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Browsing Protocols by Author "Matambo, Ernest"

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    Investigating effects of topoisomerase mutations on topoisomeraseciprofloxacin interaction in Salmonella typhi isolated in Blantyre
    (Kamuzu Universiyt of Health Sciences, 2021-10-06) Matambo, Ernest
    Introduction Typhoid fever accounts for about 135, 000 deaths in adults and children in south Asia, central and southern Africa. The recommended antibiotic treatment of typhoid fever in Malawi is the fluoroquinolone ciprofloxacin, however, Salmonella enterica subspecies enterica serovar Typhi (S. Typhi) decreased susceptibility to ciprofloxacin has been detected in Blantyre, Malawi. S. Typhi can become resistant to fluoroquinolones by two mechanisms; either due to the acquisition of plasmid mediated resistance genes or mutations in gyrA, gyrB, parC and parE genes in topoisomerase II and IV. This study will use in silico methods to identify mutations in gyrA, gyrB, parC and parE genes in S. Typhi from Blantyre and to investigate the effects of topoisomerase II and IV mutations on topoisomerase-ciprofloxacin interaction. Main objective To investigate the effect of gyrA, gyrB, parC and parE mutations on ciprofloxacintopoisomerase interaction in S. Typhi isolated in Blantyre. Specific objectives To identify mutations in Quinolone Resistance Determining Region of S. Typhi with decreased ciprofloxacin susceptibility isolated in Blantyre. To describe effects of mutations in gyrA, gyrB, parC and parE genes on their protein structure in S. Typhi with decreased ciprofloxacin susceptibility isolated in Blantyre. To compare folding energy of topoisomerase protein structure of S. Typhi with decreased ciprofloxacin susceptibility to topoisomerase protein structure of ciprofloxacin-sensitive S. Typhi. To compare ciprofloxacin-topoisomerase interaction in topoisomerase of S. Typhi with decreased ciprofloxacin susceptibility to ciprofloxacin-sensitive S. Typhi Methodology This will be a retrospective study. Reads of S. Typhi with reduced susceptibility to ciprofloxacin (n=14) and of ciprofloxacin sensitive S. Typhi (n=14) will be assembled using de novo assembly. Topoisomerase II and IV genes will then be extracted from the assembled genomes. Topoisomerase II and IV gene mutations will be identified in the genomes of S. Typhi with decreased susceptibility to ciprofloxacin by comparing the 06-Oct-2021 Ver1.1 September 2021 gene sequences to the CT18 reference genome. The topoisomerase II and IV gene sequences will be translated into protein sequences and then their protein structures predicted. The protein structures will be analysed for structural differences in the S. Typhi with decreased ciprofloxacin susceptibility and ciprofloxacin-sensitive S. Typhi. Folding energy between S. Typhi with decreased ciprofloxacin susceptibility and ciprofloxacin-sensitive S. Typhi protein structures will be compared. Bonding energy with ciprofloxacin between the two groups of protein structures will also be compared. Expected findings and their dissemination Expected findings are that there will be mutations in topoisomerase II and IV gene sequences and that the mutations will be in the ciprofloxacin binding pockets of the predicted protein structures in the S. Typhi with decreased ciprofloxacin susceptibility. Folding energy is expected to be low in protein structures without mutations as compared to protein structures with mutations. Protein structures with mutations will have high binding energy as compared to those without mutations. The study findings and write up will be submitted to COMREC, Kamuzu University of Health Sciences Library and to a peer-reviewed journal for publication. 06