Isolation of bacterial extrachromosomal DNA from human dental plaque associated with periodontal disease, using transposon-aided capture (TRACA)

Warburton, P.J.; Allan, Elaine; Hunter, Stephanie J.; Ward, John M.; Booth, '; Wade, William; Mullany, Peter

doi:10.1111/j.1574-6941.2011.01166.x

Cited by 18 publications

(19 citation statements)

References 31 publications

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“…These proteins promote the integration and excision of mobile genetic elements from genomes. Such elements frequently go through a circular intermediate phase which is expected to be isolated by the TRACA approach, as we have shown here [9].…”

Section: Isolation Of Bacterial Extra‐chromosomal Metagenomic Dna Usimentioning

confidence: 59%

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Tetracycline resistance genes and mobile genetic elements from the oral metagenome

Mullany

Allan

Warburton

2012

Clinical Microbiology and Infection

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Tetracycline resistance genes are common in the human oral cavity. However, a complete understanding of tetracycline resistance and the vectors responsible for spread of resistance requires that we understand the contribution of organisms that cannot be cultivated in the laboratory. To do this, metagenomic approaches have been applied and this has allowed the isolation of novel tetracycline resistance genes and mobile genetic elements.

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Section: Isolation Of Bacterial Extra‐chromosomal Metagenomic Dna Usimentioning

confidence: 59%

“…The method used was adapted from a method originally published by Jones and Marchesi [8]. The metagenomic DNA was prepared from supragingival and subgingival plaque samples [9]. The technique relies on using a plasmid origin of replication which is contained on a Tn 5 derivative.…”

Section: Isolation Of Bacterial Extra‐chromosomal Metagenomic Dna Usimentioning

confidence: 99%

Tetracycline resistance genes and mobile genetic elements from the oral metagenome

Mullany

Allan

Warburton

2012

Clinical Microbiology and Infection

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“…This method has been used to characterize plasmids from environments, such as human gut, human dental plaque, or activated sludge from sewage treatment plants. [129][130][131][132] TRACA allows capturing plasmids from widely different origins, but shows also a bias for recovering small plasmids, since they resist the in vitro manipulation procedures and transform with higher efficiency than large ones.…”

Section: Methods For Analyzing the Mobilome And For Extracting Mobilomentioning

confidence: 99%

Genomic and metagenomic technologies to explore the antibiotic resistance mobilome

Martínez

Coque

Lanza

et al. 2016

Annals of the New York Academy of Sciences

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Antibiotic resistance is a relevant problem for human health that requires global approaches to establish a deep understanding of the processes of acquisition, stabilization, and spread of resistance among human bacterial pathogens. Since natural (nonclinical) ecosystems are reservoirs of resistance genes, a health‐integrated study of the epidemiology of antibiotic resistance requires the exploration of such ecosystems with the aim of determining the role they may play in the selection, evolution, and spread of antibiotic resistance genes, involving the so‐called resistance mobilome. High‐throughput sequencing techniques allow an unprecedented opportunity to describe the genetic composition of a given microbiome without the need to subculture the organisms present inside. However, bioinformatic methods for analyzing this bulk of data, mainly with respect to binning each resistance gene with the organism hosting it, are still in their infancy. Here, we discuss how current genomic methodologies can serve to analyze the resistance mobilome and its linkage with different bacterial genomes and metagenomes. In addition, we describe the drawbacks of current methodologies for analyzing the resistance mobilome, mainly in cases of complex microbiotas, and discuss the possibility of implementing novel tools to improve our current metagenomic toolbox.

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“…Furthermore, a circular molecule that did not contain a plasmid origin of replication was isolated from the oral metagenome. This molecule contained an integrase gene 23 . Integrases typically generate circular molecules as an intermediate in their site-specific recombination reaction.…”

Section: Functional Metagenomics Aimed At Isolating Mobile Genetic Elmentioning

confidence: 99%

Functional metagenomics for the investigation of antibiotic resistance

Mullany

2014

Virulence

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Antibiotic resistance is a major threat to human health and well-being. To effectively combat this problem we need to understand the range of different resistance genes that allow bacteria to resist antibiotics. To do this the whole microbiota needs to be investigated. As most bacteria cannot be cultivated in the laboratory, the reservoir of antibiotic resistance genes in the non-cultivatable majority remains relatively unexplored. Currently the only way to study antibiotic resistance in these organisms is to use metagenomic approaches. Furthermore, the only method that does not require any prior knowledge about the resistance genes is functional metagenomics, which involves expressing genes from metagenomic clones in surrogate hosts. In this review the methods and limitations of functional metagenomics to isolate new antibiotic resistance genes and the mobile genetic elements that mediate their spread are explored.

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Isolation of bacterial extrachromosomal DNA from human dental plaque associated with periodontal disease, using transposon-aided capture (TRACA)

Cited by 18 publications

References 31 publications

Tetracycline resistance genes and mobile genetic elements from the oral metagenome

Tetracycline resistance genes and mobile genetic elements from the oral metagenome

Genomic and metagenomic technologies to explore the antibiotic resistance mobilome

Functional metagenomics for the investigation of antibiotic resistance

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