Activités de recherche du CNR des Escherichia coli, Shigella, Salmonella

Les recherches de l’Unité des Bactéries Pathogènes Entériques concernent, la structure et l’évolution génétique des populations bactériennes entéropathogènes (E. coli, Shigella, Salmonella et vibrions), en particulier les populations émergentes, et/ou épidémiques et/ou résistantes aux antibiotiques et le développement de nouveaux outils diagnostiques.
Le séquençage complet de génome bactérien est désormais utilisé en routine dans les CNR de l’Institut Pasteur.

LISTE DES PUBLICATIONS DU CENTRE NATIONAL DE RÉFÉRENCE DES E. COLI, SHIGELLA ET SALMONELLA

• Cointe A, Mariani-Kurkdjian P, Bonacorsi S. Conduite à tenir et prise en charge d’un patient présentant une gastroentérite à Escherichia coli entérohémorragique. Revue de Biologie Médicale /N° 364 – 2021, Janv-Fev 2022.
• Yassine I, Lefèvre S, Hansen EE, Ruckly C, Carle I, Lejay-Collin M, Fabre L, Rafei R, Clermont D, Pardos de la Gandara M, Dabboussi F, Thomson NR, Weill FX. Population structure analysis and laboratory monitoring of Shigella by core-genome multilocus sequence typing. Nat Commun. 2022 Jan 27;13(1):551.
• Bizot E, Cointe A, Smadja N, Sergentet D, Lefèvre S, Weill FX, Levy C, Cohen R, Mariani-Kurkdjian P, Bonacorsi S. Improved Molecular Diagnosis and Culture of the Emerging Heteropathotype Enterohemorrhagic Escherichia coli O80:H2 Using Its Non-Melibiose-Fermenting and Antibiotic-Resistance Properties. J Clin Microbiol. 2022 Jan 19;60(1):e0153021.
• Bizot E, Cointe A, Bidet P, Mariani-Kurkdjian P, Hobson CA, Courroux C, Liguori S, Bridier-Nahmias A, Magnan M, Merimèche M, Caméléna F, Berçot B, Weill FX, Lefèvre S, Bonacorsi S, Birgy A. Azithromycin Resistance in Shiga Toxin-Producing Escherichia coli in France between 2004 and 2020 and Detection of mef(C)-mph(G) Genes. Antimicrob Agents Chemother. 2022 Feb 15;66(2):e0194921.
• Cherchame E, Guillier L, Lailler R, Vignaud ML, Jourdan-Da Silva N, Le Hello S, Weill FX, Cadel-Six S. Salmonella enterica subsp. enterica Welikade: guideline for phylogenetic analysis of serovars rarely involved in foodborne outbreaks. BMC Genomics. 2022 Mar 19;23(1):217.
• Larkin L, Pardos de la Gandara M, Hoban A, Pulford C, Jourdan-Da Silva N, de Valk H, Browning L, Falkenhorst G, Simon S, Lachmann R, Dryselius R, Karamehmedovic N, Börjesson S, van Cauteren D, Laisnez V, Mattheus W, Pijnacker R, van den Beld M, Mossong J, Ragimbeau C, Vergison A, Thorstensen Brandal L, Lange H, Garvey P, Nielsen CS, Herrera León S, Varela C, Chattaway M, Weill FX, Brown D, McKeown P. Investigation of an international outbreak of multidrug-resistant monophasic Salmonella Typhimurium associated with chocolate products, EU/EEA and United Kingdom, February to April 2022. Euro Surveill. 2022 Apr;27(15):2200314.
• Truong J, Cointe A, Le Roux E, Bidet P, Michel M, Boize J, Mariani-Kurkdjian P, Caseris M, Hobson CA, Desmarest M, Titomanlio L, Faye A, Bonacorsi S. Clinical impact of a gastrointestinal PCR panel in children with infectious diarrhoea. Arch Dis Child. 2022 Jun;107(6):601-605.
• De Sousa Violante M, Podeur G, Michel V, Guillier L, Radomski N, Lailler R, Le Hello S, Weill FX, Mistou MY, Mallet L. A retrospective and regional approach assessing the genomic diversity of Salmonella Dublin. NAR Genom Bioinform. 2022 Jul 9;4(3):lqac047.
• Minary K, Tanne C, Kwon T, Faudeux C, Clave S, Langevin L, Pietrement C, Enoch C, Parmentier C, Mariani-Kurkdjian P, Weill FX, Jones G, Djouadi N, Morin D, Fila M. Outbreak of hemolytic uremic syndrome with unusually severe clinical presentation caused by Shiga toxin-producing Escherichia coli O26:H11 in France. Arch Pediatr. 2022 Aug;29(6):448-452.
• Moussiegt A, Birgy A, Cointe A, Duval X, Bidet P, Bonacorsi S. Escherichia coli community-acquired meningitis in adults: a case series of 29 patients in France. Clin Microbiol Infect. 2022 Sep;28(9):1304-1305.
• Falay D, Hardy L, Tanzito J, Lunguya O, Bonebe E, Peeters M, Mattheus W, Van Geet C, Verheyen E, Akaibe D, Katuala P, Ngbonda D, Weill FX, Pardos de la Gandara M, Jacobs J. Urban rats as carriers of invasive Salmonella Typhimurium sequence type 313, Kisangani, Democratic Republic of Congo. PLoS Negl Trop Dis. 2022 Sep 6;16(9):e0010740.
