Next-Generation Sequencing and MALDI Mass Spectrometry in the Study of Multiresistant Processed Meat Vancomycin-Resistant Enterococci (VRE)
Vancomycin-resistant enterococci (VRE), due to their intrinsic resistance to various commonly used antibiotics and their malleable genome, make the treatment of infections caused by these bacteria less effective. The aims of this work were to characterize isolates of <i>Enterococcus</i>...
| Main Authors: | , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2020-04-01
|
| Series: | Biology |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2079-7737/9/5/89 |
| _version_ | 1797569528301879296 |
|---|---|
| author | Carolina Sabença Telma de Sousa Soraia Oliveira Didier Viala Laetitia Théron Christophe Chambon Michel Hébraud Racha Beyrouthy Richard Bonnet Manuela Caniça Patrícia Poeta Gilberto Igrejas |
| author_facet | Carolina Sabença Telma de Sousa Soraia Oliveira Didier Viala Laetitia Théron Christophe Chambon Michel Hébraud Racha Beyrouthy Richard Bonnet Manuela Caniça Patrícia Poeta Gilberto Igrejas |
| author_sort | Carolina Sabença |
| collection | DOAJ |
| description | Vancomycin-resistant enterococci (VRE), due to their intrinsic resistance to various commonly used antibiotics and their malleable genome, make the treatment of infections caused by these bacteria less effective. The aims of this work were to characterize isolates of <i>Enterococcus</i> spp. that originated from processed meat, through phenotypic and genotypic techniques, as well as to detect putative antibiotic resistance biomarkers. The 19 VRE identified had high resistance to teicoplanin (89%), tetracycline (94%), and erythromycin (84%) and a low resistance to kanamycin (11%), gentamicin (11%), and streptomycin (5%). Based on a Next-Generation Sequencing NGS technique, most isolates were <i>vanA</i>-positive. The most prevalent resistance genes detected were <i>erm</i>(B) and <i>aac</i>(6’)-<i>Ii,</i> conferring resistance to the classes of macrolides and aminoglycosides, respectively. MALDI-TOF mass spectrometry (MS) analysis detected an exclusive peak of the <i>Enterococcus</i> genus at m/z (mass-to-charge-ratio) 4428 ± 3, and a peak at m/z 6048 ± 1 allowed us to distinguish <i>Enterococcus</i> <i>faecium</i> from the other species. Several statistically significant protein masses associated with resistance were detected, such as peaks at m/z 6358.27 and m/z 13237.3 in ciprofloxacin resistance isolates. These results reinforce the relevance of the combined and complementary NGS and MALDI-TOF MS techniques for bacterial characterization. |
| first_indexed | 2024-03-10T20:12:50Z |
| format | Article |
| id | doaj.art-d6046ddb08874c83a5cbec75e6e7cd16 |
| institution | Directory Open Access Journal |
| issn | 2079-7737 |
| language | English |
| last_indexed | 2024-03-10T20:12:50Z |
| publishDate | 2020-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biology |
| spelling | doaj.art-d6046ddb08874c83a5cbec75e6e7cd162023-11-19T22:50:41ZengMDPI AGBiology2079-77372020-04-01958910.3390/biology9050089Next-Generation Sequencing and MALDI Mass Spectrometry in the Study of Multiresistant Processed Meat Vancomycin-Resistant Enterococci (VRE)Carolina Sabença0Telma de Sousa1Soraia Oliveira2Didier Viala3Laetitia Théron4Christophe Chambon5Michel Hébraud6Racha Beyrouthy7Richard Bonnet8Manuela Caniça9Patrícia Poeta10Gilberto Igrejas11Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, PortugalDepartment of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, PortugalDepartment of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, PortugalINRAE, Plateforme d’Exploration du Métabolisme, composante protéomique (PFEMcp), 63122 Saint-Genès Champanelle, FranceINRAE, UR0370 Qualité des Produits Animaux (QuaPA), 63122 Saint-Genès Champanelle, FranceINRAE, Plateforme d’Exploration du Métabolisme, composante protéomique (PFEMcp), 63122 Saint-Genès Champanelle, FranceINRAE, Plateforme d’Exploration du Métabolisme, composante protéomique (PFEMcp), 63122 Saint-Genès Champanelle, FranceCentre National de Référence de la Résistance aux Antibiotiques, Centre Hospitalier Universitaire, 63003 Clermont-Ferrand, FranceCentre National de Référence de la Résistance aux Antibiotiques, Centre Hospitalier Universitaire, 63003 Clermont-Ferrand, FranceNational Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, National Institute of Health Dr. Ricardo Jorge, 1649-016 Lisbon, PortugalDepartment of Animal and Veterinary Science, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, PortugalDepartment of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, PortugalVancomycin-resistant enterococci (VRE), due to their intrinsic resistance to various commonly used antibiotics