The increasing emergence of multi-resistant bacteria in healthcare settings, in the community and in the environment represents a major health threat worldwide. In 2016, we started a pilot project to investigate antimicrobial resistance in surface water. Bacteria were enriched, cultivated on selective chromogenic media and species identification was carried out by MALDI-TOF analysis. From a river in southern Austria a methicillin resistant Staphylococcus aureus (MRSA) was isolated. Whole genome sequence analysis identified the isolate as ST8, spa type t008, SCCmecIV, PVL and ACME positive, which are main features of CA-MRSA USA300. Whole genome based cgMLST of the water isolate and comparison to 18 clinical MRSA USA300 isolates from the Austrian national reference laboratory for coagulase positive staphylococci originating from 2004, 2005 and 2016 and sequences of 146 USA300 isolates arbitrarily retrieved from the Sequence Read Archive revealed a close relatedness to a clinical isolate from Austria. The presence of a CA-MRSA USA300 isolate in an aquatic environment might pose a public health risk by serving as a potential source of infection or a source for emergence of new pathogenic MRSA clones.
", "keywords": ["Methicillin-Resistant Staphylococcus aureus", "0301 basic medicine", "METHICILLIN-RESISTANT", "GENES", "TRANSMISSION", "Article", "Applied microbiology", "EMERGENCE", "03 medical and health sciences", "106005 Bioinformatik", "SDG 3 - Good Health and Well-being", "Rivers", "Sequence Homology", " Nucleic Acid", "Infectious-disease epidemiology", "ENVIRONMENT", "0303 health sciences", "ANTIMICROBIAL RESISTANCE", "RESISTANT STAPHYLOCOCCUS-AUREUS", "ANTIBIOTIC-RESISTANCE", "EVOLUTION", "3. Good health", "Community-Acquired Infections", "SDG 3 \u2013 Gesundheit und Wohlergehen", "Austria", "VIRULENCE", "Bacterial infection", "106005 Bioinformatics", "Genome", " Bacterial"]}, "links": [{"href": "https://www.nature.com/articles/s41598-018-27781-8.pdf"}, {"href": "https://doi.org/10.1038/s41598-018-27781-8"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Scientific%20Reports", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41598-018-27781-8", "name": "item", "description": "10.1038/s41598-018-27781-8", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41598-018-27781-8"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-06-21T00:00:00Z"}}, {"id": "10.1038/s41467-019-14197-9", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:18:21Z", "type": "Journal Article", "created": "2020-01-24", "title": "High-quality genome sequence of white lupin provides insight into soil exploration and seed quality", "description": "AbstractWhite lupin (Lupinus albus L.) is an annual crop cultivated for its protein-rich seeds. It is adapted to poor soils due to the production of cluster roots, which are made of dozens of determinate lateral roots that drastically improve soil exploration and nutrient acquisition (mostly phosphate). Using long-read sequencing technologies, we provide a high-quality genome sequence of a cultivated accession of white lupin (2n\uffe2\uff80\uff89=\uffe2\uff80\uff8950, 451\uffe2\uff80\uff89Mb), as well as de novo assemblies of a landrace and a wild relative. We describe a modern accession displaying increased soil exploration capacity through early establishment of lateral and cluster roots. We also show how seed quality may have been impacted by domestication in term of protein profiles and alkaloid content. The availability of a high-quality genome assembly together with companion genomic and transcriptomic resources will enable the development of modern breeding strategies to increase and stabilize white lupin yield.
