ABSTRACT
We report here the complete genome sequences of two of the earliest known strains of Legionella pneumophila subsp. fraseri. Detroit-1 is serogroup 1 and was isolated from a lung biopsy specimen in 1977. Dallas 1E is serogroup 5 and was isolated in 1978 from a cooling tower.
GENOME ANNOUNCEMENT
Legionella pneumophila can colonize manmade water systems and, when present in aerosolized water, the organism can be inhaled by susceptible individuals, resulting in a potentially fatal form of pneumonia known as Legionnaires’ disease (1). The species is genetically diverse and contains three known subspecies: L. pneumophila subsp. pneumophila, L. pneumophila subsp. fraseri, and L. pneumophila subsp. pascullei (2). Strains Detroit-1 and Dallas 1E represent L. pneumophila subsp. fraseri. Detroit-1 was isolated in 1977 from lung biopsy material from a kidney transplant patient who died after developing pneumonia (3, 4). While the strain is serogroup 1, early studies (including DNA-DNA hybridization) revealed that it was genetically distinct from representatives of other serogroup 1 strains (2, 5, 6). Dallas 1E was isolated from a cooling tower sampled during a Legionnaires’ disease outbreak investigation in Dallas, TX in 1978 (7). Dallas 1E is a serogroup 5 type strain and was also recognized as belonging to L. pneumophila subsp. fraseri (2, 5).
Both strains were sequenced using the Illumina MiSeq (San Diego, CA, USA) and Pacific Biosciences RSII (PacBio; Menlo Park, CA, USA) platforms. The PacBio data were assembled into a single-contig sequence using HGAP 3, and Illumina reads were mapped to this sequence to ensure that nucleotide accuracy was >99.9%. The total genome length was 3,515,377 bp for Detroit-1 and 3,500,943 bp for Dallas 1E. Prokka version 1.8 was used to predict 3,126 (Detroit-1) and 3,101 (Dallas 1E) protein-coding sequences (8). Additionally, both isolates contained 44 predicted tRNAs. The pairwise average nucleotide identity (ANI) (9) between strains Dallas 1E and Detroit-1 was 99.26%. In addition, the pairwise ANI between these two isolates and D-7119 (a representative of L. pneumophila subsp. pascullei) was ~93.55%, while the pairwise ANI between the same two isolates (Dallas 1E and Detroit-1) and Philadelphia-1 (L. pneumophila subsp. pneumophila) was ~91.89%. Although 95% ANI has been proposed to delineate bacterial species (9), the L. pneumophila subsp. fraseri sequences displayed lower ANI with sequences of L. pneumophila subsp. pneumophila and L. pneumophila subsp. pascullei, illustrating the high genetic diversity of this species.
These genomes may be useful to researchers examining the molecular basis for serogroup differences between related strains similar to that reported among L. pneumophila subsp. pascullei isolates (10). Moreover, these complete reference sequences may help support further analysis of L. pneumophila subsp. fraseri isolates, such as those recovered recently from an outbreak in Portugal (11).
Accession number(s).
The genome sequences reported here have been deposited at GenBank under GenBank accession numbers CP017457 and CP017458 for Detroit-1 and Dallas 1E, respectively.
ACKNOWLEDGMENT
The findings and conclusions in this presentation are those of the authors and do not necessarily represent the official position of the Centers for Disease Control and Prevention.
Footnotes
Citation Raphael BH, Kozak-Muiznieks NA, Morrison SS, Mercante JW, Winchell JM. 2017. Complete genome sequences of Legionella pneumophila subsp. fraseri strains Detroit-1 and Dallas 1E. Genome Announc 5:e01525-16. https://doi.org/10.1128/genomeA.01525-16.
REFERENCES
- 1.Mercante JW, Winchell JM. 2015. Current and emerging Legionella diagnostics for laboratory and outbreak investigations. Clin Microbiol Rev 28:95–133. doi: 10.1128/CMR.00029-14. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2.Brenner DJ, Steigerwalt AG, Epple P, Bibb WF, McKinney RM, Starnes RW, Colville JM, Selander RK, Edelstein PH, Moss CW. 1988. Legionella pneumophila serogroup Lansing 3 isolated from a patient with fatal pneumonia, and descriptions of L. pneumophila subsp. pneumophila subsp. nov., L. pneumophila subsp. fraseri subsp. nov., and L. pneumophila subsp. pascullei subsp. nov. J Clin Microbiol 26:1695–1703. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3.Neblett TR, Riddle JM, Dumoff M. 1979. Surface topography and fine structure of the Legionnaires’ disease bacterium: a study of six isolates from hospitalized patients. Ann Intern Med 90:648–651. doi: 10.7326/0003-4819-90-4-648. [DOI] [PubMed] [Google Scholar]
- 4.Saravolatz LD, Burch KH, Fisher E, Madhavan TOM, Kiani D, Neblett T, Quinn EL. 1979. The compromised host and Legionnaires’ disease. Ann Intern Med 90:533–537. doi: 10.7326/0003-4819-90-4-533. [DOI] [PubMed] [Google Scholar]
- 5.Selander RK, McKinney RM, Whittam TS, Bibb WF, Brenner DJ, Nolte FS, Pattison PE. 1985. Genetic structure of populations of Legionella pneumophila. J Bacteriol 163:1021–1037. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Riffard S, Lo Presti F, Vandenesch F, Forey F, Reyrolle M, Etienne J. 1998. Comparative analysis of infrequent-restriction-site PCR and pulsed-field gel electrophoresis for epidemiological typing of Legionella pneumophila serogroup 1 strains. J Clin Microbiol 36:161–167. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.England AC III, McKinney RM, Skaliy P, Gorman GW. 1980. A fifth serogroup of Legionella pneumophila. Ann Intern Med 93:58–59. doi: 10.7326/0003-4819-93-1-58. [DOI] [PubMed] [Google Scholar]
- 8.Seemann T. 2014. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068–2069. doi: 10.1093/bioinformatics/btu153. [DOI] [PubMed] [Google Scholar]
- 9.Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM. 2007. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57:81–91. doi: 10.1099/ijs.0.64483-0. [DOI] [PubMed] [Google Scholar]
- 10.Kozak-Muiznieks NA, Morrison SS, Sammons S, Rowe LA, Sheth M, Frace M, Lucas CE, Loparev VN, Raphael BH, Winchell JM. 2016. Three genome sequences of Legionella pneumophila subsp. pascullei associated with colonization of a health care facility. Genome Announc 4(3):e00335-16. doi: 10.1128/genomeA.00335-16. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11.Borges V, Nunes A, Sampaio DA, Vieira L, Machado J, Simões MJ, Gonçalves P, Gomes JP. 2016. Legionella pneumophila strain associated with the first evidence of person-to-person transmission of Legionnaires’ disease: a unique mosaic genetic backbone. Sci Rep 6:26261. doi: 10.1038/srep26261. [DOI] [PMC free article] [PubMed] [Google Scholar]