondents with positive attitudes, were more likely to have good practices towards rabies management (OR: 2.22; 95% CI: 1.01–4.86).ConclusionRespondents had low knowledge, negative attitude and limited good practices of rabies management. Regular refresher trainings about rabies to broaden staff knowledge and improve their attitudes and hence practices of rabies management should be conducted by the District leaders. Harnessing multi-sectoral and multi-disciplinary collaborative efforts (“One Health” approach) for rabies control should be instituted to reduce the incidence of the disease in the District.

Swine erysipelas is an economically significant disease affecting all stages of pork production. The biggest losses may occur in growers-finishers because of sudden death or acute septicemia. Survivors often suffer from chronic lameness, arthritis and endocarditis leading to poor body growth. The causative agent is the ubiquitous bacterium Erysipelothrix (E.) rhusiopathiae, which is also able to enter the skin of people handling infected animals and meat and cause infection. In order to show the presence of E. rhusiopathiae in pigs, serum samples from 426 randomly selected pigs were collected in four subcounties (Bugulumbya, Butansi, Kitayunwa and Namwendwa) in Kamuli District in Uganda, as part of a multipathogen survey conducted by the International Livestock Research Institute in 2013. Subsequently, 100 samples of fresh pork were collected from all 67-pork slaughterhouses operating in the same subcounties for isolation and bacterial culture. Overall, 308/460 (67%) of the pig sera carried antibodies against E. rhusiopathiae and 45/100 (45%) of the fresh pork samples were contaminated with E. rhusiopathiae. This is the first ever report of E. rhusiopathiae in pigs and pork in Uganda.

Studies on waterborne parasites from natural environment and domestic water sources in Uganda are very scarce and unpublished. Water dwelling free-living amoebae (FLA) of the genus Acanthamoeba, Hartmannella, and Naegleria are often responsible for causing morbidities and mortalities in individuals with recent contact with contaminated water, but their presence in Uganda’s public water supply sources is not known. We cultivated and genotyped FLA from natural and domestic water from Queen Elizabeth Protected Area (QEPA) and Kampala (KLA). The cultivated parasites were observed microscopically and recorded. The overall prevalence of FLA in QEPA (Acanthamoeba spp., 35%; Hartmannella spp., 18.9%; Naegleria spp., 13.5%) and KLA (Acanthamoeba spp., 28.3%; Naegleria spp., 16.6%; Hartmannella spp., 23.1%) were not significantly different. The highest prevalence across water sources in QEPA and KLA was observed for Acanthamoeba spp., followed by Hartmannella spp., and Naegleria spp. Overall FLA mean (±SE) and mean (±SE) across water sources were highest for Acanthamoeba spp. compared to other FLA but were not statistically significant (p > 0.05). Analysis of the FLA sequences produced 1 Cercomonas, 1 Nuclearia, 1 Bodomorpha, 2 Hartmannella, 5 Echinamoeba, and 7 Acanthamoeba partial sequences, indicating a muliplicity of water contaminants that need to be controlled by proper water treatment.

Background: Contagious Caprine Pleuropneumonia (CCPP) is a devastating disease of goats caused by Mycoplasma capricolum subsp. Capripneumoniae (Mccp). The disease was first confirmed in Uganda in 1995 in Karamoja region. Contagious Caprine Pleuropneumonia negatively impacts on goats’ productivity but its extent and magnitude among the local communities in Uganda remain unknown. A cross sectional study was conducted in the districts of Agago and Otuke neighboring Karamoja in Northern Uganda during the months of July and August 2011 to explore for the status of the disease. Methods: Five hundred and four serum samples from goats were obtained from randomly selected unvaccinated herds and 100 goats from vaccinated herds. Serum samples were examined for antibodies against Mycoplasma capricolum subsp. Capripneumoniae (Mccp) by ELISA method. A total of 162 semi-structured questionnaires were administered to selected farmers to obtain information on their understanding of the disease and the risk factors they associated with CCPP. Eight focus group discussions were also conducted with selected farmer groups to obtain detailed qualitative information on CCPP. Results: Among the unvaccinated goats, seroprevalence of CCPP was 32 (17.7%) and 52 (23.3%) for Agago and Otuke districts respectively. Levels of antibodies against Mccp were higher among vaccinated goats than unvaccinated ones (mean optical densities (ODs) of 0.905 and 0.776, p = 0.08). Majority of the farmers 121 (74.7%) had knowledge on CCPP and recognized that CCPP was among the major challenges to goat production in Uganda. Conclusions: This study demonstrated that CCPP was prevalent in Agago and Otuke districts, which are outside but close to Karamoja region where the disease was previously confirmed. There is a need for wider and detailed studies to investigate further CCPP in other districts of Uganda for effective preventive and control of CCPP in Uganda and the neighboring countries.

