Investigated strains cover the spectrum of bacterial life conditions.

<p>Specific media were used for bacteria cultivation before and after inactivation treatment.</p

Reverse transcription qPCR: comparison of Cq values of PAXgene and formalin-fixed CMV samples.

<p>RT-qPCR sensitivity assay was performed to detect CMV early-immediate gene <i>TRS1</i> and reference gene <i>GAPDH</i> after fixation of CMV infected MRC-5 cells with PAXgene (<i>TRS1</i>_PF, <i>GAPDH</i>_PF), formalin (<i>TRS1</i>_FF, <i>GAPDH</i>_FF) and not fixed control samples (<i>TRS1</i>_PBS; <i>GAPDH</i>_PBS) in triple biological samples. Low Cq values indicate early detection. Statistical significance p < 0.0001 (***) or p < 0.03 (*).</p

a,b: Results of inactivation experiments of human-relevant fungi by two hours fixation with PBS as positive control, PAXgene Fix, PAXgene Fix and Stab, and formalin.

<p>At least two assays per species (1–3 experiments) were performed. a) Cfu/mL was normalised to 10⁵. The dashed line indicates the threshold for minimum of reduction of 10⁴ used for disinfectants for fungi. b) Bold printed numbers indicate minimal growth after inactivation.</p

Human relevant fungi cultivated, treated with PAXgene and formalin and investigated for viability.

<p>Human relevant fungi cultivated, treated with PAXgene and formalin and investigated for viability.</p

a,b,c,d,e,f,g: Results of bacterial inactivation experiments after treatment with PAXgene and formalin.

<p>Bacterial strains show variable viability after treatment with PAXgene Fix, PAXgene Fix and Stab compared to formalin and PBS (viability control) for 30 minutes (a, b, c, e, f, g) and 2 hours (d). The x-axis indicates the amount of experiments, the y-axis cfu/ml. To obtain comparable results all counted cfus were normalised to 10⁶. Columns represent the mean values (and error bars) calculated from the results of a series of different dilutions for one experiment. Dashed lines indicate the reduction limit of 10⁵.</p

Work flow of bacterial and fungal inactivation experiments.

<p>Work flow of bacterial and fungal experiments. Bacteria experiments were performed with four (<i>Pa</i>) and six (<i>Ms</i>) independent experiments, respectively, when no colony was detected after inactivation, six experiments if colonies were detected (<i>Bs</i>, <i>Sa and Mt</i>) and seven experiments with the most variable strain <i>Cs</i>. Two-hour-treatments were performed with fungi (two experiments and all strains listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0151383#pone.0151383.t001" target="_blank">Table 1</a>) and additionally with <i>Cs</i> (three experiments).</p

Relative abundance of fungal microbiota in lower respiratory tract samples.

<p>Healthy adults (bar group 1a), patients with healthy respiratory tract but with antibiotic therapy for extrapulmonary infection (bar group 1b), non-neutropenic intubated and mechanically ventilated ICU patients without antibiotic therapy (bar group 2a), non-neutropenic intubated and mechanically ventilated ICU patients with antibiotic therapy for extrapulmonary infection (bar group 2b), and patients with antibiotic therapy due to pneumonia (bar group 3b). Fungi are shown at genus level. Yellow bars represent the sum of <i>Candida</i> sequences across all samples per group related to the total number of detected fungal sequences within each of the groups. By conventional culture <i>Candida spp</i>. were detected in 0/8 (group 1a), 0/7 (group 1b), 1/7 (group 2a), 3/6 (group 2b), and 11/26 (group 3b) patients. No other fungi were cultured.</p

Demographic data and clinical characteristics of study patients.

<p>ICU patients were all intubated and mechanically ventilated.</p

Average relative <i>Candida</i> abundance in lower respiratory tract samples.

<p>Healthy adults (bar group 1a), patients with healthy respiratory tract but with antibiotic therapy for extrapulmonary infection (bar group 1b), non-neutropenic intubated and mechanically ventilated ICU patients without antibiotic therapy (bar group 2a), non-neutropenic intubated and mechanically ventilated ICU patients with antibiotic therapy for extrapulmonary infection (bar group 2b), and patients with antibiotic therapy due to pneumonia (bar group 3b). Significant differences of average relative <i>Candida</i> abundance between groups are shown with bars representing the average <i>Candida</i> abundance and standard errors in given groups (* = p <0.05 for groups 2a, 2b, 3b versus 1a or 1b).</p

Bray-Curtis distances between study groups indicating differences in fungal species composition.

<p>Distance of zero indicates that groups are completely similar for every species. Distance of 1 indicates that groups are completely dissimilar and do not share any species. Group 1a, healthy adults; group 1b, healthy respiratory tract but with antibiotic therapy for extrapulmonary infection; group 2a, non-neutropenic intubated and mechanically ventilated ICU patients without antibiotic therapy; group 2b, non-neutropenic intubated and mechanically ventilated ICU patients with antibiotic therapy for extrapulmonary infection; group 3b, non-neutropenic intubated and mechanically ventilated ICU patients with antibiotic therapy due to pneumonia.</p