NRU :: Browsing by Author "Bazira, Joel"

Browsing by Author "Bazira, Joel"

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AmpC-BETA Lactamases among Enterobacteriaceae Isolated at a Tertiary Hospital, South Western Uganda
(British biotechnology journal, 2014) Nakaye, Martha; Bwanga, Freddie; Itabangi, Herbert; Iramiot, J. Stanley; Mwambi, Bashir; Bazira, Joel
To characterize AmpC-beta lactamases among Enterobacteriaceae isolates from clinical samples at Mbarara Regional Referral Hospital. Study Design—Laboratory-based descriptive cross-sectional study Place and Duration of Study—Microbiology Department, Mbarara Regional Referral Hospital and MBN clinical Laboratories, between May to September 2013. Methodology—This study included 293 Enterobacteriaceae isolates recovered from clinical specimens that included blood, urine, stool and aspirates. AmpC Beta lactamase production was determined using disc placement method for cefoxitin at a break point of <18mm. Common AmpC plasmid mediated genes were EBC, ACC, FOX, DHA, CIT and MOX were; was determined by Multiplex PCR as described by Hanson and Perez-Perez. Results—Plasmid mediated AmpC phenotype was confirmed in 107 of the 293 (36.5%) cefoxitin resistant isolates with 30 isolates having more than one gene coding for resistance. The commonest source that harbored AmpC beta lactamases was urine and E. coli was the most common AmpC producer (59.5%). The genotypes detected in this study, included EBC (n=36), FOX (n=18), ACC (n=11), CIT (n=10), DHA (n=07) and MOX (n=1). Conclusion—Our findings showed that prevalence of AmpC beta-lactamase at MRRH was high (39.6), with EBC as the commonest genotype among Enterobacteriaceae Urine and E. coli were the commonest source and organism respectively that harbored AmpC beta-lactamases. There‘s rational antimicrobial therapy and antibiotic susceptibility tests should be requested by health workers especially patients presenting with urinary tract infections and bacteraemias.
Antimicrobial resistance at the human-animal interface in the Pastoralist Communities of Kasese District, South Western Uganda
(Nature Publishing Group, 2020-09) Iramiot, Jacob Stanley; Kajumbula, Henry; Bazira, Joel; Kansiime, Catherine; Asiimwe, Benon B
Abstract Intensive usage of antimicrobials in the management of animal diseases leads to selection for resistance among microorganisms. This study aimed to assess antimicrobial use and to describe factors associated with the transmission of antimicrobial resistance between humans and animals in pastoralist communities of Kasese district. A mixed-methods approach was employed in this study. Rectal swabs were collected from the participants and cattle and transported in Carry–Blaire transport medium to the laboratory within 24 h of collection for culture and sensitivity to confirm carriage of multi-drug resistant bacteria. In-depth interviews were conducted among veterinary officers, veterinary drug vendors, human health facility in-charges in both public and private health facilities, and operators of human pharmacies and drug shops. Carriage of multi-drug resistant bacteria among humans was 88 (93%) and 76(80%) among cattle. Consumption of lakeshore water and carriage of multi-drug resistant bacteria in cattle were associated with carriage of multi-drug resistant bacteria in the human population. The prevalence of multi-drug resistance among organisms Isolated from both humans and animals was high. There is a high likelihood of transmission of multi-drug resistance between humans and animals.
The Bacterial and Viral Complexity of Postinfectious Hydrocephalus in Uganda
(Science translational medicine, 2020) Paulson, Joseph N.; Williams, Brent L.; Hehnly, Christine; Mishra, Nischay; Sinnar, Shamim A.; Zhang, Lijun; Ssentongo, Paddy; Kabachelor, Edith Mbabazi; Wijetunge, Dona S. S.; Bredow, Benjamin von; Mulondo, Ronnie; Kiwanuka, Julius; Bajunirwe, Francis; Bazira, Joel; Bebell, Lisa M.; Burgoine, Kathy; Couto-Rodriguez, Mara; Ericson, Jessica E.; Erickson, Tim; Ferrari, Matthew; Gladstone, Melissa; Guo, Cheng; Haran, Murali; Hornig, Mady; Isaacs, Albert M.; Kaaya, Brian Nsubuga; Kangere, Sheila M.; Kulkarni, Abhaya V.; Kumbakumba, Elias; Li, Xiaoxiao; Limbrick, David D.; Magombe, Joshua; Morton, Sarah U.; Mugamba, John; Ng, James; Olupot, Peter Olupot; Onen, Justin; Peterson, Mallory R.; Roy, Farrah; Sheldon, Kathryn; Townsend, Reid; Weeks, Andrew D.; Whalen, Andrew J.; Quackenbush, John; Ssenyonga, Peter; Galperin, Michael Y.; Almeida, Mathieu; Atkins, Hannah; Warf, Benjamin C.; Lipkin, W. Ian; Broach, James R.; Schiff, Steven J.
