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Open AccessArticle

Next-Generation Sequencing and MALDI Mass Spectrometry in the Study of Multiresistant Processed Meat Vancomycin-Resistant Enterococci (VRE)

1
Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
2
Department of Animal and Veterinary Science, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
3
Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
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LAQV-REQUIMTE, Faculty of Science and Technology, University Nova of Lisbon, 2829-516 Lisbon, Caparica, Portugal
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INRAE, Plateforme d’Exploration du Métabolisme, composante protéomique (PFEMcp), 63122 Saint-Genès Champanelle, France
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INRAE, UR0370 Qualité des Produits Animaux (QuaPA), 63122 Saint-Genès Champanelle, France
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INRAE, UMR0454 Microbiologie Environnement Digestif Santé (MEDiS), Université Clermont Auvergne, 63122 Saint-Genès Champanelle, France
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Centre National de Référence de la Résistance aux Antibiotiques, Centre Hospitalier Universitaire, 63003 Clermont-Ferrand, France
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UMR1071 INSERM, USC1382 INRAE Microbiologie Intestin Inflammation et Susceptibilité de l’Hôte (M2iSH), Université Clermont Auvergne, 63001 Clermont-Ferrand, France
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National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, National Institute of Health Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal
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Centre for the Studies of Animal Science, Institute of Agrarian and Agri-Food Sciences and Technologies, Oporto University, 4051-401 Oporto, Portugal
*
Author to whom correspondence should be addressed.
Both authors contributed equally.
Biology 2020, 9(5), 89; https://doi.org/10.3390/biology9050089
Received: 25 February 2020 / Revised: 18 April 2020 / Accepted: 21 April 2020 / Published: 27 April 2020
(This article belongs to the Section Microbiology)
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’)-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 ± 3, and a peak at m/z 6048 ± 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. View Full-Text
Keywords: Enterococcus spp.; processed meat; antibiotic resistance; next-generation sequencing; MALDI-TOF MS Enterococcus spp.; processed meat; antibiotic resistance; next-generation sequencing; MALDI-TOF MS
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MDPI and ACS Style

Sabença, C.; de Sousa, T.; Oliveira, S.; Viala, D.; Théron, L.; Chambon, C.; Hébraud, M.; Beyrouthy, R.; Bonnet, R.; Caniça, M.; Poeta, P.; Igrejas, G. Next-Generation Sequencing and MALDI Mass Spectrometry in the Study of Multiresistant Processed Meat Vancomycin-Resistant Enterococci (VRE). Biology 2020, 9, 89. https://doi.org/10.3390/biology9050089

AMA Style

Sabença C, de Sousa T, Oliveira S, Viala D, Théron L, Chambon C, Hébraud M, Beyrouthy R, Bonnet R, Caniça M, Poeta P, Igrejas G. Next-Generation Sequencing and MALDI Mass Spectrometry in the Study of Multiresistant Processed Meat Vancomycin-Resistant Enterococci (VRE). Biology. 2020; 9(5):89. https://doi.org/10.3390/biology9050089

Chicago/Turabian Style

Sabença, Carolina; de Sousa, Telma; Oliveira, Soraia; Viala, Didier; Théron, Laetitia; Chambon, Christophe; Hébraud, Michel; Beyrouthy, Racha; Bonnet, Richard; Caniça, Manuela; Poeta, Patrícia; Igrejas, Gilberto. 2020. "Next-Generation Sequencing and MALDI Mass Spectrometry in the Study of Multiresistant Processed Meat Vancomycin-Resistant Enterococci (VRE)" Biology 9, no. 5: 89. https://doi.org/10.3390/biology9050089

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