Research / Core Facilities / Genopole / Microbial Biodiversity and Populations group

Research aims

Our group aims at understanding patterns and processes of microbial diversity at the micro-evolutionary level. We focus mainly on bacterial pathogens and the links between genetic and functional diversity, such as disease potential or ecological adaptation. Our projects include large-scale population structure analyses, fine-typing and evolution of monomorphic pathogens, analyses of the environmental distribution of bacterial genotypes, and experimental and theoretical approaches of the bacterial species concept.

Group members

  • Sylvain Brisse, Head of group
  • Virginie Passet, research Technician
  • Alexis Criscuolo, Post-doc
  • Yen-Chin Li, Master's student
  • Ulises Garza-Ramos, visiting Scientist
  • Suzanne Bialek, Post-doc

Selected publications


  • Truman, R. W., P. Singh, R. Sharma, P. Busso, J. Rougemont, A. Paniz-Mondolfi, A. Kapopoulou, S. Brisse, D. M. Scollard, T. P. Gillis, and S. T. Cole. 2011. Probable zoonotic leprosy in the southern United States. N Engl J Med 364:1626-33.

  • Nemec, A., L. Krizova, M. Maixnerova, T. J. van der Reijden, P. Deschaght, V. Passet, M. Vaneechoutte, S. Brisse, and L. Dijkshoorn. 2011. Genotypic and phenotypic characterization of the Acinetobacter calcoaceticus-Acinetobacter baumannii complex with the proposal of Acinetobacter pittii sp. nov. (formerly Acinetobacter genomic species 3) and Acinetobacter nosocomialis sp. nov. (formerly Acinetobacter genomic species 13TU). Res Microbiol 162:393-404.
  • Fevre, C., V. Passet, A. Deletoile, V. Barbe, L. Frangeul, A. S. Almeida, P. Sansonetti, R. Tournebize, and S. Brisse. 2011. PCR-Based identification of Klebsiella pneumoniae subsp. rhinoscleromatis, the agent of rhinoscleroma. PloS Negl Trop Dis 5:e1052.
  • Decre, D., C. Verdet, A. Emirian, T. Le Gourrierec, J. C. Petit, G. Offenstadt, E. Maury, S. Brisse, and G. Arlet. 2011. Emerging Severe and Fatal Infections Due to Klebsiella pneumoniae in Two University Hospitals in France. J Clin Microbiol 49:3012-4.
  • Clermont, O., D. M. Gordon, S. Brisse, S. T. Walk, and E. Denamur. 2011. Characterization of the cryptic Escherichia lineages: rapid identification and prevalence. Environ Microbiol.
  • Cheval, J., V. Sauvage, L. Frangeul, L. Dacheux, G. Guigon, N. Dumey, K. Pariente, C. Rousseaux, F. Dorange, N. Berthet, S. Brisse, I. Moszer, H. Bourhy, J. C. Manuguerra, M. Lecuit, A. Burguiere, V. Caro, and M. Eloit. 2011. Evaluation of High Throughput Sequencing for identifying known and unknown viruses in biological samples. J Clin Microbiol.
  • Chenal-Francisque, V., J. Lopez, T. Cantinelli, V. Caro, C. Tran, A. Leclercq, M. Lecuit, and S. Brisse. 2011. Worldwide distribution of major clones of Listeria monocytogenes. Emerg Infect Dis 17:1110-12.
  • Carretto, E., D. Barbarini, L. Dijkshoorn, T. J. van der Reijden, S. Brisse, V. Passet, and C. Farina. 2011. Widespread carbapenem resistant Acinetobacter baumannii clones in Italian hospitals revealed by a multicenter study. Infect Genet Evol 11:1319-1326.
  • Breurec, S., R. Michel, A. Seck, S. Brisse, D. Come, F. B. Dieye, B. Garin, M. Huerre, M. Mbengue, C. Fall, D. N. Sgouras, J. M. Thiberge, D. Dia, and J. Raymond. 2011. Clinical relevance of cagA and vacA gene polymorphisms in Helicobacter pylori isolates from Senegalese patients. Clin Microbiol Infect.
  • Breurec, S., B. Guillard, S. Hem, S. Brisse, F. B. Dieye, M. Huerre, C. Oung, J. Raymond, T. Sreng Tan, J. M. Thiberge, S. Vong, D. Monchy, and B. Linz. 2011. Evolutionary History of Helicobacter pylori Sequences Reflect Past Human Migrations in Southeast Asia. PLoS One 6:e22058.
  • Leclercq, A., V. Chenal-Francisque, H. Dieye, T. Cantinelli, R. Drali, S. Brisse, and M. Lecuit. 2011. Characterization of the novel Listeria monocytogenes PCR serogrouping profile IVb-v1. Int J Food Microbiol 147:74-7.
  • Deschaght, P., L. Van Simaey, E. Decat, E. Van Mechelen, S. Brisse, and M. Vaneechoutte. 2011. Rapid genotyping of Achromobacter xylosoxidans, Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa and Stenotrophomonas maltophilia isolates using melting curve analysis of RAPD-generated DNA fragments (McRAPD). Res Microbiol 162:386-92.
  • Coulibaly-N'Golo, G. M., E. Ekaza, B. Coulibaly, N. Aka, K. N'Guessan R, J. M. Thiberge, V. Caro, S. Brisse, and M. Bretin-Dosso. 2011. Multilocus VNTR analysis of Mycobacterium ulcerans strains isolated in Cote d'Ivoire. J Infect Dev Ctries 5:59-63.
  • Clermont, O., M. Olier, C. Hoede, L. Diancourt, S. Brisse, M. Keroudean, J. Glodt, B. Picard, E. Oswald, and E. Denamur. 2011. Animal and human pathogenic Escherichia coli strains share common genetic backgrounds. Infect Genet Evol 11:654-62


