{"type": "FeatureCollection", "features": [{"id": "10.1016/j.ijfoodmicro.2021.109043", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-22T16:16:07Z", "type": "Journal Article", "created": "2021-01-08", "title": "Unraveling the emergence and population diversity of Listeria monocytogenes in a newly built meat facility through whole genome sequencing", "description": "The food processing environments of a newly opened meat processing facility were sampled in ten visits carried out during its first 1.5\u00a0years of activity and analyzed for the presence of Listeria monocytogenes. A total of 18 L. monocytogenes isolates were obtained from 229 samples, and their genomes were sequenced to perform comparative genomic analyses. An increase in the frequency of isolation of L. monocytogenes and in the diversity of sequence types (STs) detected was observed along time. Although the strains isolated belonged to six different STs (ST8, ST9, ST14, ST37, ST121 and ST155), ST9 was the most abundant (8 out of 18 strains). Low (0 and 2) single nucleotide polymorphism (SNP) distances were found between two pairs of ST9 strains isolated in both cases 3\u00a0months apart from the same processing room (Lm-1267 and Lm-1705, with a 2 SNPs distance in the core genome; Lm-1265 and Lm-1706, with a 0 SNPs distance), which suggests that these strains may be persistent L. monocytogenes strains in the food processing environment. Most strains showed an in silico attenuated virulence potential either through the truncation of InlA (in 67% of the isolates) or the absence of other virulence factors involved in cell adhesion or invasion. Twelve of the eighteen L. monocytogenes isolates contained a plasmid, which ranged in size from 4 to 87 Kb and harbored stress survival, in addition to heavy metals and biocides resistance determinants. Identical or highly similar plasmids were identified for various sets of L. monocytogenes ST9 isolates, which suggests the clonal expansion and persistence of plasmid-containing ST9 strains in the processing environments of the meat facility. Finally, the analysis of the L. monocytogenes genomes available in the NCBI database, and their associated metadata, evidenced that strains from ST9 are more frequently reported in Europe, linked to foods, particularly to meat and pork products, and less represented among clinical isolates than other L. monocytogenes STs. It also showed that the ST9 strains here isolated were more closely related to the European isolates, which clustered together and separated from ST9 North American isolates.", "keywords": ["0301 basic medicine", "Meat", "Food Handling", "Swine", "Virulence Factors", "Tecnolog\u00eda de los alimentos", "Food processing environment", "Persistence", "03 medical and health sciences", "Manufacturing and Industrial Facilities", "Floors and Floorcoverings", "Animals", "2. Zero hunger", "0303 health sciences", "Virulence", "Whole Genome Sequencing", "Genetic Variation", "Gen\u00e9tica", "Listeria monocytogenes", "Europe", "Genes", " Bacterial", "Whole genome sequencing", "Food Microbiology", "Equipment Contamination", "Disinfectants", "Plasmids"]}, "links": [{"href": "https://doi.org/10.1016/j.ijfoodmicro.2021.109043"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/International%20Journal%20of%20Food%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.ijfoodmicro.2021.109043", "name": "item", "description": "10.1016/j.ijfoodmicro.2021.109043", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.ijfoodmicro.2021.109043"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-02-01T00:00:00Z"}}, {"id": "10.1146/annurev-food-052720-010751", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-22T16:18:13Z", "type": "Journal Article", "created": "2021-10-22", "title": "Next-generation food research: Use of meta-omic approaches for characterizing microbial communities along the food chain", "description": "<p> Microorganisms exist along the food chain and impact the quality and safety of foods in both positive and negative ways. Identifying and understanding the behavior of these microbial communities enable the implementation of preventative or corrective measures in public health and food industry settings. Current culture-dependent microbial analyses are time-consuming and target only specific subsets of microbes. However, the greater use of culture-independent meta-omic approaches has the potential to facilitate a thorough characterization of the microbial communities along the food chain. Indeed, these methods have shown potential in contributing to outbreak investigation, ensuring food authenticity, assessing the spread ofantimicrobial resistance, tracking microbial dynamics during fermentation and processing, and uncovering the factors along the food chain that impact food quality and safety. This review examines the community-based approaches, and particularly the application of sequencing-based meta-omics strategies, for characterizing microbial communities along the food chain. </p>", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "High-throughput sequencing", "Food Chain", "Food microbiome", "Microbiota", "high-throughput