• Li Y, Teng L, Xu X, Li X, Peng X, Zhou X, Du J, Tang Y, Jiang Z, Wang Z, Jia C, Müller A, Kehrenberg C, Wang H, Wu B, Weill FX, Yue M. A nontyphoidal Salmonella serovar domestication accompanying enhanced niche adaptation. EMBO Mol Med. 2022 Nov 8;14(11):e16366.
• Tack B, Phoba MF, Thong P, Lompo P, Hupko C, Desmet S, Martiny D, Mattheus W, Pardos de la Gandara M, Mbuyi-Kalonji L, Kuijpers L, Prevost B, Barbé B, Vandenberg O, Lunguya O, Ruiz J, Jacobs J, Hardy L. Epidemiological cut-off value and antibiotic susceptibility test methods for azithromycin in a collection of multi-country invasive non-typhoidal Salmonella. Clin Microbiol Infect. 2022 Dec;28(12):1615-1623.
• Vignaud ML, Noel V, Saussac M, Pardos de Gándara M, Amat JP, Moury F, Leclerc V, Leblanc JC, Lailler R, Danan C. Approche combinée d’analyses de séries temporelles et génomiques / exemple de la détection d’une augmentation de la présence de Salmonella Goldcoast en filière avicole. Bull Sant Anim Alim. 2021;92 : 1-6.
• Achtman M, Zhou Z, Alikhan NF, Tyne W, Parkhill J, Cormican M, Chiou CS, Torpdahl M, Litrup E, Prendergast DM, Moore JE, Strain S, Kornschober C, Meinersmann R, Uesbeck A, Weill FX, Coffey A, Andrews-Polymenis H, Curtiss Rd R, Fanning S. Genomic diversity of Salmonella enterica -The UoWUCC 10K genomes project. Wellcome Open Res. 2021;5: 223.
• Pulford CV, Perez-Sepulveda BM, Canals R, Bevington JA, Bengtsson RJ, Wenner N, Rodwell EV, Kumwenda B, Zhu X, Bennett RJ, Stenhouse GE, Malaka De Silva P, Webster HJ, Bengoechea JA, Dumigan A, Tran-Dien A, Prakash R, Banda HC, Alufandika L, Mautanga MP, Bowers-Barnard A, Beliavskaia AY, Predeus AV, Rowe WPM, Darby AC, Hall N, Weill FX, Gordon MA, Feasey NA, Baker KS, Hinton JCD. Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa. Nat Microbiol. 2021;6: 327–338.
• Osman M, Papon N, Weill FX. Endocannabinoids attenuate the virulence of certain enteropathogenic bacteria. Trends Microbiol. 2021;29(3): 185-187.
• Mollo B, Hobson CA, Le Hello S, Azria E, Le Monnier A, Pilmis B, Mizrahi A. Intrauterine infection caused by nontyphoidal Salmonella: a literature review. J Matern Fetal Neonatal Med. 2021;34(23): 4000-4004.
• Hawkey J, Paranagama K, Baker KS, Bengtsson RJ, Weill FX, Thomson NR, Baker S, Cerdeira L, Iqbal Z, Hunt M, Ingle DJ, Dallman TJ, Jenkins C, Williamson DA, Holt KE. Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, Shigella sonnei. Nat Commun. 2021;12(1): 2684.
• Nikiema MEM, Pardos de la Gándara M, Compaore KAM, Ky Ba A, Soro KD, Nikiema PA, Barro N, Sangare L, Weill FX. Contamination of street food with multidrug- resistant Salmonella, in Ouagadougou, Burkina Faso. PLoS One. 2021;16(6): e0253312.
• Fabre L, Njamkepo E, Weill FX. Comment on Tanmoy et al. CRISPR-Cas diversity in clinical Salmonella enterica serovar Typhi isolates from South Asian sountries. Genes (Basel). 2021;12(8): 1142.
• Cointe A, Bizot E, Delannoy S, Fach P, Bidet P, Birgy A, Weill FX, Lefèvre S, Mariani-Kurkdjian P, Bonacorsi S. Emergence of new ST301 Shiga toxin-producing Escherichia coli clones harboring extra-intestinal virulence traits in Europe. Toxins (Basel). 2021;13(10): 686.
• Ksibi B, Ktari S, Othman H, Ghedira K, Maalej S, Mnif B, Abbassi MS, Fabre L, Rhimi F, Le Hello S, Hammami A. Comparison of conventional molecular and whole-genome sequencing methods for subtyping Salmonella enterica serovar Enteritidis strains from Tunisia. Eur J Clin Microbiol Infect Dis. 2021;40(3): 597-606.
• Travert B, Rafat C, Mariani P, Cointe A, Dossier A, Coppo P, Joseph A. Shiga toxin-associated hemolytic uremic syndrome: Specificities of adult patients and implications for critical care management. Toxins (Basel). 2021;13(5): 306.
• Denamur E, Clermont O, Bonacorsi S, Gordon D. The population genetics of pathogenic Escherichia coli. Nat Rev Microbiol. 2021;19(1): 37-54.
