Molecular characterization and distribution of cephalosporin resistance determinants in Escherichia coli and Klebsiella pneumoniae isolated from patients attending Kampala International University Teaching Hospital in Bushenyi, Western Uganda

Cephalosporins are the first-line therapy antibiotics used in the treatment of gram-negative bacterial infections. However, high prevalence of cephalosporins resistance in Klebsiella pneumoniae and Escherichia coli has been reported worldwide. Studies conducted in Uganda reported high incidences of cephalosporin resistance (CR). Successive studies at Mulago National Referral Hospital indicated a decline in the resistance levels pointing to the need for regular antibiotic resistance surveillance. Therefore, this study carried out molecular characterization of CR determinants in E. coli and K. pneumoniae isolated from patients attending Kampala International University Teaching Hospital (KIU-TH). A retrospective study using E. coli and K. pnuemoniae samples previously obtained from surgical wounds and urinary tract infections among patients treated at KIU-TH between September 2016 and August 2018 was conducted. Biochemical assays were used to confirm the identity of the samples. Combined disc and boronic acid assays were used to determine the cephalosporine resistance profile of the isolates. Multiplex PCR amplification was used to characterize the extended spectrum betalactmase (ESBL) encoding genes. The study revealed that E. coli (130/81.2%) isolates were more predominant than K. pneumoniae (30/18.8%) among the archived samples. K. pneumoniae showed the highest phenotypic resistance with a mean prevalence of 90.6% but comparable to that of E. coli (89.3%). Of the 160 isolates screened, 105 (65.6%) were ESBL producers. Multiplex PCR revealed that the most predominant ESBL encoding gene was blaSHV at a prevalence of 42.0%, followed by blaTEM at 27.3%, blaCTX-M at 22.4% and blaCTX-M-15 at 8.4%. The incidence of phenotypic resistance and distribution of ESBL genes were significantly higher in patients of Ishaka division. Our study reports a high prevalence of cephalosporin-resistant E. coli and K. pnuemoniae isolated from patients attending KIU-TH and highlights the need forr routine screening of antimicrobial resistance in health-care facilities so as to guide clinicians on the rational prescription of antibiotics.List of abbreviations: ATCC: American Type Culture Collection; ESBL: extended spectrum betalactmases; AmpC: aminopenicillin cephalosporinase; CTX-M: cephotaxime (M-first detected in Munich) hydrolyzing capabilities; CTX-M-U: cephotaxime hydrolyzing capabilities gene Universal primer; SHV: sulfhydryl variables (variant-2); CMY-2: cephamycins (variant-2); TEM: temoneira; ACT-1: AmpC type (variant-1); Bla: Beta lactam; DNA: deoxyribonucleic acid; PCR: Polymerase chain reaction; MNRH: Mulago National Referral Hospital; MRRH: Mbarara Regional Referral Hospital; KRRH: Kabale Regional Referral Hospital (KRRH); KIU-TH: Kampala International University Teaching Hospital; CDL: Central Diagnostic Laboratory; CoVAB: College of Veterinary Medicine, Animal Resources and Biosecurity; CR: cephalosporin resistanc

Antimicrobial resistance of Salmonella enterica in pork and vegetable servings at pork joints in Kampala, Uganda

