Data_Sheet_1_Pangenomic analysis of Coxiella burnetii unveils new traits in genome architecture.xlsx

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 patients but 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 strains including 63 newly sequenced genomes. Our analysis demonstrated that C. burnetii has an open pangenome, unique genes being found in many strains. In addition, pathogenicity islands were detected in all genomes. In consequence C. burnetii has a high genomic plasticity, higher than that of other intracellular bacteria. The core- and pan-genomes are made of 1,211 and 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 and were 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).</p

Comparison of different eukaryotic components extracted in 13 samples from HIV-infected patients using 4 methods of DNA extraction.

<p>Comparison of different eukaryotic components extracted in 13 samples from HIV-infected patients using 4 methods of DNA extraction.</p

Abundance and distribution of the fungal OTUs obtained from the amplification of the ITS2 region in fecal samples of HIV-infected patients and healthy subjects.

<p>Abundance and distribution of the fungal OTUs obtained from the amplification of the ITS2 region in fecal samples of HIV-infected patients and healthy subjects.</p

The distribution of the major eukaryotic MOTUs detected in the fecal samples of HIV-infected patients and healthy subjects using cloning and sequencing methods.

<p>The heatmap shows read counts for the 33 MOTUs identified as contributing most to the variance (up to 86% across all samples) as determined by Similarity Percentage (SIMPER) analysis. The dendrogram shows the clustering of samples based on Bray-Curtis similarity distance.</p

The distribution of the major fungal OTUs recovered from the amplification of the ITS2 region in the fecal samples of HIV-infected patients and healthy subjects.

<p>The heatmap shows read counts for the 13 OTUs identified as contributing most to the variance (up to 86% across all samples) as determined by SIMPER analysis. The dendrogram shows the clustering of samples based on Bray-Curtis similarity distance.</p

The distribution of the major fungal OTUs obtained from the amplification of the ITS1 region in the fecal samples of HIV-infected patients and healthy subjects.

<p>The heatmap shows read counts for the 15 OTUs identified as contributing most to the variance (up to 86% across all samples) as determined by SIMPER analysis. The dendrogram shows the clustering of samples based on Bray-Curtis similarity distance.</p