sequencing", "Meta-omic approaches", "food processing environment", "3. Good health", "meta-omic approaches", "03 medical and health sciences", "food-processing environment", "food microbiome; food-processing environment; high-throughput sequencing; meta-omic approaches; Fermentation; Food Industry; Food Chain; Microbiota", "food microbiome", "Fermentation", "Food Industry", "Food-processing environment"]}, "links": [{"href": "https://www.annualreviews.org/doi/pdf/10.1146/annurev-food-052720-010751"}, {"href": "https://doi.org/10.1146/annurev-food-052720-010751"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Annual%20Review%20of%20Food%20Science%20and%20Technology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1146/annurev-food-052720-010751", "name": "item", "description": "10.1146/annurev-food-052720-010751", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1146/annurev-food-052720-010751"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-03-25T00:00:00Z"}}, {"id": "10.1186/s40168-021-01131-9", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-22T16:18:16Z", "type": "Journal Article", "created": "2021-10-14", "title": "Microbial colonization and resistome dynamics in food processing environments of a newly opened pork cutting industry during 1.5 years of activity", "description": "AbstractBackground<p>The microorganisms that inhabit food processing environments (FPE) can strongly influence the associated food quality and safety. In particular, the possibility that FPE may act as a reservoir of antibiotic-resistant microorganisms, and a hotspot for the transmission of antibiotic resistance genes (ARGs) is a concern in meat processing plants. Here, we monitor microbial succession and resistome dynamics relating to FPE through a detailed analysis of a newly opened pork cutting plant over 1.5 years of activity.</p>Results<p>We identified a relatively restricted principal microbiota dominated byPseudomonasduring the first 2 months, while a higher taxonomic diversity, an increased representation of other taxa (e.g.,Acinetobacter,Psychrobacter), and a certain degree of microbiome specialization on different surfaces was recorded later on. An increase in total abundance, alpha diversity, and \uffce\uffb2-dispersion of ARGs, which were predominantly assigned toAcinetobacterand associated with resistance to certain antimicrobials frequently used on pig farms of the region, was detected over time. Moreover, a sharp increase in the occurrence of extended-spectrum \uffce\uffb2-lactamase-producingEnterobacteriaceaeand vancomycin-resistantEnterococcaceaewas observed when cutting activities started. ARGs associated with resistance to \uffce\uffb2-lactams, tetracyclines, aminoglycosides, and sulphonamides frequently co-occurred, and mobile genetic elements (i.e., plasmids, integrons) and lateral gene transfer events were mainly detected at the later sampling times in drains.</p>Conclusions<p>The observations made suggest that pig carcasses were a source of resistant bacteria that then colonized FPE and that drains, together with some food-contact surfaces, such as equipment and table surfaces, represented a reservoir for the spread of ARGs in the meat processing facility.</p>", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Bacteria", "Food Handling", "Swine", "Tecnolog\u00eda de los alimentos", "Research", "QR100-130", "610", "Food processing environments", "Antimicrobial resistance", "Gen\u00e9tica", "630", "Anti-Bacterial Agents", "Microbial ecology", "Red Meat", "03 medical and health sciences", "Genes", " Bacterial", "Pork Meat", "Animals", "Metagenomics"]}, "links": [{"href": "https://link.springer.com/content/pdf/10.1186/s40168-021-01131-9.pdf"}, {"href": "https://doi.org/10.1186/s40168-021-01131-9"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbiome", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1186/s40168-021-01131-9", "name": "item", "description": "10.1186/s40168-021-01131-9", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1186/s40168-021-01131-9"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-10-14T00:00:00Z"}}], "links": [{"rel": "self", "type": "application/geo+json", "title": "This document as GeoJSON", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=food+processing+environment&f=json", "hreflang": "en-US"}, {"rel": "alternate", "type": "text/html", "title": "This document as HTML", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=food+processing+environment&f=html", "hreflang": "en-US"}, {"rel": "collection", "type": "application/json", "title": "Collection URL", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main", "hreflang": "en-US"}, {"type": "application/geo+json", "rel": "first", "title": "items (first)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=food+processing+environment&", "hreflang": "en-US"}, {"rel": "last", "type": "application/geo+json", "title": "items (last)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=food+processing+environment&offset=3", "hreflang": "en-US"}], "numberMatched": 3, "numberReturned": 3, "distributedFeatures": [], "timeStamp": "2026-09-23T02:46:52.039009Z"}