title: Investigation of the population structure of Legionella pneumophila by analysis of tandem repeat copy number and internal sequence variation.
abstract: The population structure of the species Legionella pneumophila was investigated by multilocus variable number of tandem repeats (VNTR) analysis (MLVA) and sequencing of three VNTRs (Lpms01, Lpms04 and Lpms13) in selected strains. Of 150 isolates of diverse origins, 136 (86 %) were distributed into eight large MLVA clonal complexes (VACCs) and the rest were either unique or formed small clusters of up to two MLVA genotypes. In spite of the lower degree of genome-wide linkage disequilibrium of the MLVA loci compared with sequence-based typing, the clustering achieved by the two methods was highly congruent. The detailed analysis of VNTR Lpms04 alleles showed a very complex organization, with five different repeat unit lengths and a high level of internal variation. Within each MLVA-defined VACC, Lpms04 was endowed with a common recognizable pattern with some interesting exceptions. Evidence of recombination events was suggested by analysis of internal repeat variations at the two additional VNTR loci, Lpms01 and Lpms13. Sequence analysis of L. pneumophila VNTR locus Lpms04 alone provides a first-line assay for allocation of a new isolate within the L. pneumophila population structure and for epidemiological studies.
authors.affiliation: Dipartimento di Biologia, Università Roma Tre, Rome, Italy.
authors.forename: Paolo
authors.initials: P
authors.lastname: Visca
authors.affiliation: Istituto Nazionale per le Malattie Infettive 'Lazzaro Spallanzani' IRCCS, Rome, Italy.
authors.forename: Silvia
authors.initials: S
authors.lastname: D'Arezzo
authors.affiliation: Division of Analytical Microbiology, DGA CBRN Defence, Vert le Petit, France.
authors.forename: Françoise
authors.initials: F
authors.lastname: Ramisse
authors.affiliation: Department of Computer Science, Department of Biology, Program in Bioinformatics, Boston University, Boston, MA, USA.|Laboratory for Biocomputing and Informatics, Boston University, Boston, MA, USA.
authors.forename: Yevgeniy
authors.initials: Y
authors.lastname: Gelfand
authors.affiliation: Laboratory for Biocomputing and Informatics, Boston University, Boston, MA, USA.
authors.forename: Gary
authors.initials: G
authors.lastname: Benson
authors.affiliation: DGA/MRIS, Mission pour la Recherche et l'Innovation Scientifique, Bagneux, France.|Université Paris-Sud, Institut de Génétique et Microbiologie, Orsay, France.
authors.forename: Gilles
authors.initials: G
authors.lastname: Vergnaud
authors.affiliation: Respiratory and Systemic Infection Laboratory, Health Protection Agency Centre for Infections, London, UK.
authors.forename: Norman K
authors.initials: NK
authors.lastname: Fry
authors.affiliation: Université Paris-Sud, Institut de Génétique et Microbiologie, Orsay, France.
authors.forename: Christine
authors.initials: C
authors.lastname: Pourcel
mesh_terms: D001483:Base Sequence; D056915:DNA Copy Number Variations; D056426:Genetic Loci; D014644:Genetic Variation; D005828:Genetics, Population; D005838:Genotype; D016952:Legionella pneumophila / Q000235:genetics*; D015810:Linkage Disequilibrium; D008969:Molecular Sequence Data; D016415:Sequence Alignment; D012689:Sequence Homology, Nucleic Acid; D020080:Tandem Repeat Sequences