• Truong J, Cointe A, Le Roux E, Bidet P, Michel M, Boize J, Mariani-Kurkdjian P, Caseris M, Hobson CA, Desmarest M, Titomanlio L, Faye A, Bonacorsi S. Clinical impact of a gastrointestinal PCR panel in children with infectious diarrhoea. Arch Dis Child. 2021;107(6): 601-605.
• Ando N, Sekizuka T, Yokoyama E, Aihara Y, Konishi N, Matsumoto Y, Ishida K, Nagasawa K, Jourdan-Da Silva N, Suzuki M, Kimura H, Le Hello S, Murakami K, Kuroda M, Hirai S, Fukaya S. Whole genome analysis detects the emergence of a single Salmonella enterica serovar Chester clone in Japan's Kanto region. Front Microbiol. 2021;12: 705679.
• Bizot E, Cointe A, Béchet S, Sobral E, Cohen R, Mariani-Kurkdjian P, Levy C, Bonacorsi S. Shiga toxin-producing Escherichia coli carriage in 959 healthy French infants. Arch Dis Child. 2021;106(12): 1239-1240.
• Travert B, Dossier A, Jamme M, Cointe A, Delmas Y, Malot S, Wynckel A, Seguin A, Presne C, Hie M, Benhamou Y, Ribes D, Choukroun G, Grangé S, Hertig A, Le Gall EC, Galicier L, Daugas E, Bouadma L, Weill FX, Azoulay E, Fakhouri F, Veyradier A, Bonacorsi S, Hogan J, Frémeaux-Bacchi V, Rondeau E, Mariani-Kurkdjian P, Coppo P, Centre de Référence des Microangiopathies Thrombotiques. Shiga toxin-associated hemolytic uremic syndrome in adults, France, 2009-2017. Emerg Infect Dis. 2021;27(7): 1876-1885.
• Lignieres G, Birgy A, Jung C, Bonacorsi S, Levy C, Angoulvant F, Grimprel E, Dommergues MA, Gillet Y, Craiu I, Rybak A, De Pontual L, Dubos F, Cixous E, Gajdos V, Pinquier D, Andriantahina I, Soussan-Banini V, Georget E, Launay E, Vignaud O, Cohen R, Madhi F.  Relay oral therapy in febrile urinary tract infections caused by extended spectrum beta-lactamase-producing Enterobacteriaceae in children: A French multicenter study. PLoS One. 2021;16(9): e0257217.
• Bonacorsi S, Visseaux B, Bouzid D, Pareja J, Rao SN, Manissero D, Hansen G, Vila J. Systematic review on the correlation of quantitative PCR cycle threshold values of gastrointestinal pathogens with patient clinical presentation and outcomes. Front Med (Lausanne). 2021;8: 711809.
• Birgy A, Madhi F, Jung C, Levy C, Cointe A, Bidet P, Hobson CA, Bechet S, Sobral E, Vuthien H, Ferroni A, Aberrane S, Cuzon G, Beraud L, Gajdos V, Launay E, Pinquier D, Haas H, Desmarest M, Dommergues MA, Cohen R, Bonacorsi S, Group of the National Observatory of Urinary tract Infection due to ESBL-producing Enterobacteriaceae in children.  Clavulanate combinations with mecillinam, cefixime or cefpodoxime against ESBL-producing Enterobacterales frequently associated with bla_OXA-1 in a paediatric population with febrile urinary tract infections. J Antimicrob Chemother. 2021;76(11): 2839-2846.
• Cointe A, Birgy A, Pascault A, Louillet F, Dufougeray A, Mariani-Kurkdjian P, Bonacorsi S. Be aware of Shiga-toxin 2f-producing Escherichia coli: case report and false-negative results with certain rapid molecular panels. Diagn Microbiol Infect Dis. 2020;98(4): 115177.
• Ktari S, Ksibi B, Ghedira K, Fabre L, Bertrand S, Maalej S, Mnif B, Rhimi F, Le Hello S, Hammami A. Genetic diversity of clinical Salmonella enterica serovar Typhimurium in a university hospital of south Tunisia, 2000-2013. Infect Genet Evol. 2020;85: 104436.
• Payen M, Pardos de la Gándara M, Cointe A, Massiot A, Bidet P, Weill FX, Bonacorsi S. Diagnostic challenge of gastrointestinal infection due to lactose-fermenting Salmonella enterica subsp. enterica serovar 4,5:i:- Diagn Microbiol Infect Dis. 2020;98(2): 115105.
• Cohen R, Madhi F, Levy C, Bonacorsi S. Treatment of urinary tract infections caused by ESBL-producing Enterobacteriaceae: Have all treatment options been considered? Pediatr Infect Dis J. 2020;39(8): e216-e217
• Schwarz C, Brehon A, Mousseaux C, Luque Y, Senet P, Mariani P, Mohamadou I, Zafrani L, Frémeaux-Bacchi V, Rondeau E, Buob D, Rafat C. Ockham's razor defeated: about two atypical cases of hemolytic uremic syndrome. BMC Nephrol. 2020;21(1): 269.
