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BackgroundIsoniazid preventive therapy (IPT) is given to HIV patients to reduce the risk of active tuberculosis (TB). However, treatment completion remains sub-optimal among those that are initiated. This study aimed to determine the completion level of IPT and the factors associated with non-completion among people on antiretroviral therapy (ART) at Kisenyi Health Center IV in Kampala, Uganda.MethodsA facility-based retrospective cohort study utilizing routinely collected data of 341 randomly selected HIV patients initiated on IPT was conducted. Data extracted from the registers were used to determine the IPT completion. Modified Poisson regression with robust error variances was used to determine the associated factors of IPT non-completion while in-depth interviews were conducted to explore barriers to IPT completion from the patient’s perspective.ResultsA total of 341 patients who started on isoniazid (INH) were retrospectively followed up, with 69% (236/341) being female. Overall IPT completion was at 83%. Multivariable analysis revealed the prevalence of IPT non-completion among males was 2.24 times the prevalence among females [aPR 2.24, 95% CI: 1.40-3.58]. The prevalence of IPT non-completion among patients with a non-suppressed HIV viral load was 3.00 times the prevalence among those with a suppressed HIV viral load [aPR 3.00, 95% CI: 1.44-6.65]. Patients who were married/cohabiting had a 69% lower prevalence of IPT non-completion compared to those who were single [aPR 0.31, 95% CI: 0.17-0.55]. Lack of IPT-related health education, pill burden, distance to the health facility, and patient relocation were reported as the barriers to IPT completion.ConclusionIPT completion was found to be at 83% among the cohort studied. However, lower completion levels persist among males and HIV virally non-suppressed patients. Lack of IPT-related health education, pill burden, distance to the health facility, and patient relocation were reported as the barriers to IPT completion. Interventions that target these groups of people need to be intensified.

With shortages of face masks being reported worldwide, it is critical to consider alternatives to commercially manufactured face masks. This study aimed to test and compare the efficacy of various makes of locally made or homemade cloth face masks obtained from face-mask vendors in Kampala, Uganda, during the COVID-19 pandemic. The testing was performed to assess the bacterial filtration efficiency (BFE), breathability, distance-dependent fitness, and reusability of the locally made or homemade cloth face masks, while considering the most commonly used non-published face-mask decontamination approaches in Uganda. During laboratory experimentation, modified protocols from various face-mask testing organizations were adopted. Ten different face-mask types were experimented upon; each face-mask type was tested four times for every single test, except for the decontamination protocols involving washing where KN95 and surgical face masks were not included. Among the locally made or homemade cloth face masks, the double-layered cloth face masks (described as F) had better BFE and distance-dependent fitness characteristics, they could be reused, and had good breathability, than the other locally made or homemade cloth face masks. Despite these good qualities, the certainty of these face masks protecting wearers against COVID-19 remains subject to viral filtration efficiency testing.

