Diversity of gene cassettes and the abundance of the class 1 integron-integrase gene in sediment polluted by metals

Oliveira-Pinto, Clarisse; Costa, Patrícia S.; Reis, Mariana P.; Chartone-Souza, Edmar; Nascimento, Andréa M. A.

doi:10.1007/s00792-016-0820-3

Cited by 11 publications

(6 citation statements)

References 40 publications

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“…ARGs-cassettes represented a small proportion of the total of the cassette-related ORFs. This observation is consistent with other studies reports that resistance cassettes abundance is relatively low compared to their diversity [6,37]. Additionally, known ARGs-cassettes still represent a small fraction of the environmental resistance pool, despite the progressive increase in related databases [38].…”

Section: Discussionsupporting

confidence: 92%

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Exploring antibiotic resistance in environmental integron-cassettes through intI-attC amplicons deep sequencing

et al. 2020

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Introduction Freshwater ecosystems provide propitious conditions for the acquisition and spread of antibiotic resistance genes (ARGs), and integrons play an important role in this process. Material and methods In the present study, the diversity of putative environmental integron-cassettes, as well as their potential bacterial hosts in the Velhas River (Brazil), was explored through intI-attC and 16S rRNA amplicons deep sequencing. Results and discussion ORFs related to different biological processes were observed, from DNA integration to oxidationreduction. ARGs-cassettes were mainly associated with class 1 mobile integrons carried by pathogenic Gammaproteobacteria, and possibly sedentary chromosomal integrons hosted by Proteobacteria and Actinobacteria. Two putative novel ARG-cassettes homologs to fosB3 and novA were detected. Regarding 16SrRNA gene analysis, taxonomic and functional profiles unveiled Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria as dominant phyla. Betaproteobacteria, Alphaproteobacteria, and Actinobacteria classes were the main contributors for KEGG orthologs associated with resistance. Conclusions Overall, these results provide new information about environmental integrons as a source of resistance determinants outside clinical settings and the bacterial community in the Velhas River.

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Section: Discussionsupporting

confidence: 92%

“…Genomic and metagenomic studies with different hosts and environments have demonstrated that gene cassettes are extremely diverse, comprising many unknown functions [36]. Among the identified ORFs, general metabolic processes, e.g., oxidation-reduction, were more frequent, as reported elsewhere [37].…”

Section: Discussionsupporting

confidence: 52%

Exploring antibiotic resistance in environmental integron-cassettes through intI-attC amplicons deep sequencing

et al. 2020

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“…Oliveira-Pinto et al. ( 2016 ) isolated an intI gene cassette related to Nitrospirae from a metal-rich stream, and Goltsman et al. ( 2009 ) identified both integrase and ARGs on chromosomes of Nitrospirae strains isolated from acid mine drainage.…”

Section: Resultsmentioning

confidence: 99%

Community structure explains antibiotic resistance gene dynamics over a temperature gradient in soil

Dunivin

Shade

2018

FEMS Microbiology Ecology

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Soils are reservoirs of antibiotic resistance genes (ARGs), but environmental dynamics of ARGs are largely unknown. Long-term disturbances offer opportunities to examine microbiome responses at scales relevant for both ecological and evolutionary processes and can be insightful for studying ARGs. We examined ARGs in soils overlying the underground coal seam fire in Centralia, PA, which has been burning since 1962. As the fire progresses, previously hot soils can recover to ambient temperatures, which creates a gradient of fire impact. We examined metagenomes from surface soils along this gradient to examine ARGs using a gene-targeted assembler. We targeted 35 clinically relevant ARGs and two horizontal gene transfer-related genes (intI and repA). We detected 17 ARGs in Centralia: AAC6-Ia, adeB, bla_A, bla_B, bla_C, cmlA, dfra12, intI, sul2, tetA, tetW, tetX, tolC, vanA, vanH, vanX and vanZ. The diversity and abundance of bla_A, bla_B, dfra12 and tolC decreased with soil temperature, and changes in ARGs were largely explained by changes in community structure. We observed sequence-specific biogeography along the temperature gradient and observed compositional shifts in bla_A, dfra12 and intI. These results suggest that increased temperatures can reduce soil ARGs but that this is largely due to a concomitant reduction in community-level diversity.

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“…One such bioindicator gene, the class 1 integrase ( intI1) (Gillings et al, 2015) has been shown to be present in many anthropogenic samples including human stool (Phongpaichit et al, 2008), wastewater treatment plants (WWTPs, Ma et al, 2013) and surrounding airborne aerosol emissions (Li et al, 2016), river sediment near WWTP effluent discharge lines (Karkman et al, 2016), ponds (M. Wang et al, 2016), landfill sites (Sun et al, 2016), untreated hospital effluents (Spindler et al, 2012), many animal hosts (Colello et al, 2015; Lluque et al, 2015), and in sediment and soils polluted or treated with metals (Oliveira-Pinto et al, 2016) and antibiotics (Cleary et al, 2016). The intI1 gene or a similar maker could eventually play a role in regulatory environmental monitoring of ARGs (Berendonk et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

Isothermal assay targeting class 1 integrase gene for environmental surveillance of antibiotic resistance markers

Stedtfeld¹,

Stedtfeld²,

Waseem³

et al. 2017

Journal of Environmental Management

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Antimicrobial resistance genes (ARGs) present in the environment pose a risk to human health due to potential for transfer to human pathogens. Surveillance is an integral part of mitigating environmental dissemination. Quantification of the mobile genetic element class 1 integron-integrase gene (intI1) has been proposed as a surrogate to measuring multiple ARGs. Measurement of such indicator genes can be further simplified by adopting emerging nucleic acids methods such as loop mediated isothermal amplification (LAMP). In this study, LAMP assays were designed and tested for estimating relative abundance of the intI1 gene, which included design of a universal bacteria 16S rRNA gene assay. Following validation of sensitivity and specificity with known bacterial strains, the assays were tested using DNA extracted from river and lake samples. Results showed a significant Pearson correlation (R2 = 0.8) between the intI1 gene LAMP assay and ARG relative abundance (measured via qPCR). To demonstrate the ruggedness of the LAMP assays, experiments were also run in the hands of relatively “untrained” personnel by volunteer undergraduate students at a local community college using a hand-held real-time DNA analysis device - Gene-Z. Overall, results support use of the intI1 gene as an indicator of ARGs and the LAMP assays exhibit the opportunity for volunteers to monitor environmental samples for anthropogenic pollution outside of a specialized laboratory.

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Diversity of gene cassettes and the abundance of the class 1 integron-integrase gene in sediment polluted by metals

Cited by 11 publications

References 40 publications

Exploring antibiotic resistance in environmental integron-cassettes through intI-attC amplicons deep sequencing

Exploring antibiotic resistance in environmental integron-cassettes through intI-attC amplicons deep sequencing

Community structure explains antibiotic resistance gene dynamics over a temperature gradient in soil

Isothermal assay targeting class 1 integrase gene for environmental surveillance of antibiotic resistance markers

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