• Castellanos LR, van der Graaf-van Bloois L, Donado-Godoy P, Veldman K, Duarte F, Acuña MT, Jarquín C, Weill FX, Mevius DJ, Wagenaar JA, Hordijk J, Zomer AL. Antimicrobial resistance in Salmonella enterica serovar Paratyphi B variant Java in poultry from Europe and Latin America. Emerg Infect Dis. 2020;26(6): 1164-1173.
• Dortet L, Bonnin RA, Le Hello S, Fabre L, Bonnet R, Kostrzewa M, Filloux A, Larrouy-Maumus G. Detection of colistin resistance in Salmonella enterica using MALDIxin test on the routine MALDI Biotyper Sirius mass spectrometer. Front Microbiol. 2020;11: 1141.
• Goeller C, Desmarest M, Garraffo A, Bonacorsi S, Gaschignard J. Management of febrile urinary tract infection with or without bacteraemia in children: A French case-control retrospective study. Front Pediatr. 2020;8: 237.
• Sévellec Y, Granier SA, Le Hello S, Weill FX, Guillier L, Mistou MY, Cadel-Six S. Source attribution study of sporadic Salmonella Derby cases in France. Front Microbiol. 2020;11: 889.
• Robinson E, Travanut M, Fabre L, Larréché S, Ramelli L, Pascal L, Guinard A, Vincent N, Calba C, Meurice L, Le Thien MA, Fourgere E, Jones G, Fournet N, Smith-Palmer A, Brown D, Le Hello S, Pardos de la Gándara M, Weill FX, Jourdan-Da Silva N. Outbreak of Salmonella Newport associated with internationally distributed raw goats' milk cheese, France, 2018. Epidemiol Infect. 2020;148: e180.
• Cointe A, Birgy A, Bridier-Nahmias A, Mariani-Kurkdjian P, Walewski V, Lévy C, Cohen R, Fach P, Delannoy S, Bidet P, Bonacorsi S. Escherichia coli O80 hybrid pathotype strains producing Shiga toxin and ESBL: molecular characterization and potential therapeutic options. J Antimicrob Chemother. 2020;75(3): 537-542.
• Joseph A, Cointe A, Mariani Kurkdjian P, Rafat C, Hertig A. Shiga toxin-associated hemolytic uremic syndrome: A narrative review. Toxins (Basel). 2020;12(2): 67.
• Birgy A, Madhi F, Jung C, Levy C, Cointe A, Bidet P, Hobson CA, Bechet S, Sobral E, Vuthien H, Ferroni A, Aberrane S, Cuzon G, Beraud L, Gajdos V, Launay E, Pinquier D, Haas H, Desmarest M, Dommergues MA, Cohen R, Bonacorsi S, Group of the National Observatory of Urinary tract Infection due to ESBL-producing Enterobacteriaceae in children. Diversity and trends in population structure of ESBL-producing Enterobacteriaceae in febrile urinary tract infections in children in France from 2014 to 2017. J Antimicrob Chemother. 2020;75(1): 96-105
• Zhou Z, Alikhan NF, Mohamed K, Fan Y, Agama Study Group, Achtman M. The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity. Genome Res. 2020;30(1): 138-152.
• Geslain G, Birgy A, Adiba S, Magnan M, Courroux C, Levy C, Cohen R, Bidet P, Bonacorsi S. Genome sequencing of strains of the most prevalent clonal group of O1:K1:H7 Escherichia coli that causes neonatal meningitis in France. BMC Microbiol. 2019;19(1): 17.
• Breurec S, Reynaud Y, Frank T, Farra A, Costilhes G, Weill FX, Le Hello S. Serotype distribution and antimicrobial resistance of human Salmonella enterica in Bangui, Central African Republic, from 2004 to 2013. PLoS Negl Trop Dis. 2019;13(12): e0007917.
• Ville S, Ydee A, Garandeau C, Canet E, Tissot A, Cantarovich D, Frémeaux-Bacchi V, Mariani-Kurkdjian P, Provôt F, Fakhouri F. Shiga toxin-producing Escherichia coli-associated hemolytic uremic syndrome in solid organ transplant recipients. Kidney Int. 2019;96(6): 1423-1424.
• Gardette M, Le Hello S, Mariani-Kurkdjian P, Fabre L, Gravey F, Garrivier A, Loukiadis E, Jubelin G. Identification and prevalence of in vivo-induced genes in enterohaemorrhagic Escherichia coli. Virulence. 2019;10(1): 180-193.
• Genuini M, Bidet P, Benoist JF, Schlemmer D, Lemaitre C, Birgy A, Bonacorsi S. ShiF acts as an auxiliary factor of aerobactin secretion in meningitis Escherichia coli strain S88. BMC Microbiol. 2019;19(1): 298.
• Radomski N, Cadel-Six S, Cherchame E, Felten A, Barbet P, Palma F, Mallet L, Le Hello S, Weill FX, Guillier L, Mistou MY. A Simple and robust statistical method to define genetic relatedness of samples related to outbreaks at the genomic scale - Application to retrospective Salmonella foodborne outbreak investigations. Front Microbiol. 2019;10: 2413.
