Masters Degrees (Medical Microbiology)

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Browsing Masters Degrees (Medical Microbiology) by Subject "Antibiotic resistance"

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    The carriage of antibiotic resistant Gram-negative organisms in children in the Cape Town community and the impact of antibiotic exposure on the development of resistance (a TB-CHAMP sub-study)
    (Stellenbosch : Stellenbosch University, 2019-12) Ocloo, Remous; Whitelaw, Andrew; Newton-Foot, Mae; Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Pathology. Medical Microbiology.
    Introduction Antibiotic resistance has become a major issue across the globe and the situation is worsening in low- and middle-income countries. In sub-Saharan Africa and the world at large, antibiotic resistance research is localized and focused on hospitalized individuals. There is, therefore, little or no data on antibiotic resistance in the community; especially in children. This study described the carriage of resistant isolates in children in Cape Town and investigated the effects of antibiotic exposure on the development of resistance in stool using an in-vitro model. Materials and Methods Stool samples from fifty participants of the Tuberculosis Child Multidrug-resistant Preventive Therapy Trial (TB-CHAMP) were cultured onto McConkey agar (MCC) with the addition of ertapenem and cefpodoxime discs to select for carbapenem and cephalosporin-resistant and susceptible E. coli and Klebsiella isolates. Antibiotic susceptibility testing was performed using Kirby Bauer disk diffusion. Carbapenem-, quinolone- and cephalosporin-resistance genes were detected by PCR and resistance-conferring mutations were detected using Sanger sequencing. Ten stool samples were exposed to two sub-clinical concentrations of amoxicillin, ciprofloxacin and colistin for 48 hours, whereafter they were plated onto MCC with the addition of various antibiotic discs (amoxicillin, ertapenem, ciprofloxacin, colistin, cefotaxime and nalidixic acid). The impact of antibiotic exposure on the development of resistance was assessed by enumeration of presumptive resistant E. coli and Klebsiella colonies within the zones of inhibition around the antibiotic discs. Results Twenty-one (42%) of the participants were colonized by quinolone-resistant isolates and 18 (36%) by cephalosporin-resistant isolates (predicted ESBL-producing organisms). Of the 21 quinolone-resistant E. coli isolates, 5 (24%) harbored qnrS while of the 6 quinolone-resistant Klebsiella isolates, 4 (67%) had qnrB. The most common quinolone resistance mutations were S83L in gyrA and S80I, A141V and S129A in parC. blaCTX-M was the only ESBL gene detected. All of the blaSHV and blaTEM genes detected were β-lactamases without extended spectrum activity. One of the participants was colonized by a carbapenem resistant Klebsiella isolate, which carried the blaNDM carbapenemase gene. Exposure of the stool samples to ciprofloxacin selected for resistant bacteria, however exposure to amoxicillin and colistin did not. Conclusion Children in Cape Town are frequently colonized by resistant bacteria and are at risk of becoming infected by these resistant organisms. The presence of plasmid-mediated resistance genes is concerning because they can be transferred between bacteria of the same and different species. There is also a need to further investigate what might be driving the high prevalence of quinolone resistance in the community. This study is the first to report the carriage of carbapenemase resistant bacteria in healthy children in South Africa. Although the in-vitro antibiotic exposure model was crude, the approach provides some evidence for the development of resistance during exposure to sub-clinical concentrations of antibiotics (especially ciprofloxacin); and notably, to agents other than those to which the sample had been exposed. This highlights the need for further investigations into the impact of sublethal antibiotic concentrations on the selection of resistance.
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    Characterisation of fosfomycin resistance in urinary pathogens from the Western Cape, South Africa.
    (Stellenbosch : Stellenbosch University, 2021-03) Mosime, Lesedi Bridget; Nel, Pieter; Newton-Foot, Mae; Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Pathology.
    ENGLISH ABSTRACT: Introduction: Urinary tract infections (UTI) are the most commonly acquired bacterial infections worldwide. The South African Department of Health advised that fosfomycin, nitrofurantoin and gentamicin be used for the treatment of uncomplicated UTI due to other antibiotics showing adverse side effects. Fosfomycin has effectively been utilised in the management of UTI, however resistance has been detected in urinary pathogens at the Tygerberg Hospital National Health Laboratory Service (NHLS) Medical Microbiology diagnostic laboratory. This study aimed to determine the prevalence of fosfomycin resistance among community-acquired urinary pathogens in the Western Cape and to characterise fosfomycin resistance mechanisms in fosfomycin resistant Escherichia coli and Klebsiella pneumoniae isolates. Methods and Materials: Two-hundred urinary isolates (Enterobacterales and Enterococcus spp.) from antenatal clinics in the Western Cape were collected from the Tygerberg Hospital NHLS Medical Microbiology laboratory during 2019 and 2020 and used to determine the prevalence of fosfomycin resistance. Fosfomycin susceptibility was determined using disc diffusion and Etest®. Fosfomycin resistant E. coli and K. pneumoniae isolates from the prevalence study and another set of fosfomycin resistant isolates (5 E. coli and 19 K. pneumoniae) collected from urine samples submitted to the NHLS at Tygerberg Hospital in 2017 (Ethics #: U17/05/026) were used to characterise fosfomycin mechanisms. FosA mediated resistance was determined using a phenotypic assay and fosA genes were detected by PCR. Mutations in the fosfomycin target gene murA and transporter genes, glpT and uhpT, were characterised by polymerase chain reaction (PCR) and Sanger sequencing. Results: Fosfomycin resistance was detected in 3.5% of community-acquired urinary pathogens. Fosfomycin resistance rates were 2.2% in E. coli (3/139) and 12.9% in other Enterobacterales. All Enterococcus spp. isolates were susceptible to fosfomycin. In the combined sample set of 31 fosfomycin resistant isolates, the phenotypic assay detected FosA in only 7 isolates, while fosA genes were detected by PCR in 25. Chromosomal mutations were identified in 6 isolates, of which three isolates (1 K. pneumoniae and 2 E. coli) had deletions in the uhpT gene, which has previously been reported to confer fosfomycin resistance. The role of other mutations found in the glpT gene of E. coli and the murA and glpT of K. pneumoniae isolates has not been determined. Conclusion: The fosfomycin resistance rate in community-acquired UTI was low, which supports the careful ongoing use of fosfomycin for the treatment of uncomplicated community-acquired UTI. FosA mediated resistance was the most common mechanism of fosfomycin resistance identified in this population.