Metagenomic strategies identify diverse integron‐integrase and antibiotic resistance genes in the Antarctic environment
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....
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ftcdlib:oai:escholarship.org:ark:/13030/qt99p986hq 2023-10-01T03:52:02+02:00 Metagenomic strategies identify diverse integron‐integrase and antibiotic resistance genes in the Antarctic environment Antelo, Verónica Giménez, Matías Azziz, Gastón Valdespino‐Castillo, Patricia Falcón, Luisa I Ruberto, Lucas AM Cormack, Walter P Mac Mazel, Didier Batista, Silvia e1219 2021-10-01 application/pdf https://escholarship.org/uc/item/99p986hq unknown eScholarship, University of California qt99p986hq https://escholarship.org/uc/item/99p986hq public MicrobiologyOpen, vol 10, iss 5 Biotechnology Genetics Antarctic Regions Bacteria Computational Biology Drug Resistance Microbial Genes Bacterial High-Throughput Nucleotide Sequencing Integrases Integrons Metagenome Metagenomics Phylogeny Soil Microbiology antibiotic resistance bioinformatics horizontal gene transfer microbial genomics Microbiology article 2021 ftcdlib 2023-09-04T18:04:42Z 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 17metagenomes 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 15metagenomes, but only four were classified as GCs, one in MTG12metagenome (Continental Antarctica), encoding an aminoglycoside-modifying enzyme (AAC(6´)acetyltransferase) and the other three in CS1metagenome (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 qacG2gene. Article in Journal/Newspaper Antarc* Antarctic Antarctica University of California: eScholarship Antarctic The Antarctic |
institution |
Open Polar |
collection |
University of California: eScholarship |
op_collection_id |
ftcdlib |
language |
unknown |
topic |
Biotechnology Genetics Antarctic Regions Bacteria Computational Biology Drug Resistance Microbial Genes Bacterial High-Throughput Nucleotide Sequencing Integrases Integrons Metagenome Metagenomics Phylogeny Soil Microbiology antibiotic resistance bioinformatics horizontal gene transfer microbial genomics Microbiology |
spellingShingle |
Biotechnology Genetics Antarctic Regions Bacteria Computational Biology Drug Resistance Microbial Genes Bacterial High-Throughput Nucleotide Sequencing Integrases Integrons Metagenome Metagenomics Phylogeny Soil Microbiology antibiotic resistance bioinformatics horizontal gene transfer microbial genomics Microbiology Antelo, Verónica Giménez, Matías Azziz, Gastón Valdespino‐Castillo, Patricia Falcón, Luisa I Ruberto, Lucas AM Cormack, Walter P Mac Mazel, Didier Batista, Silvia Metagenomic strategies identify diverse integron‐integrase and antibiotic resistance genes in the Antarctic environment |
topic_facet |
Biotechnology Genetics Antarctic Regions Bacteria Computational Biology Drug Resistance Microbial Genes Bacterial High-Throughput Nucleotide Sequencing Integrases Integrons Metagenome Metagenomics Phylogeny Soil Microbiology antibiotic resistance bioinformatics horizontal gene transfer microbial genomics Microbiology |
description |
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 17metagenomes 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 15metagenomes, but only four were classified as GCs, one in MTG12metagenome (Continental Antarctica), encoding an aminoglycoside-modifying enzyme (AAC(6´)acetyltransferase) and the other three in CS1metagenome (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 qacG2gene. |
format |
Article in Journal/Newspaper |
author |
Antelo, Verónica Giménez, Matías Azziz, Gastón Valdespino‐Castillo, Patricia Falcón, Luisa I Ruberto, Lucas AM Cormack, Walter P Mac Mazel, Didier Batista, Silvia |
author_facet |
Antelo, Verónica Giménez, Matías Azziz, Gastón Valdespino‐Castillo, Patricia Falcón, Luisa I Ruberto, Lucas AM Cormack, Walter P Mac Mazel, Didier Batista, Silvia |
author_sort |
Antelo, Verónica |
title |
Metagenomic strategies identify diverse integron‐integrase and antibiotic resistance genes in the Antarctic environment |
title_short |
Metagenomic strategies identify diverse integron‐integrase and antibiotic resistance genes in the Antarctic environment |
title_full |
Metagenomic strategies identify diverse integron‐integrase and antibiotic resistance genes in the Antarctic environment |
title_fullStr |
Metagenomic strategies identify diverse integron‐integrase and antibiotic resistance genes in the Antarctic environment |
title_full_unstemmed |
Metagenomic strategies identify diverse integron‐integrase and antibiotic resistance genes in the Antarctic environment |
title_sort |
metagenomic strategies identify diverse integron‐integrase and antibiotic resistance genes in the antarctic environment |
publisher |
eScholarship, University of California |
publishDate |
2021 |
url |
https://escholarship.org/uc/item/99p986hq |
op_coverage |
e1219 |
geographic |
Antarctic The Antarctic |
geographic_facet |
Antarctic The Antarctic |
genre |
Antarc* Antarctic Antarctica |
genre_facet |
Antarc* Antarctic Antarctica |
op_source |
MicrobiologyOpen, vol 10, iss 5 |
op_relation |
qt99p986hq https://escholarship.org/uc/item/99p986hq |
op_rights |
public |
_version_ |
1778517522886164480 |