Investigating effects of topoisomerase mutations on topoisomerase-ciprofloxacin interaction in Salmonella typhi isolated in Blantyre
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Date
2021-09-20
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Kamuzu University of Health Sciences
Abstract
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:
i. To identify mutations in Quinolone Resistance Determining Region of
S. Typhi with decreased ciprofloxacin susceptibility isolated in Blantyre
ii. 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
iii. To compare folding energy of topoisomerase protein structure of S. Typhi with
decreased ciprofloxacin susceptibility to topoisomerase protein structure of
ciprofloxacin-sensitive S. Typhi
iv. 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
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.