The aim of this study was to investigate the prevalence and antimicrobial resistance of Salmonella enterica subsp. enterica serovars including the presence of shared plasmids in pork and related fresh vegetables served in pork joints in Kampala, Uganda. Pork butcheries in three of the five administrative divisions of Kampala were included for the survey. Samples included raw pork, roasted pork, water, onions, tomatoes, cabbage, butcher’s hands (swabs), utensils (swabs) and fly midgut extracts. A total of 693 samples were collected from 77 pork butcheries from June- October 2014. Overall 53.2% pork joints had samples positive for Salmonella enterica subsp. enterica serovars. Isolation rates ranged from 31.2% (24/77) for raw pork, 1.3% (1/77) for roasted pork, 7.8% (6/77) for tomatoes, 2.6% (2/77) for onions, 5.2% (4/77) for cabbage, 9.1% (7/77) in water, and 22.1% (17/77) from fly midguts. Swab samples taken from utensil and butcher’s hands swabs were found negative (Heilmann et al., 2015). In the isolates obtained, resistance towards 22 antibiotics was tested. Resistances were found towards 11 out of the 22 antibiotics tested. High resistances were found to Cephazolin (97%), Cefotixime (93%), Gentamicin (88%), and Ceftazidime (86%). Intermediate resistance was found to Ciprofloxacin (59%) and Amoxicillin-Clavulanic acid (57.6%). Most isolates (85%) were susceptible to Levofloxacin, Ofloxacin, Sulfamethoxazole and Trimethoprim. Identification of plasmids by PCR-based replicon typing was performed recognizing FIA,FIB,FIC,HI1,HI2,I1- 1ᵞ,L/M,N,P,W,T,A/C,K,B/O,X,Y,F and FIIA. Six incompatibility groups were identified: FIA, W, FIC, FIB, P, Y with more than one incompatibility group existing among different isolates. A high resistance rate among Salmonella strains was found while the total number of incompatibility groups detected was with approximation 2.4. Thus, even though the total number of plasmids per strain is low, resistance rates detected remain high. The high resistance rates are probably resulting from intensified food animal production driving a greater use of antibiotics, which is a crucial aspect of public health concern

A review of phage mediated antibacterial applications

Background: For over a decade, resistance to newly synthesized antibiotics has been observed worldwide. The challenge of antibiotic resistance has led to several pharmaceutical companies to abandon the synthesis of new drugs in fear of bacteria developing resistance in a short period hence limiting initial investment return. To this effect, alternative approaches such as the use of bacteriophages to treat bacterial infections are being explored. This review explores the recent advances in phage-mediated antibacterial applications and their limitations.Methods: We conducted a comprehensive literature search of PubMed, Lib Hub and Google Scholar databases from January 2019 to November 2019. The search key words used were the application of bacteriophages to inhibit bacterial growth and human phage therapy to extract full-text research articles and proceedings from International Conferences published only in English.Results: The search generated 709 articles of which 95 full-text research articles fulfilled the inclusion guidelines. Transmission Electron Microscopy morphological characterization conducted in 23 studies registered Myoviruses, Siphoviruses, Podoviruses, and Cytoviruses phage families while molecular characterization revealed that some phages were not safe to use as they harbored undesirable genes. All in vivo phage therapy studies in humans and model animals against multidrug-resistant (MDR) bacterial infection provided 100% protection. Ex vivo and in vitro phage therapy experiments exhibited overwhelming results as they registered high efficacies of up to 100% against MDR clinical isolates. Phage-mediated bio-preservation of foods and beverages and bio-sanitization of surfaces were highly successful with bacterial growth suppression of up to 100%. Phage endolysins revealed efficacies statistically comparable to those of phages and restored normal ethanol production by completely eradicating lactic acid bacteria in ethanol fermenters. Furthermore, the average multiplicity of infection was highest in ex vivo phage therapy (557,291.8) followed by in vivo (155,612.4) and in vitro (434.5)

Phylogenetic Characterization of Crimean-Congo Hemorrhagic Fever Virus Detected in African Blue Ticks Feeding on Cattle in a Ugandan Abattoir.