Background: Brucellosis is a disease with significant public and economic implications but strategies for controlling this disease remain problematic. Objectives: This study sought to determine the sero-prevalence of brucellosis in prolonged fever patients and to identify modifiable risk factors for the infection in humans in post conflict Northern Uganda. Methods: The study employed a cross-sectional method among prolonged fever patients who had visited selected health facilities in the study districts in Northern Uganda. Sero-prevalence of brucellosis was calculated for i-ELISA IgG/IgM. A structured questionnaire was used to obtain data on possible risk factors for brucellosis. Associations between sero-prevalence and risk factors were measured using the Odds Ratio. Results: Brucellosis was confirmed in 18.7% of the 251 patients that tested positive for the disease, with the rapid Brucella Plate Agglutination Test, and ages 10-84 years (median age 47+0.86). Sex (p = 0.001; OR 3.79; 95% CI 1.75 - 8.24), rearing livestock (p < 0.005; OR 8.44; 95% CI 2.84-25.03) and consumption of unpasteurised milk (p = 0.023; OR 2.57; 95% CI 1.14-5.80) were factors associated with brucellosis. Conclusion: Control of brucellosis in animals, training and sensitisation of the community on brucellosis is needed to stimulate action on human brucellosis control. Keywords: Brucellosis, human, fever, prevalence, Uganda, zoonosis.

Brucellosis is a key zoonosis of major public health, animal welfare and economic significance, and is endemic in livestock in Uganda. A cross-sectional epidemiological study was carried out to estimate the sero-prevalence of brucellosis and identify factors associated with sero-positivity in cattle in urban and pen-urban Gulu and Soroti towns of Northern and Eastern Uganda, respectively. A total of 1007 sera and data on biologically plausible risk factors from 166 herds and their spatial locations, were collected from cattle reared in urban and pen-urban Gulu and Soroti towns of Uganda. The sera were analyzed using indirect ELISA and sero-positive reactors confirmed by competitive ELISA. Multivariable models were used to investigate for risk factors. The overall animal-level and herd-level sero-prevalence was 7.5% (76/1007, 95% Confidence Interval (CI): 6.15-9.4%) and 27.1% (45/166, 95% CI: 20.9-34.3%), respectively. Herd-level sero-prevalence was significantly (P

Brucellosis is endemic in livestock and humans in Uganda and its transmission involves a multitude of risk factors like consumption of milk from infected cattle. To shed new light on the epidemiology of brucellosis in Uganda the present study used phenotypic and molecular approaches to delineate theBrucellaspecies, biovars, and genotypes shed in cattle milk.Brucella abortuswithout a biovar designation was isolated from eleven out of 207 milk samples from cattle in Uganda. These isolates had a genomic monomorphism at 16 variable number tandem repeat (VNTR) loci and showed in turn high levels of genetic variation when compared with other African strains or otherB. abortusbiovars from other parts of the world. This study further highlights the usefulness of MLVA as an epidemiological tool for investigation ofBrucellainfections.

This study identified and characterized Brucella species in the informal milk chain in Uganda. A total of 324 cattle bulk milk samples were screened for the genus Brucella by real-time PCR with primers targeting the bcsp31 gene and further characterized by the omp25 gene. Of the samples tested, 6.5% were positive for Brucella species. In the omp25 phylogeny, the study sequences were found to form a separate clade within the branch containing B. abortus sequences. The study shows that informally marketed cattle milk in Uganda is a likely risk factor for human brucellosis and confirms that B. abortus is present in the cattle population. This information is important for potential future control measures, such as vaccination of cattle. Keywords: Africa; brucellosis; bulk milk; milk delivery chain; PCR; bcsp31; omp25 (Published: 11 November 2016) Citation: Infection Ecology and Epidemiology 2016, 6: 32442 - http://dx.doi.org/10.3402/iee.v6.32442