• Chung The H, Boinett C, Pham Thanh D, Jenkins C, Weill FX, Howden BP, Valcanis M, De Lappe N, Cormican M, Wangchuk S, Bodhidatta L, Mason CJ, Nguyen TNT, Ha Thanh T, Voong VP, Duong VT, Nguyen PHL, Turner P, Wick R, Ceyssens PJ, Thwaites G, Holt KE, Thomson NR, Rabaa MA, Baker S. Dissecting the molecular evolution of fluoroquinolone-resistant Shigella sonnei. Nat Commun. 2019;10(1): 4828.
• Pouzol S, Tanmoy AM, Ahmed D, Khanam F, Brooks WA, Bhuyan GS, Fabre L, Bryant JE, Gustin MP, Vanhems P, Carman B, Weill FX, Qadri F, Saha S, Endtz H. Clinical evaluation of a multiplex PCR for the detection of Salmonella enterica serovars Typhi and Paratyphi A from blood specimens in a high-endemic setting. Am J Trop Med Hyg. 2019;101(3): 513-520.
• Pulford CV, Perez-Sepulveda BM, Rodwell EV, Weill FX, Baker KS, Hinton JCD. Salmonella enterica serovar Panama, an understudied serovar responsible for extraintestinal salmonellosis worldwide. Infect Immun. 2019;87(9): e00273-19.
• Nadimpalli ML, de Lauzanne A, Phe T, Borand L, Jacobs J, Fabre L, Naas T, Le Hello S, Stegger M. Escherichia coli ST410 among humans and the environment in Southeast Asia. Int J Antimicrob Agents. 2019;54(2): 228-232.
• Criscuolo A, Issenhuth-Jeanjean S, Didelot X, Thorell K, Hale J, Parkhill J, Thomson NR, Weill FX, Falush D, Brisse S. The speciation and hybridization history of the genus Salmonella. Microb Genom. 2019;5(8): e000284.
• Guyomard-Rabenirina S, Weill FX, Le Hello S, Bastian S, Berger F, Ferdinand S, Legreneur P, Loraux C, Malpote E, Muanza B, Richard V, Talarmin A, Breurec S. Reptiles in Guadeloupe (French West Indies) are a reservoir of major human Salmonella enterica serovars. PLoS One. 2019;14(7): e0220145.
• Pijnacker R, Dallman TJ, Tijsma ASL, Hawkins G, Larkin L, Kotila SM, Amore G, Amato E, Suzuki PM, Denayer S, Klamer S, Pászti J, McCormick J, Hartman H, Hughes GJ, Brandal LCT, Brown D, Mossong J, Jernberg C, Müller L, Palm D, Severi E, Gołębiowska J, Hunjak B, Owczarek S, Le Hello S, Garvey P, Mooijman K, Friesema IHM, van der Weijden C, van der Voort M, Rizzi V, Franz E, International Outbreak Investigation Team. An international outbreak of Salmonella enterica serotype Enteritidis linked to eggs from Poland: a microbiological and epidemiological study. Lancet Infect Dis. 2019;19(7): 778-786.
• Hawkey J, Le Hello S, Doublet B, Granier SA, Hendriksen RS, Fricke WF, Ceyssens PJ, Gomart C, Billman-Jacobe H, Holt KE, Weill FX. Global phylogenomics of multidrug-resistant Salmonella enterica serotype Kentucky ST198. Microb Genom. 2019;5(7): e000269.
• Birgy A, Levy C, Nicolas-Chanoine MH, Cointe A, Hobson CA, Magnan M, Bechet S, Bidet P, Cohen R, Bonacorsi S. Independent host factors and bacterial genetic determinants of the emergence and dominance of Escherichia coli sequence type 131 CTX-M-27 in a community pediatric cohort study. Antimicrob Agents Chemother. 2019;63(7): e00382-19.
• Aldrich C, Hartman H, Feasey N, Chattaway MA, Dekker D, Al-Emran HM, Larkin L, McCormick J, Sarpong N, Le Hello S, Adu-Sarkodie Y, Panzner U, Park SE, Im J, Marks F, May J, Dallman TJ, Eibach D. Emergence of phylogenetically diverse and fluoroquinolone resistant Salmonella Enteritidis as a cause of invasive nontyphoidal Salmonella disease in Ghana. PLoS Negl Trop Dis. 2019;13(6): e0007485.
• Jones G, Lefèvre S, Donguy MP, Nisavanh A, Terpant G, Fougère E, Vaissière E, Guinard A, Mailles A, de Valk H, Fila M, Tanné C, Le Borgne C, Weill FX, Bonacorsi S, Jourdan-Da Silva N, Mariani-Kurkdjian P. Outbreak of Shiga toxin- producing Escherichia coli (STEC) O26 paediatric haemolytic uraemic syndrome (HUS) cases associated with the consumption of soft raw cow's milk cheeses, France, March to May 2019. Euro Surveill. 2019;24(22): 1900305.
• Sévellec Y, Felten A, Radomski N, Granier SA, Le Hello S, Petrovska L, Mistou MY, Cadel-Six S. Genetic diversity of Salmonella Derby from the poultry dector in Europe. Pathogens. 2019;8(2): 46.