Crimean-Congo hemorrhagic fever virus (CCHFV) is the most geographically widespread of the tick-borne viruses. However, African strains of CCHFV are poorly represented in sequence databases. In addition, almost all sequence data collected to date have been obtained from cases of human disease, while information regarding the circulation of the virus in tick and animal reservoirs is severely lacking. Here, we characterize the complete coding region of a novel CCHFV strain, detected in African blue ticks (Rhipicephalus (Boophilus) decoloratus) feeding on cattle in an abattoir in Kampala, Uganda. These cattle originated from a farm in Mbarara, a major cattle-trading hub for much of Uganda. Phylogenetic analysis indicates that the newly sequenced strain belongs to the African genotype II clade, which predominantly contains the sequences of strains isolated from West Africa in the 1950s, and South Africa in the 1980s. Whilst the viral S (nucleoprotein) and L (RNA polymerase) genome segments shared >90% nucleotide similarity with previously reported genotype II strains, the glycoprotein-coding M segment shared only 80% nucleotide similarity with the next most closely related strains, which were derived from ticks in Western India and Northern China. This genome segment also displayed a large number of non-synonymous mutations previously unreported in the genotype II strains. Characterization of this novel strain adds to our limited understanding of the natural diversity of CCHFV circulating in both ticks and in Africa. Such data can be used to inform the design of vaccines and diagnostics, as well as studies exploring the epidemiology and evolution of the virus for the establishment of future CCHFV control strategies

Phylogenetic Characterization of Crimean-Congo Hemorrhagic Fever Virus Detected in African Blue Ticks Feeding on Cattle in a Ugandan Abattoir.

Crimean-Congo hemorrhagic fever virus (CCHFV) is the most geographically widespread of the tick-borne viruses. However, African strains of CCHFV are poorly represented in sequence databases. In addition, almost all sequence data collected to date have been obtained from cases of human disease, while information regarding the circulation of the virus in tick and animal reservoirs is severely lacking. Here, we characterize the complete coding region of a novel CCHFV strain, detected in African blue ticks (Rhipicephalus (Boophilus) decoloratus) feeding on cattle in an abattoir in Kampala, Uganda. These cattle originated from a farm in Mbarara, a major cattle-trading hub for much of Uganda. Phylogenetic analysis indicates that the newly sequenced strain belongs to the African genotype II clade, which predominantly contains the sequences of strains isolated from West Africa in the 1950s, and South Africa in the 1980s. Whilst the viral S (nucleoprotein) and L (RNA polymerase) genome segments shared >90% nucleotide similarity with previously reported genotype II strains, the glycoprotein-coding M segment shared only 80% nucleotide similarity with the next most closely related strains, which were derived from ticks in Western India and Northern China. This genome segment also displayed a large number of non-synonymous mutations previously unreported in the genotype II strains. Characterization of this novel strain adds to our limited understanding of the natural diversity of CCHFV circulating in both ticks and in Africa. Such data can be used to inform the design of vaccines and diagnostics, as well as studies exploring the epidemiology and evolution of the virus for the establishment of future CCHFV control strategies

A retrospective analysis of antimicrobial resistance in pathogenic Escherichia coli and Salmonella spp. isolates from poultry in Uganda

There are increasing reports of antimicrobial treatment failures for bacterial diseases of poultry in Uganda. The paucity of data on antimicrobial resistance (AMR) of pathogenic bacteria in Uganda is a major setback to AMR control. This study investigated the occurrence of fowl typhoid, colibacillosis, and AMR in associated pathogens from 2012 to 2018. Laboratory records from the Central Diagnostic Laboratory (CDL), a National Veterinary Diagnostic Facility located at Makerere University, were reviewed. Archived isolates of the causative bacteria for the two diseases were also evaluated for AMR. The frequencies of the two disease conditions, their clinical and necropsy presentations and the demographic data of the diagnostic samples were summarized from the records. Archived bacterial isolates were revived before antimicrobial susceptibility testing. This was done on Mueller Hinton agar using the disk diffusion method, against 16 antimicrobials of medical and veterinary importance according to the Clinical Laboratory Standards Institute guidelines. A total of 697 poultry cases were presented for bacteriological investigations in the review period. Colibacillosis and salmonellosis had prevalence rates of 39.7% (277/697) and 16.2% (113/697), respectively. A total of 63 and 92 isolates of Escherichia coli and Salmonella spp., respectively, were archived but 43 (68.3%) E. coli and 47 (51.1%) Salmonella spp. isolates were recovered and evaluated for AMR. Multidrug resistance was more frequent in E. coli (38; 88.4%) than salmonellae (25; 53.2%), (p < 0.001). The high prevalence of colibacillosis, salmonellosis and the AMR of associated pathogens warrants immediate institution of appropriate disease control measures

