Genetic and in-silico approaches for investigating the mechanisms of ciprofloxacin resistance in Salmonella typhi: Mutations, extrusion, and antimicrobial resistance

<i>Salmonella enterica serovar Typhi</i> spreads typhoid infection in humans through the consumption of contaminated food and water. Poor sanitation plays a pivotal role in its dissemination. Over time, the bacterium has acquired resistance to many promising antibiotics, posing a growing global health concern and hindering the achievement of sustainable development goals. This study aims to elucidate the molecular complexity of fluoroquinolone resistance, a first-line treatment for typhoid infection. To achieve this aim, 80 clinical isolates were collected from various diagnostic laboratories. These isolates were confirmed based on morphological characteristics and biochemical tests. Multidrug-resistant (MDR) and extensively drug-resistant (XDR) isolates were identified using the Kirby-Bauer disc diffusion method. The mechanism of ciprofloxacin resistance was investigated by sequencing the quinolone resistance-determining region (QRDR) genes and identifying the presence of the <i>qnrS1</i> gene. As a result of this study, 60 % of isolates showed resistance to ciprofloxacin. At the same time, <i>the qnrS1</i> gene was present in all the selected strains while mutation analysis identified significant mutation in QRDR of DNA gyrase subunit A <i>(gyrA</i>) and Topoisomerase IV (<i>parC</i>) gene. The combinatorial effect was further investigated by downloading 286 draft genomes. The Mutation analysis reveals significant mutations at <i>gyrA</i> S83F<i>, gyrA</i> D87N<i>, gyrA</i> S83Y<i>, gyrB</i> S464F<i>, parC</i> S80I<i>, and parE</i> L416F. Additionally, docking analysis indicates reduced binding affinity and altered solvent accessibility, which show the structural changes at mutation sites. This study provides crucial insights that mutation reduces the binding affinity while <i>qnrS1</i> acts as a transport channel to extrude the ciprofloxacin. In the future, further validation through experimental mutagenesis is recommended, for targeted therapeutic interventions against the mounting threat of antibiotic-resistant <i>S. Typhi.</i>