FARMED

FARMED: Fast Antimicrobial Resistance and Mobile-Element Detection using metagenomics for animal and human on-site tests

Start: 1 January 2020
Duration: 2.5 Years
Domain: Antimicrobial Resistance
Key Words: metagenomics, pathogen detection, mobile genetic elements
Contact: Manal AbuOun (APHA)

The Project #FARMED

Antimicrobial resistance (AMR) threatens some of the greatest medical advances in modern times. Current AMR and pathogen detection is primarily reliant on classical culturing techniques, which may be slow. The development of new tools for real-time detection of resistant pathogens is a priority topic of the One Health EJP. On-site and real-time analysis requires independence from culturing techniques to facilitate rapid interventions, especially during outbreaks. Furthermore, it requires robust protocols using minimal technical equipment that can be used outside of the normal laboratory environment. Metagenomic sequencing using short-read data can detect the composition of microbial communities for the assessment of potential pathogens and AMR or virulence genes, which could become an invaluable diagnostic tool. However, short-read technologies cannot reliably associate individual genes in a community to specific organisms and is a potential limitation for detecting AMR in pathogens.

The FARMED project aims to address these issues by using the ONT MinION, comparing this technology to other metagenomic sequencing technologies, and assessing its ability for diagnostic use on a range of sample matrices within both the laboratory and the field. Using long-read metagenomic sequencing, the local genetic context of AMR genes can be derived, and as such, the presence of the AMR genes can be attributed to specific species and plasmids, within the bacterial community. This technology will enable the identification of a plethora of bacterial species and linkage of particular species to a range of AMR genes. We will create harmonised protocols for on-site metagenomic DNA extraction and sequencing library preparation on the MinION. We will simultaneously adapt existing methods for DNA extraction with the ONT VolTRAX system. Further, we will develop efficient real-time mapping strategies that identify the origin of the genetic context of AMR genes, identify the host bacterial species to enable specific pathogen detection.

In addition to on-site metagenome analysis, we will investigate and establish best practice for ‘off-site’ analysis of plasmids sequences by comparing with purified isolates. We will compare the use of long-read and short-read data, as well as a combination of the technologies such as Hi-C, to assemble complete plasmids from metagenomics data. Hi-C sequencing is a novel method that uses proximity ligation of DNA molecules to determine the genetic context of AMR genes in relation to linkage to the bacterial host chromosome. Defined communities, containing isolates harbouring known plasmids, will be used to determine whether plasmid sequences can be derived from these metagenomic data.

We will provide an interactive workshop to transfer our extensive wet- and dry-lab experiences, including molecular and bioinformatic expertise, gained from this project. We predict that the methodologies and tools emerging from FARMED will be highly attractive and imminently applicable to a wide range of users beyond the consortium, to rapidly monitor AMR present in pathogens in many different environments. We envisage this technique, will be especially useful in low or middle-income countries where the burden of pathogen occurrence and AMR may be high but there is limited access to specialist or even ‘standard’ laboratory equipment for diagnosis.

Publications

Buytaers, F E., Fraiture, M-A., Berbers, B., Vandermassen, E., Hoffman, S., Papazova, N., Vanneste, K., Marchal, K., Roosens, N H C., De Keersmaecker, S C J. (2021). A shotgun metagenomics approach to detect and characterise unauthorised genetically modified microorganisms in microbial fermentation products. Food Chemistry: Molecular Sciences. 2, 100023. DOI: https://doi.org/10.1016/j.fochms.2021.100023