Medicinal herbs are commonly used worldwide as immune boosters and immunomodulators in the management of various disease conditions. Many of these herbs commonly used have not been scientifically evaluated for their immune modulating activities. The study investigated the immunomodulatory activity of the total crude leaf extract of Hibiscus sabdariffa in Wistar albino rats. It was an experimental study that was conducted on four groups of animals each with 6 healthy adult rats. Group I was dosed each with 1mL of normal saline. Groups II, III and IV were dosed 1mL of 125, 250 and 500 mg/Kg bwt of total crude extract, daily for 14 days respectively. On the 15th day, whole blood was collected into a clean ethlenediaminetetracetic acid (EDTA)-vacutainer. The complete blood count (CBC), immune blood cell count, hemagglutination antibody (HA) titers, neutrophil adhesion and delayed-type hypersensitivity (DTH) response were determined. All the doses caused an increase in mean red blood cell (RBC) counts as compared to control group. Similarly, the mean percentage neutrophils, monocytes, basophils and eosinophils increased with dose while the opposite was true for percentage lymphocytes. The mean HA titers for the herb were higher than control though no statistical difference (p≥0.05) was observed. Similar effects were observed with neutrophil adhesions response as that of HA titers. For DTH, the highest footpad thickness (175.2% increment) was observed at a dose of 500 mg/Kg bwt after 12 h and was statistically significant (p≤0.05) as compared to control. H. sabdariffa contain compounds with immunomodulatory activity in Wistar albino rats. Key words: Immunomodulation, Hibiscus sabdariffa, total crude extracts.

Heat-labile enterotoxin (LT) produced by enterotoxigenic Escherichia coli (ETEC) increases bacterial adherence to porcine enterocytes in vitro and enhances small intestinal colonization in swine. Heat-stable enterotoxin-b (STb) is not known to affect colonization; however, through an induction of net fluid accumulation it might reduce bacterial adherence. The relationship between fluid accumulation and bacterial adherence in jejunal loops inoculated with ETEC strains that produce LT, STb, both, or neither toxin was studied. Ligated jejunal loops were constructed in weaned Yorkshire pigs in two independent experiments (Exp. 1, n=5, 8-week-old; Exp. 2, n=6, 6-8-week-old). Each pig was inoculated with six F4ac(+)E. coli strains: (1) LT(+), STb(+) parent (WAM2317); (2) STb(-) (ΔestB) mutant (MUN297); (3) MUN297 complemented with STb (MUN298); (4) LT(-) STb(-) (ΔeltAB ΔestB) mutant (MUN300); (5) MUN300 complemented with LT (MUN301); and (6) 1836-2 (non-enterotoxigenic, wild-type). Pigs were confirmed to be K88 (F4)ab/ac receptor-positive in Exp. 2 by testing for intestinal mucin-type glycoproteins and inferred to be receptor-positive in both Exp. 1 and 2 based on histopathologic evidence of bacterial adherence. Strains that produced STb induced marked fluid accumulation with the response (ml/cm) to WAM2317 and MUN298 significantly greater than that to the other strains (P

Background Pathogenic water dwelling protozoa such as Acanthamoeba spp., Hartmannella spp., Naegleria spp., Cryptosporidium spp. and Giardia spp. are often responsible for devastating illnesses especially in children and immunocompromised individuals, yet their presence and prevalence in certain environment in sub-Saharan Africa is still unknown to most researchers, public health officials and medical practitioners. The objective of this study was to establish the presence and prevalence of pathogenic free-living amoeba (FLA), Cryptosporidium and Giardia in Queen Elizabeth Protected Area (QEPA). Methods Samples were collected from communal taps and natural water sites in QEPA. Physical water parameters were measured in situ. The samples were processed to detect the presence of FLA trophozoites by xenic cultivation, Cryptosporidium oocysts by Ziehl-Neelsen stain and Giardia cysts by Zinc Sulphate floatation technique. Parasites were observed microscopically, identified, counted and recorded. For FLA, genomic DNA was extracted for amplification and sequencing. Results Both natural and tap water sources were contaminated with FLA, Cryptosporidium spp. and Giardia spp. All protozoan parasites were more abundant in the colder rainy season except for Harmannella spp. and Naegleria spp. which occurred more in the warmer months. The prevalence of all parasites was higher in tap water than in natural water samples. There was a strong negative correlation between the presence of Acanthamoeba spp., Hartmannella spp., Cryptosporidium spp. and Giardia spp. with Dissolved Oxygen (DO) (P