", "keywords": ["Repetitive Sequences", " Nucleic Acid/genetics", "0301 basic medicine", "[SDV]Life Sciences [q-bio]", "Plant Roots/genetics", "Gene Dosage", "Plant Science", "Crop", "Alkaloids/chemistry", "Plant Roots", "Gene", "Repetitive Sequences", "630", "Agricultural and Biological Sciences", "Domestication", "Soil", "Models", "Symbiotic Nitrogen Fixation in Legumes", "Gene Duplication", "[SDV.BV] Life Sciences [q-bio]/Vegetal Biology", "http://aims.fao.org/aos/agrovoc/c_3224", "Plant Proteins/metabolism", "Plant Proteins", "2. Zero hunger", "0303 health sciences", "Genome", "Q", "http://aims.fao.org/aos/agrovoc/c_27583", "Life Sciences", "Transcriptome/genetics", "http://aims.fao.org/aos/agrovoc/c_92382", "Polymorphism", " Single Nucleotide/genetics", "Lupinus", "[SDV] Life Sciences [q-bio]", "Protein Crop", "Seeds", "http://aims.fao.org/aos/agrovoc/c_5956", "White (mutation)", "Single Nucleotide/genetics", "Sequence Analysis", "Genome", " Plant", "expression des g\u00e8nes", "http://aims.fao.org/aos/agrovoc/c_4464", "Synteny/genetics", "Evolution", "Lupin Seeds", "Science", "Centromere", "Lupinus/genetics", "Polymorphism", " Single Nucleotide", "Article", "g\u00e9nomique", "Evolution", " Molecular", "Evolution and Nutritional Properties of Lupin Seeds", "physiologie v\u00e9g\u00e9tale", "03 medical and health sciences", "Alkaloids", "Genetic", "Nucleic Acid/genetics", "Seeds/physiology", "Centromere/genetics", "Genetics", "[SDV.BV]Life Sciences [q-bio]/Vegetal Biology", "Polymorphism", "Biology", "Ecology", " Evolution", " Behavior and Systematics", "Repetitive Sequences", " Nucleic Acid", "Sequence assembly", "http://aims.fao.org/aos/agrovoc/c_25189", "Ecotype", "Models", " Genetic", "g\u00e9nome", "Botany", "Molecular", "Genetic Variation", "Molecular Sequence Annotation", "Plant", "DNA", "Sequence Analysis", " DNA", "s\u00e9quence nucl\u00e9otidique", "15. Life on land", "http://aims.fao.org/aos/agrovoc/c_27527", "Agronomy", "Plant Leaves", "Evolution and Ecology of Endophyte-Grass Symbiosis", "Lupinus albus", "FOS: Biological sciences", "Genomic Structural Variation", "Plant Leaves/metabolism", "Gene expression", "Transcriptome", "am\u00e9lioration des plantes"]}, "links": [{"href": "https://www.nature.com/articles/s41467-019-14197-9.pdf"}, {"href": "https://doi.org/10.1038/s41467-019-14197-9"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Nature%20Communications", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41467-019-14197-9", "name": "item", "description": "10.1038/s41467-019-14197-9", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41467-019-14197-9"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-01-24T00:00:00Z"}}, {"id": "21.15107/rcub_nardus_23157", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-27T16:26:55Z", "type": "Report", "title": "Optimization of the method for Loop-mediated isothermal amplification (LAMP) of nucleic acids for field detection of food- and waterborne pathogens", "description": "The UN Food and Agriculture Organization (FAO) estimates that by 2050 there will be close to 10 billion people on Earth. The major global challenge is how to provide enough food for everyone, that is safe, ample and produced in a sustainable way. In regard to food safety, large-scale epidemics of foodborne diseases are a persistent threat to public health, as the number of food- and waterborne diseases significantly increases year by year, resulting in the on-going global public health issue. Foodand waterborne microbiological pathogens can be found in a variety of foodstuffs, and their early detection is extremely important to increase overall food safety, and to prevent enormous economic losses. The problems with health-unsafe food in the last 20 years, and a related rise in food poisoning cases internationally, have led to a growing and urgent demand for safe food products that will not pose a danger to consumers. On the other hand, it is equally important to ensure the absence of microbiological pathogens in the whole process of food production e.g. during crop cultivation where it is very important to perform early detection of pathogens to prevent their further spread and avoid the negative effects on yield and quality of crops or during food processing and storage. Classical microbiological cultivation methods are still considered the 'gold standard' in detection of different types of pathogens (bacteria, viruses, pathogenic fungi) during quality analysis, due to their sensitivity, relative low cost and ability to generate qualitative and quantitative information regarding the number and nature of microorganisms of a different origin. However, what is considered perhaps the biggest drawback of these methods is the fact that they require at least 3-4 days to get the first results, and even up to 7 days for confirmatory results. In addition, there are pathogens that cannot be cultivated i.e., so-called viable but non-culturable - VBNC pathogens that do not have the ability to form visible colonies, which further hinders the ability to use classical microbiological cultivation methods for their detection. Application of polymerase chain reaction, i.e. PCR, changed the way microbiological analyses are performed in the direction of detecting specific microbial DNA as a target. PCR-based methods that detect pathogen-derived nucleic acids are faster (last up to several hours), very reliable and allow the analysis of VBNC pathogens. However, these techniques depend on precise instruments, clean working conditions and hence, cannot be used in the field. In addition, PCR can give falsepositive or false-negative results due to the use of nonspecific primers or to the lack of differentiation between nucleic acids of the living (active) and dead (inactive) cells. To address these challenges, the primary focus of this doctoral