Browsing by Author "Asiimwe, Benon B."
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Item Community Perceptions on Integrating Animal Vaccination and Health Education by Veterinary and Public Health Workers in the Prevention of Brucellosis among Pastoral Communities of South Western Uganda(PLoS ONE, 2015) Kansiime, Catherine; Atuyambe, Lynn M.; Asiimwe, Benon B.; Mugisha, Anthony; Mugisha, Samuel; Guma, Victor; Rwego, Innocent B.; Rutebemberwa, ElizeusBrucellosis is a zoonotic disease of veterinary, public health, and economic significance in most developing countries, yet there are few studies that show integrated human and veterinary health care intervention focusing on integration at both activity and actors levels. The aim of our study, therefore, was to explore community perceptions on integration of animal vaccination and health education by veterinary and public health workers in the management of brucellosis in Uganda. Methods This study used a qualitative design where six Focus Group Discussions (FGDs) that were homogenous in nature were conducted, two from each sub-county, one with the local leaders, and another with pastoralists and farmers. Five Key Informant Interviews (KIIs) with two public health workers and three veterinary extension workers from three sub-counties in Kiruhura district, Uganda were conducted. All FGDs were conducted in the local language and tape recorded with consent from the participants. KIIs were in English and later transcribed and analyzed using latent content data analysis method.Item Comparison of transformation frequencies among selected Streptococcus pneumoniae serotypes(International journal of antimicrobial agents, 2010) Joloba, Moses L.; Kidenya, Benson R.; Kateete, David P.; Katabazi, Fred A.; Muwanguzi, Julian K.; Asiimwe, Benon B.; Alarakol, Simon P.; Nakavuma, Jessica L.; Bajaksouzian, Saralee; Windau, Anne; Jacobs, Michael R.Although there are over 90 serotypes of Streptococcus pneumoniae, antimicrobial resistance is predominantly found in a limited number of serotypes/serogroups, namely 6, 9, 14, 19 and 23. There is no compelling mechanism to account for this restriction. We aimed to determine whether serotypes commonly associated with drug resistance have higher transformation frequencies than those that are susceptible to antimicrobial agents. An in vitro investigation of the genetic transformation frequency of drug-resistant serotypes compared with that of susceptible serotypes under the influence of synthetic competence-stimulating peptides was performed. The transforming DNA was genomic DNA carrying a Tn916-like transposon containing the mefE gene that confers resistance to erythromycin. It was observed that serotypes 6, 9, 14, 19 and 23, which are highly associated with drug resistance, do not exhibit a higher degree of transformation efficiency than other serotypes. These findings suggest that the association of serotype with drug resistance is likely due to prolonged exposure to transforming DNA resulting from longer nasopharyngeal carriage and to a greater selective pressure from antimicrobials, particularly in children. This is the first study to compare the transformation frequencies of pneumococcal clinical isolates using genomic DNA that carries the composite Tn916-like element.Item Determinants of Patients’ Choice of Provider in Accessing Brucellosis Care among Pastoral Communities Adjacent to Lake Mburo National Park in Kiruhura District, Uganda(PLoS ONE, 2014) Kansiime, Catherine; Rutebemberwa, Elizeus; Mugisha, Anthony; Mugisha, Samuel; Asiimwe, Benon B.; Rwego, Innocent B.; Kiwanuka, Suzanne N.Brucellosis is the commonest zoonotic infection worldwide with symptoms similar to other febrile syndromes such as malaria and typhoid fever. It is often easily misdiagnosed, resulting in underreporting and misdirected treatments. Understanding of the factors that influence brucellosis care seeking is essential in enhancing its effective management. Our study sought to determine the factors associated with choice of provider in accessing care for brucellosis among pastoral communities in Uganda. Methods: This was a cross-sectional survey involving 245 randomly selected respondents previously diagnosed and treated for brucellosis, two months before the study. They were enrolled from