{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T13:07:06Z","timestamp":1790687226674,"version":"4.1.0"},"reference-count":68,"publisher":"MDPI AG","issue":"5","license":[{"start":{"date-parts":[[2020,4,27]],"date-time":"2020-04-27T00:00:00Z","timestamp":1587945600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Biology"],"abstract":"<jats:p>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 Enterococcus 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 vanA-positive. The most prevalent resistance genes detected were erm(B) and aac(6\u2019)-Ii, conferring resistance to the classes of macrolides and aminoglycosides, respectively. MALDI-TOF mass spectrometry (MS) analysis detected an exclusive peak of the Enterococcus genus at m\/z (mass-to-charge-ratio) 4428 \u00b1 3, and a peak at m\/z 6048 \u00b1 1 allowed us to distinguish Enterococcus faecium 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.<\/jats:p>","DOI":"10.3390\/biology9050089","type":"journal-article","created":{"date-parts":[[2020,4,28]],"date-time":"2020-04-28T05:05:32Z","timestamp":1588050332000},"page":"89","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":19,"title":["Next-Generation Sequencing and MALDI Mass Spectrometry in the Study of Multiresistant Processed Meat Vancomycin-Resistant Enterococci (VRE)"],"prefix":"10.3390","volume":"9","author":[{"given":"Carolina","family":"Saben\u00e7a","sequence":"first","affiliation":[{"name":"Department of Genetics and Biotechnology, University of Tr\u00e1s-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal"},{"name":"Department of Animal and Veterinary Science, University of Tr\u00e1s-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal"},{"name":"Functional Genomics and Proteomics Unit, University of Tr\u00e1s-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal"},{"name":"LAQV-REQUIMTE, Faculty of Science and Technology, University Nova of Lisbon, 2829-516 Lisbon, Caparica, Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2326-6226","authenticated-orcid":false,"given":"Telma","family":"de Sousa","sequence":"additional","affiliation":[{"name":"Department of Genetics and Biotechnology, University of Tr\u00e1s-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal"},{"name":"Department of Animal and Veterinary Science, University of Tr\u00e1s-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal"},{"name":"Functional Genomics and Proteomics Unit, University of Tr\u00e1s-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal"},{"name":"LAQV-REQUIMTE, Faculty of Science and Technology, University Nova of Lisbon, 2829-516 Lisbon, Caparica, Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Soraia","family":"Oliveira","sequence":"additional","affiliation":[{"name":"Department of Genetics and Biotechnology, University of Tr\u00e1s-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal"},{"name":"Department of Animal and Veterinary Science, University of Tr\u00e1s-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal"},{"name":"Functional Genomics and Proteomics Unit, University of Tr\u00e1s-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal"},{"name":"LAQV-REQUIMTE, Faculty of Science and Technology, University Nova of Lisbon, 2829-516 Lisbon, Caparica, Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4221-9700","authenticated-orcid":false,"given":"Didier","family":"Viala","sequence":"additional","affiliation":[{"name":"INRAE, Plateforme d\u2019Exploration du M\u00e9tabolisme, composante prot\u00e9omique (PFEMcp), 63122 Saint-Gen\u00e8s Champanelle, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3879-1496","authenticated-orcid":false,"given":"Laetitia","family":"Th\u00e9ron","sequence":"additional","affiliation":[{"name":"INRAE, UR0370 Qualit\u00e9 des Produits Animaux (QuaPA), 63122 Saint-Gen\u00e8s Champanelle, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christophe","family":"Chambon","sequence":"additional","affiliation":[{"name":"INRAE, Plateforme d\u2019Exploration du M\u00e9tabolisme, composante prot\u00e9omique (PFEMcp), 63122 Saint-Gen\u00e8s Champanelle, France"},{"name":"INRAE, UR0370 Qualit\u00e9 des Produits Animaux (QuaPA), 63122 Saint-Gen\u00e8s Champanelle, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0478-2575","authenticated-orcid":false,"given":"Michel","family":"H\u00e9braud","sequence":"additional","affiliation":[{"name":"INRAE, Plateforme d\u2019Exploration du M\u00e9tabolisme, composante prot\u00e9omique (PFEMcp), 63122 Saint-Gen\u00e8s Champanelle, France"},{"name":"INRAE, UMR0454 Microbiologie Environnement Digestif Sant\u00e9 (MEDiS), Universit\u00e9 Clermont Auvergne, 63122 Saint-Gen\u00e8s Champanelle, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Racha","family":"Beyrouthy","sequence":"additional","affiliation":[{"name":"Centre National de R\u00e9f\u00e9rence de la R\u00e9sistance aux Antibiotiques, Centre Hospitalier Universitaire, 63003 Clermont-Ferrand, France"},{"name":"UMR1071 INSERM, USC1382 INRAE Microbiologie Intestin Inflammation et Susceptibilit\u00e9 de l\u2019H\u00f4te (M2iSH), Universit\u00e9 Clermont Auvergne, 63001 Clermont-Ferrand, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richard","family":"Bonnet","sequence":"additional","affiliation":[{"name":"Centre National de R\u00e9f\u00e9rence de la R\u00e9sistance aux Antibiotiques, Centre Hospitalier Universitaire, 63003 Clermont-Ferrand, France"},{"name":"UMR1071 INSERM, USC1382 INRAE Microbiologie Intestin Inflammation et Susceptibilit\u00e9 de l\u2019H\u00f4te (M2iSH), Universit\u00e9 Clermont Auvergne, 63001 Clermont-Ferrand, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2077-6231","authenticated-orcid":false,"given":"Manuela","family":"Cani\u00e7a","sequence":"additional","affiliation":[{"name":"National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, National Institute of Health Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal"},{"name":"Centre for the Studies of Animal Science, Institute of Agrarian and Agri-Food Sciences and Technologies, Oporto University, 4051-401 Oporto, Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0925-689X","authenticated-orcid":false,"given":"Patr\u00edcia","family":"Poeta","sequence":"additional","affiliation":[{"name":"Department of Animal and Veterinary Science, University of Tr\u00e1s-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal"},{"name":"LAQV-REQUIMTE, Faculty of Science and Technology, University Nova of Lisbon, 2829-516 Lisbon, Caparica, Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6365-0735","authenticated-orcid":false,"given":"Gilberto","family":"Igrejas","sequence":"additional","affiliation":[{"name":"Department of Genetics and Biotechnology, University of Tr\u00e1s-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal"},{"name":"Functional Genomics and Proteomics Unit, University of Tr\u00e1s-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal"},{"name":"LAQV-REQUIMTE, Faculty of Science and Technology, University Nova of Lisbon, 2829-516 Lisbon, Caparica, Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2020,4,27]]},"reference":[{"key":"ref_1","unstructured":"Gilmore, M.S., Clewell, D.B., Ike, Y., and Shankar, N. 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