title: Whole genome PCR scanning (WGPS) of Coxiella burnetii strains from ruminants.
abstract: Coxiella burnetii is the causative agent of Q fever, a zoonosis that spreads from ruminants to humans via the inhalation of aerosols contaminated by livestock's birth products. This study aimed to compare the genomes of strains isolated from ruminants by "Whole Genome PCR Scanning (WGPS)" in order to identify genomic differences. C. burnetii isolated from different ruminant hosts were compared to the Nine Mile reference strain using WGPS. The identified genomic regions of differences (RDs) were confirmed by sequencing. A set of 219 primers for amplification of 10 kbp segments covering the entire genome was obtained. The analyses revealed the presence of: i) conserved genomic regions, ii) genomic polymorphism including insertions and deletions and iii) amplification failures in some cases as well. WGPS, a descriptive approach, allowed the identification and localization of divergent genetic loci from various strains of C. burnetii which consisted of deletions, insertions and maybe genomic rearrangements. It also substantiates the role played by the IS1111 element in the genomic plasticity of C. burnetii. We believe that this approach could be combined with new sequencing technologies, as a selective/directed sequencing approach, particularly when repeated sequences are present in the analysed genomes.
authors: Anses, Sophia-Antipolis Laboratory, Animal Q Fever Unit, Sophia-Antipolis, France. Electronic address: Karim.SIDI-BOUMEDINE@anses.fr.
authors: Karim
authors: K
authors: Sidi-Boumedine
authors: Anses, Sophia-Antipolis Laboratory, Animal Q Fever Unit, Sophia-Antipolis, France.
authors: Gilbert
authors: G
authors: Adam
authors: Norwegian Veterinary Institute, PO Box 750 Sentrum, N-0106, Oslo, Norway.
authors: Øysten
authors: Ø
authors: Angen
authors: National Veterinary Insitute, Dept of Bacteriology, SE 751 89, Uppsala, Sweden.
authors: Anna
authors: A
authors: Aspán
authors: Central Veterinary Institute, Part of Wageningen UR (CVI), P.O. Box 65, 8200 AB, Lelystad, The Netherlands.
authors: Alex
authors: A
authors: Bossers
authors: Central Veterinary Institute, Part of Wageningen UR (CVI), P.O. Box 65, 8200 AB, Lelystad, The Netherlands.
authors: Hendrik-Jan
authors: HJ
authors: Roest
authors: Anses, Sophia-Antipolis Laboratory, Animal Q Fever Unit, Sophia-Antipolis, France.
authors: Myriam
authors: M
authors: Prigent
authors: Anses, Sophia-Antipolis Laboratory, Animal Q Fever Unit, Sophia-Antipolis, France.
authors: Richard
authors: R
authors: Thiéry
authors: Anses, Sophia-Antipolis Laboratory, Animal Q Fever Unit, Sophia-Antipolis, France.
authors: Elodie
authors: E
authors: Rousset
mesh_terms: D000818:Animals; D001483:Base Sequence; D002417:Cattle; D002418:Cattle Diseases / Q000382:microbiology; D016997:Coxiella burnetii / Q000235:genetics* / Q000302:isolation & purification*; D004269:DNA, Bacterial / Q000235:genetics*; D016680:Genome, Bacterial / Q000235:genetics*; D015511:Goat Diseases / Q000382:microbiology; D006041:Goats / Q000382:microbiology*; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D011778:Q Fever / Q000382:microbiology / Q000635:transmission / Q000662:veterinary*; D017422:Sequence Analysis, DNA; D012756:Sheep / Q000382:microbiology*; D012757:Sheep Diseases / Q000382:microbiology; D015047:Zoonoses / Q000382:microbiology
chemical_list: D004269:DNA, Bacterial
keywords: Coxiella burnetii; Genomic comparison; Q fever; WGPS; Whole Genome PCR Scanning; Zoonosis