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Abstract Background Non-malarial febrile illnesses (NMFI) pose significant challenges in HIV-infected children, often leading to severe complications and increased morbidity. While traditional diagnostic approaches focus on specific pathogens, shotgun metagenomic sequencing offers a comprehensive tool to explore the microbial landscape underlying NMFI in this vulnerable population ensuring effective management. Methods In this study, we employed shotgun metagenomics to analyse stool samples from HIV-infected children at the Baylor Children’s Clinic Uganda presenting with non-malarial febrile illness. Samples were collected and subjected to DNA extraction at the Molecular and Genomics Laboratory, Makerere University followed by shotgun metagenomics sequencing at the Chan Zuckerberg Biohub San Francisco. Bioinformatics analysis was conducted to identify and characterise the microbial composition and potential pathogenic taxa associated with NMFI using the CZID pipeline. Results Our findings reveal a diverse array of microbial taxa in the stool samples of HIV-infected children with NMFI. Importantly, shotgun metagenomics revealed potentially pathogenic players including Trichomonas vaginalis, Candida albicans, Giardia, and Bacteroides in stool from this patient population. This sheds light on the complexities of microbial interactions that potentially underpin non-malarial febrile illness in this group. Taxonomic profiling identified recognised pathogens and comorbidities and revealed possible new correlations with NMFI, shedding light on the pathophysiology of fever in HIV-infected children. Conclusion Shotgun metagenomics is a valuable method for understanding the gut microbial landscape of NMFI in HIV-infected children, providing a comprehensive approach to pathogen identification and characterisation. By revealing potential pathogenic actors beyond the fever, this work demonstrates how metagenomic sequencing may improve our knowledge of infectious illnesses in vulnerable groups and inspire targeted therapies for better clinical care and outcomes.

Objectives: We investigated the genomic epidemiology of extended-spectrum β-lactamase-producing Enterobacter cloacae (ESBL-Ec) isolates from patients and hospital environment to better understand their distribution to help devising effective strategies for infection prevention and control. Methods: We screened ESBL-Ec at Bugando Medical Center (BMC) in Mwanza, Tanzania. Rectal swabs from orthopedic patients on admission and swabs from the neighboring inanimate environment were collected. Following microbial culture, DNA was extracted from pure ESBL-Ec, and whole-genome sequencing was done. Sequence typing (ST), plasmid replicons, drug resistance, and virulence genes were deciphered using the Rapid Microbial Analysis Pipeline (rMAP). Results: We obtained 209 ESBL isolates, of which 15 (7.2 %) were ESBL-Ec [8 (53.3 %) from patients and 7 (46.7 %) from the environment]. Seven isolates were novel and eight were diverse, each with a unique ST. All isolates harbored two to five β-lactamase genes, with the predominance of blaCTX-M-15 (15/15), blaOXA-1 (14/15), blaTEM (14/15) and blaACT (12/15). The most common non β-lactam drug resistance genes were aac(3)-IIa (14/15), aac(6′)-Ib-cr (14/15), fosA (14/15), and qnrB1 (12/15), aph(3″)-Ib (10/15) and aph(6)-Id (10/15). Eleven different types of plasmid replicons were identified in 14/15 of the isolates, harboring one to five plasmids, with the most common plasmids being IncFII (11/15) and IncFIB (10/15). All isolates harbored the outer membrane protein (ompA), and curli protein (csg) was in 14/15 isolates. Conclusion: Admitted orthopedic patients and the hospital environment act as a reservoir of ESBL-Ec with diverse STs and endowed with drug resistance and arsenals of virulence genes, calling for their routine screening on admission for mitigation of potential subsequent infections.

The routine genomic surveillance of pathogens in diverse geographical settings and equitable data sharing are critical to inform effective infection control and therapeutic development. The coronavirus disease 2019 (COVID-19) pandemic highlighted the importance of routine genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to detect emerging variants of concern. However, the majority of high-income countries sequenced >0.5% of their COVID-19 cases, unlike low- and middle-income countries. By the end of 2022, many countries around the world had managed to establish capacity for pathogen genomic surveillance. Notably, Beta and Omicron; 2 of the 5 current SARS-CoV-2 variants of concern were first discovered in Africa through an aggressive sequencing campaign led by African scientists. To sustain such infrastructure and expertise beyond this pandemic, other endemic pathogens should leverage this investment. Therefore, countries are establishing multi-pathogen genomic surveillance strategies. Here we provide a catalog of the current landscape of sequenced and publicly shared pathogens in different countries in Africa. Drawing upon our collective knowledge and expertise, we review the ever-evolving challenges and propose innovative recommendations.