three sub-counties neighboring Lake Mburo National Park between December 2012 to April 2013. Data on socio-demographics, availability, accessibility, affordability and acceptability of health services were collected. A multivariable logistic regression model was fitted to determine association between independent and outcome variables using odds ratios and 95% confidence intervals with p-value#0.05 considered statistically significant. Results: Of the 245 respondents, 127(51.8%) sought health care at government facilities and the rest at private. Respondents who were less likely to choose a government facility were either single (OR: 0.50, CI: 0.26–0.97), had general weakness (OR: 0.09, CI: 0.01–0.72) or whom family took a decision (OR: 0.52, CI: 0.28–0.97). At multivariable analysis, choice of government facility was influenced by primary education (aOR: 0.46, CI: 0.22–0.97), having six to ten household members (aOR:3.71, CI:1.84–7.49), family advice (aOR:0.64, CI: 0.23–0.91), distance $10 kms (aOR:0.44, CI: 0.21–0.92), high costs at private clinics (aOR:0.01, CI:0.02–0.15) and no diagnosis at government facility (aOR:0.11, CI:0.01–0.97). Females were more likely to seek health care at government facilities, while those with tertiary education were less likely, after the first provider. Conclusions: Females and households with six to ten members were more likely to choose government facilities. Government facilities need to be equipped to attract more patients.Item The Effect of Financial Record Keeping on Financial Performance of Development Groups in Rural Areas of Western Uganda(International Journal of Economics and Finance, 2018) Mwebesa, Lawrence Collins Kihamaiso; Kansiime, Catherine; Asiimwe, Benon B.; Mugambe, Paddy; Rwego, Innocent B.Good financial recordkeeping enables business organizations to plan properly and also check for misappropriations of resources. This manuscript expounds a study on financial record keeping as an integral part of managing development groups’ business environment. The study was carried out in three rural districts of Rubirizi, Kasese and Rukungiri in Western Uganda with the aim of determining the effects of financial record keeping on financial performance of Development groups. A total of 99 respondents were obtained from 33 development groups. In every development group, three leaders i.e. the Chairperson, Treasurer and Secretary were interviewed. Data were entered in Epi data 3.1 and descriptive and correlational analyses were done using SPSS version 21. Using the Likert scale with five categories from strongly agree to strongly disagree, a mean value of 3.5 indicated a strong agreement to the questions asked. The mean value (4.32) on access to information implied that when members have access to information; transparency and accountability are ensured. Findings indicated that 67 (67.7%) knew the type of financial books recognized by international accounting standards board (IASB). 36 (36.4%) respondents reported keeping money in boxes while 22 (22.2%) kept money in the bank. Findings revealed a significant positive relationship between the financial record keeping and financial performance (r=0.297**, P>0.05). Notwithstanding the above findings, there is need to train group leaders in financial recordkeeping.Item Epidemiology and Antibiotic Susceptibility of Vibrio Cholerae associated with the 2017 outbreak in Kasese district, Uganda(BMC public health, 2019) Iramiot, Jacob Stanley; Rwego, Innocent B.; Kansiime, Catherine; Asiimwe, Benon B.Uganda is among the 51 countries where cholera outbreaks are common with epidemics occurring predominantly along the western border with Democratic Republic of Congo (DRC), Kampala city slums, Busia district which is a border town with Western Kenya, Mbale district and the Karamoja Sub-region. This report summarizes findings from the epidemiologic investigation, which aimed at identifying the mode of transmission and antibiotic susceptibility patterns of the Vibrio cholerae isolated in Kasese district, Uganda.A descriptive cross-sectional study was carried out between 2017 and 2018 to describe the epidemiology of the cholera epidemic in Kasese district, Uganda. Rectal swabs were collected from 69 suspected case-persons and cultured on Thiosulphate-Citrate-Bile-Salts Sucrose (TCBS™; SEIKEN Japan) agar and incubated at 37 °C for 18–24 h. The isolates were serotyped with polyvalent 01 antiserum and monovalent serotype Inaba and Ogawa antisera (Denka Seiken, Tokyo, Japan) to determine which serotype was responsible for the outbreak. Antimicrobial susceptibility testing was performed using the Kirby-Bauer disk diffusion method on Mueller-Hinton agar.A list of discharged patients was obtained from the isolation units of Bwera hospital and Kagando hospital and the individuals were followed to the community where they live. Questionnaires were administered to a total of 75 participants who were either the cases or relatives to the case. GPS points of the homes of the cases and pictures of potential source infection were also taken and cases were mapped.A total of 222 cases were recorded in the Kasese District outbreak between the month of September 2017 and January 2018 with the case fatality rate (CFR) of 1.4%. Children below the age of 14 years contributed the biggest proportion of the cases (70%) and out of these, 33% were aged below 5 years. Culture isolated 69 V. cholerae 01 serotype Inaba from the total of 71 samples. Salmonella typhi was Isolated from the other two samples which were negative for V. cholerae. Antibiotic susceptibility using Kirby-Bauer disc diffusion method was done on isolates from 69 participants and showed 100% resistance to Ampicillin and over 50% were resistant to trimethoprim/Sulfamethoxazole whereas gentamicin showed 100% susceptibility. Environmental assessment revealed rampant cases of open defecation.Though we did not culture water to confirm contamination with Vibrio cholerae, we hypothesize that the cholera epidemic in Kasese 2017 was sparked off by consumption of contaminated water following the heavy floods that washed away latrines into water sources in Bwera, Isango and Nakiyumbu sub-counties. V. cholerae was also highly resistant to the commonly used antibiotics.Item Evaluation of in-house PCR for diagnosis of smear-negative pulmonary tuberculosis in Kampala, Uganda(BMC Research Notes, 2012) Nakiyingi, Lydia; Kateete, David P.; Ocama, Ponsiano; Worodria, William; Sempa, Joseph B.; Asiimwe, Benon B.; Katabazi, Fred A.; Katamba, Achilles; Huang, Laurence; Joloba, Moses L.; Mayanja-Kizza, HarrietNucleic acid amplification tests (NAATs) have offered hope for rapid diagnosis of tuberculosis (TB). However, their efficiency with smear-negative samples has not been widely studied in low income settings. Here, we evaluated in-house PCR assay for diagnosis of smear-negative TB using Lowenstein-Jensen (LJ) culture as the baseline test. Two hundred and five pulmonary TB (PTB) suspects with smear-negative sputum samples, admitted on a short stay emergency ward at Mulago Hospital in Kampala, Uganda, were enrolled. Two smear-negative sputum samples were obtained from each PTB suspect and processed simultaneously for identification of MTBC using in-house PCR and LJ culture. Results: Seventy two PTB suspects (35%, 72/205) were LJ culture positive while 128 (62.4%, 128/205) were PCR-positive. The sensitivity and specificity of in-house PCR for diagnosis of smear-negative PTB were 75% (95% CI 62.6-85.0) and 35.9% (95% CI 27.2-45.3), respectively. The positive and negative predictive values were 39% (95% CI 30.4-48.2) and 72.4% (95% CI 59.1-83.3), respectively, while the positive and negative likelihood ratios were 1.17 (95% CI 0.96-1.42) and 0.70 (95% CI 0.43-1.14), respectively. One hundred and seventeen LJ culturenegative suspects (75 PCR-positive and 42 PCR-negative) were enrolled for follow-up at 2 months. Of the PCR-positive suspects, 45 (60%, 45/75) were still alive, of whom 29 (64.4%, 29/45) returned for the follow-up visit; 15 (20%, 15/75) suspects died while another 15 (20%, 15/75) were lost to follow-up. Of the 42 PCR-negative suspects, 22 (52.4%, 22/42) were still alive, of whom 16 (72.7%, 16/22) returned for follow-up; 11 (26.2%, 11/42) died while nine (21.4%, 9/42) were lost to follow-up. Overall, more PCR-positive suspects were diagnosed with PTB during follow-up visits but the difference was not statistically significant (27.6%, 8/29 vs. 25%, 4/16, p = 0.9239). Furthermore, mortality was higher for the PCR-negative suspects but the difference was also not statistically significant (26.2% vs. 