Postinfectious hydrocephalus (PIH), often following neonatal sepsis, is the most common cause of pediatric hydrocephalus world-wide, yet the microbial pathogens remain uncharacterized. Characterization of the microbial agents causing PIH would lead to an emphasis shift from surgical palliation of cerebrospinal fluid (CSF) accumulation to prevention. We examined blood and CSF from 100 consecutive cases of PIH and control cases of non-postinfectious hydrocephalus (NPIH) in infants in Uganda. Genomic testing was undertaken for bacterial, fungal, and parasitic DNA, DNA and RNA sequencing for viral identification, and extensive bacterial culture recovery. We uncovered a major contribution to PIH from Paenibacillus, upon a background of frequent cytomegalovirus (CMV) infection. CMV was only found in CSF in PIH cases. A facultatively anaerobic isolate was recovered. Assembly of the genome revealed a strain of P. thiaminolyticus. In mice, this isolate designated strain Mbale, was lethal in contrast with the benign reference strain. These findings point to the value of an unbiased pan-microbial approach to characterize PIH in settings where the organisms remain unknown, and enables a pathway towards more optimal treatment and prevention of the proximate neonatal infections.
Diversity and Distribution of Spa types among Methicillin Resistant Staphylococcus Aureus Isolated from Humans and Livestock in Kabale District - South Western Uganda
(Research Square, 2021) Baguma, Andrew; Musinguzi, Benson; Orikiriza, Patrick; Bazira, Joel
S. aureus is a skin and mucosal bacterial commensal of both humans and animals which has evolved as an important pathogen implicated to cause various infections. High levels of antibiotic use have resulted into multi-drug resistance MRSA, especially among HA-MRSA, CA-and LA - MRSA. Awareness on coexistence and diversity of MRSA clones among humans and household Livestock particularly cattle and swine in our region is limited. We used spa typing method to determine spa diversity, distribution and coexistence in outpatients, household contacts and respective livestock (cattle and swine) in Kabale region, south western Uganda. This was a cross sectional study by design consisting of outpatients, household contacts and livestock. Outpatients (n =100) colonized with MRSA were traced back to their respective homesteads where household members, domestic cattle, and, swine were tested for S. aureus and subsequently MRSA colonization. High-resolution DNA melting analysis was used to determine spa types among MRSA isolates. Overlap of MRSA isolates among humans and livestock was based on the presence of similar spa types. A total of 3371 S.aureus isolates were collected from outpatients (n =376), household contacts (n = 1531), Cattle (n = 1159) and Swine (n = 305), among which 482 had mecA gene where 27% (100/376) and 8% (123/1531) were outpatients and household contacts respectively while 11% (132/1159) and 42% (127/305) were cattle and swine respectively. Twenty different spa types were identified; t034, t4677, t108, t1451, t9377, t1081, t040, t701, t041, t002, t044, t037,t121, t127, t922, t032, t019, t018, t012 and t030, among which t034 (109/482), t4677 (53/482), t9377 (63/482) and t1081 (53/482) were most prevalent and distributed among human and livestock. All the MRSA isolates were multidrug resistant to antibiotics tested. In Kabale region, there is high diversity of spa types among MRSA. Presence of similar spa types was found circulating among humans and their respective livestock which demonstrates a possible bidirectional transmission. Presence of MDR - MRSA highlights the need for effective prevention and control of MRSA among livestock and in the community using One Health approach.