Background: Non-prescribed use of antimicrobials in Agriculture incurs a transfer risk of resistant pathogens to humans, complicating treatment. The aim of this study was to determine the potential of Zoonotic E. coli to serve as drivers of antimicrobial resistance (AMR) among animals and humans in pastoralist communities in Kasese district, so as to protect the community. Materials and Methods: A laboratory based cross-sectional study was done using archived E. coli isolates previously obtained from humans in pastoralist communities of Kasese district, Uganda. Recovery of the isolates was done by conventional culture, and Identification by biochemical methods, serotyping and PCR. Kirby Bauer disc diffusion method was adopted for AMR profiling. Isolates were screened for resistance mechanisms including Extended Spectrum β-lactamase (ESBL), Carbapenemases and AmpC production using disc diffusion based methods. Results: The prevalence of Enterohemorrhagic E. coli (EHEC) was 16% (28/180). These EHEC isolates belonged to phylogroups; B1 (94%, 26/28), B2 (3%, 1/28) and A (3%, 1/28). All the 28 EHEC isolates possessed the virulence gene stx1, 26 of the 28 EHEC isolates contained the virulence gene stx2e, but none of the 28 possessed the virulence gene stx2. Highest resistance was seen to Cotrimoxazole (89%, 25/28), Tetracycline (71%, 20/28), Ampicillin (65%, 18/28) and Nitrofurantoin (28%, 8/28), these are the most commonly used antimicrobials in the agricultural sector in Uganda. Minimal resistance was observed to the antimicrobials that are commonly used in human medicine especially β-lactams, β-lactam+inhibitors and Carbapenems. Of the 28 zoonotic E. coli isolates, 17%, (5/28) were ESBL positive and among these 1 (3%, 1/28) was a Carbapenemase producer. Conclusion: There is a high prevalence of highly pathogenic, drug resistant E. coli O157:H7 among humans in pastoralist communities in Uganda. We suspect that these were acquired from animals because they mostly contained vero toxin gene vt2e which is animal specific, predominantly swine. Also majority of these EHEC isolates belonged to phylo-group B1 which has been documented to inhabit domestic animals. We recommend future studies to investigate relatedness of drug resistant isolates from humans and animals to ascertain the zoonotic spread of resistant enterohemorrhagic E. coli in pastoralist communities.

Background Lab-based surveillance (LBS) of antimicrobial resistance (AMR) is not systematically implemented in Uganda. We aimed to identify the gaps in establishing regular LBS of AMR in Uganda. Methods This was a retrospective records review. It was done at Mulago Hospital (MH) Microbiology Lab (MHL). It analyzed lab records on bacteria and their antimicrobial susceptibility profiles (ASPs) over 6 months. Since MH is the national referral hospital, we hypothesized that (1) MHL is the best resourced and that any limitations seen here are amplified in labs at regional referral hospitals (RRHs) and health centers (HCs); (2) data from MHL on LBS mirrors that from labs at RRHs and HCs; (3) the state of records from MHL show lab performance and the presence or absence of standard operating procedures (SOPs), as would be the case at RRHs and HCs. Results The lab got 1760 samples over the six months. The most common sample was urine (659, 37.4%). From the 1760 samples, data on 478 bacterial isolates were available. Urine gave the most isolates (159, 33.3%). Most of the isolates were gram-negative (267, 55.9%). Escherichia coli (100, 37%) was the most common gram-negative (of the Enterobacteriaceae). Pseudomonas aeruginosa (17, 6%) was the most common gram-negative (of the non-Enterobacteriaceae). The gram-negative bacteria were highly resistant to β-lactams. These were highly sensitive to carbapenems. The Staphylococcus aureus were highly resistant to β-lactams. The gram-positive bacteria were highly sensitive to vancomycin. ASPs for all bacterial categories were incomplete. Conclusions The findings from MHL suggest that there is a need to improve antimicrobial susceptibility testing capacity. They also suggest that the situation at RRHs and HCs around the country could be worse. So, there is a need to extend the political will, which already exists, into operational and implementation action.

