Application of Comparative Phylogenomics To Study the Evolution ofYersinia enterocoliticaand To Identify Genetic Differences Relating to Pathogenicity

Abstract

Yersinia enterocolitica, an important cause of human gastroenteritis generally caused by the consumption of livestock, has traditionally been categorized into three groups with respect to pathogenicity, i.e., nonpathogenic (biotype 1A), low pathogenicity (biotypes 2 to 5), and highly pathogenic (biotype 1B). However, genetic differences that explain variation in pathogenesis and whether different biotypes are associated with specific nonhuman hosts are largely unknown. In this study, we applied comparative phylogenomics (whole-genome comparisons of microbes with DNA microarrays combined with Bayesian phylogenies) to investigate a diverse collection of 94 strains of Y. enterocolitica consisting of 35 human, 35 pig, 15 sheep, and 9 cattle isolates from nonpathogenic, low-pathogenicity, and highly pathogenic biotypes. Analysis confirmed three distinct statistically supported clusters composed of a nonpathogenic clade, a low-pathogenicity clade, and a highly pathogenic clade. Genetic differences revealed 125 predicted coding sequences (CDSs) present in all highly pathogenic strains but absent from the other clades. These included several previously uncharacterized CDSs that may encode novel virulence determinants including a hemolysin, a metalloprotease, and a type III secretion effector protein. Additionally, 27 CDSs were identified which were present in all 47 low-pathogenicity strains and Y. enterocolitica 8081 but absent from all nonpathogenic 1A isolates. Analysis of the core gene set for Y. enterocolitica revealed that 20.8% of the genes were shared by all of the strains, confirming this species as highly heterogeneous, adding to the case for the existence of three subspecies of Y. enterocolitica. Further analysis revealed that Y. enterocolitica does not cluster according to source (host).

An aflagellate mutant Yersinia enterocolitica biotype 1A strain displays altered invasion of epithelial cells, persistence in macrophages, and cytokine secretion profiles in vitro

“…As there are high levels of homology between fleA, B and C, the failure to amplify individual genes may not be surprising; however, our results seem to confirm that the flagellin region in BT1A isolates is variable (Tennant et al, 2003). Interestingly, the three flagellin genes successfully hybridized with BT1A strains in a comparative microarray study (Howard et al, 2006), suggesting that the sequence variation may be occurring at a low level. The flagellin-coding region of BT1A strains is currently the focus of further investigation.…”

Evolutionary Dynamics of the Yersinia enterocolitica Complex

“…Biotyping is reasonably robust, and reflects the human pathogenic potential. There have been reports however of strains with atypical biotyping reactions (Guiyoule, et al, 1998) as well as high-pathogenic strains that lack the typical invasive phenotype, and which cluster with non-pathogenic BTs in microarray and AFLP analysis (Fearnly, et al, 2005;Howard, et al, 2006;McNally, et al, 2006;personal communication M. Prentice). This variability arises because biotyping is affected by the media used for culturing of the strain before typing and is subject to incubation time and temperature (Wauters, Kandolo and Janssens, 1987;Bottone, 1999;Cornelis, et al, 1987;Farmer, et al, 1992;Stock, Henrichfreise and Wiedemann, 2002;personal communication E. Carniel).…”

“…enterocolitica are understudied and knowledge is currently limited to microarray and amplified fragment length polymorphism studies (Fearnley, et al, 2005;Howard, et al, 2006) …”

The detection of Yersinia enterocolitica in surface water by quantitative PCR amplification of the ail and yadA genes

“…There are a number of genes involved in Y. enterocolitica virulence pathways (Revell & Miller 2001). The chromosomal ail gene plays a role in the attachment and invasion of host cells (Bottone 1997), and has been found primarily in Y. enterocolitica serotypes associated with disease (Miller et al 1989;Revell & Miller 2001;Howard et al 2006). The yadA gene is located on the pYV virulence plasmid and codes for a protein that promotes adherence to mucus layers, attachment to host cells and enhances serum resistance (Bottone 1997;Cornelis et al 1998), and is only associated with pathogenic subtypes of Y. enterocolitica (Robins-Browne et al 1989;Fredriksson-Ahomaa et al 2006).…”