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HAVBRUK2-Stort program for havbruksforskning

Mattrygghet:Developing fish-food safety control measures against antimicrobial resistance by reprogramming metabolism in farmed fish

Alternative title: Utvikling av kontrolltiltak for overføring av antimikrobiell resistens fra fisk ved omprogrammering av bakterienes stoffskifte

Awarded: NOK 5.0 mill.

DURATION: The project started on 15th September 2022 and is expected to end 14 September 2024. Although the funding duration by the Research council of Norway was supposed to start on 1st January 2022, we could not start because the Faculty of Veterinary Medicine at the Norwegian University of Life Sciences (NMBU) was in the process of moving from the Adamstuen Campus in Oslo to the NMBU campus in Ås. As a result, old equipment was discarded while new laboratory equipment was being installed at the new Campus in Ås during the period January to August 2021. Therefore, we advised to wait because it was not conducive to start the new project during this period until after moving to the New Building having functional equipment at Campus Ås in August 2021. Thus, we employed the Researcher after moving to Campus Ås on 15th September 2021. This was the start of the project with an expected completion date of 14th September 2024. SUMMARY OF ACTIVITIES: Antimicrobial resistance (AMR) has increased to be one of the biggest global health threats. Many AMR bacteria enter the food chain from farmed animals and a control strategy is to reduce transmission of AMR from food to humans. In the present study, we have collected fish samples from the freshwater and marine stages of the Atlantic salmon production cycle for screening of AMR genes using metagenomics analysis. In addition, fish food samples were obtained from fish processing industry? and retail shops. Currently, bacteria isolation and characterization using standard bacteriology procedures, MALD-TF and 16S rRNA is going on. Using the bacteria species identified from some of the samples collected this far compared with archived bacterial isolates, our preliminary findings show that some of the archived Aeromonas spp. collected from fish and the environment in Norway before the mid-1990s had tetracycline resistance genes and yet no tetracycline resistance genes were detected from bacteria isolates collected after 2000. These findings point to a considerable reduction in the prevalence of AMR in Norwegian aquaculture. In addition, our preliminary findings also show that that Aeromonas spp. found in marine sediments carry different intrinsic AMR genes that are found in the chromosomes. These genes are not easily transferred to other species because the Aeromonas spp. examined this far were found not to carry plasmids response for horizontal gene transfer. However, more analysis is going on using environment samples and fish samples. Currently, DNA extraction is ongoing and samples will be sent for metagenomics sequencing to the Norwegian sequencing centre. Bioinformatics analysis will done by the Post-Doctoral Scientist employed on the Project together with the Project Manager. The results from this study will be used for the reversal of AMR in zebrafish and Atlantic salmon experiments using nutrient metabolites as planned in the project activities. MILESTONES: 1. PROJECT MANAGEMENT: Project planning and coordination meeting Norwegian and Chinese partners a. October 2021 b. May 2022 c. October 2022 2. SAMPLE COLLECTION: More than 50 bacteria isolated from fish and aquatic environments were characterised biochemically and by PCR. 3. LABORATORY ANALYSIS: All 50 bacteria isolates were tested against important antibiotics listed by the World Health Organizations as priority using disk diffusion assay. 4. LABORATORY ANALYSIS: 24 bacteria showing multiple drug resistance were further used for DNA extraction and whole genome sequencing using the Illumina platform at the Norwegian sequencing centre, University of Oslo. 5. Bioinformatic analysis: 24 Multiple drug resistance (MDR) bacteria genome sequences including Aeromonas salmonicida, Aeromonas hydrophila, Aeromonas veronii, Aliivibrio salmonicida and deposited at NCBI with accession number: • JAJVCT000000000-JAJVCY000000000, • JAKZZS000000000-JAKZZZ000000000, • JAKZZL000000000-JAKZZM000000000, • JAKKZO000000000-JAKKZR000000000, • JALLAB000000000-JALLAC000000000, • JAKZZN000000000. 6. The antimicrobial resistance genes found in the bacterial genome were compared with the GenBank database which resulted in two manuscripts published, one submitted two are in pipeline (List are given below). 7. Course attended by the Post-Doctoral Scientist: a. Antibiotic and Antibiotic resistance: Organized by The National Graduate School in Infection Biology and Antimicrobials (IBA), University of Oslo and NDPIA, Sweden. b. Principles of Infection Biology: The National Graduate School in Infection Biology and Antimicrobials (IBA), University of Oslo https://iba2021.ipostersessions.com/GetFile.ashx?file=meetingagendaiba.pdf c. Orion HPC Workshop in bioinformatic analysis at NMBU November 7-9, 2022.