A descriptive study was conducted to identify the different strains of Echinococcus granulosus occurring in livestock in Moroto district, Uganda. Echinococcus cysts from 104 domestic animals, including cattle, sheep, goats and camels, were taken and examined by microscopy, polymerase chain reaction with restriction fragment length polymorphism and Sanger DNA sequencing. Echinococcus granulosus genotypes or strains were identified through use of Bioinformatics tools: BioEdit, BLAST and MEGA6. The major finding of this study was the existence of a limited number of E. granulosus genotypes from cattle, goats, sheep and camels. The most predominant genotype was G1 (96.05%), corresponding to the common sheep strain. To a limited extent (3.95%), the study revealed the existence of Echinococcus canadensis G6/7 in three (n = 3) of the E. granulosus–positive samples. No other strains of E. granulosus were identified. It was concluded that the common sheep strain of Echinococcus sensu stricto and G6/7 of E. canadensis were responsible for echinococcal disease in Moroto district, Uganda.

Background Multidrug resistant Pseudomonas aeruginosa and Acinetobacter baumannii are common causes of health care associated infections worldwide. Carbapenems are effective against infections caused by multidrug resistant Gram-negative bacteria including Pseudomonas and Acinetobacter species. However, their use is threatened by the emergence of carbapenemase-producing strains. The aim of this study was to determine the prevalence of carbapenem-resistant P. aeruginosa and A. baumannii at Mulago Hospital in Kampala Uganda, and to establish whether the hospital environment harbors carbapenem-resistant Gram-negative rods. Results Between February 2007 and September 2009, a total of 869 clinical specimens were processed for culture and sensitivity testing yielding 42 (5 %) P. aeruginosa and 29 (3 %) A. baumannii isolates, of which 24 % (10/42) P. aeruginosa and 31 % (9/29) A. baumannii were carbapenem-resistant. Additionally, 80 samples from the hospital environment were randomly collected and similarly processed yielding 58 % (46/80) P. aeruginosa and 14 % (11/80) A. baumannii, of which 33 % (15/46) P. aeruginosa and 55 % (6/11) A. baumannii were carbapenem-resistant. The total number of isolates studied was 128. Carbapenemase genes detected were blaIMP-like (36 %, 9/25), blaVIM-like (32 %, 8/25), blaSPM-like (16 %, 4/25); blaNDM-1-like (4 %, 1/25) in carbapenem-resistant P. aeruginosa, and blaOXA-23-like (60 %, 9/15), blaOXA-24-like (7 %, 1/15), blaOXA-58-like (13 %, 2/15), and blaVIM-like (13 %, 2/15) in carbapenem-resistant A. baumannii. Furthermore, class 1 integrons were detected in 38 % (48/128) of P. aeruginosa and Acinetobacter, 37 % (26/71) of which were in clinical isolates and 39 % (22/57) in environment isolates. Gene cassettes were found in 25 % (12/48) of integron-positive isolates. These were aminoglycoside adenylyltransferase ant(4′)-IIb (3 isolates); trimethoprim-resistant dihydrofolate reductase dfrA (2 isolates); adenyltransferase aadAB (3 isolates); QacE delta1 multidrug exporter (2 isolates); quinolone resistance pentapeptide repeat protein qnr (1 isolate); and metallo-β-lactamase genes blaVIM-4-like, blaIMP-19-like, and blaIMP-26-like (1 isolate each). Gene cassettes were missing in 75 % (36/48) of the integron-positive isolates. Conclusions The prevalence of carbapenem-resistant P. aeruginosa and Acinetobacter among hospitalized patients at Mulago Hospital is low compared to rates from South-East Asia. However, it is high among isolates and in the environment, which is of concern given that the hospital environment is a potential source of infection for hospitalized patients and health care workers. Electronic supplementary material The online version of this article (doi:10.1186/s40064-016-2986-7) contains supplementary material, which is available to authorized users.

