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

Autor: Indio V; Department of Veterinary Medical Science, University of Bologna, Ozzano dell'Emilia, Italy., Oliveri C; Department of Physics and Astronomy 'Augusto Righi', University of Bologna, Italy., Lucchi A; Department of Agricultural and Food Sciences, University of Bologna, Italy., Savini F; Department of Veterinary Medical Science, University of Bologna, Ozzano dell'Emilia, Italy., Gonzales-Barron U; Mountain Research Center (CIMO), Polytechnic Institute of Bragança, Portugal., Skandamis P; Laboratory of Food Quality Control and Hygiene, Department of Food Science and Human Nutrition, Agricultural University of Athens, Greece., Achemchem F; LASIME Laboratory, Agadir Superior School of Technology, Ibn Zohr University, Agadir, Morocco., Manfreda G; Department of Agricultural and Food Sciences, University of Bologna, Italy., Serraino A; Department of Veterinary Medical Science, University of Bologna, Ozzano dell'Emilia, Italy., De Cesare A; Department of Veterinary Medical Science, University of Bologna, Ozzano dell'Emilia, Italy.
Jazyk: angličtina
Zdroj: Italian journal of food safety [Ital J Food Saf] 2024 May 10; Vol. 13 (2), pp. 12210. Date of Electronic Publication: 2024 May 10 (Print Publication: 2024).
DOI: 10.4081/ijfs.2024.12210
Abstrakt: 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.
Competing Interests: Conflict of interest: the authors declare no potential conflict of interest.
(Copyright © 2024, the Author(s).)
Databáze: MEDLINE
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