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Pangenomic analysis of Coxiella burnetii unveils new traits in genome architecture

Rita Abou Abdallah1,2, Matthieu Million2,3, Jeremy Delerce2,3, Hussein Anani1,2, Awa Diop1,2, Aurelia Caputo2,3, Rita Zgheib1,2, Elodie Rousset4, Karim Sidi Boumedine4, Didier Raoult2,3 and Pierre-Edouard Fournier1,2*

Coxiella burnetii is the etiological agent of Q fever, a worldwide zoonosis able to cause large outbreaks. The disease is polymorphic. Symptomatic primary infection is named acute Q fever and is associated with hepatitis, pneumonia, fever, and auto-immune complications while persistent focalized infections, mainly endocarditis, and vascular infections, occur in a minority of patientsbut are potentially lethal. In order to evaluate the genomic features, genetic diversity, evolution, as well as genetic determinants of antibiotic resistance, pathogenicity, and ability to cause outbreaks of Q fever, we performed a pangenomic analysis and genomic comparison of 75 C. burnetii strainsincluding 63 newly sequenced genomes. Our analysis demonstrated thatC. burnetii has an open pangenome, unique genes being found in manystrains. In addition, pathogenicity islands were detected in all genomes. Inconsequence C. burnetii has a high genomic plasticity, higher than that ofother intracellular bacteria. The core- and pan-genomes are made of 1,211and 4,501 genes, respectively (ratio 0.27). The core gene-based phylogenetic analysis matched that obtained from multi-spacer typing and the distribution of plasmid types. Genomic characteristics were associated to clinical and epidemiological features. Some genotypes were associated to specific clinical forms and countries. MST1 genotype strains were associated to acute Q fever. A significant association was also found between clinical forms and plasmids. Strains harboring the QpRS plasmid were never found in acute Q fever andwere only associated to persistent focalized infections. The QpDV and QpH1 plasmids were associated to acute Q fever. In addition, the Guyanese strain CB175, the most virulent strain to date, exhibited a unique MST genotype, a distinct COG profile and an important variation in gene number that may explain its unique pathogenesis. Therefore, strain-specific factors play an important role in determining the epidemiological and clinical manifestations of Q fever alongside with host-specific factors (valvular and vascular defects notably).

Lien vers la publication : Frontiers Microbiol Abou Abdallah pangenome of Coxiella 2022

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