Browsing by Author "Ndekezi, Christian"

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    Genome Sequences of Bacteriophages UPEC01, UPEC03, UPEC06, and UPEC07 Infecting Avian Pathogenic Escherichia coli
    (Microbiology Resource Announcements, 2022) Kazibwe, George; Ndekezi, Christian; Alinaitwe, Ruth; Alafi, Stephen; Nanteza, Ann; Magambo, Phillip K.; Nakavuma, Jesca L.
    Here, we present the genome sequences of four bacteriophages that infect avian pathogenic Escherichia coli. The phages were isolated from raw sewage in Kampala, Uganda. The genome sizes of the phages ranged between 143,140 bp and 178,307 bp, with an average G1C content of 41.25%. Phages infecting avian pathogenic Escherichia coli (APEC) have the potential to be applied as phage therapy in the management of avian colibacillosis, a devastating disease that is responsible for significant economic losses in the poultry industry (1). The emergence of multidrug-resistant pathogenic E. coli strains has sparked interest in the search for alternative control measures for bacterial pathogens, including, among others, the use of phages (2). In this study, whole-genome sequencing of bacteriophages was carried out to determine the genetic characteristics and the taxonomic identification or classification of these phages as part of a larger study aimed at identifying and establishing phage stocks that can be used to supplement the use of antibiotics in managing avian colibacillosis in Uganda. The bacteriophages in this study were isolated from sewage at the National Water and Sewerage Corporation treatment plant (Kampala, Uganda). Several E. coli field isolates (Table 1) obtained from chicken droppings were used as isolation hosts for the phages following previously described methods (3). Briefly, 10 mL of raw sewage was centrifuged (10,000 g for 10 min) to obtain a supernatant, which was added to 10 mL of 2 tryptic soy broth (TSB) containing 100 mL of overnight E. coli broth culture. The mixture was incubated (30°C for 48 h at 120 rpm) and centrifuged (7,000 rpm for 5 min at 4°C), and the supernatant was filtered (0.45mm). The phage lysate obtained was plaque purified three times to produce a uniform phage stock. The isolated phages that could infect the APEC isolates from chickens that had died from colibacillosis were selected (4). Genomic DNA was extracted from the phages using 2% SDS and purified using a Qiagen Genomic-tip 100/G kit according to the manufacturer’s instructions.
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    Genome Sequences of Bacteriophages UPEC01, UPEC03, UPEC06, and UPEC07 Infecting Avian Pathogenic Escherichia coli
    (Microbiology Resource Announcements, 2022) Kazibwe, George; Ndekezi, Christian; Alinaitwe, Ruth; Alafi, Stephen; Nanteza, Ann; Kimuda, Magambo Phillip; Nakavuma, Jesca Lukanga
    Here, we present the genome sequences of four bacteriophages that infect avian pathogenic Escherichia coli. The phages were isolated from raw sewage in Kampala, Uganda. The genome sizes of the phages ranged between 143,140 bp and 178,307 bp, with an average G+C content of 41.25%.
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    Identification of Peste des Petits Ruminants Transmission Hotspots in the Karamoja Subregion of Uganda for Targeting of Eradication Interventions
    (Frontiers in veterinary science, 2019) Nkamwesiga, Joseph; Coffin-Schmitt, Jeanne; Ochwo, Sylvester; Mwiine, Frank Norbert; Palopoli, Annabella; Ndekezi, Christian; Isingoma, Emmanuel; Nantima, Noelina; Nsamba, Peninah; Adiba, Rogers; Hendrickx, Saskia; Mariner, Jeffrey C.
