Dairy Products and Dairy-Processing Environments as a Reservoir of Antibiotic Resistance and Quorum-Quenching Determinants as Revealed through Functional Metagenomics
ABSTRACT 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...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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American Society for Microbiology
2020-02-01
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| Series: | mSystems |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/mSystems.00723-19 |
| _version_ | 1818742268998189056 |
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| author | Elena A. Alexa (Oniciuc) Calum J. Walsh Laura M. Coughlan Amal Awad Cezara A. Simon Lorena Ruiz Fiona Crispie Paul D. Cotter Avelino Alvarez-Ordóñez |
| author_facet | Elena A. Alexa (Oniciuc) Calum J. Walsh Laura M. Coughlan Amal Awad Cezara A. Simon Lorena Ruiz Fiona Crispie Paul D. Cotter Avelino Alvarez-Ordóñez |
| author_sort | Elena A. Alexa (Oniciuc) |
| collection | DOAJ |
| description | ABSTRACT 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. |
| first_indexed | 2024-12-18T02:09:50Z |
| format | Article |
| id | doaj.art-e5c7246a828b44ac90d24e0502bc01a0 |
| institution | Directory Open Access Journal |
| issn | 2379-5077 |
| language | English |
| last_indexed | 2024-12-18T02:09:50Z |
| publishDate | 2020-02-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | mSystems |
| spelling | doaj.art-e5c7246a828b44ac90d24e0502bc01a02022-12-21T21:24:31ZengAmerican Society for MicrobiologymSystems2379-50772020-02-015110.1128/mSystems.00723-19Dairy Products and Dairy-Processing Environments as a Reservoir of Antibiotic Resistance and Quorum-Quenching Determinants as Revealed through Functional MetagenomicsElena A. Alexa (Oniciuc)0Calum J. Walsh1Laura M. Coughlan2Amal Awad3Cezara A. Simon4Lorena Ruiz5Fiona Crispie6Paul D. Cotter7Avelino Alvarez-Ordóñez8Department of Food Hygiene and Technology, Universidad de León, León, SpainTeagasc Food Research Centre, Fermoy, County Cork, IrelandTeagasc Food Research Centre, Fermoy, County Cork, IrelandBacteriology, Mycology and Immunology Department, Faculty of Veterinary Medicine, Mansoura University, Mansoura, EgyptDepartment of Food Hygiene and Technology, Universidad de León, León, SpainDairy Research Institute, Spanish National Research Council, Instituto de Productos Lácteos de Asturias—CSIC, Villaviciosa, SpainTeagasc Food Research Centre, Fermoy, County Cork, IrelandTeagasc Food Research Centre, Fermoy, County Cork, IrelandDepartment of Food Hygiene and Technology, Universidad de León, León, SpainABSTRACT 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.https://journals.asm.org/doi/10.1128/mSystems.00723-19antibiotic resistancefood safetyfunctional metagenomicsdairy productsquorum quenching |
| spellingShingle | Elena A. Alexa (Oniciuc) Calum J. Walsh Laura M. Coughlan Amal Awad Cezara A. Simon Lorena Ruiz Fiona Crispie Paul D. Cotter Avelino Alvarez-Ordóñez Dairy Products and Dairy-Processing Environments as a Reservoir of Antibiotic Resistance and Quorum-Quenching Determinants as Revealed through Functional Metagenomics mSystems antibiotic resistance food safety functional metagenomics dairy products quorum quenching |
| title | Dairy Products and Dairy-Processing Environments as a Reservoir of Antibiotic Resistance and Quorum-Quenching Determinants as Revealed through Functional Metagenomics |
| title_full | Dairy Products and Dairy-Processing Environments as a Reservoir of Antibiotic Resistance and Quorum-Quenching Determinants as Revealed through Functional Metagenomics |
| title_fullStr | Dairy Products and Dairy-Processing Environments as a Reservoir of Antibiotic Resistance and Quorum-Quenching Determinants as Revealed through Functional Metagenomics |
| title_full_unstemmed | Dairy Products and Dairy-Processing Environments as a Reservoir of Antibiotic Resistance and Quorum-Quenching Determinants as Revealed through Functional Metagenomics |
| title_short | Dairy Products and Dairy-Processing Environments as a Reservoir of Antibiotic Resistance and Quorum-Quenching Determinants as Revealed through Functional Metagenomics |
| title_sort | dairy products and dairy processing environments as a reservoir of antibiotic resistance and quorum quenching determinants as revealed through functional metagenomics |
| topic | antibiotic resistance food safety functional metagenomics dairy products quorum quenching |
| url | https://journals.asm.org/doi/10.1128/mSystems.00723-19 |
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