• Jones G, Pardos de la Gándara M, Herrera-Leon L, Herrera-Leon S, Varela Martinez C, Hureaux-Roy R, Abdallah Y, Nisavanh A, Fabre L, Renaudat C, Mossong J, Mattheus W, Huard C, Le Borgne C, de Valk H, Weill FX, Jourdan-Da Silva N. Outbreak of Salmonella enterica serotype Poona in infants linked to persistent Salmonella contamination in an infant formula manufacturing facility, France, August 2018 to February 2019. Euro Surveill. 2019;24(13): 1900161.
• Caméléna F, Birgy A, Smail Y, Courroux C, Mariani-Kurkdjian P, Le Hello S, Bonacorsi S, Bidet P. Rapid and simple universal Escherichia coli genotyping method based on multiple-locus variable-number tandem-repeat analysis using single-tube multiplex PCR and standard gel electrophoresis. Appl Environ Microbiol. 2019;85(6): e02812-18.
• Cavaco LM, Hansen F, Mushtaq S, Hill RLR, Woodford N, Le Hello S, Hendriksen RS, Hammerum AM, Hasman H. Evaluation of temocillin for phenotypic carbapenemase screening of Escherichia coli and Salmonella enterica isolates in relation to the presence of genes encoding ESBLs and carbapenemase production. J Antimicrob Chemother. 2019;74(3): 639-644.
• Frémeaux-Bacchi V, Sellier-Leclerc AL, Vieira-Martins P, Limou S, Kwon T, Lahoche A, Novo R, Llanas B, Nobili F, Roussey G, Cailliez M, Ulinski T, Deschênes G, Alberti C, Weill FX, Mariani P, Loirat C. Complement gene variants and Shiga toxin-producing Escherichia coli-associated hemolytic uremic syndrome: retrospective genetic and clinical study. Clin J Am Soc Nephrol. 2019;14(3): 364-377.
• Bruyand M, Mariani-Kurkdjian P, Le Hello S, King LA, Van Cauteren D, Lefevre S, Gouali M, Jourdan-da Silva N, Mailles A, Donguy MP, Loukiadis E, Sergentet- Thevenot D, Loirat C, Bonacorsi S, Weill FX, de Valk H, Réseau Français Hospitalier de surveillance du SHU pédiatrique. Paediatric haemolytic uraemic syndrome related to Shiga toxin-producing Escherichia coli, an overview of 10 years of surveillance in France, 2007 to 2016. Euro Surveill. 2019;24(8): 1800068.
• Nadimpalli M, Fabre L, Yith V, Sem N, Gouali M, Delarocque-Astagneau E, Sreng N, Le Hello S, BIRDY study group. CTX-M-55-type ESBL-producing Salmonella enterica are emerging among retail meats in Phnom Penh, Cambodia. J Antimicrob Chemother. 2019;74(2): 342-348.
• Nadimpalli M, Vuthy Y, de Lauzanne A, Fabre L, Criscuolo A, Gouali M, Huynh BT, Naas T, Phe T, Borand L, Jacobs J, Kerléguer A, Piola P, Guillemot D, Le Hello S, Delarocque-Astagneau E, BIRDY study group. Meat and fish as sources of extended-spectrum β-lactamase-producing Escherichia coli, Cambodia. Emerg Infect Dis. 2019;25(1): 126-131.
• Ung A, Baidjoe AY, Van Cauteren D, Fawal N, Fabre L, Guerrisi C, Danis K, Morand A, Donguy MP, Lucas E, Rossignol L, Lefèvre S, Vignaud ML, Cadel-Six S, Lailler R, Jourdan-Da Silva N, Le Hello S. Disentangling a complex nationwide Salmonella Dublin outbreak associated with raw-milk cheese consumption, France, 2015 to 2016. Euro Surveill. 2019;24(3): 1700703.
• Geslain G, Birgy A, Adiba S, Magnan M, Courroux C, Levy C, Cohen R, Bidet P, Bonacorsi S. Genome sequencing of strains of the most prevalent clonal group of O1:K1:H7 Escherichia coli that causes neonatal meningitis in France. BMC Microbiol. 2019;19(1): 17.
• Weill FX, Le Hello S et Grimont PAD Salmonella. In 3^e édition du Précis de bactériologie clinique. Eds : Riegel P, Favennec L, Paugam A, Pozetto B. 2018, Editions ESKA.
• El Sayed F, Sapriel G, Fawal N, Gruber A, Bauer T, Heym B, Dupont C, Garchon HJ, Gaillard JL, Rottman M, Le Hello S. In-host adaptation of Salmonella enterica serotype Dublin during prosthetic hip joint infection. Emerg Infect Dis. 2018;24(12): 2360-2363.
• Cointe A, Birgy A, Mariani-Kurkdjian P, Liguori S, Courroux C, Blanco J, Delannoy S, Fach P, Loukiadis E, Bidet P, Bonacorsi S. Emerging multidrug-resistant hybrid pathotype Shiga toxin-producing Escherichia coli O80 and related strains of clonal complex 165, Europe. Emerg Infect Dis. 2018;24(12): 2262-2269.
• Ingelbeen B, Bruyand M, Mariani-Kurkjian P, Le Hello S, Danis K, Sommen C, Bonacorsi S, de Valk H. Emerging Shiga-toxin-producing Escherichia coli serogroup O80 associated hemolytic and uremic syndrome in France, 2013-2016: Differences with other serogroups. PLoS One. 2018;13(11): e0207492.
