Masters Degrees (Medical Microbiology)

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Browsing Masters Degrees (Medical Microbiology) by Author "Cloete, Stephanie Simone"

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    The characterization of antimicrobial resistance and virulence in Coagulase-Negative Staphylococci isolated from neonatal blood cultures in the Western Cape
    (Stellenbosch : Stellenbosch University, 2023-03) Cloete, Stephanie Simone; Whitelaw, Andrew Christopher; Matukane, Siphiwe Ruthy; Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Pathology: Division of Medical Microbiology.
    ENGLISH SUMMARY: Introduction: Coagulase-Negative Staphylococci (CoNS) are frequently isolated from the neonatal intensive care unit. However, it is difficult to discriminate between invasive CoNS and coincident contaminants since they are commensals of skin, and the nonspecific clinical signs of neonatal sepsis may be even more subtle due to the low virulence of CoNS. The extensive range of virulence factors in CoNS, some of which may be regulated by mobile genetic elements, contributes to their pathogenicity. This study aims to describe the species distribution, antimicrobial resistance, and molecular virulence markers in CoNS from neonatal blood cultures to identify potential pathogenicity markers. Methods: Between February and July 2021, 127 CoNS isolates were collected from neonatal blood cultures submitted to Tygerberg Hospital National Health Laboratory Services microbiology laboratory. Species identification was performed on all isolates using MALDI-TOF mass spectrometry. Antimicrobial susceptibility testing (AST) using Kirby Bauer disc diffusion was performed on 82 isolates representing the two predominant CoNS species from the most represented hospitals. Twenty isolates, representing a range of susceptibility patterns, were chosen for Oxford Nanopore whole genome sequencing (WGS). The assembled genomes were analysed using the Center for Genomic Epidemiology, pubMLST, Virulence Factor Database, ISsaga, and Resistance Gene Identifier. Reverse-transcription real-time PCR was used to explore the potential association of insertion sequence (IS)256 with the expression of the biofilm associated virulence gene icaA. The icaA normalised cycle threshold (ΔCt) was calculated relative to that of the house-keeping gene (tpi). Results: The most common species identified were Staphylococcus epidermidis (80/127, 63 %) and Staphylococcus hominis (29/127, 23 %). Among the 62 S. epidermidis and 20 S. hominis isolates selected for AST, 81.7 % (67/82) were non-susceptible to at least one antibiotic, and 54 % (44/82) were resistant to three or more antibiotic classes (multidrug resistant). The highest rates of resistance were to erythromycin (64.6%), trimethoprim-sulfamethoxazole (56.1 %), and cloxacillin (54.9 %). There was considerable concordance between the observed phenotypes and the predicted genotype, especially for cefoxitin, linezolid and vancomycin. The WGS data predicted all 20 isolates (14 S. epidermidis and six S. hominis isolates) as possible human pathogens, with a probability pathogen score higher for S. epidermidis (=0.93) than S. hominis (=0.89) isolates (p<0.001). In-silico MLST revealed substantial diversity, reflected by nine S. epidermidis sequence types identified. The ica operon was present in 10/14 S. epidermidis isolates, and 7/14 isolates contained the IS256. None of the S. hominis isolates contained the ica operon. The ΔCt values in isolates with and without IS256 were not significantly different, suggesting that IS256 was not related to ica operon expression. Conclusion: There was a high-level of genetic diversity among CoNS isolates, enriched with virulence factors, antimicrobial resistance genes and mobile genetic elements. S. epidermidis harboured a greater array of virulence factors than S. hominis isolates, which require further investigation to be used as markers of clinical significance. Antimicrobial resistance was common among these isolates, which may complicate treatment strategies. There was no effect of IS256 on ica gene expression, which may relate to the distance of IS256 from the ica operon.