Abstract Escherichia coli significantly causes nosocomial infections and rampant spread of antimicrobial resistance (AMR). There is limited data on genomic characterization of extended-spectrum β-lactamase (ESBL)-producing E. coli from African clinical settings. This hospital-based longitudinal study unraveled the genetic resistance elements in ESBL E. coli isolates from Uganda and Tanzania using whole-genome sequencing (WGS). A total of 142 ESBL multi-drug resistant E. coli bacterial isolates from both Tanzania and Uganda were sequenced and out of these, 36/57 (63.1%) and 67/85 (78.8%) originated from Uganda and Tanzania respectively. Mutations in RarD, yaaA and ybgl conferring resistances to chloramphenicol, peroxidase and quinolones were observed from Ugandan and Tanzanian isolates. We reported very high frequencies for bla CTX−M−15 with 11/18(61.1%), and bla CTX−M−27 with 12/23 (52.1%), bla TEM−1B with 13/23 (56.5%) of isolates originating from Uganda and Tanzania respectively all conferring resistance to Beta-lactam-penicillin inhibitors. We observed chloramphenicol resistance-conferring gene mdfA in 21/23 (91.3%) of Tanzanian isolates. Extraintestinal E. coli sequence type (ST) 131 accounted for 5/59 (8.4%) of Tanzanian isolates while enterotoxigenic E. coli ST656 was reported in 9/34 (26.4%) of Ugandan isolates. Virulence factors originating from Shigella dysenteriae Sd197 (gspC, gspD, gspE, gspF, gspG, gspF, gspH, gspI), Yersinia pestis CO92 (irp1, ybtU, ybtX, iucA), Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (csgF and csgG), and Pseudomonas aeruginosa PAO1 (flhA, fliG, fliM) were identified in these isolates. Overall, this study highlights a concerning prevalence and diversity of AMR-conferring elements shaping the genomic structure of multi-drug resistant E. coli in clinical settings in East Africa. It underscores the urgent need to strengthen infection-prevention controls and advocate for the routine use of WGS in national AMR surveillance and monitoring programs. Availability of WGS analysis pipeline: the rMAP source codes, installation, and implementation manual can free be accessed via https://github.com/GunzIvan28/rMAP .

Abstract Background Uganda remains one of the countries with the highest burden of TB/HIV. Drug-resistant TB remains a substantial challenge to TB control globally and requires new strategic effective control approaches. Drug resistance usually develops due to inadequate management of TB patients including improper treatment regimens and failure to complete the treatment course which may be due to an unstable supply or a lack of access to treatment, as well as patient noncompliance. Methods Two sputa samples were collected from Xpert MTB/RIF® assay-diagnosed multi-drug resistant tuberculosis (MDR-TB) patient at Lira regional referral hospital in northern Uganda between 2020 and 2021 for comprehensive routine mycobacterial species identification and drug susceptibility testing using culture-based methods. Detection of drug resistance-conferring genes was subsequently performed using whole-genome sequencing with Illumina MiSeq platform at the TB Supranational Reference Laboratory in Uganda. Results In both isolates, extensively drug-resistant TB (XDR-TB) was identified including resistance to Isoniazid (katG p.Ser315Thr), Rifampicin (rpoB p.Ser450Leu), Moxifloxacin (gyrA p.Asp94Gly), Bedaquiline (Rv0678 Glu49fs), Clofazimine (Rv0678 Glu49fs), Linezolid (rplC Cys154Arg), and Ethionamide (ethA c.477del). Further analysis of these two high quality genomes revealed that this 32 years-old patient was infected with the Latin American Mediterranean TB strain (LAM). Conclusions This is the first identification of extensively drug-resistant Mycobacterium tuberculosis clinical isolates with bedaquiline, linezolid and clofazimine resistance from Uganda. These acquired resistances were because of non-adherence as seen in the patient’s clinical history. Our study also strongly highlights the importance of combating DR-TB in Africa through implementing next generation sequencing that can test resistance to all drugs while providing a faster turnaround time. This can facilitate timely clinical decisions in managing MDR-TB patients with non-adherence or lost to follow-up.

