Browsing by Author "Erima, Bernard"
Now showing 1 - 11 of 11
Results Per Page
Sort Options
Item Draft genome sequence of Acinetobacter haemolyticus strain MUWRP1017 isolated from the pus of a female inpatient at Bwera General Hospital in Uganda(American Society for Microbiology, 2024-08-20) Wokorach, Godfrey; Erima, Bernard; Alafi, Stephen; Kabatesi, Hope O; Muhindo, Julius T; Najjuka, Florence; Kiyengo, James; Kibuuka, Hannah; Musinguzi, Ambrose K.; Wabwire-Mangen, Fred; Byarugaba, Denis K.The bacterium Acinetobacter haemolyticus, with a genome size of 3.4 Mb, was isolated from a pus swab of a wound on the left lower limb above the ankle joint of a female patient. This strain carries the antimicrobial resistance genes cephalosporinase blaADC-25, oxallinase blaOXA-264, floR, and sul2 and other resistance and virulence genes.Item Epidemiology and Surveillance of Influenza Viruses in Uganda between 2008 and 2014(PLoS ONE, 2016) Wabwire-Mangen, Fred; Mimbe, Derrick E.; Erima, Bernard; Mworozi, Edison A.; Millard, Monica; Kibuuka, Hannah; Lukwago, Luswa; Bwogi, Josephine; Kiconco, Jocelyn; Tugume, Titus; Mulei, Sophia; Ikomera, Christine; Tsui, Sharon; Malinzi, Stephen; Kasasa, Simon; Coldren, Rodney; Byarugaba, Denis K.Influenza surveillance was conducted in Uganda from October 2008 to December 2014 to identify and understand the epidemiology of circulating influenza strains in out-patient clinic attendees with influenza-like illness and inform control strategies. Methodology Surveillance was conducted at five hospital-based sentinel sites. Nasopharyngeal and/or oropharyngeal samples, epidemiological and clinical data were collected from enrolled patients. Real-time reverse transcription polymerase chain reaction (RT-PCR) was performed to identify and subtype influenza strains. Data were double-entered into an Epi Info 3.5.3 database and exported to STATA 13.0 software for analysis. Results Of the 6,628 patient samples tested, influenza virus infection was detected in 10.4% (n = 687/ 6,628) of the specimens. Several trends were observed: influenza circulates throughout the year with two peaks; the major one from September to November and a minor one from March to June. The predominant strains of influenza varied over the years: Seasonal Influenza A(H3) virus was predominant from 2008 to 2009 and from 2012 to 2014; Influenza A (H1N1)pdm01 was dominant in 2010; and Influenza B virus was dominant in 2011. The peaks generally coincided with times of higher humidity, lower temperature, and higher rainfall. Conclusion Influenza circulated throughout the year in Uganda with two major peaks of outbreaks with similar strains circulating elsewhere in the region. Data on the circulating strains of influenza and its patterns of occurrence provided critical insights to informing the design and timing of influenza vaccines for influenza prevention in tropical regions of sub-Saharan Africa.Item Genetic analysis of influenza B viruses isolated in Uganda during the 2009–2010 seasons(Virology Journal, 2013) Byarugaba, Denis K.; Erima, Bernard; Millard, Monica; Kibuuka, Hannah; Lukwago, L.; Bwogi, Josephine; Mimbe, Derrick; Mworozi, Edison A.; Sharp, Bridget; Krauss, Scott; Webby, Richard J.; Webster, Robert G.; Martin, Samuel K.; Wabwire-Mangen, Fred; Ducatez, Mariette F.Influenza B viruses can cause morbidity and mortality in humans but due to the lack of an animal reservoir are not associated with pandemics. Because of this, there is relatively limited genetic sequences available for influenza B viruses, especially from developing countries. Complete genome analysis of one influenza B virus and several gene segments of other influenza B viruses isolated from Uganda from May 2009 through December 2010 was therefore undertaken in this study. Methods: Samples were collected from patients showing influenza like illness and screened for influenza A and B by PCR. Influenza B viruses were isolated on Madin-Darby Canine Kidney cells and selected isolates were subsequently sequenced and analyzed phylogenetically.Item