Background Acanthamoeba is an emerging potentially pathogenic amoeba that has been receiving increasing attention worldwide as a reservoir and potential vector for the transmission of pathogenic bacteria. It is also associated with brain cell damage, keratitis and skin irritation in humans. Its effects are more severe in immunocompromised individuals. This study provides for the first time in Uganda, information on the prevalence and genotypes of Acanthamoeba in environmental and domestic (tap) water. Methods A total of 324 environmental and 84 tap water samples were collected between November 2013 and September 2014. The samples were centrifuged, cultured (Non-Nutrient agar seeded with gram-negative bacteria) and observed under a microscope. After confirmation of Acanthamoeba, genomic DNA was extracted for PCR assays by chemical lysis and purification with phenol/chloroform/isoamyl alcohol. Samples that showed the strongest positive bands (400–600 bp) were subjected to cycle sequencing. Results Among environmental and tap water samples, 107 (33 %) and 36 (42.9 %) tested positive for Acanthamoeba spp., respectively. Prevalence of Acanthamoeba from specific environmental locations was as follows; Kazinga channel banks (60.7 %), Fish landing sites (50 %), River Kyambura (39.6 %) and Kazinga mid channel (5.3 %). There was a significant difference (p = 0.001) in the prevalence of Acanthamoeba between sampling sites. The mean (Mean ± SE) occurrence of the organism was higher in Kazinga channel banks (3.44 ± 0.49) and Fish landing sites (3.08 ± 0.53). Correlation between in situ parameters and Acanthamoeba was insignificant except for the Dissolved Oxygen (mg/ML) which was negatively correlated (r = −0.231, p = 0.001) to Acanthamoeba. Six distinct partial Acanthamoeba T-genotype groups T1, T2, T4, T5, T6 and T11 were obtained. Ultimately, Acanthamoeba spp., Acanthamoeba hatchetti and Acanthamoeba polyphaga were isolated in the current study. Conclusions There was a high prevalence of Acanthamoeba in communal piped tap and environmental water used by communities, indicating poor environmental and domestic water quality.

Sequencing and analysis of three discrete genome regions of African swine fever viruses (ASFV) from archival samples collected in 2007-2011 and active and passive surveillance between 2012 and 2015 in Nigeria were carried out. Analysis was conducted by genotyping of three single-copy African swine fever (ASF) genes. The E183L and B646L genes that encode structural proteins p54 and p72, respectively, were utilized to delineate genotypes before intragenotypic resolution by characterization of the tetrameric amino acid repeat region within the hypervariable central variable region of the B602L gene. The results showed no variation in the p72 and p54 gene regions sequenced. Phylogeny of p72 sequences revealed that all the Nigerian isolates belonged to genotype I, while that of the p54 recovered the Ia genotype. Analysis of B602L gene revealed the differences in the number of tetrameric repeats. Four new variants (Tet-15, Tet-17a, Tet-17b and Tet-48) were recovered, while a fifth variant (Tet-20) was the most widely distributed in the country displacing Tet-36 reported previously in 2003-2006. The viruses responsible for ASF outbreaks in Nigeria are from very closely related but mutated variants of the virus that have been circulating since 1997. A practical implication of the genetic variability of the Nigerian viral isolates in this study is the need for continuous sampling and analysis of circulating viruses, which will provide epidemiological information on the evolution of ASFV in the field versus new incursion for informed strategic control of the disease in the country.

Post-weaning diarrhea (PWD) caused by enterotoxigenic Escherichia coli (ETEC) is an important disease of newly weaned piglets. ETEC strains commonly express F4 and/or F18 fimbriae that attach to carbohydrate receptors present on the intestinal epithelium during colonization. The disease status in the Ugandan piggeries had previously not been studied. In this cross-sectional sero-survey and clinical outbreak monitoring, we found very high sero-prevalence levels of both anti-F4 (70.5%) and anti-F18 (73.7%) antibodies, despite limited cases of clinical outbreaks. Strains isolated from these cases were typically F18(+) ETEC. High antibiotic resistance and multi-drug resistance were characteristics of the isolates, with highest resistance level of over 95% to commonly used antibiotics such as penicillin and tetracycline. We conclude that ETEC infections are widely spread on farms in Central Uganda but clinical disease outbreaks were masked by the management practices on these farms, like the use of extensive antibiotic prophylaxis.