• Rincé A, Balière C, Hervio-Heath D, Cozien J, Lozach S, Parnaudeau S, Le Guyader FS, Le Hello S, Giard JC, Sauvageot N, Benachour A, Strubbia S, Gourmelon M. Occurrence of bacterial pathogens and human noroviruses in shellfish-harvesting areas and their catchments in France. Front Microbiol. 2018;9: 2443.
• Sévellec Y, Granier SA, Radomski N, Felten A, Le Hello S, Feurer C, Mistou MY, Cadel-Six S. Complete genome sequence of Salmonella enterica subsp. enterica serotype Derby, associated with the pork sector in France. Microbiol Resour Announc. 2018;7(12):  e01027-18.
• Joseph A, Rafat C, Zafrani L, Mariani-Kurkdjian P, Veyradier A, Hertig A, Rondeau E, Mariotte E, Azoulay E. Early differentiation of Shiga toxin-associated hemolytic uremic syndrome in critically ill adults with thrombotic microangiopathy syndromes. Crit Care Med. 2018;46(9): e904-e911.
• Guyomard-Rabenirina S, Muanza B, Bastian S, Malpote E, Jestin P, Guerin M, Talarmin A, Weill FX, Legrand A, Breurec S. Salmonella enterica serovars Panama and Arechavaleta: Risk Factors for iinvasive non-typhoidal Salmonella disease in Guadeloupe, French West Indies. Am J Trop Med Hyg. 2018;99(3): 584-589.
• Breurec S, Rafaï C, Onambele M, Frank T, Farra A, Legrand A, Weill FX. Serotype distribution and antimicrobial resistance of Shigella species in Bangui, Central African Republic, from 2002 to 2013. 2018;Am J Trop Med Hyg. 99(2): 283-286.
• Zhou Z, Lundstrøm I, Tran-Dien A, Duchêne S, Alikhan NF, Sergeant MJ, Langridge G, Fotakis AK, Nair S, Stenøien HK, Hamre SS, Casjens S, Christophersen A, Quince C, Thomson NR, Weill FX, Ho SYW, Gilbert MTP, Achtman M. Pan-genome analysis of ancient and modern Salmonella enterica demonstrates genomic stability of the invasive Para C lineage for millennia. Curr Biol. 2018;28(15): 2420-2428.e10.
• Togarsimalemath SK, Si-Mohammed A, Puraswani M, Gupta A, Vabret A, Liguori S, Mariani-Kurkdjian P, Bagga A, Dragon-Durey MA. Gastrointestinal pathogens in anti-FH antibody positive and negative Hemolytic Uremic Syndrome. Pediatr Res. 2018;84(1): 118-124.
• Sadikalay S, Reynaud Y, Guyomard-Rabenirina S, Falord M, Ducat C, Fabre L, Le Hello S, Talarmin A, Ferdinand S. High genetic diversity of extended-spectrum β-lactamases producing Escherichia coli in feces of horses. Vet Microbiol. 2018;219: 117-122.
• Sévellec Y, Vignaud ML, Granier SA, Lailler R, Feurer C, Le Hello S, Mistou MY, Cadel-Six S. Polyphyletic nature of Salmonella enterica serotype Derby and lineage-specific host-association revealed by genome-wide analysis. Front Microbiol. 2018;9: 891.
• Baker S, Thomson N, Weill FX, Holt KE. Genomic insights into the emergence and spread of antimicrobial-resistant bacterial pathogens. Science. 2018;360(6390): 733-738.
• Baker KS, Dallman TJ, Field N, Childs T, Mitchell H, Day M, Weill FX, Lefèvre S, Tourdjman M, Hughes G, Jenkins C, Thomson N. Genomic epidemiology of Shigella in the United Kingdom shows transmission of pathogen sublineages and determinants of antimicrobial resistance. Sci Rep. 2018;8(1): 7389.
• Bruyand M, Mariani-Kurkdjian P, Gouali M, de Valk H, King LA, Le Hello S, Bonacorsi S, Loirat C. Hemolytic uremic syndrome due to Shiga toxin-producing Escherichia coli infection. Med Mal Infect. 2018;48(3): 167-174.
• Baker KS, Dallman TJ, Field N, Childs T, Mitchell H, Day M, Weill FX, Lefèvre S, Tourdjman M, Hughes G, Jenkins C, Thomson N. Horizontal antimicrobial resistance transfer drives epidemics of multiple Shigella species. Nat Commun. 2018;9(1): 1462.
• Birgy A, Madhi F, Hogan J, Doit C, Gaschignard J, Caseris M, Bidet P, Cohen R, Bonacorsi S. CTX-M-55-, MCR-1-, and FosA-producing multidrug-resistant Escherichia coli infection in a child in France. Antimicrob Agents Chemother. 2018;62(4): e00127-18.
• Tran-Dien A, Le Hello S, Bouchier C, Weill FX. Early transmissible ampicillin resistance in zoonotic Salmonella enterica serotype Typhimurium in the late 1950s: a retrospective, whole-genome sequencing study. Lancet Infect Dis. 2018;18(2): 207-214.