Epidemiology of Microbial Keratitis in Uganda: A Cohort Study
(Ophthalmic Epidemiology, 2020) Arunga, Simon; Kintoki, Guyguy M.; Mwesigye, James; Ayebazibwe, Bosco; Onyango, John; Bazira, Joel; Newton, Rob; Gichuhi, Stephen; Leck, Astrid; Macleod, David; Hu, Victor H.; Burton, Matthew J.
To describe the epidemiology of Microbial Keratitis (MK) in Uganda. Methods: We prospectively recruited patients presenting with MK at two main eye units in Southern Uganda between December 2016 and March 2018. We collected information on clinical history and presentation, microbiology and 3-month outcomes. Poor vision was defined as vision < 6/60). Results: 313 individuals were enrolled. Median age was 47 years (range 18–96) and 174 (56%) were male. Median presentation time was 17 days from onset (IQR 8–32). Trauma was reported by 29% and use of Traditional Eye Medicine by 60%. Majority presented with severe infections (median infiltrate size 5.2 mm); 47% were blind in the affected eye (vision < 3/60). Microbiology was available from 270 cases: 62% were fungal, 7% mixed (bacterial and fungal), 7% bacterial and 24% no organism detected. At 3 months, 30% of the participants were blind in the affected eye, while 9% had lost their eye from the infection. Delayed presentation (overall p = .007) and prior use of Traditional Eye Medicine (aOR 1.58 [95% CI 1.04–2.42], p = .033) were responsible for poor presentation. Predictors of poor vision at 3 months were: baseline vision (aOR 2.98 [95%CI 2.12–4.19], p < .0001), infiltrate size (aOR 1.19 [95%CI 1.03–1.36], p < .020) and perforation at presentation (aOR 9.93 [95% CI 3.70–26.6], p < .0001). Conclusion: The most important outcome predictor was the state of the eye at presentation, facilitated by prior use of Traditional Eye Medicine and delayed presentation. In order to improve outcomes, we need effective early interventions.
Implementation of the World Health Organization Global Antimicrobial Resistance Surveillance System in Uganda, 2015-2020: Mixed-Methods Study Using National Surveillance Data
(JMIR public health and surveillance, 2021) Nabadda, Susan; Kakooza, Francis; Kiggundu, Reuben; Walwema, Richard; Bazira, Joel; Mayito, Jonathan; Mugerwa, Ibrahimm; Sekamatte, Musa; Kambugu, Andrew; Lamorde, Mohammed; Kajumbula, Henry; Mwebasa, Henry
Antimicrobial resistance (AMR) is an emerging public health crisis in Uganda. The World Health Organization (WHO) Global Action Plan recommends that countries should develop and implement National Action Plans for AMR. We describe the establishment of the national AMR program in Uganda and present the early microbial sensitivity results from the program. Objective: The aim of this study is to describe a national surveillance program that was developed to perform the systematic and continuous collection, analysis, and interpretation of AMR data. Methods: A systematic qualitative description of the process and progress made in the establishment of the national AMR program is provided, detailing the progress made from 2015 to 2020. This is followed by a report of the findings of the isolates that were collected from AMR surveillance sites. Identification and antimicrobial susceptibility testing (AST) of the bacterial isolates were performed using standard methods at both the surveillance sites and the reference laboratory. Results: Remarkable progress has been achieved in the establishment of the national AMR program, which is guided by the WHO Global Laboratory AMR Surveillance System (GLASS) in Uganda. A functional national coordinating center for AMR has been established with a supporting designated reference laboratory. WHONET software for AMR data management has been installed in the surveillance sites and laboratory staff trained on data quality assurance. Uganda has progressively submitted data to the WHO GLASS reporting system. Of the 19,216 isolates from WHO GLASS priority specimens collected from October 2015 to June 2020, 22.95% (n=4411) had community-acquired infections, 9.46% (n=1818) had hospital-acquired infections, and 68.57% (n=12,987) had infections of unknown origin. The highest proportion of the specimens was blood (12,398/19,216, 64.52%), followed by urine (5278/19,216, 27.47%) and stool (1266/19,216, 6.59%), whereas the lowest proportion was urogenital swabs (274/19,216, 1.4%). The mean age was 19.1 (SD 19.8 years), whereas the median age was 13 years (IQR 28). Approximately 49.13% (9440/19,216) of the participants were female and 50.51% (9706/19,216) were male. Participants with community-acquired infections were older (mean age 28, SD 18.6 years; median age 26, IQR 20.5 years) than those with hospital-acquired infections (mean age 17.3, SD 20.9 years; median age 8, IQR 26 years). All gram-negative (Escherichia coli, Klebsiella pneumoniae, and Neisseria gonorrhoeae) and gram-positive (Staphylococcus aureus and Enterococcus sp) bacteria with AST showed resistance to each of the tested antibiotics. Conclusions: Uganda is the first African country to implement a structured national AMR surveillance program in alignment with the WHO GLASS. The reported AST data indicate very high resistance to the recommended and prescribed antibiotics for treatment of infections. More effort is required regarding quality assurance of laboratory testing methodologies to ensure optimal adherence to WHO GLASS–recommended pathogen-antimicrobial combinations. The current AMR data will inform the development of treatment algorithms and clinical guidelines.
