Tetracycline resistance genes and mobile genetic elements from the oral metagenome

Mullany, Peter; Allan, Elaine; Warburton, P.J.

doi:10.1111/j.1469-0691.2012.03858.x

Cited by 12 publications

(12 citation statements)

References 11 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Metagenomic analysis and massive sequencing techniques have been used to monitor antibiotic resistance genes in environmental (Hatosy and Martiny, 2015), animal (Kazimierczak et al, 2009), and human ecosystems (Diaz-Torres et al, 2003; Seville et al, 2009; Mullany et al, 2012; Forslund et al, 2014), and would appear promising as means of characterizing the same in dairy environments. These techniques allow for the molecular characterization of the resistance genes and their associated genetic elements; this may further help to estimate the risk for their horizontal transference.…”

Section: Introductionmentioning

confidence: 99%

A Functional Metagenomic Analysis of Tetracycline Resistance in Cheese Bacteria

2017

View full text Add to dashboard Cite

Metagenomic techniques have been successfully used to monitor antibiotic resistance genes in environmental, animal and human ecosystems. However, despite the claim that the food chain plays a key role in the spread of antibiotic resistance, metagenomic analysis has scarcely been used to investigate food systems. The present work reports a functional metagenomic analysis of the prevalence and evolution of tetracycline resistance determinants in a raw-milk, blue-veined cheese during manufacturing and ripening. For this, the same cheese batch was sampled and analyzed on days 3 and 60 of manufacture. Samples were diluted and grown in the presence of tetracycline on plate count milk agar (PCMA) (non-selective) and de Man Rogosa and Sharpe (MRS) agar (selective for lactic acid bacteria, LAB). DNA from the cultured bacteria was then isolated and used to construct four fosmid libraries, named after the medium and sampling time: PCMA-3D, PCMA-60D, MRS-3D, and MRS-60D. Clones in the libraries were subjected to restriction enzyme analysis, PCR amplification, and sequencing. Among the 300 fosmid clones analyzed, 268 different EcoRI restriction profiles were encountered. Sequence homology of their extremes clustered the clones into 47 groups. Representative clones of all groups were then screened for the presence of tetracycline resistance genes by PCR, targeting well-recognized genes coding for ribosomal protection proteins and efflux pumps. A single tetracycline resistance gene was detected in each of the clones, with four such resistance genes identified in total: tet(A), tet(L), tet(M), and tet(S). tet(A) was the only gene identified in the PCMA-3D library, and tet(L) the only one identified in the PCMA-60D and MRS-60D libraries. tet(M) and tet(S) were both detected in the MRS-3D library and in similar numbers. Six representative clones of the libraries were sequenced and analyzed. Long segments of all clones but one showed extensive homology to plasmids from Gram-positive and Gram-negative bacteria. tet(A) was found within a sequence showing strong similarity to plasmids pMAK2 and pO26-Vir from Salmonella enterica and Escherichia coli, respectively. All other genes were embedded in, or near to, sequences homologous to those of LAB species. These findings strongly suggest an evolution of tetracycline resistance gene types during cheese ripening, which might reflect the succession of the microbial populations. The location of the tetracycline resistance genes in plasmids, surrounded or directly flanked by open reading frames encoding transposases, invertases or mobilization proteins, suggests they might have a strong capacity for transference. Raw-milk cheeses should therefore be considered reservoirs of tetracycline resistance genes that might be horizontally transferred.

show abstract

Section: Introductionmentioning

confidence: 99%

A Functional Metagenomic Analysis of Tetracycline Resistance in Cheese Bacteria

2017

View full text Add to dashboard Cite

show abstract

“…Culture-independent analysis is also faster and more accurate than culture-based methods. Indeed, several AR identification and AR gene quantification techniques that require no culturing have recently been developed, such as denaturing gradient gel electrophoresis (DGGE) [ 15 , 16 ], real-time quantitative PCR (qPCR) [ 13 , 14 , 17 ], construction and functional analysis of gene libraries [ 18 – 20 ], AR gene microarrays [ 21 , 22 ], and analysis of metagenomic sequences [ 23 , 24 ]. Knowledge of the types and loads of AR genes in foods could ultimately be of help to estimate the risk of their transmission during cheese manufacturing and after consumption.…”

