Sequencing-based analysis of the microbiomes of Spanish food processing facilities reveals environment-specific variation in the dominant taxa and antibiotic resistance genes

Alvarez-Molina, Adrián; Cobo-Díaz, José F.; Alexa, Elena A.; Crispie, Fiona; Prieto, Miguel; López, Mercedes; Cotter, Paul D.; Alvarez-Ordóñez, Avelino

doi:10.1016/j.foodres.2023.113442

Cited by 3 publications

(6 citation statements)

References 52 publications

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“…Other taxa, mainly within the Pseudomonas genus, showed higher abundance in the preparation area, although these species represented a minor proportion of the whole community (<0.125%). Adaptation of the microbial communities to different types of food processing environments [59] and different environments within food production facilities [13,55] have been described before, highlighting the importance of monitoring individual ecological niches within the same facilities to identify the key microbial taxa characteristic of FPE.…”

Section: Discussionmentioning

confidence: 97%

“…Previous studies have described the microbiome of FPE's such as abattoirs and meat processing plants [54][55][56][57][58][59], fermented-products production facilities [13,54,[59][60][61][62][63] and fruit and vegetables processing plants [14,64,65], and identified distinctive microbiomes depending on the type of commodities [59,66]. However, very few studies describe the FPE of RTE meals [67], despite the importance of this type of food in the contamination with foodborne pathogens during processing [15].…”

Section: Discussionmentioning

confidence: 99%

“…and Psychrobacter spp. are frequently the dominant taxa in a variety of food processing environments [55,58,59,64] due to their tolerance to low temperatures [68] and their ability to form biofilms [69,70] which often results in contamination of food products [71,72]. To our knowledge, the presence of Sphingomonas spp.…”

Section: Discussionmentioning

confidence: 99%

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Microbial composition and dynamics in environmental samples from a ready-to-eat food production facility with a long-term colonisation of Listeria monocytogenes

Maria,

Aird,

Viet

et al. 2024

Preprint

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Background: Listeria monocytogenes is a foodborne pathogen of significant concern for the food industry due to the potential health threat to consumers and a remarkable ability to persist through food safety control efforts. Even with rigorous cleaning and disinfection practices in food production settings, L. monocytogenes and resident microbes can thrive and then potentially spillover from the environment to foods. Understanding the composition and interactions within microbial communities in food processing environments can reveal mechanisms on L. monocytogenes survival and persistence in these settings. In this study, we used metagenomic analysis to monitor the resident microbiota in non-food contact surfaces located in the preparation and production areas of the high care zone of a facility producing ready-to-eat foods that was previously known to have a persistent ST121 strain of L. monocytogenes. Results: A consistent composition and relative abundance of most microbial taxa over sampling sites and times were observed in environmental metagenomes, with the genus Pseudomonas (principally Pseudomonas fluorescens) representing a major constituent of the metagenome. While there were highly related populations between the production and preparation areas, individual taxa characteristic of each area were observed (e.g., Sphingomonas aerolata was more abundant in the production area). Notably Listeria spp. were not observed in the metagenomes, but were detected in cultured samples, suggesting the abundance of Listeria was below the detection threshold for direct metagenomics. As such, a quasimetagenomics approach (sequencing of microbiological culture enrichments) was used to detect and subtype Listeria spp. and L. monocytogenes. While possible to classify Listeria seeligeri sequence types using quasimetagenomes, the classification of the L. monocytogenes sequence types was limited to a low proportion of the samples. Conclusions: A stable resident microbiota was observed with multiple environmental-associated microbial taxa, emphasizing that non-contact food surfaces represent a niche that can be colonised by a community of interdependent microbes. This community was likely selected for by their collective ability to survive cleaning and disinfection control efforts in this environment. Listeria spp. was a member of this microbial community, albeit at very low abundance, and likewise may be benefiting from the mutualism of the overall microbial community.

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Section: Discussionmentioning

confidence: 97%

Section: Discussionmentioning

confidence: 99%

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Microbial composition and dynamics in environmental samples from a ready-to-eat food production facility with a long-term colonisation of Listeria monocytogenes

Maria,

Aird,

Viet

et al. 2024

Preprint

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“…Microbial colonization can occur at various stages of meat processing, with operations such as dehairing or evisceration being among the most significant ones in terms of cross‐contamination of carcasses (Gill, 2004 ). Several metagenomic studies have been carried out to identify critical points of contamination on food contact and non‐contact surfaces in slaughterhouses and cutting plants (Alvarez‐Molina et al., 2023 ; Cobo‐Díaz et al., 2021 ; Li, Xiao, et al., 2022 ). Sanitation protocols are designed to remove a significant proportion of the microorganisms found in slaughterhouses and meat cutting plants, thereby reducing the spread of these microorganisms along the meat chain via carcasses and meat.…”

Section: The Resistome Of Food Productsmentioning

confidence: 99%

“…Sanitation protocols are designed to remove a significant proportion of the microorganisms found in slaughterhouses and meat cutting plants, thereby reducing the spread of these microorganisms along the meat chain via carcasses and meat. However, a small fraction may still remain viable and contaminate meat, potentially impacting the safety of the product (Alvarez‐Molina et al., 2023 ; Li, Xiao, et al., 2022 ).…”

Section: The Resistome Of Food Productsmentioning

confidence: 99%

The resistome of the food chain: A One Health perspective

Fernández‐Trapote,

Oliveira,

Cobo‐Díaz

et al. 2024

Microbial Biotechnology

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Antimicrobial resistance (AMR) represents a significant global health problem which challenges Sustainable Development Goal 3 of the United Nations, with growing concerns about the possibility of AMR transmission through the food chain. The indiscriminate use of antimicrobials for the treatment of food production animals and for agricultural crop improvement, in addition to the direct discharge of livestock farm residues to sewage and the use of animal manure in agriculture, are among the factors that can facilitate the selection and transmission of AMR throughout the food chain. The study of food microbiomes has been boosted by the advent of next‐generation sequencing techniques, which have enabled gaining in‐depth understanding of the diversity of antimicrobial resistance genes present in food and associated environments (the so‐called resistome). The aim of this review is to provide an accurate and comprehensive overview of the knowledge currently available on the resistome of the most frequently consumed foods worldwide, from a One Health perspective. To this end, the different metagenomic studies which have been conducted to characterize the resistome of foods are compiled and critically discussed.

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