Molecular detection and characterization of emerging pathogens of Rickettsia- felis and felis-like organisms from peri-domestic eas in Uganda(Research Article, 2023) Eneku, Wilfred; Erima, Bernard; Maranda Byaruhanga, Anatoli; Nora, G. Cleary; Atim, Gladys; Tugume, Titus; Ukuli, Qouilazoni A.; Kibuuka, Hannah; Mworozi, Edison; Christina Douglas; Jeffrey W. Koehler; Michael E. Fricken; Biryomumaisho, Savino; Matovu, Enock; Tweyongyere, Robert; Wabwire-Mangen, Fred; Byarugaba, Denis K.Background: Flea-borne spotted fever is an emerging zoonosis caused by Rikecttsia felis, a Gram-negative obligate intracellular bacterium. The agent is believed to be cosmopolitan, following the distribution pattern of its host and reservoir, Ctenocephalides felis. However, the epidemiology and public health risk it poses remains poorly understood in sub-Saharan Africa, including Uganda. Yersinia pestis, is primarily transmitted by rodent fleas, Xenopsylla cheopis, but other fleas, particularly C. felis, have vectoral capacity. They are neglected in Ugandan entomological surveillance and public health practices, particularly outside endemic foci of bubonic plague. Methods: We collected 14,641 fleas from domestic animals, rodents and homestead environment; compared their diversity and abundance. Pooled into 714 flea pools by species, collection time, host, and host species, 172 pools were selected based on seasons and analyzed for Yersinia pestis Pla genes, while 62 pools were tested for Rickettsia species gltA, ompA, and 17kDA genes by qPCR and Sanger sequencing. Results: Five flea species were identified from the collections: Ctenocephalides canis, C. felis, Echidnophaga gallinacea, Pulex irritans, and Xenopsylla cheopis. Ctenocephalides was the predominant genus, accounting for 84.8% of fleas collected, mostly found on dogs and goats. Except for P. irritans (which was found in Gulu district) the other four flea species were found across all districts, year-round, with higher numbers collected in dry seasons compared to rainy seasons (c2=47.64, df=20, p<0.001). Rattus rattus constituted 74% of rodents captured from human dwellings and was the only rodent species with fleas, where X. cheopis was the predominant species and E. gallinacea found on only three rodents. All 172 pools of fleas tested negative for Yersinia pestis. Of the 62 pools tested for Rickettsia spp., 29 (46.8%) were positive. Twenty-five PCR amplicons were successfully sequenced for 17kDa and two for ompA genes. Based on 17kDa, two were identified as R. felis from C. canis and 23 were R. asembonensis from multiple flea species, including C. canis collected goats and C. felis from cats. Conclusion: Our survey identified a high pooled detection rate (~50%) of Rickettsia spp. in fleas tested, suggesting a potential risk of human exposure and infection. Rickettsia felis and R. asembonensis were the predominant flea-borne Rickettsia spp. identified, with this study also representing the first report of Rickettsia spp. in E. gallinacea in Uganda.Item Molecular detection of Coxiella burnetii in ticks collected from animals and the environment in Uganda(Zoonoses and Public Health, 2024) Eneku, Wilfred; Erima, Bernard; Maranda Byaruhanga, Anatoli; Nora, Cleary; Atim, Gladys; Tugume, Titus; Ukuli, Qouilazoni Aquino; Kibuuka, Hannah; Mworozi, Edison; Tweyongyere, Robert; Christina, E. Douglas; Jeffrey, W. Koehler; Michael, E. von Fricken; Wabwire-Mangen, Fred; Byarugaba, Denis K.Aims Coxiella burnetii is a highly infectious organism that is easily spread through aerosols causing Q fever in humans. Ticks can harbour and transmit C. burnetii to animals, contributing to disease maintenance. Our aim was to examine the presence of C. burnetii in ticks in Uganda. Methods and Results In this study, ticks were collected from five Ugandan districts and tested by real-time PCR for C. burnetii (Coxiella outer membrane protein 1 gene). A total of 859 tick pools (9602 individual ticks) were tested, and pool positivity for C. burnetii was 5.5% (n = 47). Pooled