Section: Introductionmentioning

confidence: 99%

Molecular Identification and Quantification of Tetracycline and Erythromycin Resistance Genes in Spanish and Italian Retail Cheeses

Flórez

Alegría

Rossi

et al. 2014

BioMed Research International

View full text Add to dashboard Cite

Large antibiotic resistance gene pools in the microbiota of foods may ultimately pose a risk for human health. This study reports the identification and quantification of tetracycline- and erythromycin-resistant populations, resistance genes, and gene diversity in traditional Spanish and Italian cheeses, via culturing, conventional PCR, real-time quantitative PCR (qPCR), and denaturing gradient gel electrophoresis (DGGE). The numbers of resistant bacteria varied widely among the antibiotics and the different cheese varieties; in some cheeses, all the bacterial populations seemed to be resistant. Up to eight antibiotic resistance genes were sought by gene-specific PCR, six with respect to tetracycline, that is, tet(K), tet(L), tet(M), tet(O), tet(S), and tet(W), and two with respect to erythromycin, that is, erm(B) and erm(F). The most common resistance genes in the analysed cheeses were tet(S), tet(W), tet(M), and erm(B). The copy numbers of these genes, as quantified by qPCR, ranged widely between cheeses (from 4.94 to 10.18log⁡10/g). DGGE analysis revealed distinct banding profiles and two polymorphic nucleotide positions for tet(W)-carrying cheeses, though the similarity of the sequences suggests this tet(W) to have a monophyletic origin. Traditional cheeses would therefore appear to act as reservoirs for large numbers of many types of antibiotic resistance determinants.

show abstract

“…The high percentage of tetracycline and quinolone resistance genes might be caused not only by antibiotic selection pressure, but also by horizontal transmission due to high-density feeding pattern. More and more evidences showed that the MGEs was an important way in the mechanism of resistance to tetracycline and quinolones (47) (48)(49)(50). On the other hand, there was a correlation between these ARGs that might lead to multidrug resistance.…”

Section: Discussionmentioning

confidence: 99%

The Difference of Antibiotic Resistance Genes in Gut Microbiota Among Yak, Beef and Dairy Cattle by Metagenomic Approach

Wang

Wei

et al. 2020

Preprint

View full text Add to dashboard Cite

The drug resistance has been partly driven by the overuse of antimicrobials in agricultural feeding. Better understanding of the antibiotic resistance in gut of bovine is needed to assess its potential effects based on metagenomic approach and analysis. In this study, we collected 40 fecal samples to explore the drug resistance deriving from antibiotics in bacterial community by an analysis of the diversity and difference of antibiotic resistant genes (ARGs) in gut microbiota from yak, beef and dairy cattle. 1688 genes were annotated, including 734 ARG subtypes in summary. The ARGs were related with tetracycline, quinolone, β-lactam, aminoglycoside, in accordance with the antibiotics widely used in clinic for humans or animals. The emergence, prevalence and differences in resistance genes in the intestines of yaks, beef and dairy cattle may be caused by the selective pressure of different feeding patterns. Additionally, the abundance of ARGs in yak was lower than in beef and dairy cattle, while the abundance of integron, a kind of mobile genetic elements (MGEs), was higher than those in beef and dairy cattle. Furthermore, the results of this study demonstrated that a comprehensive profile of various ARGs among yak, beef and dairy cattle for providing a basic research.

show abstract

Tetracycline resistance genes and mobile genetic elements from the oral metagenome

Cited by 12 publications

References 11 publications

A Functional Metagenomic Analysis of Tetracycline Resistance in Cheese Bacteria

A Functional Metagenomic Analysis of Tetracycline Resistance in Cheese Bacteria

Molecular Identification and Quantification of Tetracycline and Erythromycin Resistance Genes in Spanish and Italian Retail Cheeses

The Difference of Antibiotic Resistance Genes in Gut Microbiota Among Yak, Beef and Dairy Cattle by Metagenomic Approach

Contact Info

Product

Resources

About