20% p = 0.7094). Conclusion: In-house PCR correlates poorly with LJ culture for diagnosis of smear-negative PTB. Therefore, in-house PCR may not be adopted as an alternative to LJ culture.Item Health service delay among pulmonary tuberculosis patients presenting to a National Referral Hospital, Kampala, Uganda: a cross sectional study(Pan African Medical Journal, 2013) Kansiime, Catherine; Kiwuwa, Stephen M.; Levi, Mugenyi; Asiimwe, Benon B.; Katamba, AchillesDelay in the diagnosis of pulmonary tuberculosis (PTB) is common in many countries in Sub-Saharan Africa. Timely diagnosis of active tuberculosis is crucial in minimizing morbidity and mortality in the community as well as nosocomial transmission in health care facilities. This study aimed at determining factors associated with health service delay in the diagnosis and initiation of treatment among new PTB patients presenting to the National Referral Hospital-Mulago. Methods: This was a cross-sectional study among eligible new PTB patients presenting at the National referral TB treatment center Mulago hospital, between March to May 2009. The patients were consecutively recruited and interviewed using a semi-structured questionnaire to assess socio- demographic and health service factors. Multivariate logistic regression using odds ratios and 95% confidence intervals was done. Results: Two hundred and sixty six newly diagnosed PTB patients were enrolled, of which 65.4% experienced health systems delay. The median health service delay was 9days (IQR=8-19). Factors associated with health service delay were: 1n-patient (OR= 4.68, 95% CI: 1.91-11.45), secondary as highest level of education attained (OR= 3.56, 95% CI: 1.18-10.74), primary as highest level of education attained (OR= 6.70, 95% CI: 2.13-21.02), presence of fever (OR= 3.28, 95% CI: 1.05-10.79), and patient delay at health facility (OR= 5.01, 95% CI: 1.33-18.9). Conclusion: The study found a significant proportion of Health service delay among pulmonary tuberculosis patients presenting at the referral hospital. Being an in-patient and having fever as a symptom of tuberculosis needs further attention in order to have timely diagnosis. There is need for awareness on TB especially that most of the TB symptoms present like other febrile illnesses such as malaria and needs consideration when patients present to a health facility.Item Knowledge and perceptions of brucellosis in the pastoral communities adjacent to Lake Mburo National Park, Uganda(BMC Public Health, 2014) Kansiime, Catherine; Mugisha, Anthony; Makumbi, Fredrick; Mugisha, Samuel; Rwego, Innocent B.; Sempa, Joseph; Kiwanuka, Suzanne N.; Asiimwe, Benon B.; Rutebemberwa, ElizeusBrucellosis is one of the most common zoonotic infections globally. Lack of knowledge about brucellosis may affect the health-seeking behavior of patients, thus leading to sustained transmission in these communities. Our study assessed knowledge and perceptions of brucellosis among pastoral communities adjacent to Lake Mburo National Park (LMNP), Kiruhura District, Uganda. Methods: A community cross-sectional questionnaire survey involving 371 randomly selected household heads from three sub-counties neighboring LMNP were interviewed between June and August 2012. Data collected included communities’ knowledge on causes, symptoms, transmission, treatment, prevention and risk factors of brucellosis. Multivariable logistic regression analysis was performed to explore strength of association between overall knowledge of brucellosis and various individual factors using odds ratios and 95% confidence intervals. Results: Only 70 (19%) knew the symptoms of brucellosis in animals, and three quarters (279, 75.5%) mentioned joint and muscle pain as a common symptom in humans. Almost all participants (370, 99.3%) had ever heard about brucellosis, majority (311, 84.7%) believed it affects all sexes and two thirds (67.7%) of the respondents believed close proximity to wildlife contributes to the presence of the disease. Almost all (352, 95.4%) knew that brucellosis in humans could be treatable using modern drugs. The main routes of infection in humans such as consumption of unpasteurized dairy products were known by 97% (360/371); eating of half-cooked meat by 91.4% and eating contaminated pasture in animals by 97.4%. There