• Jourdan-da Silva N, Fabre L, Robinson E, Fournet N, Nisavanh A, Bruyand M, Mailles A, Serre E, Ravel M, Guibert V, Issenhuth-Jeanjean S, Renaudat C, Tourdjman M, Septfons A, de Valk H, Le Hello S. Ongoing nationwide outbreak of Salmonella Agona associated with internationally distributed infant milk products, France, December 2017. Euro Surveill. 2018;23(2): 17-00852.
• Gossner CM, Le Hello S, de Jong B, Rolfhamre P, Faensen D, Weill FX, Giesecke J. Around the world in 1475 Salmonella geo-serotypes. Emerg Infect Dis. 2017;22(7): 1298-1302.
• Fonteneau L, Jourdan Da Silva N, Fabre L, Ashton P, Torpdahl M, Bouchrif B, El Boulani A, Valkanou E, Mattheus W, Friesema I, Varela Martínez C, Herrera Leon S, Mossong J, Severi E, Grant K, Weill FX, Gossner CM, Bertrand S, Dallman T, Le Hello S. Salmonella Chester multinational outbreak linked to travel exposures in Morocco, summer 2014 – 2015. Euro Surveill. 2017;22(7): 30463.
• Peters T, Bertrand S, Björkman JT, Brandal LT, Brown DJ, Erdõsi T, Heck M, Ibrahem S, Johansson K, Kornschober C, Kotila SM, Le Hello S, Lienemann T, Mattheus W, Nielsen EM, Ragimbeau C, Rumore J, Sabol A, Torpdahl M, Trees E, Tuohy A, de Pinna E. Multi-laboratory validation study of multilocus variable-number tandem repeat analysis (MLVA) for Salmonella enterica serovar Enteritidis, 2015. Euro Surveill. 2017;22(9): 30477.
• Vignaud ML, Cherchame E, Marault M, Chaing E, Le Hello S, Michel V, Jourdan-Da Silva N, Lailler R, Brisabois A, Cadel-Six S. MLVA for Salmonella enterica subsp. enterica serovar Dublin: Development of a method suitable for inter-laboratory surveillance and application in the context of a raw milk cheese outbreak in France in 2012. Front Microbiol. 2017;8: 295.
• Mohammed M, Le Hello S, Leekitcharoenphon P, Hendriksen R. The invasome of Salmonella Dublin as revealed by whole genome sequencing. BMC Infect Dis. 2017;17(1): 544.
• Kuijpers LMF, Phe T, Veng CH, Lim K, Ieng S, Kham C, Fawal N, Fabre L, Le Hello S, Vlieghe E, Weill FX, Jacobs J, Peetermans WE. The clinical and microbiological characteristics of enteric fever in Cambodia, 2008-2015. PLoS Negl Trop Dis. 2017;11(9): e0005964.
• Bruyand M, Mariani P, Gouali M, de Valk H, King LA, Le Hello S, Bonacorsi S, Loirat C. Hemolytic uremic syndrome related to Shiga toxin-producing Escherichia coli infection, an overview. Med Mal Infect. 2017;S0399-077X(16)30859-9.
• Delannoy S, Mariani-Kurkdjian P, Webb HE, Bonacorsi S, Fach P. The Mobilome; A major contributor to Escherichia coli stx2-positive O26:H11 strains intra-serotype diversity. Front Microbiol. 2017;8: 1625.
• Gaschignard J, Geslain G, Mallet C, Lorrot M, Blot N, Alison M, Bonacorsi S. Spondylodiscitis in a healthy 12-year-old girl with Extraintestinal pathogenic Escherichia coli (ExPEC) bacteraemia. BMC Infect Dis. 2017;17(1): 380.
• Birgy A, Bidet P, Levy C, Sobral E, Cohen R, Bonacorsi S. CTX-M-27-producing Escherichia coli of sequence type 131 and clade C1-M27, France. Emerg Infect Dis. 2017;23(5): 885.
• Birgy A, Delecourt M, Geslain G, Desselas E, Caseris M, Magnan M, Mariani-Kurkdjian P, Bidet P, Bonacorsi S. A combination of mecillinam and amoxicillin/clavulanate can restore susceptibility of high-level TEM-1-producing Escherichia coli to mecillinam. J Antimicrob Chemother. 2017;72(7): 1911-1914.
• Delannoy S, Beutin L, Mariani-Kurkdjian P, Fleiss A, Bonacorsi S, Fach P. The Escherichia coli serogroup O1 and O2 lipopolysaccharides are encoded by multiple O-antigen gene clusters. Front Cell Infect Microbiol. 2017;7: 30.
• Robin F, Beyrouthy R, Bonacorsi S, Aissa N, Bret L, Brieu N, Cattoir V, Chapuis A, Chardon H, Degand N, Doucet-Populaire F, Dubois V, Fortineau N, Grillon A, Lanotte P, Leyssene D, Patry I, Podglajen I, Recule C, Ros A, Colomb-Cotinat M, Ponties V, Ploy MC, Bonnet R. Inventory of extended-spectrum-β-lactamase-producing Enterobacteriaceae in France as assessed by a multicenter study. Antimicrob Agents Chemother. 2017;61(3): e01911-16.

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