prevalence differed by district; the highest was Luwero (7.3%), then Gulu (6.6%), and Kasese had the lowest (1.3%). However, district variation was not statistically significant (Fisher's exact = 0.07). Ticks collected from dogs and cats had the highest positivity rates [23/47, (48.9%)] followed by livestock (cattle, goats, sheep, and pigs) [18/47, (38.3%)] and vegetation [6/47, (12.8%)]. Haemaphysalis elliptica had the highest infection rates, followed by Rhipicephalus appendiculatus, Amblyomma variegatum and Rhipicephalus decoloratus had similar prevalence. Conclusions Although ticks are not the primary transmitters of C. burnetii to humans, pathogen detection in ticks can be an indirect indicator of risk among animal hosts. Vulnerable populations, including occupations with close animal contact such as farming, butchery, and veterinary practice, have an increased risk of C. burnetii exposure. Veterinarians and clinicians should be aware that C. burnetii may cause human and animal illness in these regions.Item Molecular Epidemiology of Influenza A/H3N2 Viruses Circulating in Uganda(PLoS ONE, 2011) Byarugaba, Denis K.; Ducatez, Mariette F.; Erima, Bernard; Mworozi, Edison A.; Millard, Monica; Kibuuka, Hannah; Lukwago, Luswa; Bwogi, Josephine; Kaira, Blanche B.; Mimbe, Derrick; Schnabel, David C.; Krauss, Scott; Darnell, Daniel; Webby, Richard J.; Webster, Robert G.; Wabwire-Mangen, FredThe increasing availability of complete influenza virus genomes is deepening our understanding of influenza evolutionary dynamics and facilitating the selection of vaccine strains. However, only one complete African influenza virus sequence is available in the public domain. Here we present a complete genome analysis of 59 influenza A/H3N2 viruses isolated from humans in Uganda during the 2008 and 2009 season. Isolates were recovered from hospital-based sentinel surveillance for influenza-like illnesses and their whole genome sequenced. The viruses circulating during these two seasons clearly differed from each other phylogenetically. They showed a slow evolution away from the 2009/10 recommended vaccine strain (A/ Brisbane/10/07), instead clustering with the 2010/11 recommended vaccine strain (A/Perth/16/09) in the A/Victoria/208/09 clade, as observed in other global regions. All of the isolates carried the adamantane resistance marker S31N in the M2 gene and carried several markers of enhanced transmission; as expected, none carried any marker of neuraminidase inhibitor resistance. The hemagglutinin gene of the 2009 isolates differed from that of the 2008 isolates in antigenic sites A, B, D, and to a lesser extent, C and E indicating evidence of an early phylogenetic shift from the 2008 to 2009 viruses. The internal genes of the 2009 isolates were similar to those of one 2008 isolate, A/Uganda/MUWRP-050/2008. Another 2008 isolate had a truncated PB1-F2 protein. Whole genome sequencing can enhance surveillance of future seasonal changes in the viral genome which is crucial to ensure that selected vaccine strains are protective against the strains circulating in Eastern Africa. This data provides an important baseline for this surveillance. Overall the influenza virus activity in Uganda appears to mirror that observed in other regions of the southern hemisphere.Item Online Learning Resources Enhanced Teaching and Learning of Medical Mycology among Medical Students in Gulu University, Uganda(Education Research International, 2020) Bongomin, Felix; Erima, Bernard; Kwizera, Richard; Odongo-Aginya, Emmanuel I.The burden of serious fungal diseases has significantly increased in the past few decades; however, the number of health-care workers with expertise in the management of fungal diseases remains low, especially in low- and middle-income countries (LMICs). This study aimed to evaluate the use of freely available online teaching material to enhance teaching and learning of medical mycology among medical students in Gulu University Medical School, Uganda. Methods. We conducted a cross-sectional study