    This paper describes an assessment of the patterns of peste des petits ruminants virus circulation in the Karamoja subregion of Uganda conducted to identify the communities that maintain the virus and inform the development of a targeted vaccination strategy. Participatory epidemiological methods were used to develop an operational hypothesis for the patterns of PPR in Karamoja that was subsequently validated through outbreak investigation and genomics. The participatory epidemiological assessment included risk mapping with livestock owners, community animal health workers and veterinarians and indicated there were two critical foci of virus transmission on the Uganda-Kenya border. One was located in two adjacent subcounties of Kotido and Kaabong Districts in northern Karamoja and the other in Loroo subcounty of Amudat District in southern Karamoja. Participants reported that these were locations where outbreaks were usually first observed in Karamoja and subsequently spread to other areas. Following the participatory assessment, surveillance activities were implemented across the Karamoja subregion in 2018. Three outbreak were detected, investigated and sampled. Two outbreaks were located in the northern and one on the southern focus of transmission. No Outbreaks were diagnosed in Karamoja outside of these foci during 2018. Genomics indicated different clusters of viruses were associated with the northern and southern foci that were more closely related to other East African isolates than to each other. This indicates these are two separate systems of virus circulation which should be explicitly addressed in eradication as separate cross-border systems that require integrated cross-border interventions.
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    Invasive Cattle Ticks in East Africa: Morphological and Molecular Confirmation of The Presence of Rhipicephalus Microplus in South‑Eastern Uganda
    (Parasites & Vectors, 2020) Muhanguzi, Dennis; Byaruhanga, Joseph; Amanyire, Wilson; Ndekezi, Christian; Ochwo, Sylvester; Nkamwesiga, Joseph; Mwiine, Frank Norbert; Tweyongyere, Robert; Fourie, Josephus; Madder, Maxime; Schetters, Theo; Horak, Ivan; Juleff, Nick; Jongejan, Frans
    Rhipicephalus microplus, an invasive tick species of Asian origin and the main vector of Babesia species, is considered one of the most widespread ectoparasites of livestock. The tick has spread from its native habitats on translocated livestock to large parts of the tropical world, where it has replaced some of the local populations of Rhipicephalus decoloratus ticks. Although the tick was reported in Uganda 70 years ago, it has not been found in any subsequent surveys. This study was carried out to update the national tick species distribution on livestock in Uganda as a basis for tick and tick-borne disease control, with particular reference to R. microplus.The study was carried out in Kadungulu, Serere district, south-eastern Uganda, which is dominated by small scale livestock producers. All the ticks collected from 240 cattle from six villages were identified microscopically. Five R. microplus specimens were further processed for phylogenetic analysis and species confirmation.The predominant tick species found on cattle was Rhipicephalus appendiculatus (86.9 %; n = 16,509). Other species found were Amblyomma variegatum (7.2 %; n = 1377), Rhipicephalus evertsi (2.3 %; n = 434) and R. microplus (3.6 %; n = 687). Phylogenetic analysis of the 12S rRNA, 16S rRNA and ITS2 gene sequences of R. microplus confirmed the morphological identification.It is concluded that R. microplus has replaced R. decoloratus in the sampled villages in Kadungulu sub-county, since the latter was not any longer found in this area. There is currently no livestock movement policy in force in Uganda, which could possibly limit the further spread of R. microplus ticks. Future surveys, but also retrospective surveys of museum specimens, will reveal the extent of distribution of R. microplus in Uganda and also for how long this tick has been present on livestock without being noticed.
