Wide distribution of Mediterranean and African spotted fever agents and the first identification of Israeli spotted fever agent in ticks in Uganda.

Rickettsia microorganisms are causative agents of several neglected emerging infectious diseases in humans transmitted by arthropods including ticks. In this study, ticks were collected from four geographical regions of Uganda and pooled in sizes of 1-179 ticks based on location, tick species, life stage, host, and time of collection. Then, they were tested by real-time PCR for Rickettsia species with primers targeting gltA, 17kDa and ompA genes, followed by Sanger sequencing of the 17kDa and ompA genes. Of the 471 tick pools tested, 116 (24.6%) were positive for Rickettsia spp. by the gltA primers. The prevalence of Rickettsia varied by district with Gulu recording the highest (30.1%) followed by Luwero (28.1%) and Kasese had the lowest (14%). Tick pools from livestock (cattle, goats, sheep, and pigs) had the highest positivity rate, 26.9%, followed by vegetation, 23.1%, and pets (dogs and cats), 19.7%. Of 116 gltA-positive tick pools, 86 pools were positive using 17kDa primers of which 48 purified PCR products were successfully sequenced. The predominant Rickettsia spp. identified was R. africae (n = 15) in four tick species, followed by R. conorii (n = 5) in three tick species (Haemaphysalis elliptica, Rhipicephalus appendiculatus, and Rh. decoloratus). Rickettsia conorii subsp. israelensis was detected in one tick pool. These findings indicate that multiple Rickettsia spp. capable of causing human illness are circulating in the four diverse geographical regions of Uganda including new strains previously known to occur in the Mediterranean region. Physicians should be informed about Rickettsia spp. as potential causes of acute febrile illnesses in these regions. Continued and expanded surveillance is essential to further identify and locate potential hotspots with Rickettsia spp. of concern.

Whole strains vs MGEs in short and longterm transmission of ESBL genes between healthcare and community settings in Uganda.

Multidrug-resistant ESBL-producing Escherichia coli are a leading cause of infections in hospital and community settings. Based on samples from two hospitals in Uganda and households of inpatients we tested the hypothesis that ESBL E. coli and/or their resistance determinants could spread within the healthcare and community settings through discharged patients that were still colonized. We used bacterial culture, susceptibility testing whole genome sequencing and detailed bioinformatics analysis to test the above hypothesis. Genome analysis revealed presence of predominantly blaCTX-M-15 and blaOXA-1 genes with a total resistome with genes belonging to 14 different classes of antimicrobials. Short-term cases of strain sharing were reported within each setting and strains from the two settings were found to cluster together based on their overall resistome. Long-term horizontal transfer of ESBL genes by various IncF and IncY types of plasmids shared between healthcare and community settings was demonstrated. Based on hybrid assembly, plasmid reconstruction and phylogenetic analyses, our study suggests that while the dissemination of AMR between healthcare and community settings in the short-term is possible at whole strain level, the long-term transmission between healthcare and communities is sustained by the transfer of plasmids circulating across niches and disseminating related resistomes.

Co-Surveillance of Rotaviruses in Humans and Domestic Animals in Central Uganda Reveals Circulation of Wide Genotype Diversity in the Animals.

Rotavirus genotypes are species specific. However, interspecies transmission is reported to result in the emergence of new genotypes. A cross-sectional study of 242 households with 281 cattle, 418 goats, 438 pigs, and 258 humans in Uganda was undertaken between 2013 and 2014. The study aimed to determine the prevalence and genotypes of rotaviruses across co-habiting host species, as well as potential cross-species transmission. Rotavirus infection in humans and animals was determined using NSP3 targeted RT-PCR and ProSpecT Rotavirus ELISA tests, respectively. Genotyping of rotavirus-positive samples was by G- and P-genotype specific primers in nested RT-PCR assays while genotyping of VP4 and VP7 proteins for the non-typeable human positive sample was done by Sanger sequencing. Mixed effect logistic regression was used to determine the factors associated with rotavirus infection in animals. The prevalence of rotavirus was 4.1% (95% CI: 3.0-5.5%) among the domestic animals and 0.8% (95% CI: 0.4-1.5%) in humans. The genotypes in human samples were G9P[8] and P[4]. In animals, six G-genotypes, G3(2.5%), G8(10%), G9(10%), G11(26.8%), G10(35%), and G12(42.5%), and nine P-genotypes, P[1](2.4%), P[4](4.9%), P[5](7.3%), P[6](14.6%), P[7](7.3%), P[8](9.8%), P[9](9.8%), P[10](12.2%), and P[11](17.1%), were identified. Animals aged 2 to 18 months were less likely to have rotavirus infection in comparison with animals below 2 months of age. No inter-host species transmission was identified.

Multilocus sequence analysis revealed a high genotypic diversity of Aeromonas hydrophila infecting fish in Uganda.

