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

• Published in: MicrobiologyOpen (Weinheim) Vol. 10; no. 5; pp. e1219 - n/a
• Main Authors: Antelo, Verónica, Giménez, Matías, Azziz, Gastón, Valdespino‐Castillo, Patricia, Falcón, Luisa I., Ruberto, Lucas A. M., Mac Cormack, Walter P., Mazel, Didier, Batista, Silvia
• Format: Journal Article
• Language: English
• Published: England John Wiley & Sons, Inc 01-10-2021; Wiley; John Wiley and Sons Inc
• Subjects: Acetyltransferase; Adenyltransferase; Amino acids; Aminoglycoside antibiotics; Aminoglycosides; Antarctic Regions; Antibiotic resistance; Antibiotics; Bacteria - genetics; BASIC BIOLOGICAL SCIENCES; bioinformatics; Cassettes; Chromosomes; Computational Biology - methods; Drug Resistance, Microbial - genetics; Gene amplification; Genes; Genes, Bacterial; Genomes; High-Throughput Nucleotide Sequencing; horizontal gene transfer; Integrase; Integrases - genetics; Integrons - genetics; Islands; Metagenome; Metagenomics; Metagenomics - methods; microbial genomics; Microbial mats; Microbiology; Microorganisms; Original; Phylogeny; Polar environments; Soil analysis; Soil Microbiology; Terrestrial environments; Antarctic Regions; Antarctic Peninsula; Antarctica; King George Island; antibiotic resistance; horizontal gene transfer; microbial genomics; bioinformatics
• ISSN: 2045-8827; 2045-8827
• DOI: 10.1002/mbo3.1219

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 objective of this study is to identify and analyze integrons and antibiotic resistance genes (ARGs) in samples collected from diverse sites in terrestrial Antarctica. The metagenomic analysis allowed us to identify novel predicted intI integrases and gene cassettes (GCs), which mostly encode unknown functions.