Jeremiah Seni,1 Inyasi Lawrence Akaro,2,3 Baraka Mkinze,2,3 Zengo Kashinje,1 Modest Benard,1 Gerald Mboowa,4 Dickson Aruhomukama,4 Ivan Sserwadda,4 Moses L Joloba,4 Stephen E Mshana,1 Benson R Kidenya5 1Department of Microbiology and Immunology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, Mwanza, Tanzania; 2Department of Surgery, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, Mwanza, Tanzania; 3Department of Orthopaedic Surgery, Bugando Medical Centre, Mwanza, Tanzania; 4Department of Immunology and Molecular Biology, Makerere University College of Health Sciences, Kampala, Uganda; 5Department of Biochemistry and Molecular Biology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, Mwanza, TanzaniaCorrespondence: Jeremiah SeniDepartment of Microbiology and Immunology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, P.O. Box 1464, Bugando, Mwanza, TanzaniaTel: +255 784 593000Email senijj80@gmail.comBackground: The dual burden of road traffic accidents and antimicrobial resistance in orthopaedic infections is challenging already strained health-care systems. Limited information exists in Tanzania on antimicrobial resistance surveillance to delineate the potential sources of multi-drug-resistant bacteria for specific mitigation strategies among orthopaedic patients.Methods: A longitudinal study was conducted at Bugando Medical Centre in Mwanza city between January and May 2020. It involved the collection of rectal swabs/stools, hand swabs, and environmental sampling to identify extended-spectrum beta-lactamase (ESBL)-producing gram-negative bacteria. Participants’ data were collected using a structured questionnaire and analysed to determine factors associated with ESBL colonization among index orthopaedic patients and correlates with other ESBL sources using OR (95% CI) and a cut-off p-value of ≤ 0.05.Results: We found that 47.2% (125/265) of index patients, 77.8% (14/18) of neighbouring patients, 8.3% (2/24) of health-care workers, 72.2% (13/18) of non-medical caregivers, and 31.4% (27/86) of samples taken from the hospital environment had ESBL producers. Escherichia coli and Klebsiella spp. predominated among participants and Acinetobacter spp. predominated in the environmental samples. Patients with open fractures had increased odds of being colonized with ESBL producers [OR (95% CI): 2.08 (1.16– 3.75); p=0.015]. The floor below patients’ beds was commonly contaminated; however, the odds of environmental contamination decreased on the third round of sampling [OR (95% CI: 0.16 (0.04– 0.67); p=0.012], apparently as a result of parallel infection prevention and control responsive measures against coronavirus disease 2019 (COVID-19).Conclusion: We found a high occurrence of ESBL colonization among participants and in the environmentat this tertiary hospital. The importance of routine ESBL surveillance among orthopaedic patients with open fractures on admission and strengthened decontamination of health-care premises is reiterated.Keywords: ESBL colonization, orthopaedic patients, Mwanza, Tanzania

Despite the poor genomics research capacity in Africa, efforts have been made to empower African scientists to get involved in genomics research, particularly that involving African populations. As part of the Human Heredity and Health in Africa (H3Africa) Consortium, an initiative was set to make genomics research in Africa an African endeavor and was developed through funding from the United States’ National Institutes of Health Common Fund and the Wellcome Trust. H3Africa is intended to encourage a contemporary research approach by African investigators and to stimulate the study of genomic and environmental determinants of common diseases. The goal of these endeavors is to improve the health of African populations. To build capacity for bioinformatics and genomics research, organizations such as the African Society for Bioinformatics and Computational Biology have been established. In this article, we discuss the current status of the bioinformatics infrastructure in Africa as well as the training challenges and opportunities.

Background: Infections caused by gram-negative antibiotic-resistant bacteria continue to increase. Despite recommenda- tions by the Clinical Laboratory Standards Institute (CLSI) and the European Committee on Antimicrobial Susceptibility Testing (EUCAST) with regards to detection of antibiotic degrading enzymes secreted by these bacteria, the true prevalence of extended-spectrum β-lactamase (ESBL) and carbapenemase producers remains a difficult task to resolve. Describing of previously designed phenotypic detection assays for ESBLs and carbapenemases in a single document avails a summary that allows for multiple testing which increases the sensitivity and specificity of detection. Methods and aims: This review, therefore, defined and classified ESBLs and carbapenemases, and also briefly described how the several previously designed phenotypic detection assays for the same should be performed. Conclusion: Extended-spectrum β-lactamase and carbapenemase detection assays, once performed correctly, can precisely discriminate between bacteria producing these enzymes and those with other mechanisms of resistance to β-lactam antibi- otics. Keywords: Extended-spectrum β-lactamases; carbapenemases; phenotypic detection.

