Shotgun metagenomic investigation of foodborne pathogens and antimicrobial resistance genes in artisanal fermented meat products from the Mediterranean area
-
Published:2024-05-10
Issue:
Volume:
Page:
-
ISSN:2239-7132
-
Container-title:Italian Journal of Food Safety
-
language:
-
Short-container-title:Ital J Food Safety
Author:
Indio ValentinaORCID, Olivieri ChiaraORCID, Lucchi Alex, Savini Federica, Gonzales-Barron UrsulaORCID, Skandamis PanagiotisORCID, Achemchem FouadORCID, Manfreda Gerardo, Serraino Andrea, De Cesare AlessandraORCID
Abstract
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.
Publisher
PAGEPress Publications
Reference22 articles.
1. Alcock BP, Huynh W, Chalil R, Smith KW, Raphenya AR, Wlodarski MA, Edalatmand A, Petkau A, Syed SA, Tsang KK, Baker SJC, Dave M, Mccarthy MC, Mukiri KM, Nasir JA, Golbon B, Imtiaz H, Jiang X, Kaur K, Kwong M, Liang ZC, Niu KC, Shan P, Yang JYJ, Gray KL, Hoad GR, Jia B, Bhando T, Carfrae LA, Farha MA, French S, Gordzevich R, Rachwalski K, Tu MM, Bordeleau E, Dooley D, Griffiths E, Zubyk HL, Brown ED, Maguire F, Beiko RG, Hsiao WWL, Brinkman FSL, Van Domselaar G, Mcarthur AG, 2023. CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic resistance database. Nucleic Acids Res 51:D690-9. 2. Álvarez M, Andrade MJ, Cebrián E, Roncero E, Delgado J, 2023. Perspectives on the probiotic potential of indigenous moulds and yeasts in dry-fermented sausages. Microorganisms 11:1746. 3. Cruxen CE dos S, Funck GD, Haubert L, Dannenberg G da S, Marques J de L, Chaves FC, da Silva WP, Fiorentini ÂM, 2019. Selection of native bacterial starter culture in the production of fermented meat sausages: application potential, safety aspects, and emerging technologies. Food Res Int 122:371-82. 4. Delgado J, Álvarez M, Cebrián E, Martín I, Roncero E, Rodríguez M, 2023. Biocontrol of pathogen microorganisms in ripened foods of animal origin. Microorganisms 11:1578. 5. Franciosa I, Alessandria V, Dolci P, Rantsiou K, Cocolin L, 2018. Sausage fermentation and starter cultures in the era of molecular biology methods. Int J Food Microbiol 279:26-32.
|
|