was moderate overall knowledge of brucellosis 197 (53.1%). Factors associated with higher overall knowledge were being agro-pastoralists (aOR: 2.08, CI: 1.17-3.71) compared to pure pastoralists while those who reported that the disease was a health problem (aOR: 0.18, CI: 0.06-0.56) compared to those who said it was not were less likely to be knowledgeable. Conclusions: There was moderate overall knowledge of human and animal brucellosis among the participants. Majority of the participants believed that close proximity to wildlife contributes to the presence of the disease in the area. There is a need for collaboration between the public health, veterinary and wildlife sectors to provide health education on brucellosis for better management of the disease in the communities.Item Long-term dominance of Mycobacterium tuberculosis Uganda family in peri-urban Kampala-Uganda is not associated with cavitary disease(BMC Infectious Diseases, 2013) Wampande, Eddie M.; Mupere, Ezekiel; Debanne, SaraM; Asiimwe, Benon B.; Nsereko, Mary; Mayanja, Harriet; Eisenach, Kathleen; Kaplan, Gilla; Boom, Henry W.; Gagneux, Sebastien; Joloba, Moses L.Previous studies have shown that Mycobacterium tuberculosis (MTB) Uganda family, a sub-lineage of the MTB Lineage 4, is the main cause of tuberculosis (TB) in Uganda. Using a well characterized patient population, this study sought to determine whether there are clinical and patient characteristics associated with the success of the MTB Uganda family in Kampala. A total of 1,746 MTB clinical isolates collected from1992-2009 in a household contact study were genotyped. Genotyping was performed using Single Nucleotide Polymorphic (SNP) markers specific for the MTB Uganda family, other Lineage 4 strains, and Lineage 3, respectively. Out of 1,746 isolates, 1,213 were from patients with detailed clinical data. These data were used to seek associations between MTB lineage/sub-lineage and patient phenotypes.Item Multidrug Resistance among Escherichia Coli and Klebsiella Pneumoniae Carried in the Gut of Out-Patients from Pastoralist Communities of Kasese District, Uganda(PloS one, 2018) Stanley, Iramiot Jacob; Kajumbula, Henry; Bazira, Joel; Kansiime, Catherine; Rwego, Innocent B.; Asiimwe, Benon B.Antimicrobial resistance is a worldwide public health emergency that requires urgent attention. Most of the effort to prevent this coming catastrophe is occurring in high income countries and we do not know the extent of the problem in low and middle-income countries, largely because of low laboratory capacity coupled with lack of effective surveillance systems. We aimed at establishing the magnitude of antimicrobial resistance among Escherichia coli and Klebsiella pneumoniae carried in the gut of out-patients from pastoralist communities of rural Western Uganda.A cross-sectional study was carried out among pastoralists living in and around the Queen Elizabeth Protected Area (QEPA). Stool samples were collected from individuals from pastoralist communities who presented to the health facilities with fever and/or diarrhea without malaria and delivered to the microbiology laboratory of College of Health Sciences-Makerere University for processing, culture and drug susceptibility testing.A total of 300 participants fulfilling the inclusion criteria were recruited into the study. Three hundred stool samples were collected, with 209 yielding organisms of interest. Out of 209 stool samples that were positive, 181 (89%) grew E. coli, 23 (11%) grew K. pneumoniae and five grew Shigella. Generally, high antibiotic resistance patterns were detected among E. coli and K. pneumoniae isolated. High resistance against cotrimoxazole 74%, ampicillin 67%, amoxicillin/clavulanate 37%, and ciprofloxacin 31% was observed among the E. coli. In K. pneumoniae, cotrimoxazole 68% and amoxicillin/clavulanate 46%, were the most resisted antimicrobials. Additionally, 57% and 82% of the E. coli and K. pneumoniae respectively were resistant to at least three classes of the antimicrobials tested. Resistance to carbapenems was not detected among K. pneumoniae and only 0.6% of the E. coli were resistant to carbapenems. Isolates producing ESBLs comprised 12% and 23% of E. coli and K. pneumoniae respectively.We demonstrated high antimicrobial resistance, including