A Functional Metagenomic Analysis of Tetracycline Resistance in Cheese Bacteria

Flórez, Ana Belén; Vázquez, Lucía; Mayo, Baltasar

doi:10.3389/fmicb.2017.00907

Cited by 24 publications

(20 citation statements)

References 57 publications

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“…enterica and E. coli. In addition, these authors showed that various tetracycline resistance determinants were embedded or in proximity to sequences homologous to those of LAB-derived species (9). It is reasonable to believe that members of LAB isolated from dairy products can act as reservoirs for different AR genes, as was previously reported (9,12,(28)(29)(30).…”

Section: Discussionmentioning

confidence: 54%

“…In addition, these authors showed that various tetracycline resistance determinants were embedded or in proximity to sequences homologous to those of LAB-derived species (9). It is reasonable to believe that members of LAB isolated from dairy products can act as reservoirs for different AR genes, as was previously reported (9,12,(28)(29)(30). In our study, the use of a combined approach involving both function-based and in silico sequencing-based analyses to characterize a large metagenomics library built with DNA isolated from different compartments of the cheese production chain allowed us to identify L. lactis as a major reservoir and source of AR determinants within the dairy production chain.…”

Section: Discussionmentioning

confidence: 99%

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Dairy Products and Dairy-Processing Environments as a Reservoir of Antibiotic Resistance and Quorum-Quenching Determinants as Revealed through Functional Metagenomics

et al. 2020

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Here, the role of the dairy-processing chain as a reservoir of antimicrobial resistance (AR) determinants and a source of novel biocontrol quorum-sensing inhibitors is assessed through a functional metagenomics approach. A metagenomic library comprising ∼22,000 recombinant clones was built from DNA isolated from raw milk, raw milk cheeses, and cheese-processing environment swab samples. The high-throughput sequencing of 9,216 recombinant clones showed that lactic acid bacteria (LAB) dominated the microbial communities of raw milk cheese, while Gram-negative microorganisms of animal or soil origin dominated the microbiota of raw milk and cheese-processing environments. Although functional screening of the metagenomic library did not recover potential quorum-sensing inhibitors, in silico analysis using an in-house database built specifically for this study identified homologues to several genes encoding proteins with predicted quorum-quenching activity, among which, the QsdH hydrolase was the most abundant. In silico screening of the library identified LAB, and especially Lactococcus lactis, as a relevant reservoir of AR determinants in cheese. Functional screening of the library allowed the isolation of 13 recombinant clones showing an increased resistance toward ampicillin, which in all cases was accompanied by a reduced susceptibility to a wide range of β-lactam antibiotics. This study shows that the dairy-processing environment is a rich reservoir of AR determinants, which vary by sample source, and suggests that combining next-generation sequencing with functional metagenomics can be of use in overcoming the limitations of both approaches. IMPORTANCE The study shows the potential of functional metagenomics analyses to uncover the diversity of functions in microbial communities prevailing in dairy products and their processing environments, evidencing that lactic acid bacteria (LAB) dominate the cheese microbiota, whereas Gram-negative microorganisms of animal or soil origin dominate the microbiota of milk and cheese-processing environments. The functional and in silico screening of the library allowed the identification of LAB, and especially Lactococcus lactis, as a relevant reservoir of antimicrobial resistance (AR) determinants in cheese. Quorum-quenching (QQ) determinants were not recovered through the execution of wet-lab function-based screenings but were detected through in silico sequencing-based analyses.

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Section: Discussionmentioning

confidence: 54%

Section: Discussionmentioning

confidence: 99%

Dairy Products and Dairy-Processing Environments as a Reservoir of Antibiotic Resistance and Quorum-Quenching Determinants as Revealed through Functional Metagenomics

et al. 2020

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“…Surveillance of AMR is currently based on the isolation of indicator microorganisms and their phenotypic characterisation, but this culture‐dependent approach does not provide complete information on the mechanisms driving AMR or on the presence or spread of AMR genes throughout the food chain. Metagenomics is a powerful tool that allows culture‐independent analysis of complex microbial communities and thus has potential applications in AMR surveillance (Bonham et al., ; Flórez et al., ; Walsh et al., ). It can provide access to all the genetic resources in a given environmental niche, which is essential for obtaining the genomes of fastidious or non‐culturable microorganisms.…”

Section: Introductionmentioning

confidence: 91%

“…The ability of bacteria to resist the action of one or several antimicrobial agents through bacterial gene mutations or by acquiring exogenous resistance genes carried on mobile elements is defined as antimicrobial resistance (AMR) (ECDC, 2017). Acquired resistance to some antimicrobials is already so widespread as to compromise their value for the treatment of life-threatening infections (EFSA BIOHAZ Panel, 2008). Harmonised outcome indicators have been jointly established by the European Centre for Disease Prevention and Control (ECDC), the European Food Safety Authority (EFSA) and the European Medicines Agency (EMA) to assist Member States in assessing the progress made in reducing antimicrobial use and AMR both in humans and food-producing animals (ECDC, EFSA BIOHAZ Panel and CVMP, 2017).…”

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confidence: 99%

Risk assessment of antimicrobial resistance along the food chain through culture‐independent methodologies

Likotrafiti¹,

Oniciuc²,

Prieto³

et al. 2018

EFS2

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Antimicrobial resistance (AMR) represents a major challenge for Public Health and the scientific community, and requires immediate and drastic solutions. Acquired resistance to certain antimicrobials is already widespread to such an extent that their efficacy in the treatment of certain life‐threatening infections is already compromised. To date, the emergence and spread of AMR has been attributed to the use, misuse or indiscriminate use of antibiotics as therapeutic drugs in human, animal and plant health, or as growth promoters in veterinary husbandry. In addition, there is growing concern over the possibility of AMR transmission via the food chain. Food processing environments could act as potential hotspots for AMR acquisition and spread. Indeed, biocide use and exposure to food‐related stresses and food processing technologies could presumably act as selection pressures for increased microbial resistance against clinically relevant antibiotics. Global AMR surveillance is critical for providing the necessary information to form global strategies and to monitor the effectiveness of public health interventions as well as to detect new trends and emerging threats. Surveillance of AMR is currently based on the isolation of indicator microorganisms and the phenotypic characterisation of the strains isolated. However, this approach provides very limited information on the mechanisms driving AMR or on the presence and spread of AMR genes. Whole genome sequencing (WGS) of bacterial pathogens is a powerful tool that can be used for epidemiological surveillance, outbreak detection and infection control. In addition, whole metagenome sequencing (WMS) allows for the culture‐independent analysis of complex microbial communities, providing useful information on the occurrence of AMR genes. Both approaches can be used to provide the information necessary for the implementation of quantitative risk assessment of AMR transmission routes along the food chain.

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“…Antimicrobials are used globally both for humans and animals to obviate and treat contagious diseases (O'neill, 2014). Furthermore, in some countries, antimicrobials are used in animal breeding as growth promoters (Flórez et al, 2017). Antimicrobial agents are one of the medicinal innovations of humanity that allows us to cure both human and veterinary infections of microbes.…”

Section: Introductionmentioning

confidence: 99%