and their malleable genome, make the treatment of infections caused by these bacteria less effective. The aims of this work were to characterize isolates of <i>Enterococcus</i> spp. that originated from processed meat, through phenotypic and genotypic techniques, as well as to detect putative antibiotic resistance biomarkers. The 19 VRE identified had high resistance to teicoplanin (89%), tetracycline (94%), and erythromycin (84%) and a low resistance to kanamycin (11%), gentamicin (11%), and streptomycin (5%). Based on a Next-Generation Sequencing NGS technique, most isolates were <i>vanA</i>-positive. The most prevalent resistance genes detected were <i>erm</i>(B) and <i>aac</i>(6’)-<i>Ii,</i> conferring resistance to the classes of macrolides and aminoglycosides, respectively. MALDI-TOF mass spectrometry (MS) analysis detected an exclusive peak of the <i>Enterococcus</i> genus at m/z (mass-to-charge-ratio) 4428 ± 3, and a peak at m/z 6048 ± 1 allowed us to distinguish <i>Enterococcus</i> <i>faecium</i> from the other species. Several statistically significant protein masses associated with resistance were detected, such as peaks at m/z 6358.27 and m/z 13237.3 in ciprofloxacin resistance isolates. These results reinforce the relevance of the combined and complementary NGS and MALDI-TOF MS techniques for bacterial characterization.https://www.mdpi.com/2079-7737/9/5/89<i>Enterococcus</i> spp.processed meatantibiotic resistancenext-generation sequencingMALDI-TOF MS |
| spellingShingle | Carolina Sabença Telma de Sousa Soraia Oliveira Didier Viala Laetitia Théron Christophe Chambon Michel Hébraud Racha Beyrouthy Richard Bonnet Manuela Caniça Patrícia Poeta Gilberto Igrejas Next-Generation Sequencing and MALDI Mass Spectrometry in the Study of Multiresistant Processed Meat Vancomycin-Resistant Enterococci (VRE) Biology <i>Enterococcus</i> spp. processed meat antibiotic resistance next-generation sequencing MALDI-TOF MS |
| title | Next-Generation Sequencing and MALDI Mass Spectrometry in the Study of Multiresistant Processed Meat Vancomycin-Resistant Enterococci (VRE) |
| title_full | Next-Generation Sequencing and MALDI Mass Spectrometry in the Study of Multiresistant Processed Meat Vancomycin-Resistant Enterococci (VRE) |
| title_fullStr | Next-Generation Sequencing and MALDI Mass Spectrometry in the Study of Multiresistant Processed Meat Vancomycin-Resistant Enterococci (VRE) |
| title_full_unstemmed | Next-Generation Sequencing and MALDI Mass Spectrometry in the Study of Multiresistant Processed Meat Vancomycin-Resistant Enterococci (VRE) |
| title_short | Next-Generation Sequencing and MALDI Mass Spectrometry in the Study of Multiresistant Processed Meat Vancomycin-Resistant Enterococci (VRE) |
| title_sort | next generation sequencing and maldi mass spectrometry in the study of multiresistant processed meat vancomycin resistant enterococci vre |
| topic | <i>Enterococcus</i> spp. processed meat antibiotic resistance next-generation sequencing MALDI-TOF MS |
| url | https://www.mdpi.com/2079-7737/9/5/89 |
| work_keys_str_mv | AT carolinasabenca nextgenerationsequencingandmaldimassspectrometryinthestudyofmultiresistantprocessedmeatvancomycinresistantenterococcivre AT telmadesousa nextgenerationsequencingandmaldimassspectrometryinthestudyofmultiresistantprocessedmeatvancomycinresistantenterococcivre AT soraiaoliveira nextgenerationsequencingandmaldimassspectrometryinthestudyofmultiresistantprocessedmeatvancomycinresistantenterococcivre AT didierviala nextgenerationsequencingandmaldimassspectrometryinthestudyofmultiresistantprocessedmeatvancomycinresistantenterococcivre AT laetitiatheron nextgenerationsequencingandmaldimassspectrometryinthestudyofmultiresistantprocessedmeatvancomycinresistantenterococcivre AT christophechambon nextgenerationsequencingandmaldimassspectrometryinthestudyofmultiresistantprocessedmeatvancomycinresistantenterococcivre AT michelhebraud nextgenerationsequencingandmaldimassspectrometryinthestudyofmultiresistantprocessedmeatvancomycinresistantenterococcivre AT rachabeyrouthy nextgenerationsequencingandmaldimassspectrometryinthestudyofmultiresistantprocessedmeatvancomycinresistantenterococcivre AT richardbonnet nextgenerationsequencingandmaldimassspectrometryinthestudyofmultiresistantprocessedmeatvancomycinresistantenterococcivre AT manuelacanica nextgenerationsequencingandmaldimassspectrometryinthestudyofmultiresistantprocessedmeatvancomycinresistantenterococcivre AT patriciapoeta nextgenerationsequencingandmaldimassspectrometryinthestudyofmultiresistantprocessedmeatvancomycinresistantenterococcivre AT gilbertoigrejas nextgenerationsequencingandmaldimassspectrometryinthestudyofmultiresistantprocessedmeatvancomycinresistantenterococcivre |