Identifying genetic signatures in regions around antimicrobial resistance genes
Date:
The advancement of antimicrobial resistance genes (ARGs) is one of the biggest threats to public health. Since ARGs can be found in a diverse range of genetic contexts in different species and environments, determining structural elements in the regions up- and downstream, or flanks, of ARGs can provide useful information on their evolutionary history. We will present our analysis of flanks surrounding members of the mcr gene family in metagenomic samples. The mcr genes confer resistance to colistin, a last-resort antibiotic used against multidrug-resistant bacteria. We have identified and assembled 869 mcr positive metagenomes from various origins and locations and have extracted flanks of 1939 different mcr contigs from the assemblies. Plasmid replicons and mobile genetic elements (MGEs) were identified in the flanks. By setting a minimum flank size of 1,000 bp and clustering on the pairwise k-mer distance, we can observe several unique genetic signatures for each mcr gene variant. For example, we can see that only the ISApl1 MGE appears around mcr-1 contigs and IS903 in mcr-9 flanks. As there were only 138 contigs that passed the size criteria, we are in the process of including mcr flanks from 3327 genomes of single isolates retrieved from NCBI to better understand the elements involved in the dissemination of mcr genes. Our presentation will include these results as well.