Bachelors Thesis

Over the years, numerous research projects reacting to an array of scientific questions have been pursued and most have been accomplished. However, despite the existence of several accredited, open-access- peer- reviewed- scientific journals, most of which offer waivers of publication charges to authors particularly those from low- and middle- income countries (LMICs) and potential personal and professional benefits of publishing, findings of numerous research projects remain shelved. This has left a lot of knowledge gaps in scientific literature and has negatively impacted research output in LMICs in Africa. This article explores: the benefits of publishing a research project, process of converting a research project into a publishable manuscript, and how to minimize rejections, purposely to hearten students, academics and research fellows particularly in LMICs to publish their research projects.

Face-masking could reduce the risk of COVID-19 transmission. We assessed knowledge, attitudes, perceptions, and practices toward COVID-19 and face-mask use among 644 high-risk individuals in Kampala, Uganda. In data analysis, descriptive, bivariate, and multivariate logistic regression analyses with a 95% CI were considered. Adjusted odds ratios were used to determine the magnitude of associations. P-values < 0.05 were considered statistically significant. The majority, 99.7% and 87.3% of the participants, respectively, had heard about COVID-19 and believed that face-masks were protective against COVID-19, whereas 67.9% reported having received information on face-mask use. Food-market vendors and those with no formal education were 0.5 and 0.3 times less likely to have received information about face-mask use than hospital workers and those who had completed secondary school, respectively. Those who had received information on face-mask use were 2.9 and 1.8 times more likely to own face-masks and to perceive them as protective, respectively. Food-market vendors were 3.9 times more likely to reuse their face-masks than hospital workers. Our findings suggest that Ugandan high-risk groups have good knowledge, optimistic attitudes and perceptions, and relatively appropriate practices toward COVID-19.

Reliable data on antimicrobial resistance (AMR) transmission dynamics in Uganda remains scarce; hence, we studied this area. Eighty-six index patients and “others” were recruited. Index patients were those who had been admitted to the orthopedic ward of Mulago National Referral Hospital during the study period; “others” included medical and non-medical caretakers of the index patients, and index patients’ immediate admitted hospital neighbors. Others were recruited only when index patients became positive for carrying antimicrobial-resistant bacteria (ARB) during their hospital stay. A total of 149 samples, including those from the inanimate environment, were analyzed microbiologically for ARB, and ARB were analyzed for their antimicrobial susceptibility profiles and mechanisms underlying observed resistances. We describe the diagnostic accuracy of the extended-spectrum β-lactamase (ESBL) production screening method, and AMR acquisition and transmission dynamics. Index patients were mostly carriers of ESBL-producing Enterobacteriaceae (PE) on admission, whereas non-ESBL-PE carriers on admission (61%) became carriers after 48 hours of admission (9%). The majority of ESBL-PE carriers on admission (56%) were referrals or transfers from other health-care facilities. Only 1 of 46 samples from the environment isolated an ESBL-PE. Marked resistance (> 90%) to β-lactams and folate-pathway inhibitors were observed. The ESBL screening method’s sensitivity, specificity, positive predictive value, and negative predictive value were 100%, 50%, 90%, and 100%, respectively. AMR acquisition and transmission occurs via human–human interfaces within and outside of health-care facilities compared with human–inanimate environment interfaces. However, this remains subject to further research.

BackgroundWith shortages of face-masks continuing to be reported worldwide, critical questions like whether or not there is an adequate alternative to commercially manufactured face-masks continue to linger especially in low- and middle-income settings. This study aimed at addressing this through testing and comparing various materials and forms of face-masks for filtration efficiency, breathability, microbial cleanliness, distance-dependent fitness, and re-usability of different face-masks procured from face-mask vendors in Kampala, Uganda.MethodsThis was a laboratory-based descriptive study that applied new protocols and already existing protocols with substantive modifications to ten different types of face-mask types each in quadruplicate to achieve each specified aim.ResultsSurgical face-masks had better filtration efficiency, distance-dependent fitness and breathability compared to other face-masks tested. Decontamination of these face-masks with 70% ethanol negatively affected their efficacy. Locally-made double layered face-masks had better: filtration efficiency, distance-dependent fitness and breathability compared to other locally-made cloth face-masks, and re-usability compared to all the face-mask types that had been tested.Discussion/conclusionsLocally-made double layered cloth face-masks could serve as alternative face-masks especially for populations in low- and middle-income settings like Uganda while allowing restricted use of surgical face-masks and other respirators like the KN95 to high-risk groups only.

