Comparative genomics reveals mechanism for short-term and long-term clonal transitions in pandemic Vibrio cholerae

Abstract

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 sixth and the current seventh pandemics, respectively. Cholera researchers continually face newly emerging and reemerging pathogenic clones carrying diverse combinations of phenotypic and genotypic properties, which significantly hampered control of the disease. To elucidate evolutionary mechanisms governing genetic diversity of pandemic V. cholerae, we compared the genome sequences of 23 V. cholerae strains isolated from a variety of sources over the past 98 years. The genome-based phylogeny revealed 12 distinct V. cholerae lineages, of which one comprises both O1 classical and El Tor biotypes. All seventh pandemic clones share nearly identical gene content. Using analogy to influenza virology, we define the transition from sixth to seventh pandemic strains as a ''shift'' between pathogenic clones belonging to the same O1 serogroup, but from significantly different phyletic lineages. In contrast, transition among clones during the present pandemic period is 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 O139 and V. cholerae O1 El Tor hybrid clones. Based on the comparative genomics 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.genomic islands ͉ cholera toxin prophage ͉ lateral gene transfer

Temperature regulation of virulence factors in the pathogen Vibrio coralliilyticus

“…An increased expression of RTX toxin in Vc450 at the virulent temperature of 27 1C may allow for increased survival of Vc450 owing to degradation of the host's innate immune system. V. coralliilyticus pathogenicity islands Pathogenic vibrios, like many bacteria, commonly acquire virulence factors via horizontal transfer of bacteriophages and pathogenicity islands (Chun et al, 2009). We identified two novel pathogenicity islands in the genome of Vc450.…”

“…coralliilyticus genome To investigate the presence of potential virulence factors, we performed whole genome sequencing of Vc450 and identified an asymmetrical, two-chromosome structure consistent among all Vibrio genomes examined (Okada et al, 2005;Chun et al, 2009). The larger (C1-3 416 103 bp) and smaller (C2-1 865 911 bp) chromosomes follow a gene distribution pattern typical for vibrios with C1 predominantly carrying genes for viability and growth, and C2 mostly bearing genes for adaptation to environmental change (Makino et al, 2003).…”

Unprecedented levels of horizontal gene transfer among spatially co-occurring Shewanella bacteria from the Baltic Sea

“…Extensive genetic exchange between co-occurring strains has been previously implied by metagenomic studies of natural populations (Tyson et al, 2004;Konstantinidis and DeLong, 2008), but the fragmented nature of these data sets did not allow robust estimations of the magnitude of the genetic exchange at the wholegenome level or assessment of its ecological consequences (Eppley et al, 2007;Konstantinidis and DeLong, 2008). Recent studies of isolated strains have also reported elevated levels of genetic exchange between pathogenic bacteria such as between distinct Campylobacter species (Sheppard et al, 2008) or within Vibrio cholerae (Chun et al, 2009). However, the genes exchanged in these cases are typically limited to a few environmentally selected functions and show strong biases in terms of spatial location in the genome (Caro-Quintero et al, 2009).…”

Genomic versatility and functional variation between two dominant heterotrophic symbionts of deep-sea Osedax worms

“…The predicted ORFs were annotated by searching against clusters of orthologous groups (COGs; Tatusov et al, 1997) and SEED databases (Disz et al, 2010). A comparative method was also employed, as described previously by Chun et al (2009), in which target contigs with homology to a query ORF (450% amino-acid sequence over 50% of the length of the gene) were identified using BLASTN. Nucleotide sequences of the query ORF, and selection of target homologous regions, were then aligned using a pairwise global alignment algorithm (Myers and Miller, 1988).…”