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

In 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 a...

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Published inItalian journal of food safety Vol. 13; no. 2; p. 12210
Main Authors Indio, Valentina, Olivieri, Chiara, Lucchi, Alex, Savini, Federica, Gonzales-Barron, Ursula, Skandamis, Panagiotis, Achemchem, Fouad, Manfreda, Gerardo, Serraino, Andrea, De Cesare, Alessandra
Format Journal Article
LanguageEnglish
Published PAGEPress Publications, Pavia, Italy 10.05.2024
PAGEPress Publications
Subjects
antimicrobial resistance
biological hazards
fermented meat
mediterranean productions
Shotgun metagenomic
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Summary:In 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 the 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.
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Conference presentation: this paper was presented at the XXXII National Conference of the Italian Association of Veterinary Food Hygienists (AIVI), September 13-15, 2023, Maierato, Italy.
Availability of data and materials: data and materials are available from the corresponding author upon request.
Publisher's note: all claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.
Contributions: VI, carried out the bioinformatic and biostatistics analysis and writing of the original draft; CO, AL, performed DNA extraction, library preparation and sequencing; FS, contributed to the paper drafting and editing; UGB, PS, FA, collected and shipped the samples from their own country; GM, AS, AD, conceived and planned the study, collected the Italian samples and supported in editing the final draft. All authors have commented and approved the final version as submitted.
Conflict of interest: the authors declare no potential conflict of interest.
Ethics approval and consent to participate: not applicable.
ISSN:2239-7132
2239-7132
DOI:10.4081/ijfs.2024.12210