among second year medical students undertaking Medical Mycology course on antifungal agents in the department of Medical Microbiology and Immunology in the academic year 2017-2018. The materials were synthesized and peer-reviewed by experts in fungal diseases and were made freely available on the Leading International Fungal Education website (http://www.LIFE-Worldwide.org). A local faculty in the department delivered the lectures, and pre- and posttest scores were evaluated statistically. Sixty medical students participated in the study of which 78% were male. The average score was 41% for the pretest and 52% for the posttest. There was no significant difference in the scores of males and females. Majority of the students gave an above-average rating for the course material; however, 54% preferred prerecorded videos. Using freely available online materials on medical mycology can enhance teaching and learning of medical mycology. Because of this, there is need to incorporate up-to-date information about the subject into the curriculums of medical schools especially in LMICs.Item Prevalence of influenza A viruses in livestock and free-living waterfowl in Uganda(BMC Veterinary Research, 2014) Kirunda, Halid; Erima, Bernard; Tumushabe, Agnes; Kiconco, Jocelyn; Tugume, Titus; Mulei, Sophia; Mimbe, Derrick; Mworozi, Edison; Bwogi, Josephine; Luswa, Lukwago; Kibuuka, Hannah; Millard, Monica; Byaruhanga, Achilles; Ducatez, Mariette F.; Krauss, Scott; Webby, Richard J.; Webster, Robert G.; Wurapa, Kofi; Byarugaba, Denis K.; Wabwire-Mangen, FredAvian influenza viruses may cause severe disease in a variety of domestic animal species worldwide, with high mortality in chickens and turkeys. To reduce the information gap about prevalence of these viruses in animals in Uganda, this study was undertaken. Results: Influenza A virus prevalence by RT-PCR was 1.1% (45/4,052) while sero prevalence by ELISA was 0.8% (24/2,970). Virus prevalence was highest in domestic ducks (2.7%, 17/629) and turkeys (2.6%, 2/76), followed by free-living waterfowl (1.3%, 12/929) and swine (1.4%, 7/511). A lower proportion of chicken samples (0.4%, 7/1,865) tested positive. No influenza A virus was isolated. A seasonal prevalence of these viruses in waterfowl was 0.7% (4/561) for the dry and 2.2% (8/368) for the wet season. In poultry, prevalence was 0.2% (2/863) for the dry and 1.4% (24/1,713) for the wet season, while that of swine was 0.0% (0/159) and 2.0% (7/352) in the two seasons, respectively. Of the 45 RT-PCR positive samples, 13 (28.9%) of them were H5 but none was H7. The 19 swine sera positive for influenza antibodies by ELISA were positive for H1 antibodies by HAI assay, but the subtype(s) of ELISA positive poultry sera could not be determined. Antibodies in the poultry sera could have been those against subtypes not included in the HAI test panel. Conclusions: The study has demonstrated occurrence of influenza A viruses in animals in Uganda. The results suggest that increase in volumes of migratory waterfowl in the country could be associated with increased prevalence of these viruses in free-living waterfowl and poultry.Item Seroprevalence of Q-fever, spotted fever, typhus group Rickettsia and Orientia among febrile patients visiting hospital-based sentinel sites in Uganda(PAMJ - One Health, 2023) Eneku, Wilfred; Erima, Bernard; Byaruhanga, Anatoli Maranda; Nora, Gillian Cleary; Atim, Gladys; Tugume, Titus; Ukuli, Qouilazoni Aquino; Kibuuka, Hannah; Mworozi, Edison; Christina, Douglas; Jeffrey, William Koehler; Michael, Emery von Fricken; Biryomumaisho, Savino; Tweyongyere, Robert; Wabwire-Mangen, Fred; Byarugaba, Denis KaruhizeIntroduction: rickettsioses are emerging zoonotic febrile illnesses transmitted to humans by ticks, fleas, lice, and mites. Q-fever, Spotted fever group (SFG), Typhus group (TG) rickettsia and Scrub typhus (STG) have been reported with varying prevalence across East Africa. However, little is known about the burden of exposure in Uganda. The aim of this study was to determine the seroprevalence