Generic context-dependence governs clonal emergence of ciprofloxacin resistance mutations

Ciprofloxacin is widely used against enterobacterial infections, where primary resistance-determinants are the mutations in DNA gyrase (GyrA) and topoisomerase IV (ParC) proteins. Bioinformatic analyses on 2734 isolates representing prominent enterobacterial species deciphered a high-resolution (with > 96% accuracy) septatype scheme, involving both nonsynonymous and synonymous mutations in five codon positions of gyrA , parC , and recN (encoding recombination protein N), and presence/absence of two plasmid-mediated resistance genes ( qnrB2 and qnrS1 ). Such a typing scheme should provide a framework for rapid point-of-care assays to optimize ciprofloxacin use against enterobacterial, and potentially other bacterial, infections. As expected, four amino acid positions of the topoisomerases were the most powerful contributors. Despite species-specificity, and also habitat-specificity owing to distinct intra-species clonal emergence, their tetratype combinations strictly followed a generalized context-dependence syntax, where conformational change owing to increased hydrophobicity disrupted ciprofloxacin binding to GyrA and ParC, leading to drug resistance. Moreover, in some Salmonella isolates, codon ctg over the consensus cta for leucine at codon 346 of the recN gene, owing to its drastically high usage preference, suggested better codon optimization. This might lead to higher RecN production, potentially aiding to antibiotic escape property of the organism, thereby indicating contribution of synonymous mutations in antibiotic resistance.