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.
Otomycosis among Patients Presenting with Ear Discharges at a Tertiary Hospital in South Western Uganda
(International Journal of TROPICAL DISEASE & Health, 2018) Itabangi, Herbert; Katawera, Victoria; Nyaitera, Victoria; Iramiot, Jacob Stanley; Nakaye, Martha; Mwambi, Bashir; Mukasa Kiguli, James; Bazira, Joel; Byarugaba, Fredrick
To the determine prevalence, mycology profile, associated symptoms and risk factors of otomycosis among patients that present with an ear discharge. Study Design: This was a cross-sectional study in which survey data was analysed. Place and Duration of Study: Departments of Microbiology and ENT, Faculty of Medicine, Mbarara University Teaching Hospital, between 2013 and 2015. Methodology: We recruited 117 patients (52 men, 65 women of age range 1-69 years) presenting with a discharging ear. Both newly enrolled and follow-up patients were included in the study. Clinically, patients were assessed for symptoms, possible predisposing factors, and treatment history. For laboratory diagnosis, ear swabs were aseptically collected and mycology profile determined using both direct examination and culture techniques. Fungal identification was through stimulation of fruiting bodies such as conidia or chlamydospores and biochemical identification. Results: Of the 117 participants enrolled, fungal infection was detected in 24 (20.51%) with direct microscopy and confirmed in 16 (13.68%) by culture. Otomycosis was more common among the youth (54%). There were no statistically significant symptoms associated with otomycosis. However, HIV/AIDS and mastoidectomy were significant predisposing factors (38%, p = 0.001 and 25%, p = 0.002, respectively). Aspergillus species (76.47%), Candida albicans (17.65%) and Cladosporium species (5.88%) were the agents commonly associated with otomycosis in this region. Conclusion: Otomycosis can be common and is an important disease of the external ear, especially in at-risk individuals. In southwestern Uganda, the disease is common among young males and aetiology is mainly due to Aspergillus and Candida albicans but other opportunists such as Cladosporium species may also be implicated. Thus, there is a need for routine checks followed by robust diagnostic approaches as a means for evidence-based patient management.
Pan-Resistome Characterization of Uropathogenic Escherichia coli and Klebsiella pneumoniae Strains Circulating in Uganda and Kenya, Isolated from 2017–2018
(Antibiotics, 2021) Gonzales Decano, Arun; Pettigrew, Kerry; Sabiiti, Wilber; Sloan, Derek J.; Neema, Stella; Bazira, Joel; Kiiru, John; Onyango, Hellen; Asiimwe, Benon; Holden, Matthew T. G.
