Abstract
Campylobacter jejuni ST-474 is the most important human enteric pathogen in New Zealand, and yet this genotype is rarely found elsewhere in the world. Insight into the evolution of this organism was gained by a whole genome comparison of two ST-474, flaA SVR-14 isolates and other available C. jejuni isolates and genomes. The two isolates were collected from different sources, human (H22082) and retail poultry (P110b), at the same time and from the same geographical location. Solexa sequencing of each isolate resulted in 1.659 Mb (H22082) and 1.656 Mb (P110b) of assembled sequences within 28 (H22082) and 29 (P110b) contigs. We analysed 1502 genes for which we had sequences within both ST-474 isolates and within at least one of 11 C. jejuni reference genomes. Although 94.5% of genes were identical between the two ST-474 isolates, we identified 83 genes that differed by at least one nucleotide, including 55 genes with non-synonymous substitutions. These covered 101 kb and contained 672 point differences. We inferred that 22 (3.3%) of these differences were due to mutation and 650 (96.7%) were imported via recombination. Our analysis estimated 38 recombinant breakpoints within these 83 genes, which correspond to recombination events affecting at least 19 loci regions and gives a tract length estimate of 2 kb. This includes a 12 kb region displaying non-homologous recombination in one of the ST-474 genomes, with the insertion of two genes, including ykgC, a putative oxidoreductase, and a conserved hypothetical protein of unknown function. Furthermore, our analysis indicates that the source of this recombined DNA is more likely to have come from C. jejuni strains that are more closely related to ST-474. This suggests that the rates of recombination and mutation are similar in order of magnitude, but that recombination has been much more important for generating divergence between the two ST-474 isolates.
Highlights
Our understanding of the rate and determinants of bacterial evolution has been revolutionised by the development and application of new tools in molecular biology, genomics and statistical genetics
Sequencing the genomes of the two sequence type 474 (ST-474) strains An Illumina GAII was used to generate short read sequences of 36 bases for the two ST-474 strains using a lane for each isolate. 5389820 and 3272064 sequences were obtained for P110b and H22082 respectively, with a yield of 194.03 Mb and 117.79 Mb of sequence respectively
It can be seen that there is no appreciable mapping of the ST-474 reads to any of the known C. jejuni plasmids
Summary
Our understanding of the rate and determinants of bacterial evolution has been revolutionised by the development and application of new tools in molecular biology, genomics and statistical genetics These include the advent of Generation Sequencing [1] and novel approaches to making inference on whole genome data, without the need for time-consuming, full annotation [2,3,4]. Until recently we had relatively little understanding of the evolution of Campylobacter spp. but multilocus sequence typing (MLST) of large collections of isolates, combined with coalescent modelling, has provided new insight into the possible convergence of these two species [6] and revised our estimates of the rate of mutation and recombination [7] This has led to notable advances in our ability to attribute epidemiologically significant isolate clusters to specific ecological sources, both animal and environmental [8,9]. The seven housekeeping gene MLST scheme, even when supplemented by the addition of one or more hypervariable genes [10,11,12], covers less than 0.5% of the 1.6–1.8 Mb C. jejuni genome and provides limited insight into the full extent of genomic variation between seemingly closely-related bacteria
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