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. 2021 Oct;10(5):e1219.
doi: 10.1002/mbo3.1219.

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

Verónica Antelo #  1 , Matías Giménez #  1   2 , Gastón Azziz  3 , Patricia Valdespino-Castillo  4 , Luisa I Falcón  5   6 , Lucas A M Ruberto  7   8 , Walter P Mac Cormack  7   8 , Didier Mazel  9   10 , Silvia Batista  1
Affiliations

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

Verónica Antelo et al. Microbiologyopen. 2021 Oct.

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.

Keywords: antibiotic resistance; bioinformatics; horizontal gene transfer; microbial genomics.

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Conflict of interest statement

None declared.

Figures

FIGURE 1
FIGURE 1
Phylogenetic tree of integrase protein sequences described in this work along with reference integrases. The different clusters are identified with Roman numbers. Classical reference sequences are written in blue (IntI1, IntI2, IntI3, IntI4, IntI5, XerC, and XercD sequences). Sequences recovered by NGS microbial mat metagenome analysis are written in green and by NGS soil metagenome analysis are written in red. Amplicon library sequences are written in orange. Sequences marked with * represent a cluster of sequences with more than 90% identity, the number of sequences in the cluster is shown between brackets
FIGURE 2
FIGURE 2
(a) Amino acid sequence alignment (SeaView) of IntIs recovered by amplicon library and NGS analysis. The first seven sequences were included as a reference. (b) Amino acid sequence alignment including the region with an additional domain, identified in some environmental IntIs
FIGURE 3
FIGURE 3
Heatmap of antimicrobial resistance genes in metagenomic assemblies and its association to attC sequences within the same contig
FIGURE A1
FIGURE A1
(a) Sequence map of integron detected in contig CS1_503. Only part of the contig is displayed. (b) Sequence map of integron detected in contig CS1_14211. The entire contig is displayed. (c) Sequence map of integron detected in contig CS1_5. No ARGs were detected in this integron. Only part of the contig is displayed
FIGURE A2
FIGURE A2
Sequence map of CALIN detected in contig 18109 from metagenome 12. The entire sequence is displayed
See this image and copyright information in PMC

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