Phylogenetic Reconstruction of the Legionella pneumophila Philadelphia-1 Laboratory Strains through Comparative Genomics

Abstract

Over 20 years ago, two groups independently domesticated Legionella pneumophila from a clinical isolate of bacteria collected during the first recognized outbreak of Legionnaires’ disease (at the 1976 American Legion’s convention in Philadelphia). These two laboratory strains, JR32 and Lp01, along with their derivatives, have been disseminated to a number of laboratories around the world and form the cornerstone of much of the research conducted on this important pathogen to date. Nevertheless, no exhaustive examination of the genetic distance between these strains and their clinical progenitor has been performed thus far. Such information is of paramount importance for making sense of several phenotypic differences observed between these strains. As environmental replication of L. pneumophila is thought to exclusively occur within natural protozoan hosts, retrospective analysis of the domestication and axenic culture of the Philadelphia-1 progenitor strain by two independent groups also provides an excellent opportunity to uncover evidence of adaptation to the laboratory environment. To reconstruct the phylogenetic relationships between the common laboratory strains of L. pneumophila Philadelphia-1 and their clinical ancestor, we performed whole-genome Illumina resequencing of the two founders of each laboratory lineage: JR32 and Lp01. As expected from earlier, targeted studies, Lp01 and JR32 contain large deletions in the lvh and tra regions, respectively. By sequencing additional strains derived from Lp01 (Lp02 and Lp03), we retraced the phylogeny of these strains relative to their reported ancestor, thereby reconstructing the evolutionary dynamics of each laboratory lineage from genomic data.

Resequencing of Treponema pallidum ssp. pallidum Strains Nichols and SS14: Correction of Sequencing Errors Resulted in Increased Separation of Syphilis Treponeme Subclusters

“…Several bacterial genomes recently resequenced by next generation sequencing methods [43]–[45] revealed numerous errors in the previously published sequences. Since these errors could significantly affect protein annotations and complicate further comparative studies, revisions of genome sequences are of crucial importance.…”

STING Senses Microbial Viability to Orchestrate Stress-Mediated Autophagy of the Endoplasmic Reticulum

“…Naturally occurring thymidine auxotrophs ( thyA − ) were selected as previously described (Sander et al, 2011), and were grown in Luria-Bertani (LB) supplemented with 500 μg/ ml Thymidine and 50 μg /ml Trimethoprim (Sigma). Legionella pneumophila ΔdotAΔflaA (LPO1) strain was obtained from C. Roy (Yale University) and the thymidine auxotroph strain Legionella pneumophilaΔdotAΔflaA thyA − (LPO2) was a gift from R. Vance (University of California Berkeley) (Rao et al, 2013). Both were grown on BCYE Plates (Buffered Charcoal Yeast Extract Plates) and BYE media (Buffered Yeast Extract).…”

Molecular Characterization of LubX: Functional Divergence of the U-Box Fold by Legionella pneumophila

“…Philadelphia-1 derived (Lp03) strain (Berger and Isberg, 1993; Rao et al, 2013) was patched on charcoal- N -(2-acetamido)-2-aminoethanesulfonic acid (ACES)-yeast extract-thymidine (CYET) plates and used to inoculate overnight 37°C cultures in ACES-yeast extract-thymidine (AYET) broth (Berger and Isberg, 1993). Cultures were grown to either exponential phase (OD600 = 1.6) or post-exponential phase (cessation of growth, increase in pigmentation, and an increase in motility as visualized by light microscopy).…”