OpenAIRE Publications

Project Events

Project Kick-off meeting- 13th November 2019, Berlin, Germany

Project Deliverables 

wso shellkadına özelkadın newsbacklink albacklink satışinstagram takipçi hilesimeme küçültmewso shellworld newstatto girlshacklink seoseo analysismakale programıbacklink salessite analysispubg hile alseo sorgulamahacklink panelseo analysisseo sorgulagoogle newshacklink satışbacklinkbacklink satışseo araclarıseo analizsite analizAntalya Escortwebroot shellbypass shellr57 shelladana escortcanlı bahisadana eskortnevşehir escortbedava bonus veren bahis siteleribedava bonusdeneme bonusu30 tl bonus veren bahis sitelerihoşgeldin bonusuhoşgeldin bonusu veren bahis siteleribahis siteleribahiskaçak iddaacanlı bahisTürkçe Bahis Şirketlerisex hikayeleriporno hikayelerkayseri escortpendik escortsex hikayependik escorttuzla escortpendik escortkurtkoy escortkartal escortapartman kamera sistemikamera sistemimaltepe escortporno izleporno izleümraniye escortizmit escort bayankocaeli escort bayanizmit escortc99 shellc99 shellhtml kod şifrelemeseo newshacklinkbacklink alçorlu escortçerkezköy escortsivas escortmanisa escortizmir escorthatay escorterzurum escortbalikesir escorturfa escorttrabzon escorttekirdag escortsamsun escortadana escortankara escortantep escortaydin escortbursa escortdenizli escortsakarya escortordu escortmugla escortdiyarbakir escorteskisehir escortkayseri escortkocaeli escortkonya escortmalatya escortmaras escortmardin escortmersin escortizmir escortankara escortmersin escorteskişehir escortgaziantep escortsakarya escortkayseri escortantalya escortistanbul escortbursa escortadana escortwso shellsite hız testiadıyamanescortafyon escortağrı escortaksaray escortamasya escortardahan escortartvin escortaydın escortbalıkesir escortbartın escortbatman escortbayburt escortbilecik escortbingöl escortbitlis escortçanakkale escortçankırı escortçorum escortdenizli escortdiyarbakır escortdüzce escortedirne escortelazığ escorterzincan escortbolu escortburdur escortgümüşhane escorthatay escortığdır escortısparta escortmaraş escortkarabük escortkars escortkastamonu escortkilis escortkırıkkale escortkırklareli escortkırşehir escortkocaeli escortkonya escortkütahya escortmalatya escortmanisa escortmardin escortmuğla escortmuş escortnevşehir escortniğde escortordu escortosmaniye escortrize escortsamsun escorturfa escortsiirt escortsinop escortşırnak escortsivas escorttekirdağ escorttokat escorttrabzon escorttunceli escortuşak escortvan escortyozgat escortyalova escortzonguldak escortkıbrıs escortpendik escortesenyurt escortzeytinburnu escortküçükçekmece escortbeşiktaş escorttuzla escortbeykoz escortfatih escortsancaktepe escortarnavutköy escortbağcılar escortümraniye escortbeyoğlu escortüsküdar escortesenler escortmecidiyeköy escortsarıyer escortetiler escortlevent escortbebek escortgaziosmanpaşa escortkartal escortbaşakşehir escortşişli escorthalkalı escortbahçelievler escortortaköy escorteyüp escortbahçeşehir escortkağıthane escorttaksim escortçekmeköy escortsultançiftliği escortşaşkınbakkal escortbayrampaşa escortbeylikdüzü escortkadıköy escortataşehir escortbakırköy escortmerter escortataköy escortnişantaşı escortkozyatağı escortavcılar escortbüyükçekmece escortkurtköy escortiçerenköy escortküçükyalı escortbostancı escortşirinevler escorterenköy escortadana escortadıyaman escortafyon escortağrı escortaksaray escortamasya escortankara escortantalya escortardahan escortartvin escortaydın escortbalıkesir escortbartın escortbatman escortbayburt escortbilecik escortbingöl escortbitlis escortbolu escortburdur escortbursa escortçanakkale escortçankırı escortçorum escortdenizli escortdiyarbakir escortdüzce escortedirne escortelazığ escorterzincan escorterzurum escorteskişehir escortantep escortgiresun escortgümüşhane escorthakkari escorthatay escortığdır escortistanbul escortizmir escortkarabük escortkaraman escortkars escortkastamonu escortkayseri escortkıbrıs escortkilis escortkırıkkale escortkırklareli escortkırşehir escortkocaeli escortkonya escortkütahya escortmalatya escortmanisa escortmaraş escortmardin escortmersin escortmuğla escortmuş escortnevşehir escortniğde escortordu escortosmaniye escortrize escortsakarya escortsamsun escortsiirt escortsinop escortmozrankGameloopporno izleçekiliş sitesihtml code encryptionserver scanwso shelloyun indirsunucu taramasite speed testinstagram takipçi hilesiWordpress Free Themeswordpress free temahtml kod şifrelemesunucu taramaTanıtım Yazısıwordpress themesseowordpress ücretsiz temaWho islogsuz shell indirlitespeed bypass shellindoxploit shellphp shellgoogle sıra buluculitespeed bypass shellbacklink sorgulamaeryaman escortistanbul bayan escortankara escorthacklink satışbacklink satışhacklink panelhacklinkerzurum escortgiresun escortbest stethoscoperaycon reviewsBest Dog Crateshapermint bra reviewswireless earbudsBest Gaming Monitorsviagra siparişlifta 20 mgcialis fiyatviagra 100 mg fiyatcialis jelviagra satın alcialis 5 mg fiyatviagra satın alviagra fiyatıdegravigrandedegra 100 mgorcafilcialis nedircialis 20 mg eczane fiyatıcialis fiyatcialis 20 mgcialis 100 mgviagra fiyatliftalifta 5 mghardciscialis eczanecialis 5 mg fiyatıcialis 100 mg fiyatcialis 5 mgviagra fiyatlarıviagra satışonline eczane viagraviagra eczanecialis 20 mgcialis 100 mgcialis hapcialis 20cialis eczanecialis satışcialis fiyatlarıcialis fiyatıviagra fiyatviagra fiyatlarıviagra eczaneviagra satın alpfizer viagra satışonline eczane viagrapfizer viagra satın alviagra siparişviagra sipariş hattıviagra fiyat 2021online viagra siparişviagra fiyat 2021 eczaneviagra fiyat eczanecialis 5 mgkamagra satın alkamagrakamagra jelkamagra jel siparişkamagra siparişkamagra fiyatkamagra jel fiyatıkamagra fiyatıkamagra 100mgkamagra 100mg fiyatsüper kamagrakamagra nedirSincan escortAnkara rus escortsultangazi escortbingöl escortsancaktepe escorteskişehir escortkırklareli escortçekmeköy escortbodrum escortkuşadası escortc99 shellc99 shelllifta 20 mgliftalifta 20lifta 20 mg nedirlifta nedirhacklink seokuşadası escortbeylikdüzü escortkarşıyaka escortgöztepe escortbornova escortçeşme escortbuca escortalsancak escortkonak escort