title: Molecular epidemiology of Coxiella burnetii in French livestock reveals the existence of three main genotype clusters and suggests species-specific associations as well as regional stability.
abstract: Q fever is a worldwide zoonosis caused by the bacterium Coxiella burnetii. In domestic ruminants, Q fever main clinical manifestations are abortions. Although the clinical signs may differ between ruminant species, C. burnetii's genetic diversity remains understudied in enzootic areas. Here, we focused on France, where Q fever is enzootic, with the aims to (a) identify potential associations between C. burnetii genotypes and ruminant host species; (b) assess the distribution of C. burnetii genotypes both within French farms and across France's major livestock-farming regions; and (c) suggest a subset of markers for future genotypic studies. We used DNA samples collected between 2006 and 2015 from 301 females (160 cows, 76 ewes, 65 goats) aborted of Q fever within 7 different farming regions. C. burnetii diversity was determined using a multiple-locus variable-number of tandem repeat analysis (MLVA) considering 17 markers. Using a phylogenetic approach, we identified 3 main genotypic clusters divided into 12 sub-clusters. These clusters were significantly associated with ruminant species: almost all the cattle genotypes were found in a "cattle-specific" cluster whereas small ruminants genotypes essentially grouped into the two other clusters. The clusters also proved stable over space and time, some genotypes being more specifically observed in certain farming regions. We also observed some within-farm diversity but this diversity was restricted to a same genotypic cluster. Finally, we identified 6 MLVA markers that maximized the representativeness of the diversity described. Overall, we highlighted that molecular epidemiology is a relevant approach to assess C. burnetii's genetic diversity and to reveal the existence of species-specific associations and regional stability. These results will be valuable in the field to trace genotype circulation among ruminants and from ruminants to humans. Ultimately, the potential links between genotypes and virulence traits need to be investigated to adapt control measures in livestock farms.
authors.affiliation: EPIA, INRA, 63122 Saint-Genès Champanelle, France; Université de Lyon, VetAgro Sup, 69280 Marcy l'Etoile, France; Anses (French Agency for Food, Environmental, and Occupational Health and Safety), Laboratory of Sophia Antipolis, Animal Q Fever Unit, Sophia Antipolis, France.
authors.forename: Aurelien
authors.initials: A
authors.lastname: Joulié
authors.affiliation: Anses (French Agency for Food, Environmental, and Occupational Health and Safety), Laboratory of Sophia Antipolis, Animal Q Fever Unit, Sophia Antipolis, France.
authors.forename: Karim
authors.initials: K
authors.lastname: Sidi-Boumedine
authors.affiliation: EPIA, INRA, 63122 Saint-Genès Champanelle, France.
authors.forename: Xavier
authors.initials: X
authors.lastname: Bailly
authors.affiliation: EPIA, INRA, 63122 Saint-Genès Champanelle, France.
authors.forename: Patrick
authors.initials: P
authors.lastname: Gasqui
authors.affiliation: EPIA, INRA, 63122 Saint-Genès Champanelle, France.
authors.forename: Séverine
authors.initials: S
authors.lastname: Barry
authors.affiliation: GDEC, INRA, 63039 Clermont-Ferrand, France.
authors.forename: Lydia
authors.initials: L
authors.lastname: Jaffrelo
authors.affiliation: GDEC, INRA, 63039 Clermont-Ferrand, France.
authors.forename: Charles
authors.initials: C
authors.lastname: Poncet
authors.affiliation: EPIA, INRA, 63122 Saint-Genès Champanelle, France.
authors.forename: David
authors.initials: D
authors.lastname: Abrial
authors.affiliation: Anses (French Agency for Food, Environmental, and Occupational Health and Safety), Laboratory of Sophia Antipolis, Animal Q Fever Unit, Sophia Antipolis, France.
authors.forename: Elise
authors.initials: E
authors.lastname: Yang
authors.affiliation: EPIA, INRA, 63122 Saint-Genès Champanelle, France; Université de Lyon, VetAgro Sup, 69280 Marcy l'Etoile, France.
authors.forename: Agnès
authors.initials: A
authors.lastname: Leblond
authors.affiliation: Anses (French Agency for Food, Environmental, and Occupational Health and Safety), Laboratory of Sophia Antipolis, Animal Q Fever Unit, Sophia Antipolis, France.
authors.forename: Elodie
authors.initials: E
authors.lastname: Rousset
authors.affiliation: EPIA, INRA, 63122 Saint-Genès Champanelle, France. Electronic address: elsa.jourdain@inra.fr.
authors.forename: Elsa
authors.initials: E
authors.lastname: Jourdain
mesh_terms: D000034:Abortion, Veterinary / Q000382:microbiology*; D000818:Animals; D002417:Cattle; D002418:Cattle Diseases / Q000382:microbiology*; D016997:Coxiella burnetii / Q000235:genetics* / Q000302:isolation & purification; D005260:Female; D014644:Genetic Variation; D016680:Genome, Bacterial; D042822:Genomic Instability; D015511:Goat Diseases / Q000382:microbiology*; D006041:Goats; D058507:Host Specificity; D054884:Host-Pathogen Interactions; D018598:Minisatellite Repeats; D017720:Molecular Epidemiology; D058885:Multilocus Sequence Typing; D010802:Phylogeny; D011778:Q Fever / Q000382:microbiology / Q000662:veterinary*; D017422:Sequence Analysis, DNA; D012756:Sheep; D012757:Sheep Diseases / Q000382:microbiology*; D013045:Species Specificity
keywords: France; Genotyping; Multiple-Locus Variable number tandem repeats Analysis (MLVA); Q fever; Ruminants; Zoonosis