Urinary tract infection (UTI) develops after a pathogen adheres to the inner lining of the urinary tract. Cases of UTIs are predominantly caused by several Gram-negative bacteria and account for high morbidity in the clinical and community settings. Of greater concern are the strains carrying antimicrobial resistance (AMR)-conferring genes. The gravity of a UTI is also determined by a spectrum of other virulence factors. This study represents a pilot project to investigate the burden of AMR among uropathogens in East Africa. We examined bacterial samples isolated in 2017–2018 from in- and out-patients in Kenya (KY) and Uganda (UG) that presented with clinical symptoms of UTI. We reconstructed the evolutionary history of the strains, investigated their population structure, and performed comparative analysis their pangenome contents. We found 55 Escherichia coli and 19 Klebsiella pneumoniae strains confirmed uropathogenic following screening for the prevalence of UTI virulence genes including fimH, iutA, feoA/B/C, mrkD, and foc. We identified 18 different sequence types in E. coli population while all K. pneumoniae strains belong to ST11. The most prevalent E. coli sequence types were ST131 (26%), ST335/1193 (10%), and ST10 (6%). Diverse plasmid types were observed in both collections such as Incompatibility (IncF/IncH/IncQ1/IncX4) and Col groups. Pangenome analysis of each set revealed a total of 2862 and 3464 genes comprised the core genome of E. coli and K. pneumoniae population, respectively. Among these are acquired AMR determinants including fluoroquinolone resistance-conferring genes aac(3)-Ib-cr and other significant genes: aad, tet, sul1, sul2, and cat, which are associated with aminoglycoside, tetracycline, sulfonamide, and chloramphenicol resistance, respectively. Accessory genomes of both species collections were detected several -lactamase genes, blaCTX-M, blaTEM and blaOXA, or blaNDM. Overall, 93% are multi-drug resistant in the E. coli collection while 100% of the K. pneumoniae strains contained genes that are associated with resistance to three or more antibiotic classes. Our findings illustrate the abundant acquired resistome and virulome repertoire in uropathogenic E. coli and K. pneumoniae, which are mainly disseminated via clonal and horizontal transfer, circulating in the East African region. We further demonstrate here that routine genomic surveillance is necessary for high-resolution bacterial epidemiology of these important AMR pathogens.
Phylogenetic analysis of multidrug resistant E. coli isolates from the urinary tract in Bushenyi district, Uganda using the new Clermont phylotyping method
(African Journal of Microbiology Research, 2020) Odoki, Martin; Aliero, Adamu A.; Tibyangye, Julius; Onkoba, Sarah K.; Bashir, Alkali; Maniga, Josephat N.; Eilu, Emmanuel; Wampande, Eddie; Kato, Charles D.; Agwu, Ezera; Bazira, Joel
Due to the increasing rates of multidrug resistance (MDR) among the Enterobacteriaceae that cause urinary tract infections (UTIs), selection of antimicrobial agents for empirical therapy is becoming a major challenge. This study determined the antimicrobial resistance profiles, multidrug resistance profiles, multiple antibiotic resistance indices (MARI), factors associated with MDR UTIs and the phylogenetic groups of MDR Escherichia coli strains isolated from the urinary tract among patients attending hospitals in Bushenyi District, Uganda. In this cross-sectional study, a total of 86 bacterial uropathogens isolated from 267 study participants suspected to have UTIs were subjected to antimicrobial susceptibility tests using the Kirby Bauer Disk diffusion method. Data for the factors associated with MDR were obtained by the use of questionnaires. Phylogenetic groups of the MDR E. coli were determined using the new Clermont method for phylotyping E. coli. Descriptive and multiple logistic regression statistical tools were used to determine phylogenetic groups, and assess for statistically significant relationship between MDR UTIs and factors suspected to be associated with MDR UTIs respectively. The isolates assigned as group B2 9/12 (75.0%), B1 2/5 (40.0%) and A 2/7 (28.6%) by using the old Clermont method could not be phylotyped using the new Clermont method and were grouped as non-typeable strains of E. coli. Our study demonstrated high prevalence of the non-typeable strains of MDR E. coli, we therefore recommend the use of modern DNA sequencing-based approaches which is the gold standard for genotyping bacteria, that this current study could not afford
Prevalence and Antibiotic Susceptibility Patterns of Clinical Isolates of Methicillin- Resistant Staphylococcus aureus in a Tertiary Care Hospital in Western Uganda
(British Microbiology Research Journal, 2014) Stanley, Iramiot J.; Bwanga, Freddie; Itabangi, Herbert; Nakaye, Martha; Mwambi, Bashir; Bazira, Joel
To determine the prevalence and antibiotic susceptibility patterns of clinical isolates of methicillin resistant Staphylococcus aureus isolated at Mbarara Regional Referral Hospital. Method: A total of 400 S. aureus isolates recovered from various clinical specimens at Mbarara Regional Referral Hospital were included in this study. Phenotypic screening was performed using Oxacillin. Presence of mecA gene was studied using polymerase chain reaction (PCR). The mecA positive isolates were tested for susceptibility to, Vancomycin, Imipenem, Fusidic acid, Trimethoprim/Sulfamethoxazole, Clindamycin and Linezolid using the Kirby Bauer technique. Results: Of the 300 isolates of S. aureus 31.3% (94) were phenotypically MRSA and 38% (114) had the mecA gene. All the MRSA isolates were susceptible to vancomycin and linezolid but were highly resistant to trimethoprim/sulfamethoxazole (70.2%). Of the 114 MRSA isolates 19.3% (22) were multi-drug resistant S. aureus (MDR-MRSA). The study found that there was a significant difference between genotypic and phenotypic detection methods (p < 0.001). Conclusion: The prevalence of MRSA in Mbarara is high (38%) with a high resistance to trimethoprim/sulfamethoxazole. The detection of mecA gene is a good predictor of methicillin resistance in S. aureus. There is a worrying prevalence of MDR MRSA among the clinical isolates of S. aureus in South Western Uganda.