Science education and research have the potential to drive profound change in low- and middle-income countries (LMICs) through encouraging innovation, attracting industry, and creating job opportunities. However, in LMICs, research capacity is often limited, and acquisition of funding and access to state-of-the-art technologies is challenging. The Alliance for Global Health and Science (the Alliance) was founded as a partnership between the University of California, Berkeley (USA) and Makerere University (Uganda), with the goal of strengthening Makerere University’s capacity for bioscience research. The flagship program of the Alliance partnership is the MU/UCB Biosciences Training Program, an in-country, hands-on workshop model that trains a large number of students from Makerere University in infectious disease and molecular biology research. This approach nucleates training of larger and more diverse groups of students, development of mentoring and bi-directional research partnerships, and support of the local economy. Here, we describe the project, its conception, implementation, challenges, and outcomes of bioscience research workshops. We aim to provide a blueprint for workshop implementation, and create a valuable resource for bioscience research capacity strengthening in LMICs.

BackgroundDental caries is a multifactorial disease that affects many people. Even though microorganisms play a crucial role in causing dental caries, diagnosis is routinely macroscopic. In order to improve early detection especially in HIV patients who are disproportionately affected, there is need to reconcile the macroscopic and microscopic characteristics of dental caries. Therefore, the aim of this study was to characterize the oral microbiota profile along the decayed, missing, filled teeth (DMFT) index using amplicon sequencing data.MethodsAmplicon sequencing of the V6-V8 region of the 16S rRNA gene was done on DNA recovered from whole unstimulated saliva of 59 HIV positive and 29 HIV negative individuals. The microbial structure, composition and co-occurrence networks were characterized using QIIME-2, Phyloseq, Microbiome-1.9.2 and Metacoder in R.ResultsWe characterized the oral microbiota into 2,093 operational taxonomic units (OTUs), 21 phyla and 239 genera from 2.6 million high quality sequence reads. While oral microbiota did not cluster participants into distinct groups that track with the DMFT index, we observed the following: (a) The proportion of accessory microbiota was highest in the high DMFT category while the core size (∼50% of richness) remained relatively stable across all categories. (b) The abundance of core genera such as Stomatobaculum, Peptostreptococcus and Campylobacter was high at onset of dental caries, (c) A general difference in oral microbial biomass. (d) The onset of dental caries (low DMFT) was associated with significantly lower oral microbial entropy.ConclusionsAlthough oral microbial shifts along the DMFT index were not distinct, we demonstrated the potential utility of microbiota dynamics to characterize oral disease. Therefore, we propose a microbial framework using the DMFT index to better understand dental caries among HIV positive people in resource limited settings.

Abstract 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 bla VIM 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. bla VIM was the most prevalent carbapenemase gene, and it was detected in all CRAB and CRPA isolates while bla OXA-23 and bla OXA-24 were detected in 29 and 24% of CRAB isolates, respectively. Co-carriage of bla OXA-23 and bla OXA-24 occurred in 14% of CRAB isolates. Moreover, 63% of the study isolates carried class 1 integrons; of these 31% successfully transferred bla VIM to E. coli J53. Conclusions CRAB and CRPA prevalence at the Mulago Hospital ICU is relatively low but carbapenemase genes especially bla VIM and bla OXA-23 are prevalent among them. This requires strengthening of infection control practices to curb selection and transmission of these strains in the hospital.

