Comparison of ITS, beta-tubulin and actin sequences of clinical isolates of <i>Aspergillus</i> and isolates of the same species collected from the environment.

<p>Results are expressed in number of single nucleotide polymorphisms (or deletion when indicated), compared with the sequence of the clinical isolate</p><p>*Deletion of one nucleotide; D: sequence with more than three single nucleotide polymorphisms; ND: not determined</p><p>Comparison of ITS, beta-tubulin and actin sequences of clinical isolates of <i>Aspergillus</i> and isolates of the same species collected from the environment.</p

Characteristics of 12 patients with <i>Aspergillus</i> spp. colonisation after transplantation.

<p>*Duration expressed in weeks</p><p>Abbreviations: COPD, chronic obstructive pulmonary disease; LTU, lung transplant unit; SICU, surgical intensive care unit</p><p>Characteristics of 12 patients with <i>Aspergillus</i> spp. colonisation after transplantation.</p

Univariate and multivariate analysis of relationships between fungal contamination and <i>Aspergillus</i> colonisation (Cox proportional hazards model).

<p>Univariate and multivariate analysis of relationships between fungal contamination and <i>Aspergillus</i> colonisation (Cox proportional hazards model).</p

Kinetics of <i>Pneumocystis carinii</i> air shedding and lung burden in Sprague Dawley rats inoculated intratracheally at day 0 with 10⁶ cryopreserved <i>P. carinii</i> organisms.

<p><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062155#pone-0062155-g001" target="_blank"><b>Figure 1a</b>:</a> experiment 1; <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062155#pone-0062155-g001" target="_blank"><b>Figure 1b</b>:</a> experiment 2. In each experiment, the total number of <i>P. carinii</i> organisms was determined by qPCR in lung samples (red bars) and in air samples (green bars).</p

Kinetics of anti-<i>Pneumocystis</i> antibody titres in Sprague Dawley rats inoculated intratracheally at day 0 with 10⁶ cryopreserved <i>P. carinii</i> organisms.

<p><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062155#pone-0062155-g002" target="_blank"><b>Figure 2a</b>:</a> experiment 1; <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062155#pone-0062155-g002" target="_blank"><b>Figure 2b</b>:</a> experiment 2. In each experiment, anti-<i>Pneumocystis</i> IgG (blue squares) and IgM (orange circles) antibody titres were determined by an indirect immunofluorescence assay.</p

Characteristics of the STR markers and primers used in this study.

<p>Characteristics of the STR markers and primers used in this study.</p

Transmission map of the 10 patients in whom the <i>P</i>. <i>jirovecii</i> genotype 21 was detected.

<p>The date corresponds to the time at which the patient was present in the hospital and is delineated as a circle. Colored circles show <i>P</i>. <i>jirovecii</i> exposure of a given patient on a given day. Color coding distinguishes the different groups of patients (purple for patients 01–03, blue for patients 04–06 and turquoise for patients 07–10). The red bar corresponds to transmission between two groups of patients. Colored bars show the transmission routes.</p

Summary of genotype categories for <i>P</i>. <i>jirovecii</i> samples.

<p>Summary of genotype categories for <i>P</i>. <i>jirovecii</i> samples.</p

Minimum spanning tree analysis of 61 genotypes from 55 samples harboring a unique genotype (one allele per marker) or multiple genotypes (multiple alleles in one marker).

<p>The number of allelic mismatches among STR profiles was used as distance. Each circle corresponds to one genotype (Gt), with its arbitrary number indicated next to it. The size of the circle is correlated with the number of isolates possessing the corresponding Gt, from one (smallest circle) to nine (Gt21). Dark, dashed and thin connecting bars corresponds to one, 2 or >2 different markers observed between linked genotypes. Gray zones surrounding some groups of circles indicate that these profiles belong to the same genetic cluster, meaning that they have a single allelic mismatch with at least one other member of the group. Cluster 2, which was significantly associated with renal transplant recipients, is shown by a dashed line. The color of the circles indicates the underlying disease of the patient in whom this specific genotype was recovered (Green, HIV patient; Red, hematology patient; Purple, renal transplant recipient; Yellow, other cause of immunosuppression).</p

Discriminatory power of the assay for genotyping <i>P</i>. <i>jirovecii</i>.

<p>Discriminatory power of the assay for genotyping <i>P</i>. <i>jirovecii</i>.</p