TY - JOUR T1 - Genome assortment, not serogroup, defines Vibrio cholerae pandemic strains JF - NatureNature Y1 - 2009 A1 - Brettin, Thomas S. A1 - Bruce, David C. A1 - Challacombe, Jean F. A1 - Detter, John C. A1 - Han, Cliff S. A1 - Munik, A. C. A1 - Chertkov, Olga A1 - Meincke, Linda A1 - Saunders, Elizabeth A1 - Choi, Seon Y. A1 - Haley, Bradd J. A1 - Taviani, Elisa A1 - Jeon, Yoon-Seong A1 - Kim, Dong Wook A1 - Lee, Jae-Hak A1 - Walters, Ronald A. A1 - Hug, Anwar A1 - Rita R. Colwell KW - 59 KW - CHOLERA KW - genes KW - Genetics KW - GENOTYPE KW - ISLANDS KW - ORIGIN KW - PHENOTYPE KW - PUBLIC HEALTH KW - recombination KW - STRAINS KW - Toxins AB - Vibrio cholerae, the causative agent of cholera, is a bacterium autochthonous to the aquatic environment, and a serious public health threat. V. cholerae serogroup O1 is responsible for the previous two cholera pandemics, in which classical and El Tor biotypes were dominant in the 6th and the current 7th pandemics, respectively. Cholera researchers continually face newly emerging and re-emerging pathogenic clones carrying combinations of new serogroups as well as of phenotypic and genotypic properties. These genotype and phenotype changes have hampered control of the disease. Here we compare the complete genome sequences of 23 strains of V. cholerae isolated from a variety of sources and geographical locations over the past 98 years in an effort to elucidate the evolutionary mechanisms governing genetic diversity and genesis of new pathogenic clones. The genome-based phylogeny revealed 12 distinct V. cholerae phyletic lineages, of which one, designated the V. cholerae core genome (CG), comprises both O1 classical and EI Tor biotypes. All 7th pandemic clones share nearly identical gene content, i.e., the same genome backbone. The transition from 6th to 7th pandemic strains is defined here as a 'shift' between pathogenic clones belonging to the same O1 serogroup, but from significantly different phyletic lineages within the CG clade. In contrast, transition among clones during the present 7th pandemic period can be characterized as a 'drift' between clones, differentiated mainly by varying composition of laterally transferred genomic islands, resulting in emergence of variants, exemplified by V.cholerae serogroup O139 and V.cholerae O1 El Tor hybrid clones that produce cholera toxin of classical biotype. Based on the comprehensive comparative genomics presented in this study it is concluded that V. cholerae undergoes extensive genetic recombination via lateral gene transfer, and, therefore, genome assortment, not serogroup, should be used to define pathogenic V. cholerae clones. ER -