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Shotgun metagenomic investigation of foodborne pathogens and antimicrobial resistance genes in artisanal fermented meat products from the Mediterranean area

2024Journal article Open access
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dc.contributor.authorIndio, Valentina
dc.contributor.authorOlivieri, Chiara
dc.contributor.authorLucchi, Alex
dc.contributor.authorSavini, Federica
dc.contributor.authorGonzales-Barron, Ursula
dc.contributor.authorSkandamis, Panagiotis
dc.contributor.authorAchemchem, Fouad
dc.contributor.authorManfreda, Gerardo
dc.contributor.authorSerraino, Andrea
dc.contributor.authorCesare, Alessandra
dc.date.accessioned2024-10-16T08:55:47Z
dc.date.available2024-10-16T08:55:47Z
dc.date.issued2024
dc.description.abstractIn this pilot study, we compared the metagenomic profiles of different types of artisanal fermented meat products collected in Italy, Greece, Portugal, and Morocco to investigate their taxonomic profile, also in relation to the presence of foodborne pathogens and antimicrobial resistance genes. In addition, technical replicates of the same biological sample were tested to estimate the reproducibility of shotgun metagenomics. The taxonomic analysis showed a high level of variability between different fermented meat products at both the phylum and genus levels. Staphylococcus aureus was identified with the highest abundance in Italian fermented meat; Escherichia coli in fermented meat from Morocco; Salmonella enterica in fermented meat from Greece; Klebsiella pneumoniae and Yersinia enterocolitica in fermented meat from Portugal. The fungi Aspergillus, Neosartoria, Emericella, Penicillum and Debaryomyces showed a negative correlation with Lactococcus, Enterococcus, Streptococcus, Leuconostoc and Lactobacillus. The resistome analysis indicated that genes conferring resistance to aminoglycoside, macrolide, and tetracycline were widely spread in all samples. Our results showed that the reproducibility between technical replicates tested by shotgun metagenomic was very high under the same conditions of analysis (either DNA extraction, library preparation, sequencing analysis, and bioinformatic analysis), considering both the degree of overlapping and the pairwise correlation.pt_PT
dc.description.sponsorshipThis research was funded by the EU H2020 PRIMA ARTISANEFOOD project “Innovative Bio-interventions and Risk Modeling Approaches for Ensuring Microbial Safety and Quality of Mediterranean Artisanal Fermented Foods.pt_PT
dc.description.versioninfo:eu-repo/semantics/publishedVersionpt_PT
dc.identifier.citationIndio, Valentina; Olivieri, Chiara; Lucchi, Alex; Savini, Federica; Gonzales-Barron, Ursula; Skandamis, Panagiotis; Achemchem, Fouad; Manfreda, Gerardo; Serraino, Andrea; Cesare, Alessandra (2024). Shotgun metagenomic investigation of foodborne pathogens and antimicrobial resistance genes in artisanal fermented meat products from the Mediterranean area. Italian Journal of Food Safety. ISSN 2239-7132. 13:2, p. 1-7pt_PT
dc.identifier.doi10.4081/ijfs.2024.12210pt_PT
dc.identifier.issn2239-7132
dc.identifier.urihttp://hdl.handle.net/10198/30428
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.publisherPagePresspt_PT
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/pt_PT
dc.subjectFermented meat productspt_PT
dc.subjectFoodborne pathogenspt_PT
dc.subjectAntimicrobialpt_PT
dc.subjectResistance genespt_PT
dc.subjectShotgun metagenomicspt_PT
dc.titleShotgun metagenomic investigation of foodborne pathogens and antimicrobial resistance genes in artisanal fermented meat products from the Mediterranean areapt_PT
dc.typejournal article
dspace.entity.typePublication
oaire.citation.endPage7pt_PT
oaire.citation.issue2pt_PT
oaire.citation.startPage1pt_PT
oaire.citation.titleItalian Journal of Food Safetypt_PT
oaire.citation.volume13pt_PT
person.familyNameGonzales-Barron
person.givenNameUrsula
person.identifier.ciencia-id0813-C319-B62A
person.identifier.orcid0000-0002-8462-9775
person.identifier.scopus-author-id9435483700
rcaap.rightsopenAccesspt_PT
rcaap.typearticlept_PT
relation.isAuthorOfPublication17c6b98f-4fb5-41d3-839a-6f77ec70021a
relation.isAuthorOfPublication.latestForDiscovery17c6b98f-4fb5-41d3-839a-6f77ec70021a

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