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 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.