dissertation is on development and optimization of innovative nucleic acid based methods for rapid detection of pathogens in food and water. More specifically, the research focus of the dissertation is the application of the isothermal loop-mediated amplification (LAMP) method, which allows for fast, simple, and reliable field detection. This approach for detection of pathogens in food of animal and plant origin and in the environment corresponds to the \u201cOne health\u201d paradigm, recommended by the FAO, that is encompassing methods of optimizing the health and well-being of people, animals, plants and environment. In line with this, the primary objectives (O) of this doctoral dissertation have been formulated as follows: O1) To perform advanced development of the LAMP method for research and potential practical purposes in order to detect pathogens in different complex matrices comprising foodstuffs (meat and vegetable), water, and soil-like matrix; O2) to determine applicability of the LAMP method for river water quality assessment as advised by the One health paradigm; O3) to improve and optimize procedures for nucleic acid (NA) isolation in order to enable rapid extraction in the field conditions and O4) comparison of the efficiency of the developed LAMP protocols versus both the conventional cultivation methods and the PCR method as the \u201cgold standard\u201d for NA amplification-based analyses. O1 formulated in the above described way comprises O1.1) establishing clearly defined protocols for LAMP detection of bacterial pathogens in various food matrices using Klebsiella aerogenes species as a model system; The protocol development includes de novo design of the specific primers, and O1.2) developing LAMP protocol for early detection of pathogenic fungi Trichoderma spp. in soil-like matrix. The protocol development includes de novo design of the specific primers. Final protocol includes implementation of colorimetric detection of the LAMP products using gold nanoparticles, thereby increasing the technology readiness level (TRL) for real-life application of the developed protocol. O2 focuses on evaluating the potential application of the LAMP method in detecting fecal indicator bacteria (FIB), such as E. coli, for river water quality assessment. O3 deals with enhancing extraction protocols for rapid DNA isolation O3.1.1) from the foodstuffs and O3.1.2) from soil-like real-life samples (Chelex 100 method) and O3.2) from highly contaminated river water samples (a syringe-based DNA isolation method) and provides evaluation of developed protocols for application in the field conditions. O4 aims to provide conclusions on the applicability of developed LAMP protocols for use in early detection of pathogens of bacterial and fungal origin, in field conditions. The key conclusions derived from the research conducted in this dissertation are that the LAMP method has been successfully optimized for the specific detection of K. aerogenes and Trichoderma spp. in various types of real-life samples. Additionally, the LAMP protocol development included design of novel LAMP primers for both K. aerogenes and Trichoderma spp. as the primer sequences for these pathogens were not found in the literature. The developed LAMP procedures using novel primers are characterized by high sensitivity and low detection limits for all tested samples, as well as with better efficiency compared to the PCR method. These aspects confirm the significant potential of the LAMP method as a diagnostic tool for pathogen detection. Additionally, the field application of the LAMP method combined with the Chelex 100 method for DNA isolation enables practical use of the developed LAMP protocols under various conditions. Furthermore, the results demonstrated that the LAMP method can also be used for detecting E. coli in complex samples such as highly contaminated water, positioning the LAMP method as a very good tool for application following the One Health approach. Notably, the protocols for both LAMP and DNA extraction procedures developed within this thesis still require further increase in TRL before commercial field applications. Taking all of the above into account, this dissertation represents a significant contribution to the research on molecular detection methods and development of innovative diagnostic tools for enhancing food and water safety, that can be of significant importance in addressing the global challenge of ensuring safe food and sustainable environment for the growing population. Further research and application of these methods may greatly contribute to food poisoning prevention, public health and environmental management, as defined in the \u201cOne health\u201d agenda.", "keywords": ["LAMP; isothermal method; nucleic acids; detection of pathogenic microorganisms; food safety; food security; field detection"]}, "links": [{"href": "https://doi.org/21.15107/rcub_nardus_23157"}, {"rel": "self", "type": "application/geo+json", "title": "21.15107/rcub_nardus_23157", "name": "item", "description": "21.15107/rcub_nardus_23157", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/21.15107/rcub_nardus_23157"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2025-05-28T00:00:00Z"}}], "links": [{"rel": "self", "type": "application/geo+json", "title": "This document as GeoJSON", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=+Nucleic+Acid&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=+Nucleic+Acid&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=+Nucleic+Acid&", "hreflang": "en-US"}, {"rel": "last", "type": "application/geo+json", "title": "items (last)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=+Nucleic+Acid&offset=3", "hreflang": "en-US"}], "numberMatched": 3, "numberReturned": 3, "distributedFeatures": [], "timeStamp": "2026-07-27T17:01:38.060163Z"}