RT info:eu-repo/semantics/preprint
T1 Sequencing-based analysis of the microbiomes of Spanish food processing facilities reveals environment-specific variation in the dominant taxa and antibiotic resistance genes
A1 Álvarez Molina, Adrián
A1 Cobo Díaz, José Francisco
A1 Alexa, Elena-Alexandra
A1 Crispie, Fiona
A1 Prieto Maradona, Miguel
A1 López Fernández, María Mercedes
A1 Cotter, Paul D.
A1 Álvarez Ordóñez, Avelino
A2 Tecnologia de los Alimentos
K1 Tecnología de los alimentos
K1 Food processing environments
K1 Antimicrobial resistance
K1 Metagenomics
K1 Resistome
K1 Microbiome
K1 3309 Tecnología de Los Alimentos
K1 3309.14 Elaboración de Alimentos
AB [EN] ResumenIn the last years, advances in high throughput sequencing technologies have opened the possibility to broaden environmental monitoring activities in facilities processing food, offering expanded opportunities for characterizing in an untargeted manner the microbiome and resistome of foods and food processing environments (FPE) with huge potential benefits in food safety management systems. Here the microbiome and resistome of FPE from slaughterhouses (n = 3), dairy (n = 12) and meat (n = 10) processing plants were assessed through whole metagenome sequencing of 2 composite samples for each facility, comprising 10 FPE swabs taken from food contact surfaces and 10 FPE samples from non-food contact surfaces, respectively. FPE from slaughterhouses had more diverse microbiomes and resistomes, while FPE from dairy processing plants showed the highest β-dispersion, consistent with a more heterogeneous microbiome and resistome composition. The predominant bacterial genera depended on the industry type, with Pseudomonas and Psychrobacter being highly dominant in surfaces from slaughterhouses and meat industries, while different lactic acid bacteria predominated in dairy industries. The most abundant antimicrobial resistance genes (ARG) found were associated with resistance to aminoglycosides, tetracyclines and quaternary ammonium compounds (QAC). ARGs relating to resistance to aminoglycosides and tetracyclines were significantly more prevalent in slaughterhouses than in food processing plants, while QAC resistance genes were particularly abundant in some food contact surfaces from dairy and meat processing plants, suggesting that daily sanitation under suboptimal conditions may be selecting for persistent microbiota tolerant to these biocides in some facilities. The taxonomic mapping of ARG pointed to specific bacterial genera, such as Escherichia, Bacillus, or Staphylococcus, as carriers of the most relevant resistance determinants. About 63% of all ARG reads were assigned to contigs classified as plasmid-associated, indicating that the resistome of FPE may be strongly shaped through the spread of mobile genetic elements. Overall, the relevance of FPE as reservoirs of ARG was confirmed and it was demonstrated that next generation sequencing technologies allowing a deep characterisation of sources and routes of spread of microorganisms and antimicrobial resistance determinants in food industry settings hold promise to be integrated in monitoring and food safety management programmes.
PB Springer
SN 1873-7145
LK https://hdl.handle.net/10612/17793
UL https://hdl.handle.net/10612/17793
NO Alvarez-Molina, A., Cobo-Díaz, J. F., Alexa, E. A., Crispie, F., Prieto, M., López, M., Cotter, P. D., & Alvarez-Ordóñez, A. (2023). Sequencing-based analysis of the microbiomes of Spanish food processing facilities reveals environment-specific variation in the dominant taxa and antibiotic resistance genes. Food Research International, 173. https://doi.org/10.1016/J.FOODRES.2023.113442
DS BULERIA. Repositorio Institucional de la Universidad de León
RD 03-jun-2024