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    Molecular Detection and Phylogenetic Analysis of Lumpy Skin Disease Virus from Outbreaks in Uganda 2017–2018
    (BMC veterinary research, 2020) Ochwo, Sylvester; VanderWaal, Kimberly; Ndekezi, Christian; Nkamwesiga, Joseph; Munsey, Anna; Witto, Sarah Gift; Nantima, Noelina; Mayanja, Franklin; Okurut, Anna Rose Ademun; Atuhaire, David Kalenzi
    Lumpy skin disease (LSD) is an infectious viral disease of cattle caused by a Capripoxvirus. LSD has substantial economic implications, with infection resulting in permanent damage to the skin of affected animals which lowers their commercial value. In Uganda, LSD is endemic and cases of the disease are frequently reported to government authorities. This study was undertaken to molecularly characterize lumpy skin disease virus (LSDV) strains that have been circulating in Uganda between 2017 and 2018. Secondly, the study aimed to determine the phylogenetic relatedness of Ugandan LSDV sequences with published sequences, available in GenBank.A total of 7 blood samples and 16 skin nodule biopsies were screened for LSDV using PCR to confirm presence of LSDV nucleic acids. PCR positive samples were then characterised by amplifying the GPCR gene. These amplified genes were sequenced and phylogenetic trees were constructed. Out of the 23 samples analysed, 15 were positive for LSDV by PCR (65.2%). The LSDV GPCR sequences analysed contained the unique signatures of LSDV (A11, T12, T34, S99, and P199) which further confirmed their identity. Sequence comparison with vaccine strains revealed a 12 bp deletion unique to Ugandan outbreak strains. Phylogenetic analysis indicated that the LSDV sequences from this study clustered closely with sequences from neighboring East African countries and with LSDV strains from recent outbreaks in Europe. It was noted that the sequence diversity amongst LSDV strains from Africa was higher than diversity from Eurasia.The LSDV strains circulating in Uganda were closely related with sequences from neighboring African countries and from Eurasia. Comparison of the GPCR gene showed that outbreak strains differed from vaccine strains. This information is necessary to understand LSDV molecular epidemiology and to contribute knowledge towards the development of control strategies by the Government of Uganda.
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    Retrospective in silico mutation profiling of SARS-CoV-2 structural proteins circulating in Uganda by July 2021: Towards refinement of COVID-19 disease vaccines, diagnostics, and therapeutics
    (Plos one, 2022) Odongo, Steven; Okella, Hedmon; Ndekezi, Christian; Okee, Moses; Namayanja, Monica; Mujuni, Brian; Sterckx, Yann G. J.; Kizito, Dennison; Mwiine, Frank Nobert; Lutwama, Julius Julian; Ibingira, Charles
    The SARS-CoV-2 virus, the agent of COVID-19, caused unprecedented loss of lives and economic decline worldwide. Although the introduction of public health measures, vaccines, diagnostics, and therapeutics disrupted the spread of the SARS-CoV-2, the emergence of variants poses substantial threat. This study traced SARS-CoV-2 variants circulating in Uganda by July 2021 to inform the necessity for refinement of the intervention medical products. A comprehensive in silico analysis of the SARS-CoV-2 genomes detected in clinical samples collected from COVID-19 patients in Uganda revealed occurrence of structural protein variants with potential of escaping detection, resisting antibody therapy, or increased infectivity. The genome sequence dataset was retrieved from the GISAID database and the open reading frame encoding the spike, envelope, membrane, or nucleocapsid proteins was translated. The obtained protein sequences were aligned and inspected for existence of variants. The variant positions on each of the four alignment sets were mapped on predicted epitopes as well as the 3D structures. Additionally, sequences within each of the sets were clustered by family. A phylogenetic tree was constructed to assess relationship between the encountered spike protein sequences and Wuhan-Hu-1 wild-type, or the Alpha, Beta, Delta and Gamma variants of concern. Strikingly, the frequency of each of the spike protein point mutations F157L/Del, D614G and P681H/R was over 50%. The furin and the transmembrane serine protease 2 cleavage sites were unaffected by mutation. Whereas the Delta dominated the spike sequences (16.5%, 91/550), Gamma was not detected. The envelope protein was the most conserved with 96.3% (525/545) sequences being wild-type followed by membrane at 68.4% (397/580). Although the nucleocapsid protein sequences varied, the variant residue positions were less concentrated at the RNA binding domains. The dominant nucleocapsid sequence variant was S202N (34.5%, 205/595). These findings offer baseline information required for refining the existing COVID-19 vaccines, diagnostics, and therapeutics.