Comparative genomic analysis of Vibrio cholerae: genes that correlate with cholera endemic and pandemic disease

Abstract

Historically, the first six recorded cholera pandemics occurred between 1817 and 1923 and were caused by Vibrio cholerae O1 serogroup strains of the classical biotype. Although strains of the El Tor biotype caused sporadic infections and cholera epidemics as early as 1910, it was not until 1961 that this biotype emerged to cause the 7th pandemic, eventually resulting in the global elimination of classical biotype strains as a cause of disease. The completed genome sequence of 7th pandemic El Tor O1 strain N16961 has provided an important tool to begin addressing questions about the evolution of V. cholerae as a human pathogen and environmental organism. To facilitate such studies, we constructed a V. cholerae genomic microarray that displays over 93% of the predicted genes of strain N16961 as spotted features. Hybridization of labeled genomic DNA from different strains to this microarray allowed us to compare the gene content of N16961 to that of other V. cholerae isolates. Surprisingly, the results reveal a high degree of conservation among the strains tested. However, genes unique to all pandemic strains as well as genes specific to 7th pandemic El Tor and related O139 serogroup strains were identified. These latter genes may encode gain-of-function traits specifically associated with displacement of the preexisting classical strains in South Asia and may also promote the establishment of endemic disease in previously cholera-free locations.

Figure 1

Representation of absent/present genes in nine test strains compared with N16961. Final absent/present calls for each gene were translated to binary code and analyzed using the cluster/treeview software of Eisen et al. (19). For each strain, a black line indicates the presence of a gene, whereas a white line indicates its absence. Black lines represent all genes from strain N16961, as this strain's sequence was used to construct the array.

Figure 2

Group I–III genes identified by array, Southern, and PCR analysis. Absent genes were categorized based on criteria listed in Table 2. Black squares indicate genes identified as absent by array analysis and confirmed as absent by PCR or Southern analysis; gray squares indicate genes identified as absent by array analysis alone; and white squares indicate genes identified as absent by PCR or Southern analysis. The two regions of group III genes comprising newly identified Vibrio seventh pandemic islands are labeled VSP-I and VSP-II.