Integron gene cassettes harboring novel variants of d-alanine-d-alanine ligase confer high-level resistance to d-cycloserine

Abstract

AbstractAntibiotic resistance poses an increasing threat to global health. To tackle this problem, the identification of principal reservoirs of antibiotic resistance genes (ARGs) plus an understanding of drivers for their evolutionary selection are important. During a PCR-based screen of ARGs associated with integrons in saliva-derived metagenomic DNA of healthy human volunteers, two novel variants of genes encoding ad-alanine-d-alanine ligase (ddl6andddl7) located within gene cassettes in the first position of a reverse integron were identified.Treponema denticolawas identified as the likely host of theddlcassettes. Bothddl6andddl7conferred high level resistance tod-cycloserine when expressed inEscherichia coliwithddl7conferring four-fold higher resistance to D-cycloserine compared toddl6. A SNP was found to be responsible for this difference in resistance phenotype between the twoddlvariants. Molecular dynamics simulations were used to explain the mechanism of this phenotypic change at the atomic scale. A hypothesis for the evolutionary selection ofddlcontaining integron gene cassettes is proposed, based on molecular docking of plant metabolites within the ATP andd-cycloserine binding pockets of Ddl.