Face-masking could reduce the risk of COVID-19 transmission. We assessed: knowledge, attitudes, perceptions, and practices towards COVID-19 and face-mask use among 644 high risk-individuals in Kampala, Uganda. In data analysis, descriptive, bivariate and multivariate logistic regression analyses, with a 95% confidence interval were considered. Adjusted-odds ratios were used to determine the magnitude of associations. P-values < 0.05 were considered statistically-significant. Majority: 99.7% and 87.3% of the participants respectively had heard and believed that face-masks were protective against COVID-19, while 67.9% reported having received information on face-mask use. Males, food market vendors, those with no formal education, and those aged 24-33, 44-53 and 54-63 years were 0.58, 0.47, 0.25, 1.9, 2.12, and 3.39 times less likely to have received information about face-mask use respectively. Majority, 67.8% owned locally-made, non-medical face-masks, while 77.0% of face-mask owners believed that they knew the right procedure of wearing them. Those who had received information on face-mask use were 2.85 and 1.83 times more likely to own face-masks and to perceive them as protective. Food market vendors were 3.92 times more likely to re-use their face-masks. Our findings suggest that Ugandan high-risk groups have good knowledge, optimistic attitudes and perceptions, and relatively appropriate practices towards COVID-19.

In recent times, pan-drug resistant Acinetobacter baumannii have emerged and continue to spread among critically ill patients, this poses an urgent risk to global and local human health. This study sought to provide the first genomic analysis of a pan-drug resistant Acinetobacter baumannii from Uganda and Africa, and to tell a story of mobile genetic element-mediated antibiotic resistance evolution in the isolate. It was an in-silico study in which intrinsic and acquired antibiotic resistance genes, and/or chromosomal resistance mutations were identified using PATRIC, CARD, NDARO and ResFinder. Screening for insertion sequences was done using ISfinder. Also, plasmid screening, phylogenetic analysis and sequence typing were performed using PlasmidFinder, PATRIC and Gubbin, and MLST respectively.The isolate belonged to the Sequence type 136, belonging to Clonal complex 208 and Global complex 2. This isolate shared close homology with strains from Tanzania. Resistance in the isolate was chromosomally and mobile genetic element-mediated by Acinetobacter-derived cephalosporinases and carbapenem hydrolyzing class D β-lactamses, blaOXA-2, 51, 5 88, 317, blaADC-2, 25. Colistin resistance was associated with previously documented mutants, lpxA and lpxC. Other key resistance genes identified were: aph(3”)-lb, aph(6)-ld, aph(3’)-la, aac(3)-lld, aac(3)-lla, aph(3’)-l, aph(3”)-l, aph(6)-lc, aph(6)-ld, aac(3)-II, III, IV, VI, VIII, IX, X, macA, macB, tetA, tetB, tetR, dfrA, and those of the floR family. RSF1010 like IncQ broad-host-range plasmids and features of pACICU1, pACICU2, and p3ABAYE Acinetobacter baumannii plasmids namely partitioning proteins ParA and B were present. Insertion sequences present included IS3, IS5, IS66 and those of the ISLre2 families.The study described for the first time a pan-drug resistant Acinetobacter baumannii from Uganda, and told a story of mobile genetic element-mediated antibiotic resistance evolution in the isolate despite being limited by pan-drug resistance phenotypic data. It provides a basis to track trends in antibiotic resistance and identification of emerging resistance patterns in Acinetobacter baumannii in Uganda.