Prevalence of antibodies to Brucella species in commercial raw bovine milk in Southwestern Uganda
(BMC Research Notes, 2017) Kamwine, Monicah; Orikiriza, Patrick; Taseera, Kabanda; Iramiot, Jacob Stanley; Ojuka, Patrick; Ikiriza, Steven; Atwebembeire, Jeninah; Otieno, Duncan; Tweshengyereze, Silver; Mwanga‑Amumpaire, Juliet; Bazira, Joel; Boum II, Yap
The purpose and objective of this research was to explore the prevalence of antibodies against Brucella species in raw milk samples collected in Southwestern Uganda, one of the biggest milk producing regions in the Country. We hypothesized that there is a high level of antibodies in milk samples from this region. This builds more evidence to other studies in the region on the level contamination of raw milk. Results: A total of 185 raw milk samples, collected from dairy farms and factories in southwestern region, were tested for antibodies to Brucella spp. using the milk ring test (MRT) and indirect Enzyme-Linked Immunosorbent Assay (i-ELISA).We found a prevalence of 26.5% (49/185) by the two methods. This is related to previous reports in the region and adds more evidence on the need for further investigations to confirm the source of these antibodies and their relationship with disease in milk producing animals.
Trends in Antimicrobial Resistance of Staphylococcus aureus Isolated from Clinical Samples at Mbarara Regional Referral Hospital in Rural Uganda
(British Microbiology Research Journal, 2014) Bazira, Joel; Boum II, Yap; Sempa, Joseph; Iramiot, Jacobs; Nanjebe, Deborah; Sewankambo, Nelson; Nakanjako, Damalie
This study aimed at describing the antibiotic susceptibility patterns of S. aureus isolated from clinical samples at Mbarara Regional Referral Hospital from 2003 to 2012. Methods: This was a retrospective study that included clinical specimens cultured at the Microbiology laboratory of Mbarara Regional referral hospital between 2003 and 2012. Cultures and sensitivity data were abstracted from the laboratory registers using a data abstraction form. Among the positive culture reports, the antibiotic sensitivity of the common bacteria isolated were also recorded. Analysis of susceptibility data was limited to Staphylococcus aureus, the commonest organism identified. The data were entered into Epi info and exported to Stata Version 12.1 for analysis. Results: A total of 36,080 cultures were performed over a period of 10 years. Of these 7,744 (21.5%) specimens grew an organism. S. aureus was the most prevalent organism isolated. Fifty nine percent of the S. aureus was isolated from blood samples followed by 22% from pus samples, urine (8%) and HVS (5%). During the study period, resistance of S.aureus to chloramphenicol, amoxycillin, penicillin, tetracycline, and cotrimoxazole ranged from 50-90% while S. aureus resistance to Gentamicin and ceftriaxone ranged from 10-20%. Conclusion: Over the last decade, S. aureus isolates showed up to 90% resistance to commonly prescribed oral antibiotics. We recommend regular review of antibiotic resistance patterns to inform hospitals’ on guidelines on empirical antibiotic prescription, especially in resource-limited settings where susceptibility testing may not be feasible.
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.

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