Summary of the molecular results of patients for whom plant DNA was detected in the bronchoalveolar lavage.

<p>CMV, cytomegalovirus; HSV, herpes simplex virus.</p

Summary of clinical and sociodemographic features of patients positive for plant DNA.

<p>ARDS, acute respiratory distress syndrome; CAP, community-acquired pneumonia; HIV, human immunodeficiency virus; SAPS, simplified acute physiology score; ICU, intensive care unit.</p

Primers and probes used in viral quantitative PCR.

<p>RSV, respiratory syncytial virus; VZV, varicella-zoster virus; CMV, cytomegalovirus; HSV, herpes simplex virus.</p

Bronchoalveolar lavage and blood culture results of patients with plant DNA identified by molecular methodology.

<p>Bronchoalveolar lavage and blood culture results of patients with plant DNA identified by molecular methodology.</p

Additional file 2: Table S2. of Effect of driving pressure on mortality in ARDS patients during lung protective mechanical ventilation in two randomized controlled trials

Multivariate Cox regression analysis for factors on day 1 including plateau pressure associated with ARDS mortality at day 90. (DOC 33 kb

Differences in fungal microbiota composition between community-associated pneumonia (CAP), ventilator-associated pneumonia (VAP), non-ventilator ICU pneumonia (NV ICU-P), aspiration pneumonia (AP) and control subjects (CS) cohorts.

<p>Fungi are presented according to their classes. Distribution of fungal classes in each cohort is expressed as a percentage. Fungal classes and their corresponding colours are indicated in the bottom right corner.</p

Serologic Prevalence of Amoeba-Associated Microorganisms in Intensive Care Unit Pneumonia Patients

<div><p>Background</p><p>Patients admitted to intensive care units are frequently exposed to pathogenic microorganisms present in their environment. Exposure to these microbes may lead to the development of hospital-acquired infections that complicate the illness and may be fatal. Amoeba-associated microorganisms (AAMs) are frequently isolated from hospital water networks and are reported to be associated to cases of community and hospital-acquired pneumonia.</p> <p>Methodology/Principal Findings</p><p>We used a multiplexed immunofluorescence assay to test for the presence of antibodies against AAMs in sera of intensive care unit (ICU) pneumonia patients and compared to patients at the admission to the ICU (controls). Our results show that some AAMs may be more frequently detected in patients who had hospital-acquired pneumonia than in controls, whereas other AAMs are ubiquitously detected. However, ICU patients seem to exhibit increasing immune response to AAMs when the ICU stay is prolonged. Moreover, concomitant antibodies responses against seven different microorganisms (5 <i>Rhizobiales</i>, <i>Balneatrix alpica</i>, and Mimivirus) were observed in the serum of patients that had a prolonged ICU stay.</p> <p>Conclusions/Significance</p><p>Our work partially confirms the results of previous studies, which show that ICU patients would be exposed to water amoeba-associated microorganisms, and provides information about the magnitude of AAM infection in ICU patients, especially patients that have a prolonged ICU stay. However, the incidence of this exposure on the development of pneumonia remains to assess.</p> </div

Prevalence of antibodies to amoeba-associated microorganisms in convalescent-phase sera after hospital-acquired pneumonia and in control (admission) sera.

<p>ND; not determined.</p

A phylogenetic tree inferred from 16S rDNA sequences of novel bacterial phylotypes.

<p>These novel phylotypes exhibited sequence similarities of less than 98% to known bacteria available in the GenBank database, and they were classified <i>in silico</i> using “Classifier” program. Phylotypes are reported according to their genus or by the last possible classification determined by the program. When possible, phylotypes with the same classification are clustered together. The frequency of phylotypes in each cohort is shown on the right.. <i>Bacteroidetes</i> are shown in purple, <i>Firmicutes</i> in red, <i>Proteobacteria</i> in blue, <i>Actinobacteria</i> in yellow, <i>Acidobacteria</i> in orange and <i>Spirochaetes</i> in green. CAP, community-acquired pneumonia; VAP, ventilator-associated pneumonia; NV ICU-P, non-ventilator ICU pneumonia; AP, aspiration pneumonia; and CS, control subjects.</p

Seroconversion rates to amoeba-associated microorganisms.

<p>CAP, community-acquired pneumonia; HAP, Hospital-acquired pneumonia; ND; not determined.</p