Director: Elisabeth Carniel
The research activity of the Yersinia Unit focused in 2004 on the mobility of a pathogenicity island, termed the High-Pathogenicity Island, and on the evolution of the plague bacillus, Yersinia pestis. To this aim, the genome of the recent ancestor Y. pseudotuberculosis was sequenced and compared to that of Y. pestis. Furthermore, the combination of three different multilocus molecular methods allowed the generation of a phylogenetic tree and led to a better understanding of the evolution of the plague bacillus since its emergence.
The Yersinia Research Unit was created in 2004. The genus Yersinia belongs to the family Enterobacteriaceae and includes three species pathogenic for humans and animals: the enteropathogens Y. pseudotuberculosis and Y. enterocolitica, and the plague agent Y. pestis.
The activities of the Yersinia Research Unit are primarily devoted to:
- The characterization of a pathogenicity island whose presence confers to the host bacterium the ability to cause systemic infections in humans and to be lethal in mice.
- The molecular bases for the exceptional pathogenicity of Y. pestis, using comparative genomics approaches.
- The physiopathology of Yersinia infections.
- The host's mechanisms of innate and acquired immunity and the development of a vaccine against plague.
- The genetic bases of susceptibility to plague.
- The evolution of Y. pestis since its recent emergence from Y. pseudotuberculosis.
- The resistance of pathogenic Yersinia to antibiotics and the evaluation of new treatments.
- Public health (French Reference Center, National Surveillance Network and WHO Collaborating Center for Yersinia).
The main research works published in 2004 dealt with:
1. Analysis of the conservation of the high pathogenicity island in various enterobacteria and of its excision machinery.
Contributors: B. Lesic, S. Bach and E. Carniel.
Collaborators: J-M. Ghigo, U. Dobrindt and J. Hacker.
Highly pathogenic Yersinia (Y. enterocolitica 1B, Y. pseudotuberculosis and Y. pestis) harbor a pathogenicity island termed the High-Pathogenicity Island (HPI). The Yersinia HPI carries genes involved in the biosynthesis, transport and regulation of the siderophore yersiniabactin and can thus be regarded as an iron-uptake island. Its presence confers to the bacterium the ability to disseminate in its host and cause a systemic infection. A unique characteristic of this island is its wide distribution among different enterobacteria genera such as E. coli, Klebsiella, Citrobacter, Enterobacter, Serratia and Salmonella. In E. coli, the island is prevalent in extraintestinal isolates and is associated with a higher virulence. A second and degenerate HPI is present on the chromosomes of Y. pestis and Y. pseudotuberculosis. HPI-like elements have also been recently identified in the insect pathogen Photorhabdus luminescens and the Gram-positive species Corynebacterium diphtheriae. A genetic comparison of the HPIs present in the databases indicated that the organization and sequences of the various HPIs are highly conserved among most Enterobacteriaceae, suggesting the recent acquisition of this island by these various species.
The HPI has kept the potential to be mobile within the chromosome of Y. pseudotuberculosis. It can excise itself precisely from the bacterial chromosome, by recombination between the attB-R and attB-L sites flanking the island. We have shown that upon excision, the HPI forms an episomal circular molecule. The island has thus the ability to excise from the chromosome, circularize, and reintegrate itself, either in the same location or in another asn tRNA copy. We have also demonstrated that the HPI-encoded bacteriophage P4-like integrase (Int) plays a critical role in HPI excision and that, like phage integrases, it acts as a site-specific recombinase which catalyses both excision and integration reactions. However, Int alone cannot efficiently promote recombination between the attB-R and attB-L sites, and we have further demonstrated that a newly identified HPI-borne factor, designated Hef (for HPI excision factor) is also required for this activity. Hef belongs to a family of recombination directionality factors. Like the other members of this family, Hef probably plays an architectural rather than a catalytic role and promotes HPI excision from the chromosome by driving the function of Int towards an excisionase activity. The fact that the HPI, and probably several other PAIs, carry a machinery of integration/excision highly similar to those of bacteriophages argues for a phage-mediated acquisition and transfer of these elements.
