Razavi M, Marathe NP, Gillings MR, Flach CF, Kristiansson E, Joakim Larsson DG
Microbiome 5 (1) 160 [2017-12-15; online 2017-12-15]
Over the past 75 years, human pathogens have acquired antibiotic resistance genes (ARGs), often from environmental bacteria. Integrons play a major role in the acquisition of antibiotic resistance genes. We therefore hypothesized that focused exploration of integron gene cassettes from microbial communities could be an efficient way to find novel mobile resistance genes. DNA from polluted Indian river sediments were amplified using three sets of primers targeting class 1 integrons and sequenced by long- and short-read technologies to maintain both accuracy and context. Up to 89% of identified open reading frames encode known resistance genes, or variations thereof (> 1000). We identified putative novel ARGs to aminoglycosides, beta-lactams, trimethoprim, rifampicin, and chloramphenicol, including several novel OXA variants, providing reduced susceptibility to carbapenems. One dihydropteroate synthase gene, with less than 34% amino acid identity to the three known mobile sulfonamide resistance genes (sul1-3), provided complete resistance when expressed in Escherichia coli. The mobilized gene, here named sul4, is the first mobile sulfonamide resistance gene discovered since 2003. Analyses of adjacent DNA suggest that sul4 has been decontextualized from a set of chromosomal genes involved in folate synthesis in its original host, likely within the phylum Chloroflexi. The presence of an insertion sequence common region element could provide mobility to the entire integron. Screening of 6489 metagenomic datasets revealed that sul4 is already widespread in seven countries across Asia and Europe. Our findings show that exploring integrons from environmental communities with a history of antibiotic exposure can provide an efficient way to find novel, mobile resistance genes. The mobilization of a fourth sulfonamide resistance gene is likely to provide expanded opportunities for sulfonamide resistance to spread, with potential impacts on both human and animal health.
BioProject: PRJNA400874 Sediment metagenome. Amplicon sequencing of gene cassettes from polluted sediments.
GENBANK: MG649394 Uncultured bacterium clone riv2 dihydropteroate synthase (sul4) and quaternary ammonium compound efflux genes, complete cds
GENBANK: MG649395 Uncultured bacterium clone riv3 OXA-2-like protein gene, complete cds; and QacE delta gene, partial cds
GENBANK: MG649396 Uncultured bacterium clone riv4 dihydrofolate reductase (drfb2) gene, partial cds; arr-6-like protein gene, complete cds; and class 1 integron integrase gene, partial cds
GENBANK: MG649397 Uncultured bacterium clone riv5 class 1 integron integrase gene, partial cds; and OXA-10-like protein gene, complete cds
GENBANK: MG649398 Uncultured bacterium clone riv6 chloramphenicol O-acetyltransferase gene, complete cds
GENBANK: MG649399 Uncultured bacterium clone riv7 QacE delta gene, partial cds; and OXA-46-like protein gene, complete cds
GENBANK: MG649400 Uncultured bacterium clone riv9 OXA-2-like protein gene, complete cds; and QacE delta gene, partial cds
GENBANK: MG649401 Uncultured bacterium clone riv10 CARB-PSE gene, partial cds; and dfrA-like protein gene, complete cds
GENBANK: MG649402 Uncultured bacterium clone riv8 ISCR20-like protein, dihydropteroate synthase (sul4), and hypothetical protein genes, complete cds
GENBANK: MG649403 Uncultured bacterium clone riv11 qacE gene, partial cds; and molecular chaperone, qacE, and aminoglycoside nucleotidyltransferase AadA genes, complete cds