A multilocus sequence analysis (MLSA) was carried out to delineate Aeromonas hydrophila from fish in Uganda. Five housekeeping genes including recA, gyrB, metG, gltA and pps; and the 16S rRNA gene were amplified and sequenced from a total of nine A. hydrophila isolates. The obtained sequences were edited, and consensus sequences generated for each gene locus. The housekeeping gene sequences were concatenated and phylogenetic analysis performed in MEGA version 7.0.2. Pairwise distances ranged from 0.000 to 0.118, highest within the gltA gene locus and lowest within the 16S rRNA gene. The average evolutionary diversity within isolates from the same source ranged between 0.002 and 0.037, and it was 0.033 between the different sources. Similar tree topologies were obtained from the different gene loci with recA, metG and gyrB being more consistent in discriminating isolates according to sources while the 16S rRNA gene had the lowest resolution. The concatenated tree had the highest discriminatory power. This study revealed that A. hydrophila strains infecting fish in Uganda are of diverse genotypes suggesting different sources of infection in a given outbreak. Efforts to minimize spread of the bacteria across sources should be emphasized to control infections of mixed genotypes.

Immunogenicity and protection efficacy evaluation of avian paramyxovirus serotype-1 (APMV-1) isolates in experimentally infected chickens.

Vaccine failures after Newcastle disease vaccination with the current commercial vaccines have been reported and are associated with many factors, including genotypic and antigenic differences between vaccine and outbreak strains, although all APMV-1 members belong to one serotype. We assessed the immunoprotection ability of four thermostable, low-virulent Newcastle disease-virus isolates from Ugandan waterfowl against challenge with a virulent strain (MDT = 36.8 h, ICPI = 1.78) isolated from morbid chicken. Six-week-old commercial Leghorn layers, challenged at 21 days post immunization were used. Four isolates designated: NDV-133/UG/MU/2011, NDV-177/UG/MU/2011, NDV-178/UG/MU/2011 and NDV-173/UG/MU/2011 induced mean haemagglutinin inhibition antibody titres of log2 9.3, 8.2, 6.3 and 2.0, respectively, at 21 days post immunization. The antibody titres correlated with the protection rates (R² = 0.86, p < 0.007) of 60%, 50%, 20% and 0% of birds, respectively, against challenge at 14 days post challenge. Further evaluation of these and more low-virulent isolates might provide an alternative to the current commercial vaccine failures.

Disparate thermostability profiles and HN gene domains of field isolates of Newcastle disease virus from live bird markets and waterfowl in Uganda.

BACKGROUND: Uganda poultry production is still faced with frequent outbreaks of Newcastle disease (ND) in the backyard free-range systems despite the accessibility of cross protective vaccines. Live bird markets and waterfowl has long been reported as a major source of disease spread as well as potential sources of avirulent strains that may mutate to virulent strains. ND-virus has been reported enzootic in Ugandan poultry but limited studies have been conducted to ascertain thermostability phenotypes of the Ugandan ND-virus strains and to understand how these relate to vaccine strains. METHODS: This study evaluated thermostability of 168 ND-virus field isolates recovered from live bird markets and waterfowls in Uganda compared to two live commercial vaccine strains (I2 and LaSota) by standard thermostability procedures and Hemagglutinin-Neuraminidase (HN) gene domains. The known pathotypes with thermostability profiles were compared at HN amino acid sequences. RESULTS: Field isolates displayed disparate heat stability and HN gene domains. Thermolabile isolates were inactivated within 15 min, while the most thermostable isolates were inactivated in 120 min. Four thermostable isolates had more than 2 log2 heamaglutinin (HA) titers during heat treatment and the infectivity of 9.8 geometric mean of log10 EID50 % in embryonated eggs. One isolate from this study exhibited a comparable thermostability and stable infectivity titers after serial passages, to that of reference commercial vaccine was recommended for immunogenicity and protection studies. CONCLUSION: The occurrence of ND-virus strains in waterfowl and live bird markets with disparate thermostability and varying HN gene domains indicate circulation of different thermostable and thermolabile ND-virus pathotypes in the country.

The epidemiology of rotavirus disease in under-five-year-old children hospitalized with acute diarrhea in central Uganda, 2012-2013.

A cross-sectional study was undertaken during 2012-2013 to determine the prevalence, strains and factors associated with rotavirus infection among under-5-year-old children hospitalized with acute diarrhea in Uganda. Rotaviruses were detected in 37 % (263/712) of the children. The most prevalent strains were G9P[8] (27 %, 55/204) and G12P[4] (18.6 %, 38/204). Mixed infections were detected in 22.5 % (46/204) of the children. The study suggests that consumption of raw vegetables (OR = 1.45, 95 % CI = 1.03-2.03) and family ownership of dogs (OR = 1.9, 95 % CI = 1.04-3.75) increases the risk of rotavirus infection. The study findings will be used to assess the impact of RV vaccination in Uganda.