multidrug resistance, among E. coli and K. pneumoniae isolates from pastoralist out-patients. We recommend a One Health approach to establish the sources and drivers of this problem to inform public health.Item Performance of Frontloading for Smear Microscopy in the Diagnosis of Pulmonary Tuberculosis: A Cross- Sectional Study at a Referral Hospital in Uganda(PLoS ONE, 2012) Miremba, Penelope; Kalyango, Joan N.; Worodria, William; Mugerwa, Henry; Nakakawa, Ethel; Asiimwe, Benon B.To compare the performance of frontloading and the standard WHO method for diagnosis of pulmonary TB at Mulago Hospital in order to validate the technique in this setting. Methods: This was a cross-sectional study in which 229 adult ($18 years) TB suspects were consecutively enrolled. Suspects submitted three sputum samples as follows: at initial presentation, one hour after the first sample, and the next morning. The first and next morning samples formed the standard WHO method, while the first and the one hour later samples formed the frontloading method. Sample processing was by the standard N-acetyl L-cystein (NALC)-NaOH method, and fluorescent microscopy was done for both methods, while cultures of the first sample on Lowenstein-Jensen slants acted as a gold standard. The sensitivity, specificity and predictive values for the WHO standard and frontloading methods were compared. Results: The sensitivity of both the frontloading and standard schemes was 91.1% while their specificities were 86.2% and 91.7% respectively. There was excellent agreement between the diagnostic capacity of the two methods (kappa statistic = 0.87, P,0.0001). The positive predictive value for the frontloading scheme was 87.2% and that for the standard approach was 91.9%, while the negative predictive values were 90.4% and 90.9%, respectively. Among the HIV positive patients, frontloading identified 59/79 (74.7%) culture positive samples while the standard approach identified 55/79 (69.6%). In the HIV sero-negative category, on the other hand, front-loading identified 48/110 (43.6%) culture positive samples compared to 45/110 (40.9%) by the standard approach. Conclusion: Frontloading based on smear examination of two same-day sputum samples has a similar performance to the current standard method and would not be associated with any significant missed diagnosis. It may therefore be advocated for use in our setting so as to reduce time to completion of diagnosis and patient loss to follow-up.Item Risk Factors for Human Brucellosis in Agro‑pastoralist Communities of South Western Uganda: a case–control study(BMC Research notes, 2015) Asiimwe, Benon B.; Kansiime, Catherine; Rwego, Innocent B.Brucellosis is a zoonosis of veterinary, public health and economic significance in most developing countries. The disease can result in permanent and disabling sequelae and considerable medical expenses in addition to loss of income due to loss of working hours. A case–control study was conducted in Nyabushozi, Kiruhura district, Uganda, so as to determine the risk factors for transmission of brucellosis to humans in these communities.We conducted a matched case–control study among participants in a previous study who were positive by the standard Serum Agglutination Test with titres ≥1:160. Controls were two neighbors for each case, matched by sex and age. A structured interviewer administered questionnaire was used to collect data on potential risk factors for brucellosis. Categorical variables were presented as proportions and their associations determined by Chi-square test. Bivariate analysis was performed to explore associations between the disease and the risk factors of brucellosis. Conditional logistic regression models were fitted to estimate independent associations between the disease and the risk factors using Odds Ratios and 95 % confidence intervals.A total of 45 cases and 90 controls were interviewed. Of the 45 cases, 21 (46.7 %) were male while 44/90 (48.9 %) of the controls were female. The most significant risk factors for infection being an agro-pastoralist (P = 0.05), consumption of raw cow ghee (P = 0.03) and consumption of unpasteurized milk (P = 0.02).The greatest risk factors for acquiring brucellosis in the study area were being an agro-pastoralist, consumption of raw cow ghee and consumption