Genomics of Legionella pneumophila

A major step forward in Legionella research was the determination ofthe genome sequences of three clinical serogroup 1 isolates of L. pneumophila subsp. pneumo-phila. The three strains are L. pneumophila strains Paris and strain Lens (Cazalet et al. 2004), and strain Philadelphia 1 (Chien et al. 2004). Strain Philadelphia 1 is derived from the original 1976 isolate (Fraser et al. 1977) obtained from a lung specimen from a patient who had died from Legionnaires' disease at the American Legionnaires' Convention in 1976. It is widely used in many laboratories for the study of the L. pneumophila life cycle and its virulence mechanisms. Most of our knowledge of the biology of L. pneumophila has been deduced from studies conducted with this strain and its derivatives. In contrast, strain Paris is a very abundant strain in France and Europe. It accounts for 12.7% of cases of legionel-losis in France and 33% of those that occur in the Paris area (Aurell et al. 2003). It is associated with hospital- and community-acquired disease that occurs as outbreaks or sporadic cases and is the only recognized endemic L. pneumophila strain indicating particular adaptations to the environment or the host. Strain Lens is an epidemic strain, which from November 2003 to January 2004 caused the largest outbreak that had occurred in France, with 86 cases resulting in 17 deaths (Miquel et al. 2004), suggesting that it is particularly successful in causing disease. Furthermore, strain Lens was isolated in January 2004 and sequenced in February 2004, and thus has the advantage of being freshly isolated: no genomic rearrangements, mutations, or adaptations acquired in the laboratory should have occurred in this strain.

The genome sequences of L. pneumophila strains Paris and Lens were obtained by the whole-genome shotgun strategy as described earlier (Frangeul et al. 1999). For both genomes, different libraries were used and a scaffold was obtained by end-sequencing clones from a BAC library. For the genome sequencing of strain Philadelphia 1 a combined strategy of whole-genome shotgun sequencing and sequencing of BAC clones, which covered approximately 90% of the Legionella genome, was employed.

The complete genome sequences of L. pneumophila strain Paris, Lens, and Phi-ladelphia1 comprise 3 503 610bp, 3 345 687 bp, and 3 397 754bp, respectively, with an average G+C content of 38% (Table 15.1). The genomes contain approx. 3000 genes distributed fairly evenly between the two strands (approx. 57% on the leading strand) and accounting for about 88% of the potential coding capacity. Genes were classified into 31 (strains Paris and Lens) and 27 broad functional classes (strain Philadelphia 1). No function could be predicted for 42.1% of the L. pneumophila Paris, 44.1% of the L. pneumophila Lens and for 28% of the L.pneu-mophila Philadelphia 1 genes, a proportion similar to that found in most other sequenced bacterial genomes. A high proportion of the predicted genes (21% for strain Paris, 20.4% for strain Lens, 17% for strain Philadelphia 1) are unique to the genus Legionella.

Table 15.1 General features ofthe three Legionella pneumophila genomes.

L. pneumophila L. pneumophila L. pneumophila Paris Lens Philadelphia 1

Size of the chromosome (bp)

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