Abstract Background Nosocomial infections are a major setback in the healthcare delivery system especially in developing countries due to the limited resources. The roles played by medical care equipment and work surfaces in the transmission of such organisms have inevitably contributed to the elevated mortality, morbidity and antibiotic resistances. Methods A total 138 samples were collected during the study from Kawolo general hospital. Swab samples were collected from various work surfaces and fomites which consisted of; beds, sink taps, infusion stands, switches, work tables and scissors. Cultures were done and the susceptibility patterns of the isolates were determined using Kirby Bauer disc diffusion method. Data was analyzed using Stata 13 and Microsoft Excel 2013 packages. Results A total of 44.2% (61/138) of the collected swab specimens represented the overall bacterial contamination of the sampled articles. Staphylococcus aureus and Klebsiella pneumoniae accounted for the highest bacterial contaminants constituting of 75.4% (46/61) and 11.5% (7/61) respectively. Infusion stands and patient beds were found to have the highest bacterial contamination levels both constituting 19.67% (12/61). The highest degree of transmission of organisms to patients was found to be statistically significant for patient beds with OR: 20.1 and P-value 8X10− 4. Vancomycin, ceftriaxone and ciprofloxacin were the most effective antibiotics with 100%, 80% and 80% sensitivity patterns among the isolates respectively. Multi-drug resistant (MDR) Staphylococcus aureus accounted for 52% (24/46) with 4% (1/24) classified as a possible extensively drug resistant (XDR) whereas Gram negative isolates had 27% (4/15) MDR strains out of which 50%(2/4) were classified as possible pan-drug resistant (PDR). Conclusion The high prevalence of bacterial contaminants in the hospital work environment is an indicator of poor or ineffective decontamination. The study findings reiterate the necessity to formulate drug usage policies and re-examine effectiveness of decontamination and sterilization practices within Kawolo general hospital. We also recommend installation of a sound Microbiology unit at the hospital to take on susceptibility testing to check on the empirical use of antibiotics as a way of reducing the rampant elevations in drug resistances.

Abstract Background In Africa, health practitioners and the current knowledge of the public on genetics and genomics is still very low and yet this has potential to reduce the burden of common genetic diseases. Many initiatives have promoted genomic research, infrastructure, and capacity building in Africa. What remains to be done is to improve genomics literacy among populations and communities while utilizing an array of strategies. Genomic literacy and awareness are key in the management of genetic diseases which includes diagnosis, prevention of complications and therapy. Africa is characterized by great cultural and language diversity thereby requiring a multidisciplinary approach to improving public and community genomics literacy and engagement. However, this is further complicated by having the fact that sub‐Saharan Africa is comprised of countries with the lowest literacy rates in the world. Methods We applied the Preferred Reporting Items for Systematic Reviews and Meta‐Analyses guidelines to review genomic literacy in Africa using PubMed database. Results We found very limited evidence of genomics literacy for genetic diseases in Africa. Conclusion We propose a number of approaches that if adopted will significantly increase the genomic literacy and reduce the burden of genetic diseases in Africa.

Bacterial infections involving antibiotic-resistant gram-negative bacteria continue to increase and represent a major global public health concern. Resistance to antibiotics in these bacteria is mediated by chromosomal and/or acquired resistance mechanisms, these give rise to multi-drug resistant (MDR), extensive-drug resistant (XDR) or pan-drug resistant (PDR) bacterial strains. Most recently, plasmid-mediated resistance to colistin, an antibiotic that had been set apart as the last resort antibiotic in the treatment of infections involving MDR, XDR and PDR gram-negative bacteria has been reported. Plasmid-mediated colistin resistant gram-negative bacteria have been described to be PDR, implying a state devoid of alternative antibiotic therapeutic options. This review concisely describes the evolution of antibiotic resistance to plasmid-mediated colistin resistance and discusses the potential role of high-throughput sequencing technologies, genomics, and bioinformatics towards improving antibiotic resistance surveillance, the search for novel drug targets and precision antibiotic therapy focused at combating colistin resistance, and antibiotic resistance as a whole.

Antimicrobial Resistance (AMR) and Healthcare Associated Infections (HAIs) are major global public health challenges in our time. This study provides a broader and updated overview of AMR trends in surgical wards of Mulago National Referral Hospital (MNRH) between 2014 and 2018. Laboratory data on the antimicrobial susceptibility profiles of bacterial isolates from 428 patient samples were available. The most common samples were as follows: tracheal aspirates (36.5%), pus swabs (28.0%), and blood (20.6%). Klebsiella (21.7%), Acinetobacter (17.5%), and Staphylococcus species (12.4%) were the most common isolates. The resistance patterns for different antimicrobials were: penicillins (40–100%), cephalosporins (30–100%), β-lactamase inhibitor combinations (70–100%), carbapenems (10–100%), polymyxin E (0–7%), aminoglycosides (50–100%), sulphonamides (80–100%), fluoroquinolones (40–70%), macrolides (40–100%), lincosamides (10–45%), phenicols (40–70%), nitrofurans (0–25%), and glycopeptide (0–20%). This study demonstrated a sustained increase in resistance among the most commonly used antibiotics in Uganda over the five-year study period. It implies ongoing hospital-based monitoring and surveillance of AMR patterns are needed to inform antibiotic prescribing, and to contribute to national and global AMR profiles. It also suggests continued emphasis on infection prevention and control practices (IPC), including antibiotic stewardship. Ultimately, laboratory capacity for timely bacteriological culture and sensitivity testing will provide a rational choice of antibiotics for HAI.

