Comprehensive mutational analysis of the efflux regulator marR

Abstract: Antimicrobial resistance is an increasing problem worldwide and it is therefore important to monitor resistance trends by surveillance. To collect phenotypic information is the standard method today, although genotypic surveillance has recently received more attention. To be implemented, knowledge about how to correctly interpret sequencing data needs to be complemented. In the AcrAB-TolC efflux regulator marR this is an issue. Mutations in marR can lead to a reduced susceptibility to various drugs, including ciprofloxacin. To address this issue we did a comprehensive mutational analysis of the gene marR, in order to identify the missense mutations that contribute to resistance to ciprofloxacin. Selections for mutants at low levels of ciprofloxacin and subsequent analysis of the mutation frequency at each position of marR using Illumina sequencing were performed. 24 independent selections revealed in total 25 unique missense mutations, with the majority located in the DNA-binding region of marR. However, none of the missense mutations matched previously sequenced clinical isolates, suggesting that we may be selecting on a too high concentration of ciprofloxacin.  In conclusion, our selection experiment and subsequent analysis of the mutation frequencies in marR show that marR missense mutations can be generated by this method. The selections need to be further optimized in order to find clinically relevant marR missense mutations.