Doctoral Degrees (Medical Microbiology)

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Browsing Doctoral Degrees (Medical Microbiology) by browse.metadata.advisor "Newton-Foot, Mae"

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    Colistin resistance in gram-negative pathogens in the Western Cape, South Africa
    (Stellenbosch : Stellenbosch University, 2021-12) Snyman, Yolandi; Newton-Foot, Mae; Whitelaw, Andrew Christopher; Maloba, Motlatji Reratilwe Bonnie; Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Pathology: Division of Medical Microbiology.
    ENGLISH ABSTRACT: Background Antimicrobial resistance is a public health concern and injudicious antibiotic prescribing and inadequate infection control practices have left the global community with untreatable multidrugresistant (MDR) bacteria. Colistin is a last resort antibiotic used to treat infections with MDR Gramnegative bacteria (GNB), especially carbapenem-resistant GNB. Therefore, the emergence of colistin resistance is a serious problem. This study from the Western Cape, South Africa, describes colistin resistance mechanisms in colistin-resistant GNB isolates from clinical specimens from various hospitals, stool samples from healthy children in the community, and river and storm water. Methods Colistin-resistant GNB isolates from clinical specimens from different healthcare facilities were collected from the NHLS microbiology laboratory at Tygerberg Hospital during 2016 and 2017. Fifty stool samples from healthy children (≤ 5 year of age) in the Cape Town metropolitan were collected between November 2017 and August 2018, and three surface water sources and stormwater were collected in 2019 and 2020. Selective media was used to isolate colistin-resistant GNB from the stool and water samples. Colistin resistance was confirmed using broth microdilution (BMD). The mobile colistin resistance genes, mcr-1-9, were detected by PCR and whole-genome sequencing (WGS). In selected mcr-negative isolates chromosomal colistin resistance mutations were identified by WGS. Strain typing was performed by WGS (MLST and SNP analyses) and repPCR. The functionality of mcr genes with unknown colistin resistance profiles was determined by BMD following recombinant expression or plasmid curing. Results mcr-1 was present in 55% (12/22) of Escherichia coli and 71% (5/7) of Klebsiella spp. isolates from patients at various hospitals during 2016-2017. pmrB mutations were identified in 8/10 mcrnegative E. coli and mgrB was disrupted in the two mcr-negative Klebsiella spp. isolates. Most colistin-resistant GNB isolated from hospitalised patients in 2016 and 2017 were unrelated, however, some clonal relatedness was observed in the 2017 E. coli population and a clonal expansion of an emerging colistin-resistant MDR Acinetobacter baumannii strain was noted among isolates from 2017. No previously described colistin resistance mechanism was detected in the A. baumannii isolates, but a possible novel mechanism was described. mcr-4.3 was detected in a Stellenbosch University https://scholar.sun.ac.za iii single Acinetobacter nosocomialis isolate, although recombinant mcr-4.3 did not confer colistin resistance in E. coli, plasmid curing of the mcr-4.3-containing plasmid restored colistin susceptibility. Colistin-resistant E. coli were isolated from the stools of two healthy children from the community (4%, 2/50) during 2017-2018; however, mcr genes were not detected. Colistin-resistant GNB, mainly Aeromonas spp., and mcr-5.1 and/or various mcr-3 variants were detected in the Plankenburg river, Eerste river, and Berg river and stormwater from Muizenberg and Fish Hoek in 2019 and 2020. Of the colistin-resistant Aeromonas spp. isolated from the Berg river, 25% (6/24) contained five novel mcr-3 variants, which were confirmed to confer colistin resistance. Conclusion The emergence of colistin resistance mechanisms in diverse strains obtained from hospital patients, with the limited gastrointestinal carriage of colistin-resistant Enterobacterales in community children and the disparate colistin-resistant species and mechanisms in the environment, suggest that selective pressure, and not community transmission, is the main driver of colistin resistance in clinical settings.
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    Exploring the gut microbiome of children from Cape Town communities
    (Stellenbosch : Stellenbosch University, 2021-12) Van Zyl, Kristien Nel; Newton-Foot, Mae; Whitelaw, Andrew Christopher; Stellenbosch University. Faculty of Science. Dept. Department of Pathology. Medical Microbiology.
    ENGLISH ABSTRACT: Despite the increase in microbiome investigations in the last decade, descriptions of the microbiota remain limited in developing countries, particularly in children. Little is known about the gut microbiota of young children in South Africa and there is a need for investigations of the composition and diversity of microbiota and the influence of demographic, clinical, and environmental factors on the microbiota in this setting. This study formed part of the ongoing Tuberculosis child multidrug-resistant preventive therapy (TB-CHAMP) clinical trial, which aims to determine the efficacy and safety of levofloxacin preventive therapy in a cohort of children <5 years exposed to multidrug-resistant tuberculosis in the household. This sub-study explored the composition, diversity, and factors influencing the baseline bacterial and fungal gut microbiota of these children, prior to randomisation into treatment or placebo arms. A pilot study was performed to assess the effect of stool sample storage and transport conditions on the microbiota and to develop a practical DNA extraction standard operating procedure for the remainder of the sub-study and future microbiome studies in this setting. Quantitative PCR showed that the gut microbiota was not affected by storage and transport conditions common to this setting. Targeted 16S rRNA and internal transcribed spacer 1 gene sequencing was performed on the Illumina platform to characterise the bacterial and fungal microbiota. The bacterial microbiota of young children from Cape Town communities were shown to be similar to those in children from developing countries and age was the main driver of differences in both bacterial and fungal communities. While the risk for dysbiosis was shown to be low overall, recent antibiotic use and household pollution were associated with reduced bacterial diversity. The inconsistent detection and abundance of fungi even in participants of the same age, highlighted the need for expanded research, including dietary and longitudinal analysis. The need for longitudinal analysis in paediatric populations was further emphasised by a systematic review on the effects of antibiotics on the microbiome, particularly in populations who are at risk for increased antibiotic exposure. The findings also demonstrated the population and target site-specific responses of the microbiome to antibiotics, which underlined the need for individual evaluation of the effect of antibiotics on the gut microbiome. This study set the groundwork for future investigations in the TB-CHAMP cohort, including the temporal development and stability of the gut microbiome in these children, and the impact of levofioxacin preventive therapy on the microbiota and resistance reservoirs in the gut.