Multidimensional Assessment of the Host Response in Mechanically Ventilated Patients with Suspected Pneumonia

Abstract

Rationale: The identification of informative elements of the host response to infection may improve the diagnosis and management of bacterial pneumonia.Objectives: To determine whether the absence of alveolar neutrophilia can exclude bacterial pneumonia in critically ill patients with suspected infection and to test whether signatures of bacterial pneumonia can be identified in the alveolar macrophage transcriptome.Methods: We determined the test characteristics of alveolar neutrophilia for the diagnosis of bacterial pneumonia in three cohorts of mechanically ventilated patients. In one cohort, we also isolated macrophages from alveolar lavage fluid and used the transcriptome to identify signatures of bacterial pneumonia. Finally, we developed a humanized mouse model of Pseudomonas aeruginosa pneumonia to determine if pathogen-specific signatures can be identified in human alveolar macrophages.Measurements and Main Results: An alveolar neutrophil percentage less than 50% had a negative predictive value of greater than 90% for bacterial pneumonia in both the retrospective (n = 851) and validation cohorts (n = 76 and n = 79). A transcriptional signature of bacterial pneumonia was present in both resident and recruited macrophages. Gene signatures from both cell types identified patients with bacterial pneumonia with test characteristics similar to alveolar neutrophilia. Conclusions:The absence of alveolar neutrophilia has a high negative predictive value for bacterial pneumonia in critically ill patients with suspected infection. Macrophages can be isolated from alveolar lavage fluid obtained during routine care and used for RNA-Seq analysis. This novel approach may facilitate a longitudinal and multidimensional assessment of the host response to bacterial pneumonia.

Identification of Novel Genes and Biological Pathways That Overlap in Infectious and Nonallergic Diseases of the Upper and Lower Airways Using Network Analyses

“…Overall, based on DEGs, 32 pathways (38%) overlap between the upper and lower airways, and 27 pathways were common to all three phenotypes (OM, CRS, and Lower; Supplementary Figure 5; Supplementary Table 5). Notably about half of these 27 pathways that were common in OM, CRS, and Lower also overlap with DEGs identified in previous microarray and RNA-Seq studies (Liu et al, 2004;Kwon et al, 2006;Lee et al, 2006;Payne et al, 2008;Raju et al, 2008;Stankovic et al, 2008;Rostkowska-Nadolska et al, 2011;Klenke et al, 2012;Macias et al, 2013;Wang et al, 2016;Ramakrishnan et al, 2017;Wang et al, 2017;Gao et al, 2018a;Gao et al, 2018b;Kato et al, 2018;Langelier et al, 2018;Ninomiya et al, 2018;Okada et al, 2018;Jovanovic et al, 2019;Walter et al, 2019;Yao et al, 2019). The common pathways from Part 2 RNA-Seq data that were identified in the transcriptome literature are apoptosis, cell adhesion, cell cycle, cell proliferation, chromatin organization/remodeling, Table 6).…”

Residual endotoxin induces primary graft dysfunction through ischemia-reperfusion-primed alveolar macrophages

“…Thus, both donor-derived NCMs and recipient CMs play complementary roles in neutrophil recruitment and extravasation to initiate lung transplant ischemia/ reperfusion injury. These mechanisms differ from observations in naive mice treated with LPS in which tissue-resident alveolar macrophages (TRAMs), or other cell populations in the lung, may be necessary for neutrophil recruitment (16)(17)(18)(19). We therefore hypothesized that LPS from the different bacterial pathogens and perhaps other PAMPs, persisting after successful antimicrobial therapy, contribute to excessive neutrophil recruitment after lung transplantation by augmenting signaling through NCMs or CMs, and/or activated parallel pathways through TRAMs.…”

“…This was accompanied by pulmonary edema and histologic signs of injury (Supplemental Figure 3, C and D) (27,28). We then performed RNA-Seq analysis of flow-sorted TRAMs isolated from BALF in patients with severe pneumonia resulting in respiratory failure in our medical intensive care unit (16). Specifically, we compared alveolar macrophage transcriptomes from patients with confirmed pneumonia secondary to Pseudomonas aeruginosa (based on quantitative culture of the same BALF sample) to transcriptomes of patients with negative quantitative culture and found that differentially expressed genes were associated with gene ontology (GO) processes involved in immune activation (Figure 2, A and B).…”

Metagenomic identification of severe pneumonia pathogens in mechanically-ventilated patients: a feasibility and clinical validity study

“…Genes conferring resistance phenotype are highlighted in bold Tested agents for case 6: Ampicillin/Sulbactum, Oxacillin, Imipenem, Gentamicin, Erthromycin, Tetracycline Tested agents for case 7: Piperacillin/Tazobactum, Ticarcillin/Clavulanic acid, Cefepime, Ceftazidime, Imipenem, Meropenem, Aztreonam, Gentamicin, Tobramycin, Amikacin, Ciprofloxacin, Levofloxacin similar to the ones considered for culture-based methods based on numbers of colony-forming units [38]. However, the distinction between colonization and infection cannot be based solely on culture results or microbial DNA sequencing outputs, but needs to be an integrative one, incorporating clinical, radiographic, and systemic/ focal host-responses [39][40][41]. With the introduction of RNA-based sequencing, a simultaneous assessment of microbial community profiles with the corresponding host transcriptomics at the local level may offer further diagnostic insights [40].…”