Metagenomic characterization of antibiotic resistance genes in Antarctic soils

Yuan, Ke; Yu, Ke; Yang, Ruiqiang; Zhang, Qinghua; Yang, Ying; Chen, En-Zhong; Liu, Lin; Luan, Tiangang; Chen, Wen; Chen, Baowei

doi:10.1016/j.ecoenv.2019.03.099

Cited by 65 publications

(43 citation statements)

References 60 publications

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“…Although with lesser abundance, we also found matches to genes conferring resistance to beta-lactams, aminoglycosides, rifamycin, fosmidomycin, and peptide antibiotics. These results agree with two previous studies of soil metagenomes from Mackay Glacier in South Victoria Land and King George Island in Antarctica, where a set of genes encoding putative efflux pumps and antibiotic inactivation enzymes were predicted (Goethem et al, 2018; Yuan et al, 2019).…”

Section: Resultssupporting

confidence: 92%

Mapping the microbial diversity and natural resistome of North Antarctica soils

Marcoleta

Varas

Costa

et al. 2021

Preprint

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The rising of multi-resistant bacterial pathogens is currently one of the most critical threats to global health and requires urgent actions for its control and a better understanding of the origin, evolution, and spread of antibiotic resistance. It is of consensus that this must be faced under a one-health prism that includes the environment and non-human animals as possible sources and media for resistance amplification and evolution. In this regard, the resistome extension and diversity present in natural and remote environments remain largely unexplored. Moreover, little is known about the availability of antimicrobial resistance genes (ARGs) from these environments to be disseminated through horizontal transfer, potentially mediating the rise of new resistance mechanisms among clinically relevant pathogenic microorganisms. Furthermore, the impact of the anthropogenic intervention on the presence of antibiotic resistant bacteria and the underlying genes is still a matter of controversy. In this context, the Antarctic Peninsula soils are attractive remote environments to study, since their high microbial diversity, the presence of ice-covered soils sheltering ancestral microorganisms that are being exposed as cause of the global warming, and because it is one of the most transited routes between Antarctica and the rest of the world, thus permitting genetic and microbial carriage among those places. Also, it harbors both human bases and places without noticeable human intervention. In this work, we explored the culturable resistome of soils from different places of North Antarctica, including human bases and non-intervened areas. We identified bacterial isolates resistant to a wide array of antibiotics, harboring up to 10 simultaneous resistances, most of them belonging to the genus Pseudomonas. Genomic analyses of the two top resistant bacteria revealed a dominant presence of efflux pumps although an unexpectedly low abundance of known resistance genes, suggesting the presence of unidentified new mechanisms. Moreover, using 16S rRNA amplicon and metagenomic sequencing we explored the microbial diversity in the sampled soils and evaluated the presence and abundance of antimicrobial resistance genes. Proteobacteria, Bacteroidota, Acidobacteriota, and Verrucomicrobiota corresponded to the most abundant Phyla in most of the soils, while among the most abundant genera were Candidatus Udaeobacter, RB41, Polaromonas, and Ferruginibacter. A similarly high microbial diversity was observed when comparing humanized with non-intervened sites, although beta diversity analysis, as well as sequence composition analysis revealed significant clustering of non-intervened apart from humanized areas. We identified a variety of genes potentially involved in resistance to more than 15 drug classes in both short reads based analyses and ARGs detection among assembled contigs. Further, through performing hybrid assembly by combining short and long read sequence data we searched for resistance genes located inside possible mobile genetic elements and identified the source taxa. Polaromonas, Pseudomonas, Streptomyces, Variovorax, Bhurkolderia, and Gemmatimonas were the host taxa of most of the identified ARGs. Plasmid prediction among the assembled metagenomes led to the identification of a putative OXA-like beta-lactamase from Polaromonas spp. located inside a putative plasmid, which included all the key conserved residues for the activity of this kind of beta-lactamases. Taken together, this evidence indicates that resident North Antarctica soil microbial communities harbor a highly diverse natural resistome, part of which is located inside mobile genetic elements that could act disseminating these ARGs to other bacteria.

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Section: Resultssupporting

confidence: 92%

Mapping the microbial diversity and natural resistome of North Antarctica soils

Marcoleta

Varas

Costa

et al. 2021

Preprint

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“…However, there are no reports of the presence of the vatF gene in the Antarctic environment. Yuan et al ( 2019 ) found macrolide resistance genes in soil samples, but all of them encoded efflux pumps rather than acetyltransferases. Similarly,Zaikova et al ( 2019 ) found macrolides efflux pumps in 5 assembled genomes recovered from fossil microbial mats, but not vat genes.…”

Section: Discussionmentioning

confidence: 99%

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

Antelo

Giménez

Azziz³

et al. 2021

MicrobiologyOpen

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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.

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“…The present study, to the best of our knowledge, provides a preliminary metagenomics outlook in the deeper marine sediments of the sampled region, hence the main objective was to observe the proportion of coding genes in this metagenomes against reported antibiotics and metals. Therefore, though recent studies have used a minimum cut-off of 80%, in our study, the genes with percent identity 50 as minimum were considered so that any signatures of resistant genes are not missed 14,15 . Previously, it was reported that at lower identity cut-off the sensitivity for true positives reduced, but still there was at least half the proportion was truly predicted 14 .…”

Section: Discussionmentioning

confidence: 99%

Antibiotic Resistome Biomarkers associated to the Pelagic Sediments of the Gulfs of Kathiawar Peninsula and Arabian Sea

Shekar

Nathani

Poriya³

et al. 2019

Sci Rep

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Antibiotic resistance has been one of the most persistent global issue. Specifically, marine microbiomes have served as complex reservoirs of antibiotic resistant genes. Molecular advancements have enabled exploration of the uncultured microbial portion from hitherto difficult to sample niches such as deeper oceans. The Gulfs of Kathiawar Peninsula have been known for their unique properties like extreme tidal variations, different sediment textures and physicochemical variations. Pelagic sediment cores across four coordinates each of the Gulf of Kutch, Gulf of Khambhat and an open Arabian Sea were collected, processed for metagenomic sequencing and assessed for antibiotic and metal resistome. The dominant genes were mostly resistant to macrolides, glycopeptides and tetracycline drugs. Studied samples divided into three clusters based on their resistome with carA, macB, bcrA, taeA, srmB, tetA, oleC and sav1866 among the abundant genes. Samples from creek of Gulf of Kutch and mouth of Gulf of Khambhat were most diverse in resistance gene profile. Biomarkers observed include gyrA mutation conferring resistance gene in the Arabian Sea; Proteobacteria species in Gulf of Kutch and Arabian sea; while Aquificae, Acidobacteria and Firmicutes species in the Gulf of Khambhat. Region-wise differentially abundant 23 genes and 3 taxonomic biomarkers were proposed for antibiotic resistance monitoring.

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Metagenomic characterization of antibiotic resistance genes in Antarctic soils

Cited by 65 publications

References 60 publications

Mapping the microbial diversity and natural resistome of North Antarctica soils

Mapping the microbial diversity and natural resistome of North Antarctica soils

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

Antibiotic Resistome Biomarkers associated to the Pelagic Sediments of the Gulfs of Kathiawar Peninsula and Arabian Sea

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