Genome evolution in major Escherichia coli O157:H7 lineages

Abstract

Background: Genetic analysis of Escherichia coli O157:H7 strains has shown divergence into two distinct lineages, lineages I and II, that appear to have distinct ecological characteristics, with lineage I strains more commonly associated with human disease. In this study, microarray-based comparative genomic hybridization (CGH) was used to identify genomic differences among 31 E. coli O157:H7 strains that belong to various phage types (PTs) and different lineage-specific polymorphism assay (LSPA) types.

Results: A total of 4,084 out of 6,057 ORFs were detected in all E. coli O157:H7 strains and 1,751 were variably present or absent. Based on this data, E. coli O157:H7 strains were divided into three distinct clusters, which consisted of 15 lineage I (LSPA type 111111), four lineage I/II (designated in this study) (LSPA type 211111) and 12 lineage II strains (LSPA 222222, 222211, 222212, and 222221), respectively. Eleven different genomic regions that were dominant in lineage I strains (present in > or =80% of lineage I and absent from > or = 92% of lineage II strains) spanned segments containing as few as two and up to 25 ORFs each. These regions were identified within E. coli Sakai S-loops # 14, 16, 69, 72, 78, 83, 85, 153 and 286, Sakai phage 10 (S-loops # 91, 92 and 93) and a genomic backbone region. All four lineage I/II strains were of PT 2 and possessed eight of these 11 lineage I-dominant loci. Several differences in virulence-associated loci were noted between lineage I and lineage II strains, including divergence within S-loop 69, which encodes Shiga toxin 2, and absence of the non-LEE encoded effector genes nleF and nleH1-2 and the perC homologue gene pchD in lineage II strains.

Conclusion: CGH data suggest the existence of two dominant lineages as well as LSPA type and PT-related subgroups within E. coli O157:H7. The genomic composition of these subgroups supports the phylogeny that has been inferred from other methods and further suggests that genomic divergence from an ancestral form and lateral gene transfer have contributed to their evolution. The genomic features identified in this study may contribute to apparent differences in the epidemiology and ecology of strains of different E. coli O157:H7 lineages.

Figure 1

The distribution of divergent genes among 31 E. coli O157:H7 strains as determined in CGH experiments with MWG oligonucleotides. The position of each ORF in the genome map of E. coli O157:H7 strain EDL933 is displayed on the X-axis and the percentage of E. coli O157:H7 strains that have divergent ORFs, based on GACK values, is shown on the Y-axis. Specific O islands, prophages and ORFs of interest are identified in the sequence.

Figure 2

The distribution of divergent genes among 31 E. coli O157:H7 strains as determined in CGH experiments with MWG oligonucleotides. As in Figure 1 except that the genome map of E. coli O157:H7 strain Sakai is used and S-loops and specific ORFs of interest are shown.

Figure 3

Relative positions and conservation of lineage-specific and lineage-dominant genome segments in 31 different E. coli O157:H7. Coordinates from the lineage-specific and lineage-dominant ORFs were plotted onto the genome of E. coli O157:H7 strain Sakai using the Microbial Genome Viewer [42]. The first ring (outermost) is + strand CDS, the second ring is - strand CDS, and the third ring is Codon Adaptation Index (CAI). Data from the individual strains are given in concentric rings from the periphery to the centre, with lineage I and II strains separated by a solid white ring. Green color indicates that the segment is present and red color indicates its absence. GC content is plotted on the innermost orange ring. a: S-loop#14; b: S-loop#16; c: S-loop#69; d: S-loop#69; r: S-loop#72; f: S-loop#78; g: S-loop#83; h: S-loop#85; i: Sp10 (S-loop#s91, 92, and 93); j: Backbone (ECs2126 - 27); k: S-loop#153; m:S-loop#244 (LEE); n: S-loop#274; o: S-loop#286. The origin and terminus are indicated by black bars extending from the outermost ring. Replichore 1 and replichore 2 are indicated by the outermost numbers.

Figure 4

The dendrogram generated by CGH analysis of E. coli O157:H7 strains. Data generated from two arrays for each strain have been averaged and analyzed with acuity 3.1. The 6057 locus tags of open reading frames of three E. coli strains (EDL933, Sakai, and K12 MG1655) in the image were organized alphabetically. The dendrogram was generated by hierarchical cluster analysis (Pearson correlation) of log2 (RAT2N) of each strain with Acuity 3.1. In the colour scheme at the bottom of above figure, the brightest green corresponds to spots that are absent (divergent) with high certainty, the brightest red indicates spots that are present (conserved) with the greatest certainty, the black indicates spots that are uncertain or slightly divergent.