Codes4strains: Tracking bacterial pathogens through sources, geography and time using stable phylogenetically informative genome codes

Start: October 2019
Duration: 3 Years
Domain: Foodborne Zoonoses, Antimicrobial Resistance
Members: IP, INRA, ANSES- France, PHE- UK
Contact: Dr Sylvain Brisse (IP)

The Project

The implementation of genome sequencing in public health microbiology has allowed the natural variation exhibited by pathogenic bacteria to be leveraged for infectious disease surveillance and outbreak detection. Genotype information derived from WGS allows the monitoring of pathogenic potential and the tracking of epidemic behaviour, to inform infection control, diagnostic and treatment practice. To track strains globally, and as they spread between the environment, food, animals and humans, universal strain nomenclatures are necessary. Two main strain nomenclatures approaches are currently existing. First, core genome Multilocus Sequence Typing (cgMLST) is widely applied for bacterial pathogen surveillance. It relies on predefined gene loci, the sequence variants of which are given unique identifiers (allelic numbers). Resulting allelic profiles are given unique identifiers (cgST) or are grouped based on their similarity, generally using the single-linkage clustering method. An alternative approach known as the SNP address was developed at Public Health England. Different from MLST, it is based on single nucleotide polymorphisms (SNP) compared to a reference genome. Single-linkage clustering is performed based on the resulting SNP distance between isolates. An original concept of the SNP address is to apply several thresholds upon allelic or SNP differences. The ‘address’ is a multi-positions code, where each position corresponds to the cluster membership at descending thresholds of genetic (SNP) distance among strains resulting in a multi-level nomenclature which provides a good approximation of the phylogenetic relatedness among isolates. Likewise, several cgMLST thresholds can be used to provide phylogenetic information on top of classification purposes, as was done for Listeria monocytogenes by the group of the main applicant. Providing multi-level information on phylogenetic relatedness has proved helpful for epidemiological investigations and for prospective surveillance. This has facilitated outbreak detection as well as providing the framework for case/control studies at different diversity levels, depending on the length or complexity of an outbreak. Further, utilising a flexible level of divergence to define an ‘outbreak type’ aids hypothesis generation and may allow in some cases to identify the specific source of the outbreak by maximizing the power of case-control source attribution studies. SNP and cgMLST approaches have complementary characteristics. One strength of the cgMLST approach is its standardized aspect (predefined sets of loci; unlike SNPs, which have proven difficult to standardize), which maximizes the applicability of the method for international or cross-sector strain comparisons where analysis is performed independently. In turn, whole-genome SNPs are more discriminatory than cgMLST, which relies on predefined set of ‘core’ loci. Therefore, SNP and cgMLST should be regarded as two useful approaches to be integrated jointly in future genomic epidemiology strategies. However, one major limitation of current SNP address or multi-level cgMLST classifications is that they utilise single-linkage clustering to define groups. This approach is unstable, as the fusion of predefined groups upon discovery of ‘intermediate’ genotypes is an inherent mathematical property of single-linkage. This issue is pertinent within epidemiological timescales, where intermediate genotypes have a high probability of being sampled. It is our experience in both applicants groups that the fusion of predefined groups is a challenge to handle in practice, and introduces nomenclatural confusion. Currently, no genomic nomenclature system of bacterial pathogens exists that combines complete stability of identifiers, high standardization and reproducibility and high resolution. This gap represents an important barrier to the field of genomic epidemiology and slows down communication and action against the transmission of pathogens across sectors, world regions and over long periods of time.We will address this critical gap in the present PhD project

Mélanie Hennart

About me: My name is Melanie and I am 24 years old. I have a Master’s degree in Bioinformatics and Modelling (BIM) from Sorbonne University since July 2018. My academic background in this multidisciplinary course has allowed me to develop my knowledge of biology and to acquire skills in the field of informatics, such as the use and implementation of bioinformatics tools. I have therefore chosen to focus my scientific profile on methodological development for the analysis of large genomic datasets.

What motivated me to do a PhD: My professional experience in the Unit “Biodiversity and Epidemiology of Bacterial Pathogens” at the Institut Pasteur allowed me to discover the field of molecular epidemiology and reinforced my interest in comparative genomics. In addition, pursuing my doctoral studies will allow me to explore and design methods of bacterial nomenclature that will facilitate communication between different public health actors in the future. This project will allow me to benefit from the expertise of the various laboratories in bacterial population genomics and bioanalysis in the field of microbiology.


Mélanie Hennart has been selected for this exciting PhD project! Welcome to the One Health EJP consortium!





Hennart, M., Panunzi, LG., Rodrigues, C., Gaday, Q., Baines, SL., Barros-Pinkelnig, M., Carmi-Leroy, A., Dazas, M., Wehenkel, AM., Didelot, X., Toubiana, J., Badell, E., Brisse, S. (2020). Population genomics and antimicrobial resistance in Corynebacterium diphtheriae. Genome Medicine. 12, p 1-18. DOI:

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