2. Insights into the genome evolution of Y. pestis through whole genome comparison with Y. pseudotuberculosis
Contributors: V. Chenal-Francisque, D. Dacheux, A. Derbise and E. Carniel.
Collaborators: P. Chain, F. Larimer, J. Lamerdin, P.O. Stoutland, W. M Regala, A.M. Georgescu, L.M. Vergez, M. Land, L.V. Motin, R.R. Brubaker, J. Fowler, J. Hinnebusch, M. Marceau, C. Medigue, M. Simonet, B. Souza, J.M. Elliott, L. Hauser and E. Garcia.
Y. enterocolitica and Y. pseudotuberculosis behave like true enteropathogens, i. e. they are transmitted by the fecal-oral route and cause intestinal symptoms of moderate intensity. In contrast, Y. pestis has drastically different clinical and epidemiological features. This bacterium is the etiologic agent of plague, a highly severe and often fatal disease, and is transmitted by fleabites. Nonetheless, we previously showed that Y. pestis, one of the most pathogenic bacterium currently existing on Earth, is a highly uniform clone that emerged recently from the enteric pathogen Y. pseudotuberculosis. In order to identify the genetic bases for the difference between Y. pestis and its recent ancestor, we sequenced the complete genome of Y. pseudotuberculosis strain IP32953 and used it for detailed genome comparisons with available Y. pestis sequences. Analyses of identified differences across a panel of Yersinia isolates from around the world revealed 32 Y. pestis chromosomal genes that, together with the two Y. pestis specific plasmids, represent the only new genetic material acquired by Y. pestis since its divergence from Y. pseudotuberculosis. In contrast, 202 pseudogenes and 317 genes absent from Y. pestis were detected, indicating that as many as 13% of Y. pseudotuberculosis genes no longer function in Y. pestis. Extensive insertion sequence-mediated genome rearrangements and reductive evolution through massive gene loss, resulting in elimination and modification of preexisting gene expression pathways, appear to be more important than acquisition of genes in the evolution of Y. pestis. These results provide a sobering example of how a highly virulent epidemic clone can suddenly emerge from a less virulent, closely related progenitor.
3. Microevolution and history of Yersinia pestis
Contributors: V. Chenal-Francisque and E. Carniel.
Collaborators: M. Achtman, G. Morelli, P. Zhu, T. Wirth, I. Diehl, A.J. Vogler, D.M. Wagner, C.J. Allender, W.R. Easterday, P. Worsham, .N.R. Thomson, J. Parkhill, L.E. Lindler and P. Keim.
As a young pathogen, Y. pestis has evolved too recently to allow the accumulation of extensive sequence diversity. However, this species is not totally uniform. Investigation of the microevolution of Y. pestis, using a combination of three different multilocus molecular methods targeting genome-wide synonymous SNPs, variation in size of tandem repeats, and insertion of IS100 elements, allowed the construction of an evolutionary tree rooted on Y. pseudotuberculosis. This tree indicates that Y. pestis initially evolved from Y. pseudotuberculosis along one branch, called branch 0, from which atypical Y. pestis variants named Microtus and pestoides split off. This initial phase was followed by a binary split into branch 1 and branch 2, approximately 6,500 years ago. Branch 1 includes Orientalis isolates of worldwide origin and Antiqua strains from Africa, while branch 2 comprises Medievalis and Antiqua strains from Asia. High diversity is often a good indicator of the geographical source of microbes. The isolation of representatives of the three branches from Asia suggests that Y. pestis arose in this part of the world, rather than in Africa from which branch 2 has not been isolated.
4. National Reference Laboratory, National Surveillance network and WHO Collaborating Center for Yersinia
L. Martin, A. Leclercq, F. Guinet, and E. Carniel
See the Yersinia National Reference Laboratory web site
Keywords: Yersinia, enteropathogen, plague, virulence, genomics, physiopathology