of unboiled milk. We recommend dissemination of health education packages regarding risks and prevention measures for brucellosis in these communities.Item Species And Drug Susceptibility Profiles Of Staphylococci Isolated From Healthy Children In Eastern Uganda(PloS one, 2020) Kateete, David Patrick; Asiimwe, Benon B.; Mayanja, Raymond; Najjuka, Christine Florence; Rutebemberwa, ElizeusStaphylococci are a key component of the human microbiota, and they mainly colonize the skin and anterior nares. However, they can cause infection in hospitalized patients and healthy individuals in the community. Although majority of the Staphylococcus aureus strains are coagulase-positive, some do not produce coagulase, and the isolation of coagulase-positive non-S. aureus isolates in humans is increasingly being reported. Therefore, sound knowledge of the species and characteristics of staphylococci in a given setting is important, especially isolates from children and immunocompromised individuals. The spectrum of Staphylococcus species colonizing children in Uganda is poorly understood; here, we aimed to determine the species and characteristics of staphylococci isolated from children in Eastern Uganda. Seven hundred and sixty four healthy children less than 5 years residing in Iganga and Mayuge districts in Eastern Uganda were enrolled. A total of 513 staphylococci belonging to 13 species were isolated from 485 children (63.5%, 485/764), with S. aureus being the dominant species (37.6%, 193/513) followed by S. epidermidis (25.5%, 131/513), S. haemolyticus (2.3%, 12/513), S. hominis (0.8%, 4/513) and S. haemolyticus/lugdunensis (0.58%, 3/513). Twenty four (4.95%, 24/485) children were co-colonized by two or more Staphylococcus species. With the exception of penicillin, antimicrobial resistance (AMR) rates were low; all isolates were susceptible to vancomycin, teicoplanin, linezolid and daptomycin. The prevalence of methicillin resistance was 23.8% (122/513) and it was highest in S. haemolyticus (66.7%, 8/12) followed by S. aureus (28.5%, 55/193) and S. epidermidis (23.7%, 31/131). The prevalence of multidrug resistance was 20.3% (104/513), and 59% (72/122) of methicillin resistant staphylococci were multidrug resistant. Four methicillin susceptible S. aureus isolates and a methicillin resistant S. scuiri isolate were mupirocin resistant (high-level). The most frequent AMR genes were mecA, vanA, ant(4')-Ia, and aac(6')-Ie- aph(2'')-Ia, pointing to presence of AMR drivers in the community.Item Species And Genotypic Diversity Of Non-Tuberculous Mycobacteria Isolated From Children Investigated For Pulmonary Tuberculosis In Rural Uganda(BMC infectious diseases, 2013) Asiimwe, Benon B.; Bagyenzi, Godwins B.; Ssengooba, Willy; Mumbowa, Francis; Mboowa, Gerald; Wajja, Anne; Kiiza, Harriet Mayanja; Musoke, Philippa M.; Wobudeya, Eric; Kallenius, Gunilla; Joloba, Moses L.Smear microscopy, a mainstay of tuberculosis (TB) diagnosis in developing countries, cannot differentiate M. tuberculosis complex from NTM infection, while pulmonary TB shares clinical signs with NTM disease, causing clinical and diagnostic dilemmas. This study used molecular assays to identify species and assess genotypic diversity of non-tuberculous mycobacteria (NTM) isolates from children investigated for pulmonary tuberculosis at a demographic surveillance site in rural eastern Uganda. Children were investigated for pulmonary tuberculosis as part of a TB vaccine surveillance program (2009–2011). Two cohorts of 2500 BCG vaccinated infants and 7000 adolescents (12–18 years) were recruited and followed up for one to two years to determine incidence of tuberculosis. Induced sputum and gastric aspirates were processed by the standard N-acetyl L-cysteine (NALC)-NaOH method. Sediments were cultured in the automated MGIT (Becton Dickson) liquid culture system and incubated at 37°C for at least six weeks. Capilia TB assay was used to classify mycobacteria into MTC and NTM. The GenoType CM/AS assays were performed to identify species while Enterobacterial Repetitive Intergenic Consensus (ERIC) PCR genotyping was used to assess genetic diversity of the strains within each species. Among 2859 infants and 2988 adolescents screened, the numbers of TB suspects were 710 and 1490 infants and adolescents respectively. The