and associated risk factors of rickettsial diseases in Uganda. Methods: a total of 460 archived serum samples collected from patients with fever of unknown origin after screening across five hospital-based sentinel sites were analysed. The samples were collected during 18-month period of active surveillance for acute febrile illnesses, from January 2018 through June 2019. We performed IgM ELISA tests on the 460 sera for SFG and TG rickettsia, IgM IFA for STG and Phase 2 IgG ELISA for Q-fever. We also assessed risk factors associated with the serostatus. Results: the population comprised predominantly children, had balanced gender proportions, with 66% coming from rural areas. The overall seroprevalence of SFG rickettsiosis was 6.3%; however, 11.5% and 10.8% prevalence rates were observed in Gulu and Bwera hospitals respectively. This was higher than the 3.7% observed in the capital city Kampala, although the differences were not statistically significant (Fisher's exact = 0.489). Overall seropositivity of Q-fever was 7.6%, although Bwera Hospital had the highest rate (12.5%) and Mulago had the lowest rate (2%). The differences were not considered statistically significant (Fishers exact= 0.075). Increasing age (OR-adjusted=1.4, 95%CI=1.0-1.9, p=0.026) and rural background (OR-adjusted=2.6, 95%CI=1.6- 6.4, p=0.037) were both significantly associated with seropositivity for Q-fever, while only increasing age had higher odds for seropositivity for SFG rickettsia (OR-adjusted= 1.9, 95% CI= 1.4- 2.6, p<0.001). One serum sample of a 10-monthold male from Bwera hospital was reactive to both SFG and Q-fever antibodies. We found four sera reactive cases to typhus group IgM and another four reactive to Orientia spp. IgM. However, we were not able to determine associating factors due to low seropositivity rates. Conclusion: here, we report for the first time the seroprevalence of Qfever, SFG and STG in febrile patients in Uganda. This report also provides the second study in over five decades since the earliest report of TG rickettsia. Testing for these pathogens in patients with acute febrile illness with unknown etiology may hold value, however more studies are required to provide information on disease ecology, risk factors, and transmission dynamics of these pathogens in Uganda.Item Whole-genome analysis of influenza A(H1N1)pdm09 viruses isolated in Uganda from 2009 to 2011(Influenza and Other Respiratory Viruses, 2016) Byarugaba, Denis K.; Erima, Bernard; Millard, Monica; Kibuuka, Hannah; Lukwago, Luswa; Bwogi, Josephine; Mimbe, Derrick; Kiconco, Jocelyn B.; Tugume, Titus; Mworozi, Edison A.; Turner, Jasmine; Mckenzie, Pamela P.; Webby, Richard R. J.; Webster, Robert G.; Foret, Charlotte; Ducatez, Mariette F.; Coldren, Rodney; Wabwire-Mangen, Fred; Krauss, ScottWe report a whole-genome analysis of 19 influenza A(H1N1)pdm09 isolates from four Ugandan hospitals between 2009 and 2011. The isolates differed from the vaccine strain A/California/07/2009 by three amino acid substitutions P100S, S220T, and I338V in the hemagglutinin and by two amino acid substitutions V106I and N248D in the neuraminidase proteins with consistent mutations in all gene segments distinguishing isolates from the 2009/2010 to 2010/2011 seasons. Phylogenetic analysis showed low genetic evolution, with genetic distances of 0%–1.3% and 0.1%–1.6% for HA and NA genes, respectively. The amino acid substitutions did not lead to antigenic differences from the reference strains.Item Wide distribution of Mediterranean and African spotted fever agents and the first identification of Israeli spotted fever agent in ticks in Uganda(PLOS NEGLECTED TROPICAL DISEASES, 2023) Eneku, Wilfred; Erima, Bernard; Maranda Byaruhanga, Anatoli; Atim, Gladys; Tugume, Titus; Ukuli, Qouilazoni A.; Kibuuka, Hannah; Mworozi, Edison; Christina, Douglas; Jeffrey, W. Koehler; Nora, G. Cleary; Michael, E. von Fricken; Tweyongyere, Robert; Wabwire-Mangen, Fred; Karuhize Byarugaba, DenisRickettsia 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.