HIV/AIDS, tuberculosis (TB), and malaria are 3 major global public health threats that undermine development in many resource-poor settings. Recently, the notion that positive selection during epidemics or longer periods of exposure to common infectious diseases may have had a major effect in modifying the constitution of the human genome is being interrogated at a large scale in many populations around the world. This positive selection from infectious diseases increases power to detect associations in genome-wide association studies (GWASs). High-throughput sequencing (HTS) has transformed both the management of infectious diseases and continues to enable large-scale functional characterization of host resistance/susceptibility alleles and loci; a paradigm shift from single candidate gene studies. Application of genome sequencing technologies and genomics has enabled us to interrogate the host-pathogen interface for improving human health. Human populations are constantly locked in evolutionary arms races with pathogens; therefore, identification of common infectious disease-associated genomic variants/markers is important in therapeutic, vaccine development, and screening susceptible individuals in a population. This review describes a range of host-pathogen genomic loci that have been associated with disease susceptibility and resistant patterns in the era of HTS. We further highlight potential opportunities for these genetic markers.

The routine genomic surveillance of pathogens in diverse geographical settings and equitable data sharing are critical to inform effective infection control and therapeutic development. The coronavirus disease 2019 (COVID-19) pandemic highlighted the importance of routine genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to detect emerging variants of concern. However, the majority of high-income countries sequenced >0.5% of their COVID-19 cases, unlike low- and middle-income countries. By the end of 2022, many countries around the world had managed to establish capacity for pathogen genomic surveillance. Notably, Beta and Omicron; 2 of the 5 current SARS-CoV-2 variants of concern were first discovered in Africa through an aggressive sequencing campaign led by African scientists. To sustain such infrastructure and expertise beyond this pandemic, other endemic pathogens should leverage this investment. Therefore, countries are establishing multi-pathogen genomic surveillance strategies. Here we provide a catalog of the current landscape of sequenced and publicly shared pathogens in different countries in Africa. Drawing upon our collective knowledge and expertise, we review the ever-evolving challenges and propose innovative recommendations.

The routine genomic surveillance of pathogens in diverse geographical settings and equitable data sharing are critical to inform effective infection control and therapeutic development. The coronavirus disease 2019 (COVID-19) pandemic highlighted the importance of routine genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to detect emerging variants of concern. However, the majority of high-income countries sequenced >0.5% of their COVID-19 cases, unlike low- and middle-income countries. By the end of 2022, many countries around the world had managed to establish capacity for pathogen genomic surveillance. Notably, Beta and Omicron; 2 of the 5 current SARS-CoV-2 variants of concern were first discovered in Africa through an aggressive sequencing campaign led by African scientists. To sustain such infrastructure and expertise beyond this pandemic, other endemic pathogens should leverage this investment. Therefore, countries are establishing multi-pathogen genomic surveillance strategies. Here we provide a catalog of the current landscape of sequenced and publicly shared pathogens in different countries in Africa. Drawing upon our collective knowledge and expertise, we review the ever-evolving challenges and propose innovative recommendations.

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: 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.

Bacterial infections involving antibiotic resistant gram-negative bacteria continue to increase and represent a major global public health concern. Resistance to antibiotics in these bacteria is mediated by chromosomal and/or acquired resistance mechanisms, these give rise to multi-drug resistant (MDR) or extensive drug resistant (XDR) bacterial strains. Most recently, a novel acquired plasmid mediated resistance mechanism to colistin, an antibiotic that had been set apart as the last resort antibiotic in the treatment of infections involving MDR and XDR gram-negative bacteria, has been reported. Plasmid mediated colistin resistant gram-negative bacteria have been described to be pan-drug resistant, implying a state devoid of alternative antibiotic therapeutic options. This review describes the evolution of antibiotic resistance to plasmid mediated colistin resistance, and discusses the potential role of high-throughput sequencing technologies, genomics and bioinformatics towards improving antibiotic resistance surveillance, the search for novel drug targets and precision antibiotic therapy focused at combating colistin resistance, and antimicrobial resistance as a whole.