  • Sangal, V., H. Harbottle, C. J. Mazzoni, R. Helmuth, B. Guerra, X. Didelot, B. Paglietti, W. Rabsch, S. Brisse, F. X. Weill, P. Roumagnac, and M. Achtman. 2010. Evolution and population structure of Salmonella enterica serovar Newport. J Bacteriol 192:6465-76.
  • Giannouli, M., S. Cuccurullo, V. Crivaro, A. Di Popolo, M. Bernardo, F. Tomasone, G. Amato, S. Brisse, M. Triassi, R. Utili, and R. Zarrilli. 2010. Molecular epidemiology of multidrug-resistant Acinetobacter baumannii in a tertiary care hospital in Naples, Italy, shows the emergence of a novel epidemic clone. J Clin Microbiol 48:1223-30.
  • Elhani, D., L. Bakir, M. Aouni, V. Passet, G. Arlet, S. Brisse, and F. X. Weill. 2010. Molecular epidemiology of extended-spectrum beta-lactamase-producing Klebsiella pneumoniae strains in a university hospital in Tunis, Tunisia, 1999-2005. Clin Microbiol Infect 16:157-64.
  • Diancourt, L., V. Passet, A. Nemec, L. Dijkshoorn, and S. Brisse. 2010. The population structure of Acinetobacter baumannii: expanding multiresistant clones from an ancestral susceptible genetic pool. PLoS One 5:e10034.

  • Di Popolo, A., M. Giannouli, M. Triassi, S. Brisse, and R. Zarrilli. 2010. Molecular epidemiology of multidrug-resistant Acinetobacter baumannii strains in four Mediterranean countries using a multilocus sequence typing scheme. Clin Microbiol Infect.

  • Deletoile, A., V. Passet, J. Aires, I. Chambaud, M. J. Butel, T. Smokvina, and S. Brisse. 2010. Species delineation and clonal diversity in four Bifidobacterium species as revealed by multilocus sequencing. Res Microbiol 161:82-90.

  • Berthet, N., A. Deletoile, V. Passet, G. C. Kennedy, J. C. Manuguerra, S. T. Cole, and S. Brisse. 2010. Reconstructed ancestral sequences improve pathogen identification using resequencing DNA microarrays. PLoS One 5:e15243.