prevalence of NTM in infant suspects was 3.7% (26/710) (95% CI 2.5–5.2) while that in adolescent suspects was 4.6% (69/1490) (95% CI 3.6–5.8). On culture, 127 isolates were obtained, 103 of which were confirmed as mycobacteria comprising of 95 NTM and eight M. tuberculosis complex. The Genotype CM/AS assay identified 63 of the 95 NTM isolates while 32 remained un-identified. The identified NTM species were M. fortuitum (40 isolates, 63.5%), M. szulgai (9 isolates, 14.3%), M. gordonae (6 isolates, 9.5%), M. intracellulare (3 isolates, 4.7%), M. scrofulaceum (2 isolates, 3.2%), M. lentiflavum (2 isolates, 3.2%), and M. peregrinum (1 isolate, 1.6%). Genotyping did not reveal any clustering in M. intracellulare, M. gordonae and M. szulgai species. M. fortuitum, on the other hand, had two clusters, one with three isolates of M. fortuitum 1 and the other with two isolates of M. fortuitum 2 subspecies. The remaining 35 of the 40 isolates of M. fortuitum had unique fingerprint patterns.M. fortuitum is the most common cause of infection by NTM among Infants and adolescents in rural Uganda. There is a varied number of species and genotypes, with minimal clustering within species, suggesting ubiquitous sources of infection to individuals in this community.Item Whole genome sequences of multi-drug resistant Escherichia coli isolated in a Pastoralist Community of Western Uganda: Phylogenomic changes, virulence and resistant genes(PLoS ONE, 2020) Iramiot, Jacob Stanley; Kajumbula, Henry; Bazira, Joel; Etienne, P. de Villiers; Asiimwe, Benon B.The crisis of antimicrobial resistance is already here with us, affecting both humans and animals alike and very soon, small cuts and surgeries will become life threatening. This study aimed at determine the whole genome sequences of multi-drug resistant Escherichia coli isolated in a Pastoralist Community of Western Uganda: phylogenomic changes, virulence and resistant genes. Methods This was a laboratory based cross sectional study. Bacterial isolates analyzed in this study were 42 multidrug resistant E. coli isolated from stool samples from both humans (n = 30) and cattle (n = 12) in pastoralist communities collected between January 2018-March 2019. Most of the isolates (41/42) were resistant to three or more antibiotics (multi-drug resistant) and 21/42 isolates were ESBL producers; 13/30 from human and 8/12 from cattle. Whole Genome Sequencing (WGS) was carried out at the facilities of Kenya Medical Research Institute-Wellcome trust, Kilifi, to determine the phylogenomic changes, virulence and resistant genes. Results At household level, the genomes from both human and animals clustered away from one another except for one instance where two human isolates from the same household clustered together. However, 67% of the E. coli isolated from cattle were closely related to those found in humans. The E. coli isolates were assigned to eight different phylogroups: A, B1, B2, Cladel, D, E, F and G, with a majority being assigned to phylogroup A; while most of the animal isolates were assigned to phylogroup B1. The carriage of multiple AMR genes was higher from the E. coli population from humans than those from cattle. Among these were Beta-lactamase; blaOXA-1: Class D beta-lactamases; blaTEM-1, blaTEM-235: Beta-lactamase; catA1: chloramphenicol acetyl transferase; cmlA1: chloramphenicol efflux transporter; dfrA1, dfrA12, dfrA14, dfrA15, dfrA17, dfrA5, dfrA7, dfrA8: macrolide phosphotransferase; oqxB11: RND efflux pump conferring resistance to fluoroquinolone; qacL, qacEdelta1: quinolone efflux pump; qnrS1: quinolone resistance gene; sul1, sul2, sul3: sulfonamide resistant; tet(A), tet(B): tetracycline efflux pump. A high variation of virulence genes was registered among the E. coli genomes from humans than those of cattle origin. Conclusion From the analysis of the core genome and phenotypic resistance, this study has demonstrated that the E. coli of human origin and those of cattle origin may have a common ancestry. Limited sharing of virulence genes presents a challenge to the notion that AMR in humans is as a result of antibiotic use in the farm and distorts the picture of the directionality of transmission of AMR at a human-animal interface and presents a task of exploring alternative routes of transmission of AMR.