Objective: This study aimed at providing a comprehensive genomic analysis of whole-genome sequence data obtained from V. cholerae isolates from different outbreaks in Uganda using bioinformatics approaches. Results :The ten sequenced strains of V. cholerae were found to carry virulence-associated genes MakA, ctxA, ctxB, carA, carB, trpB, clpB, ace, toxR, zot, rtxA, ompW, ompR, gmhA, fur, hlyA, rstR, Type IV secretion system genes, T6SS genes vasA-L, vgrG-2, vgrG-3, vipA/mglA, and vipB/mglB; alsD; alsR; the flagella-mediated cytotoxin gene, makA; Type IV pilus genes tcpA-F, tcpH-J, tcpN, tcpP-T, and icmF/vasK; adherence genes acfA-D, IlpA, and quorum sensing system genes luxS and cqsA. Pathogenicity islands identified were VSP-1, VSP-2, VPI-1, and VPI-2. Antimicrobial resistance genes identified in the strains included strA and B, APH(3'')-I, APH(3'')-Ib, APH(6)-Id, APH(6)-Ic, murA, pare, dfrA1, floR, catB, and catB9. The strains also contained genes of the VC1786 integrative and conjugative element. SNP-based phylogenetic analysis revealed 218 shared SNPs in the strains, of these, 98 were missense. Gene enrichment analysis of the 98 SNPs revealed enrichment in genes that mediate transmembrane-signaling activity, peptidyl-prolyl cis-trans isomerase activity, and phosphorelay response regulator activity.

Background: Antimicrobial resistance threatens the achievements of modern medicine as well as the sustainability of effective global public health responses to the threat posed by infectious diseases. Extended-spectrum β-lactamase production in bacteria provides the main mechanism of resistance in gram-negative bacteria, particularly those belonging to the Enterobacteriaceae family as well as gram-positive bacteria. This study hence aimed at providing insights into the potential role of in-patients, their immediate hospital environments, out-patients, and their communities in the transmission of antimicrobial resistance via identifying gram-negative and gram-positive bacteria commonly isolated in samples collected from each of these patients/sites as well as their antimicrobial susceptibility profiles using extended-spectrum β-lactamase production in the same as the basis. Methods: Our study reviewed four cross-sectional studies conducted at national and regional referral hospitals in Uganda. Data on bacterial aetiology and antimicrobial susceptibility testing retrieved from the studies was imported into Microsoft Excel, cleaned, sand then exported to IBM SPSS statistics (version 16) for statistical analysis. The databases used were PubMed and Embase. Results: We report that; Escherichia coli and Klebsiella pneumoniae are the most prevalent Enterobacteriaceae species in the samples that were collected in the studies reviewed; these species account for the highest proportions of extended-spectrum β-lactamase producers; Staphylococcus aureus is the most prevalent of the gram-positive bacteria isolated from the same samples, and accounts for the highest proportions of extended-spectrum β-lactamase producers in the gram-positive bacteria isolated, and similar Enterobacteriaceae species and gram-positive bacteria, are predominant in samples from in-patients, their immediate hospital environments, and out-patients. Conclusion: The insights provided indicate antimicrobial resistance transmission dynamics be re-thought and more comprehensive studies aimed at investigating the same be done to ascertain the source and transmission routes of antimicrobial-resistant bacteria in clinical settings.