  • Brisse, S., C. Fevre, V. Passet, S. Issenhuth-Jeanjean, R. Tournebize, L. Diancourt, and P. Grimont. 2009. Virulent clones of Klebsiella pneumoniae: identification and evolutionary scenario based on genomic and phenotypic characterization. PLoS ONE 4:e4982.
  • Deletoile, A., D. Decre, S. Courant, V. Passet, J. Audo, P. Grimont, G. Arlet, and S. Brisse. 2009. Phylogeny and identification of Pantoea species and typing of Pantoea agglomerans strains by multilocus gene sequencing. J Clin Microbiol 47:300-10.
  • Brisse, S., C. Pannier, A. Angoulvant, T. de Meeus, L. Diancourt, O. Faure, H. Muller, J. Peman, A. M. Viviani, R. Grillot, B. Dujon, C. Fairhead, and C. Hennequin. 2009. Uneven distribution of mating types among genotypes of Candida glabrata from clinical samples. Eukaryot Cell 8:287-295.
  • Pages, F., C. N. Peyrefitte, M. T. Mve, F. Jarjaval, S. Brisse, I. Iteman, P. Gravier, D. Nkoghe, and M. Grandadam. 2009. Aedes albopictus mosquito: the main vector of the 2007 Chikungunya outbreak in Gabon. PLoS ONE 4:e4691.
  • Ah-You, N., L. Gagnevin, P. A. Grimont, S. Brisse, X. Nesme, F. Chiroleu, L. Bui Thi Ngoc, E. Jouen, P. Lefeuvre, C. Verniere, and O. Pruvost. 2009. Polyphasic characterization of xanthomonads pathogenic to members of the Anacardiaceae and their relatedness to species of Xanthomonas. Int J Syst Evol Microbiol 59:306-18.
  • Bui, T. N., C. Verniere, P. Jarne, S. Brisse, F. Guerin, S. Boutry, L. Gagnevin, and O. Pruvost. 2009. From local surveys to global surveillance: three high-throughput genotyping methods for epidemiological monitoring of Xanthomonas citri pv. citri pathotypes. Appl Environ Microbiol 75:1173-84.
  • Bui Thi Ngoc, L., C. Verniere, K. Vital, F. Guerin, L. Gagnevin, S. Brisse, N. Ah-You, and O. Pruvost. 2009. Development of 14 minisatellite markers for the citrus canker bacterium, Xanthomonas citri pv. citri. Mol Ecol Resources 9:125-127. 


  • Ragon, M., T. Wirth, F. Hollandt, R. Lavenir, M. Lecuit, A. Le Monnier, and S. Brisse. 2008. A new perspective on Listeria monocytogenes evolution. PLoS Pathogens 4:e1000146.
  • Wirth, T., F. Hildebrand, C. Allix-Beguec, F. Wolbeling, T. Kubica, K. Kremer, D. van Soolingen, S. Rusch-Gerdes, C. Locht, S. Brisse, A. Meyer, P. Supply, and S. Niemann. 2008. Origin, Spread and Demography of the Mycobacterium tuberculosis Complex. PLoS Pathog 4:e1000160.
  • Vimont, S., B. Mnif, C. Fevre, and S. Brisse. 2008. Comparison of PFGE and multilocus sequence typing for analysis of Klebsiella pneumoniae isolates. J Med Microbiol 57:1308-10.
  • Jaureguy, F., L. Landraud, V. Passet, L. Diancourt, E. Frapy, G. Guigon, E. Carbonnelle, O. Lortholary, O. Clermont, E. Denamur, B. Picard, X. Nassif, and S. Brisse. 2008. Phylogenetic and genomic diversity of human bacteremic Escherichia coli strains. BMC Genomics 9:560.
  • Guigon, G., J. Cheval, R. Cahuzac, and S. Brisse. 2008. MLVA-NET – a standardised web database for bacterial genotyping and surveillance. Euro Surveill 13.
  • Ait Tayeb, L., M. Lefevre, V. Passet, L. Diancourt, S. Brisse, and P. Grimont. 2008. Comparative phylogenies of Burkholderia, Ralstonia, Comamonas, Brevundimonas and related organisms derived from rpoB, gyrB and rrs gene sequences. Res. Microbiol. 159:169-177.