For conservation purposes and due to growing ecotourism, free-ranging mountain gorillas (Gorilla gorilla beringei) have been habituated to humans. Fecal specimens (n = 62) collected in January 1999 from mountain gorillas of the Bwindi and Mgahinga National Parks, Uganda, were tested for Campylobacter spp., Salmonella spp., and Shigella spp., and the overall prevalence of infection was 19%, 13%, and 6%, respectively. The prevalence of positive specimens was not related to the year of habituation of a gorilla group to humans. Campylobacter spp., Salmonella, and Shigella spp. infections were not distributed equally among the age classes of gorillas; most of the enteropathogens (80%), and all Shigella spp. organisms, S. sonnei, S. boydii, and S. flexneri, were isolated from subadults and adult gorillas with ages ranging from 6.0 to 11.9 yr. The prevalence of Campylobacter spp. and Salmonella spp. infections among human-habituated gorillas has doubled during the last 4 yr, and isolation of Shigella spp. for the first time from mountain gorillas, may indicate enhanced anthropozoonotic transmission of these enteropathogens.

In this study the immunogenicity of recombinant nucleoprotein (Np) administered intranasally or intraperitoneally, and its ability to support a systemic protective anti-virus antibody response was examined, in a mouse model of measles virus (MV)-induced encephalitis. Although both intranasal and intraperitoneal routes of immunisation resulted in priming Np- and MV-specific T-cell responses, the intraperitoneal route was shown to prime for a predominantly IgG2a serum anti-MV antibody response of high avidity, which confered complete protection following intracranial challenge with a neuroadapted strain of MV. On the other hand, intranasal priming resulted in a mixed IgG1, IgG2a serum anti-MV antibody response of low avidity, and only 43% of immunised mice survived following intracranial challenge with the neuroadapted strain of MV. These findings suggest that the route of immunisation in combination with an appropriate adjuvant could influence the induction of a quality antibody response with protective capacity.

Amoebiasis is an infection caused by water borne protozoan parasite Entamoeba histolytica . In Uganda where sanitation infrastructure and health education was not adequate, amoebiasis was thought to be still an important health problem. However there was little or no data on prevalence of this very important protozoan infection. In addition, microscopy remained the main method for the diagnosis of amoebiasis but could not differentiate between Entamoeba dispar/moshkovskii and Entamoeba histolytica infections. This made determination of true prevalence of Entamoeba histolytica infections difficult. It was against this background that this study was designed to carry out species specific diagnosis of Entamoeba histolytica and Entamoeba dispar/moshkovskii in Uganda where these species had been reported to be endemic. This study used microscopy and polymerase chain reaction amplification of Serine-rich Entamoeba histolytica (SREHP) gene. It was shown that 36.7% (n=22) of the samples initially diagnosed as positive by microscopy were positive by PCR. The true prevalence of E. histolytica and E.dispar/ moshkovskii was found to be 7.31% and 12.6% respectively. It was concluded that Entamoeba infection in Soroti, Eastern Uganda is more frequently due to E. dispar /moshkovskii (13.3%) the non-pathogenic forms than to E. histolytica , the pathogen (7.31%). Key words: Entamoeba histolytica , Microscopy, Polymerase chain reaction, Prevalence.

Background: Mycobacterium tuberculosis (TB) is still a major problem globally and especially in Africa. Vitamin D deficiency has been linked to TB in the past and studies have found vitamin D deficiency to be common among Ugandan TB patients. The functional activity of vitamin D is dependent on the genotype of the vitamin D receptor (VDR) polymorphic genes. Recent findings have indicated that VDR polymorphisms may cause increased resistance or susceptibility to TB. The vitamin D ligand and its receptor play a pivotal role in innate immunity by eliciting antimicrobial activity, which is important in prevention of TB. The fok I vitamin D receptor gene has extensively been examined in TB patients but findings so far have been inconclusive. Objectives: This study sought to investigate the frequency distribution of the VDR fok I gene polymorphisms in pulmonary TB patients and controls. Methods: A pilot case control study of 41 newly diagnosed TB patients and 41 healthy workers was set up. Vitamin D receptor fok I gene was genotyped. Results: The frequency distribution of fok I genotype in Ugandan TB patients was 87.8% homozygous-dominant (FF), 7.3% (Ff) heterozygous and 4.8% (ff) homozygous recessive. For normal healthy subjects the frequencies were (FF) 92.6%, (Ff) 2.4% and (ff) 4.8%. No significant difference was observed in the FF and ff genotypes among TB patients and controls. The Ff heterozygous genotype distribution appeared more in TB patients than in controls. A significant difference was observed in the fok I genotype among gender p value 0.02. No significant difference was observed in ethnicity, p value 0.30. Conclusions: The heterozygous Ff fok I genotype may be associated with TB in the Ugandan population.