Metagenomic strategies identify diverse integron‐integrase and antibiotic resistance genes in the Antarctic environment

Abstract

The objective of this study is to identify and analyze integrons and antibiotic resistance genes (ARGs) in samples collected from diverse sites in terrestrial Antarctica. Integrons were studied using two independent methods. One involved the construction and analysis of intI gene amplicon libraries. In addition, we sequenced 17 metagenomes of microbial mats and soil by high‐throughput sequencing and analyzed these data using the IntegronFinder program. As expected, the metagenomic analysis allowed for the identification of novel predicted intI integrases and gene cassettes (GCs), which mostly encode unknown functions. However, some intI genes are similar to sequences previously identified by amplicon library analysis in soil samples collected from non‐Antarctic sites. ARGs were analyzed in the metagenomes using ABRIcate with CARD database and verified if these genes could be classified as GCs by IntegronFinder. We identified 53 ARGs in 15 metagenomes, but only four were classified as GCs, one in MTG12 metagenome (Continental Antarctica), encoding an aminoglycoside‐modifying enzyme (AAC(6´)acetyltransferase) and the other three in CS1 metagenome (Maritime Antarctica). One of these genes encodes a class D β‐lactamase (blaOXA‐205) and the other two are located in the same contig. One is part of a gene encoding the first 76 amino acids of aminoglycoside adenyltransferase ( aadA6 ), and the other is a qacG2 gene.

The Natural History of Integrons

“…Integrons have been found in every environment surveyed [20][21][22][23] and are carried by diverse bacterial taxa [8]. To date, integrons have been detected within several phyla: Acidobacteriota, Actinobacteriota, Bacteroidota, Campylobacterota, Chloroflexota, The typical structure of a chromosomal integron includes an integron integrase gene (intI), which encodes a tyrosine recombinase (IntI); an integron recombination site (attI); and a cassette array made up of 1-200+ sequential gene cassettes.…”

“…Integrons have been found in every environment surveyed [20][21][22][23] and are carried by diverse bacterial taxa [8]. To date, integrons have been detected within several phyla: Acidobacteriota, Actinobacteriota, Bacteroidota, Campylobacterota, Chloroflexota, Chrysio-genetota, Cyanobacteria, Desulfobacterota, Firmicutes, Gemmatimonadota, Proteobacteria, Planctomycetota, Spirochaetota, and Verrucomicrobiota [8,24].…”

Glacier-fed stream biofilms harbour diverse resistomes and biosynthetic gene clusters

“…Studies delving into the origins of AMR have reported that fecal pollution may explain ARG abundances in anthropogenically impacted environments [49]. This phenomenon was also observed by Antelo et al [50] and others [51] who detected ARGs in soils in Antarctica, especially in proximity to scientific bases. Although it is plausible that some of the GFSs sampled in our study may indeed be under anthropogenic influence, in pristine environments, AMR is most likely derived from natural antibiotics produced by microorganisms as a competitive advantage.…”

Novel Mobile Integrons and Strain-Specific Integrase Genes within Shewanella spp. Unveil Multiple Lateral Genetic Transfer Events within The Genus

“…The richness of integrase gene types in the environment has been previously reported; however, most studies used culture-independent techniques, where integrons cannot be assigned to a specific bacterial species or genus [36,[50][51][52][53][54]. In Shewanella spp., integrase gene types were found scattered and some of them were even shared by different species (Table S4).…”