  • Salerno, A., A. Deletoile, M. Lefevre, I. Ciznar, K. Krovacek, P. Grimont, and S. Brisse. 2007. Recombining population structure of Plesiomonas shigelloides (Enterobacteriaceae) revealed by multilocus sequence typing. J Bacteriol 189:7808-7818.
  • Diancourt, L., V. Passet, C. Chervaux, P. Garault, T. Smokvina, and S. Brisse. 2007. Multilocus Sequence Typing of Lactobacillus casei reveals a clonal population structure with low levels of homologous recombination. Appl Environ Microbiol 73:6601-6611.
  • van Belkum, A., P. T. Tassios, L. Dijkshoorn, B. Cookson, J. Green, N. J. Fry, V. Fussing, S. Haeggman, S. Brisse, and M. Struelens. 2007. Criteria for the validation and application of typing methods used to study bacterial epidemiology. 2007 Clin Microbiol Infect 13 Suppl 3:1-46.


  • Schuffenecker, I., I. Iteman, A. Michault, S. Murri, L. Frangeul, M.-C. Vaney, R. Lavenir, N. Pardigon, J.-M. Reynes, F. Pettinelli, L. Biscornet, L. Diancourt, S. Michel, S. Duquerroy, G. Guigon, M.-C. Frenkiel, A.-C. Bréhin, N. Cubito, P. Desprès, F. Kunst, F. A. Rey, H. Zeller, and S. Brisse. 2006. Genome microevolution of Chikungunya viruses causing the Indian Ocean outbreak. PLoS Med 3:e263.
  • Roumagnac, P., F. X. Weill, C. Dolecek, S. Baker, S. Brisse, N. T. Chinh, T. A. Le, C. J. Acosta, J. Farrar, G. Dougan, and M. Achtman. 2006. Evolutionary history of Salmonella typhi. Science 314:1301-4.
  • Ecker, J. A., C. Massire, T. A. Hall, R. Ranken, T. T. Pennella, C. Agasino Ivy, L. B. Blyn, S. A. Hofstadler, T. P. Endy, P. T. Scott, L. Lindler, T. Hamilton, C. Gaddy, K. Snow, M. Pe, J. Fishbain, D. Craft, G. Deye, S. Riddell, E. Milstrey, B. Petruccelli, S. Brisse, V. Harpin, A. Schink, D. J. Ecker, R. Sampath, and M. W. Eshoo. 2006. Identification of Acinetobacter species and genotyping of Acinetobacter baumannii by multilocus PCR and mass spectrometry. J Clin Microbiol 44:2921-32.


  • Gutierrez, M. C., S. Brisse, R. Brosch, M. Fabre, B. Omaïs, M. Marmiesse, P. Supply, and V. Vincent. 2005. Ancient Origin and Gene Mosaicism of the Progenitor of Mycobacterium tuberculosis. PLoS Pathogens 1:e5.
  • Fevre, C., V. Passet, F. X. Weill, P. A. Grimont, and S. Brisse. 2005. Variants of the Klebsiella pneumoniae OKP chromosomal beta-lactamase are divided into two main groups, OKP-A and OKP-B. Antimicrob Agents Chemother 49:5149-52.
  • Fevre, C., M. Jbel, V. Passet, F. X. Weill, P. A. D. Grimont, and S. Brisse. 2005. Six groups of the OXY beta-lactamase evolved over millions of years in Klebsiella oxytoca. Antimicrob Agents Chemother 49:3453-3462.
  • Diancourt, L., V. Passet, J. Verhoef, P. A. D. Grimont, and S. Brisse. 2005. Multilocus sequence typing of Klebsiella pneumoniae nosocomial isolates. J. Clin. Microbiol. 43:4178-4182.