https://doi.org/10.4081/ijfs.2024.12210

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

Vol. 13 No. 2 (2024)
Submitted: 20 December 2023
Accepted: 8 January 2024
Published: 10 May 2024
Shotgun metagenomic, fermented meat, biological hazards, antimicrobial resistance, mediterranean productions
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Authors

Valentina Indio
https://orcid.org/0000-0002-8854-3821
Department of Veterinary Medical Science, University of Bologna, Ozzano dell’Emilia, Italy.
Chiara Oliveri
https://orcid.org/0000-0002-9483-916X
Department of Physics and Astronomy “Augusto Righi”, University of Bologna, Italy.
Alex Lucchi
Department of Agricultural and Food Sciences, University of Bologna, Italy.
Federica Savini
federica.savini3@unibo.it
Department of Veterinary Medical Science, University of Bologna, Ozzano dell’Emilia, Italy.
Ursula Gonzales-Barron
https://orcid.org/0000-0002-8462-9775
Mountain Research Center (CIMO), Polytechnic Institute of Bragança, Portugal.
Panagiotis Skandamis
https://orcid.org/0000-0001-7878-5897
Laboratory of Food Quality Control and Hygiene, Department of Food Science and Human Nutrition, Agricultural University of Athens, Greece.
Fouad Achemchem
https://orcid.org/0000-0002-3298-1128
LASIME Laboratory, Agadir Superior School of Technology, Ibn Zohr University, Agadir, Morocco.
Gerardo Manfreda
Department of Agricultural and Food Sciences, University of Bologna, Italy.
Andrea Serraino
Department of Veterinary Medical Science, University of Bologna, Ozzano dell’Emilia, Italy.
Alessandra De Cesare
https://orcid.org/0000-0001-5216-6617
Department of Veterinary Medical Science, University of Bologna, Ozzano dell’Emilia, Italy.

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 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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How to Cite

1.
Indio V, Oliveri C, Lucchi A, Savini F, Gonzales-Barron U, Skandamis P, Achemchem F, Manfreda G, Serraino A, De Cesare A. Shotgun metagenomic investigation of foodborne pathogens and antimicrobial resistance genes in artisanal fermented meat products from the Mediterranean area. Ital J Food Safety [Internet]. 2024 May 10 [cited 2024 Dec. 22];13(2). Available from: https://www.pagepressjournals.org/ijfs/article/view/12210
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