title: Rapid detection and evolutionary analysis of Legionella pneumophila serogroup 1 sequence type 47.
abstract: OBJECTIVE
  Legionella pneumophila serogroup 1 (Lp1) sequence type 47 is the leading cause of legionellosis in north-western Europe, but, surprisingly, it is rarely isolated from environmental samples. Comparative genomics was applied to develop a PCR assay and to better understand the evolution of this strain.
  
  
  METHODS
  Comparative analysis of 36 genomes representative of the Lp species was used to identify specific PCR targets, which were then evaluated in silico on 545 sequenced genomes and in vitro on 436 Legionella strains, 106 respiratory samples, and three environmental samples from proven ST47 sources. Phylogenetic analyses were performed to understand the evolution of ST47.
  
  
  RESULTS
  The gene LPO_1073 was characterized as being 100% conserved in all 129 ST47 genomes analysed. A real-time PCR designed to detect LPO_1073 was positive for all 110 ST47 strains tested and agreed with culture and typing results previously obtained for 106 respiratory samples. The three environmental samples were also positive. Surprisingly, 26 of the 44 ST109 strains tested among 342 non-ST47 strains scored positive for LPO_1073. SNP-based phylogenetic analysis was undertaken to understand this result: the PCR-positive ST109 genomes were almost identical to ST47 genomes, with the exception of a recombined region probably acquired by ST47 from a ST62(-like) strain.
  
  
  CONCLUSIONS
  The genomic analysis allowed the design of a highly specific PCR assay for rapid detection of ST47 strains. Furthermore, it allowed us to uncover the evolution of ST47 strains from ST109 by homologous recombination with ST62. We hypothesize that this recombination generated the leading cause of legionellosis in north-western Europe.
authors.affiliation: Public Health England, London, UK.
authors.forename: M
authors.initials: M
authors.lastname: Mentasti
authors.affiliation: French National Reference Center of Legionella, Hospices Civils de Lyon, France.
authors.forename: P
authors.initials: P
authors.lastname: Cassier
authors.affiliation: Public Health England, London, UK; Wellcome Trust Sanger Institute, Cambridge, UK.
authors.forename: S
authors.initials: S
authors.lastname: David
authors.affiliation: French National Reference Center of Legionella, Hospices Civils de Lyon, France; International Center for Infectiology Research, Inserm U1111, CNRS, UMR5308, University Lyon1, Ecole Normale Supérieure de Lyon, Lyon, F-69008, France.
authors.forename: C
authors.initials: C
authors.lastname: Ginevra
authors.affiliation: Institut Pasteur, Unité de Biologie des Bactéries Intracellulaires, France; CNRS UMR 3525, Paris, France.
authors.forename: L
authors.initials: L
authors.lastname: Gomez-Valero
authors.affiliation: Public Health England, London, UK.
authors.forename: A
authors.initials: A
authors.lastname: Underwood
authors.affiliation: Public Health England, London, UK; The European Programme for Public Health Microbiology Training (EUPHEM), ECDC, Stockholm, Sweden.
authors.forename: B
authors.initials: B
authors.lastname: Afshar
authors.affiliation: French National Reference Center of Legionella, Hospices Civils de Lyon, France; International Center for Infectiology Research, Inserm U1111, CNRS, UMR5308, University Lyon1, Ecole Normale Supérieure de Lyon, Lyon, F-69008, France.
authors.forename: J
authors.initials: J
authors.lastname: Etienne
authors.affiliation: Wellcome Trust Sanger Institute, Cambridge, UK.
authors.forename: J
authors.initials: J
authors.lastname: Parkhill
authors.affiliation: Public Health England, London, UK.
authors.forename: V
authors.initials: V
authors.lastname: Chalker
authors.affiliation: Institut Pasteur, Unité de Biologie des Bactéries Intracellulaires, France; CNRS UMR 3525, Paris, France.
authors.forename: C
authors.initials: C
authors.lastname: Buchrieser
authors.affiliation: Public Health England, London, UK.
authors.forename: T G
authors.initials: TG
authors.lastname: Harrison
authors.affiliation: French National Reference Center of Legionella, Hospices Civils de Lyon, France; International Center for Infectiology Research, Inserm U1111, CNRS, UMR5308, University Lyon1, Ecole Normale Supérieure de Lyon, Lyon, F-69008, France. Electronic address: Sophie.jarraud@univ-lyon1.fr.
authors.forename: S
authors.initials: S
authors.lastname: Jarraud
mesh_terms: D019143:Evolution, Molecular; D016680:Genome, Bacterial; D006801:Humans; D016952:Legionella pneumophila / Q000145:classification* / Q000235:genetics*; D058889:Molecular Typing; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D060888:Real-Time Polymerase Chain Reaction; D011995:Recombination, Genetic; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA; D065288:Serogroup
keywords: L. pneumophila; PCR; Phylogeny; ST109; ST47; ST62; WGS