Reconstructing the Evolutionary Trajectory of Legionnaires' Disease Outbreaks

Legionnaires' disease is a severe, often fatal pneumonia caused by the intracellular pathogenM.Sc.2017-11-18 00:00:0

Legionella pneumophila Philadelphia-1 clinical genome (GenBank format)

GenBank formatted file derived from editing NC_002942 (Legionella pneumophila subsp. pneumophila str. Philadelphia 1). Corrects several discrepancies between the 1976 Philadelphia isolate given to the Isberg laboratory by Barry Fields and the original sequence

Data from: Phylogenetic reconstruction of the Legionella pneumophila Philadelphia-1 laboratory strains through comparative genomics.

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

Lp02-AWE genome (GenBank format)

GenBank formatted file derived from editing NC_002942 (Legionella pneumophila subsp. pneumophila str. Philadelphia 1). Lp02 is a thymidine auxotroph, derived from Lp01 by trimethoprim selection. This sequence reflects the genome of the original Lp02 isolate in Alexander Ensminger's strain collection

Lp01-CR genome (GenBank format)

GenBank formatted file derived from editing NC_002942 (Legionella pneumophila subsp. pneumophila str. Philadelphia 1). Lp01 is a common laboratory strain. This Lp01-CR sequence reflects the genome of the Lp01 isolate in Chitong Rao's strain collection

Lp03-AWE genome (GenBank format)

GenBank formatted file derived from editing NC_002942 (Legionella pneumophila subsp. pneumophila str. Philadelphia 1). Lp03 is a dotA mutant, derived from a thymidine auxotroph, originally thought to be Lp02. This sequence reflects the genome of the Lp03 isolate in Alexander Ensminger's strain collection

JR32-AWE (GenBank format)

GenBank formatted file derived from editing NC_002942 (Legionella pneumophila subsp. pneumophila str. Philadelphia 1). JR32 is a common laboratory strain, a streptomycin resistant, restriction-minus derivative of the Philadelphia-1 clinical strain. This sequence reflects the genome of the JR32 isolate in Alexander Ensminger's strain collection

Lp01 "core" genome (GenBank format)

GenBank formatted file derived from editing NC_002942 (Legionella pneumophila subsp. pneumophila str. Philadelphia 1). Lp01 is a common laboratory strain, a streptomycin resistant, restriction-minus derivative of the Philadelphia-1 clinical strain. This "core" sequence reflects the genome of the original Lp01 isolate, calculated based on the phylogeny between contemporary Lp01 strains and Lp02

Phylogeny of the <i>Legionella pneumophila</i> Philadelphia-1 laboratory strains as determined by whole-genome Illumina sequencing.

<p>Illumina sequencing was performed on the Philadelphia-1 progenitor and each of its laboratory derivatives, JR32, Lp01, Lp02, and Lp03. Each genome was aligned to the published <i>L. pneumophila</i> Philadelphia-1 sequence (GenBank accession AE017354.1). The identification of single nucleotide polymorphisms (SNPs) and insertions and deletions (INDELs) in each laboratory strain was used to determine genetic distances with maximum likelihood between each strain. To explain these relationships, intermediate ancestral strains were proposed, as represented by open circles. A previously sequenced Lp01 derivative (Lp01^JK) containing <i>luxN</i> and <i>ftsE</i> mutations, but not <i>lpg0716</i> and <i>lpg0718</i> mutations indicates that <i>luxN</i> and <i>ftsE</i> emerged first within the Lp01 lineage <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0064129#pone.0064129-Ensminger1" target="_blank">[7]</a>. Not displayed: a putative gene conversion event that emerged independently in only the Lp01^CR and JR32 strains (AGAT 608,162–608,165 GAAG). (For details of each exact isolate sequenced, see materials and methods: JR32^AE, Lp01^CR, Lp01^JK, Lp02^AE, Lp03^AE).</p

Polymorphisms between the Philadelphia-1 progenitor and the original published sequence.

1<p>Nucleotide positions within the published <i>L. pneumophila</i> Philadelphia-1 genome <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0064129#pone.0064129-Chien1" target="_blank">[18]</a> (GenBank accession AE017354.1).</p