Antimicrobial use and antimicrobial resistance in broiler farms in peri-urban Wakiso, Uganda

Objective: A cross sectional study was carried out to 1) describe the antimicrobial use patterns among poultry farmers in Wakiso 2) establish resistant profiles of Salmonella, E. coli and Enterococci among poultry farms in Wakiso. Methods: A cross sectional study in Wakiso district was carried out in October and November 2021 for a period of 6 weeks. A semi structured questionnaire was used to collect data on antimicrobial use on the farms. Boot sock sampling was used to collect samples from the whole poultry house. A composite sample of faecal material was also collected from the poultry house. The information on antimicrobial use is being analyzed for descriptive statistics. The faecal samples were cultured in the laboratory for Isolation of Salmonella, E. coli and Enterococci. The Isolates will further be tested to establish their resistant profiles. The composite sample was used to quantify resistant coliforms against cefotaxime and colistin Results: A total of 200 poultry farms in Wakiso were visited, 211 boot sock samples and 211 composite samples were collected. 29.85% of the respondents were male while 70.15% were female.37.38% had attained secondary level of education. There was observed widespread use of antimicrobials on the farms for treatment of different conditions as well as prevention of disease. The most used groups of antibiotics were, Penicillins, Tetracyclines and Aminoglycosides while Sulphonamides were the least used. From the laboratory analysis, out of the 211 samples collected, Salmonella was isolated at a rate of 8.5%, E. coli at 77.3% and Enterococcus at 62.6%. Resistant coliforms to cefotaxime (5I.7%) and colistin (45.5%) were also identified. Conclusion: There are indications of resistant coliforms among poultry farms in Wakiso. This is attributed to the observed continuous use of antibiotics on the poultry farms. There is need to improve antimicrobial use among farmers. Proper diagnosis of conditions is one possible way that will reduce the use of different antibiotics at farm level

A survey of biosecurity practices of pig farmers in selected districts affected by African swine fever in Uganda

IntroductionIn Uganda, pig production is an important source of livelihood for many people and contributes to food security. African swine fever (ASF) is a major constraint to pig production in Uganda, threatening the food supply and sustainable livelihoods. Prevention of ASF primarily relies on good biosecurity practices along the pig value chain. Previous studies showed that biosecurity along the pig value chain and on farms in Uganda is poor. However, the biosecurity practices of pig farmers in ASF affected areas of Uganda and their opinions on on-farm ASF morbidity and mortality were previously not comprehensively characterized. The objectives of this study were to document pig farmers’ experiences with ASF in their farms and to describe the pig biosecurity practices in districts of Uganda that were highly affected by ASF.MethodsA total of 99 farmers were interviewed in five districts. Data were collected by way of triangulation through farmer interviews, field observations during the farmer interviews, and a survey of key informants. However, farmer interviews were considered the primary source of data for this study. Farmers’ biosecurity practices were scored using a biosecurity scoring algorithm.ResultsForty-one out of 96 (42.7%) farmers reported having pigs with ASF in the past 12 months. The level of pig farming experience (p = 0.0083) and herd size (p &lt; 0.0001) were significantly associated with the reported occurrence of ASF. Overall, the biosecurity scores for the respondents were considered poor with 99% (98/99) scoring &lt;70% and just one farmer obtaining a fair score of 72.2%. District (p = 0.0481), type of husbandry system (p = 0.014), and type of pig breed raised (p = 0.004) were significantly associated with farmer’s biosecurity score.ConclusionContinued farmer education on ASF and the importance of good biosecurity practices is necessary. More in-depth scientific inquiry into the factors influencing the biosecurity practices among pig farmers in Uganda is necessary