Background Between January 2015 and July 2017, we investigated the frequency of carbapenem resistant Acinetobacter baumannii (CRAB) and carbapenem resistant Pseudomonas aeruginosa (CRPA) at the Mulago Hospital intensive care unit (ICU) in Kampala, Uganda. Carbapenemase production and carbapenemase gene carriage among CRAB and CRPA were determined; mobility potential of carbapenemase genes via horizontal gene transfer processes was also studied. Methods Clinical specimens from 9269 patients were processed for isolation of CRAB and CRPA. Drug susceptibility testing was performed with the disk diffusion method. Carriage of carbapenemase genes and class 1 integrons was determined by PCR. Conjugation experiments that involved blaVIM positive CRAB/CRPA (donors) and sodium azide resistant Escherichia coli J53 (recipient) were performed. Results The 9269 specimens processed yielded 1077 and 488 isolates of Acinetobacter baumannii and Pseudomonas aeruginosa, respectively. Of these, 2.7% (29/1077) and 7.4% (36/488) were confirmed to be CRAB and CRPA respectively, but 46 were available for analysis (21 CRAB and 25 CRPA). Majority of specimens yielding CRAB and CRPA were from the ICU (78%) while 20 and 2% were from the ENT (Ear Nose & Throat) Department and the Burns Unit, respectively. Carbapenemase assays performed with the MHT assay showed that 40 and 33% of CRPA and CRAB isolates respectively, were carbapenemase producers. Also, 72 and 48% of CRPA and CRAB isolates respectively, were metallo-beta-lactamase producers. All the carbapenemase producing isolates were multidrug resistant but susceptible to colistin. blaVIM was the most prevalent carbapenemase gene, and it was detected in all CRAB and CRPA isolates while blaOXA-23 and blaOXA-24 were detected in 29 and 24% of CRAB isolates, respectively. Co-carriage of blaOXA-23 and blaOXA-24 occurred in 14% of CRAB isolates. Moreover, 63% of the study isolates carried class 1 integrons; of these 31% successfully transferred blaVIM to E. coli J53. Conclusions CRAB and CRPA prevalence at the Mulago Hospital ICU is relatively low but carbapenemase genes especially blaVIM and blaOXA-23 are prevalent among them. This requires strengthening of infection control practices to curb selection and transmission of these strains in the hospital.

Background: Cholera remains a serious public health problem in Uganda and Africa. The aim of this study was to provide the complete array of antimicrobial resistance genes, integrative and conjugative elements, virulence genes, pathogenicity islands, plasmids, and insertion sequences in the strains. In addition, this study also aimed to provide a single nucleotide polymorphism (SNP) based phylogenetic analysis of the strains. Methods: In the analysis, both Linux and web-based bioinformatics approaches were used to analyze the study sequences. Databases used included; FastQC, MultiQC, Snippy, PANTHER, PATRIC, Unicycler, ISFinder, Center for Genomic Epidemiology pipelines (i.e. MLST, PlasmidFinder, MyDbFinder, and ResFinder), MashTree and IcyTree. Results: The 10 sequenced strains of Vibrio cholerae were found to carry virulence-associated genes including MakA, ctxA, ctxB, carA, carB, trpB, clpB, ace, toxR, zot, rtxA, ompW, ompR, gmhA, fur, hlyA, and rstR. Also identified were: genes of the Type VI secretion system including vasA-L, vgrG-2, vgrG-3, vipA/mglA, and vipB/mglB; alsD (VC1589), involved in the synthesis of 2,3-butanediol; alsR, involved in the acetate-responsive LysR-type regulation; makA, the flagella-mediated cytotoxin gene; Type VI pilus genes including tcpA-F, tcpH-J, tcpN, tcpP-T, and icmF/vasK; adherence genes acfA-D and IlpA; and quorum sensing system genes luxS and cqsA. Pathogenicity islands identified comprised of VSP-1 and VSP-2, as well as VPI-1 and VPI-2. In addition, strA and B, APH(3'')-I, APH(3'')-Ib, APH(6)-Id, APH(6)-Ic, murA, pare, dfrA1, floR, catB, and catB9 were among the antimicrobial resistance genes found in the sequences. Analysis for SNPs shared among the sequences showed that the sequenced strains shared 218 SNPs and of these, 98 SNPs were missense. Gene enrichment analysis of these SNPs showed enrichment in genes that mediate transmembrane-signaling receptor activity, peptidyl-prolyl cis-trans isomerase activity, and phosphor-relay response regulator activity. Conclusions: This study applied bioinformatics approaches to provide comprehensive genomic analysis of V. cholerae genomes obtained from Uganda.