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This project application addresses an emerging global challenge on antimicrobial resistance (AMR) as a food safety threat. Transmission of AMR-infections through fish-foods to humans has become a serious global food safety threat. Tilapia (Oreochromis niloticus) and Atlantic salmon (Salmo salar L) are among the top farmed fish species in the world of which China and Norway are leading producers. In this project, we intend to develop control measures against AMR in fish foods. As a first step, we will develop a metagenomics surveillance system for profiling AMR-genes found in the fish-food-production chain using samples from fish farms, feed, processed and ready-to-eat fish foods. Using this approach, we aim to determine the relative abundance of all AMR-genes present in food samples to identify stages in the fish-food-production chain prone to AMR-contamination. We will rank all AMR-genes detected based on the World Health Organization (WHO) classification of critical, highly and important resistance to antimicrobial treatment. This classification will be used to identify high-risk areas of human exposure to AMR-infections. We aim to identify high risk stages in the fish-food production chain that require intervention to prevent transmission of AMR-pathogens to humans. Bacteria identified to be antibiotic resistant by metagenomics will be isolated and cultured from collected samples. In the second step, we intend to use the host metabolites reprogramming approach to equip fish with the ability to reverse antibiotic resistant bacteria to highly susceptible bacteria using nutrient metabolites. Identification of appropriate metabolites will be done by gas-chromatography, mass-spectrometry and cluster analysis on antibiotic resistant bacteria isolated from the fish-food production chain. Metabolites with highest reversal of antibiotic resistant bacteria to highly susceptible bacteria will be used for host metabolism reprograming in Atlantic salmon and tilapia.

Funding scheme:

HAVBRUK2-Stort program for havbruksforskning

Thematic Areas and Topics

Global helseAnvendt forskningFNs BærekraftsmålMål 3 God helseFNs BærekraftsmålMål 2 Utrydde sultPortefølje Demokrati og global utviklingGlobal helseGlobal helse ErnæringLTP3 Muliggjørende og industrielle teknologierBioteknologiLTP3 Nano-, bioteknologi og teknologikonvergensLTP3 Global utvikling, ulikhet, og demokratibyggingMarinMarin bioteknologiLTP3 HelseResponsible Research & InnovationRRI MedvirkningBioteknologiMarin bioteknologiResponsible Research & InnovationLTP3 Fagmiljøer og talenterFNs BærekraftsmålPortefølje Muliggjørende teknologierInternasjonaliseringInternasjonalt prosjektsamarbeidPortefølje Banebrytende forskningHelseGrunnforskningLTP3 Bioøkonomi og forvaltningBransjer og næringerFiskeri og havbrukPortefølje HelseAntimikrobiell resistensLTP3 Et kunnskapsintensivt næringsliv i hele landetHavbrukAnnen havbruksrelevant forskningDelportefølje KvalitetBioøkonomiØvrig bioøkonomiLTP3 Hav og kystLTP3 Rettede internasjonaliseringstiltakBioøkonomiBransjer og næringerMarinHavbrukMarinDelportefølje Et velfungerende forskningssystemDelportefølje InternasjonaliseringPolitikk- og forvaltningsområderMatMat - Blå sektorInternasjonaliseringInternasjonalt samarbeid om utlysningHavbrukPolitikk- og forvaltningsområderFiskeri og kystPolitikk- og forvaltningsområderSkog, landbruk og matLTP3 Marine bioressurser og havforvaltningInternasjonaliseringPortefølje ForskningssystemetLTP3 Samfunnsikkerhet, sårbarhet og konfliktKlimarelevant forskningLTP3 Styrket konkurransekraft og innovasjonsevneLTP3 Høy kvalitet og tilgjengelighetMatLTP3 Klima, miljø og energiPortefølje Mat og bioressurserLTP3 Samfunnssikkerhet og beredskapMatTrygg verdikjede