Microbiome Profiling Demonstrates Concordance of Endotracheal Tube Aspirates With Direct Lower Airway Sampling in Intubated Patients.

Background: Endotracheal aspirates (ETAs) are widely used for microbiologic studies of the respiratory tract in intubated patients. However, they involve sampling through an established endotracheal tube using suction catheters, both of which can acquire biofilms that may confound results.

Research Question: Does standard clinical ETA in intubated patients accurately reflect the authentic lower airway bacterial microbiome?

Study Design And Methods: Comprehensive quantitative bacterial profiling using 16S rRNA V1-V2 gene sequencing was applied to compare bacterial populations captured by standard clinical ETA vs contemporaneous gold standard samples acquired directly from the lower airways through a freshly placed sterile tracheostomy tube.

The Lung Allograft Microbiome Associates with Pepsin, Inflammation, and Primary Graft Dysfunction.

Primary graft dysfunction (PGD) is the principal cause of early morbidity and mortality after lung transplantation. The lung microbiome has been implicated in later transplantation outcomes but has not been investigated in PGD. To define the peritransplant bacterial lung microbiome and relationship to host response and PGD.

Signatures of COVID-19 Severity and Immune Response in the Respiratory Tract Microbiome.

Viral infection of the respiratory tract can be associated with propagating effects on the airway microbiome, and microbiome dysbiosis may influence viral disease. Here, we investigated the respiratory tract microbiome in coronavirus disease 2019 (COVID-19) and its relationship to disease severity, systemic immunologic features, and outcomes. We examined 507 oropharyngeal, nasopharyngeal, and endotracheal samples from 83 hospitalized COVID-19 patients as well as non-COVID patients and healthy controls.

The lung microbiome: progress and promise.

The healthy lung was long thought of as sterile, but recent advances using molecular sequencing approaches have detected bacteria at low levels. Healthy lung bacteria largely reflect communities present in the upper respiratory tract that enter the lung via microaspiration, which is balanced by mechanical and immune clearance and likely involves limited local replication. The nature and dynamics of the lung microbiome, therefore, differ from those of ecological niches with robust self-sustaining microbial communities.

The lung microbiome in lung transplantation.

Culture-independent study of the lower respiratory tract after lung transplantation has enabled an understanding of the microbiome - that is, the collection of bacteria, fungi, and viruses, and their respective gene complement - in this niche. The lung has unique features as a microbial environment, with balanced entry from the upper respiratory tract, clearance, and local replication. There are many pressures impacting the microbiome after transplantation, including donor allograft factors, recipient host factors such as underlying disease and ongoing exposure to the microbe-rich upper respiratory tract, and transplantation-related immunosuppression, antimicrobials, and postsurgical changes.

Signatures of COVID-19 severity and immune response in the respiratory tract microbiome.

Rationale: Viral infection of the respiratory tract can be associated with propagating effects on the airway microbiome, and microbiome dysbiosis may influence viral disease.

Objective: To define the respiratory tract microbiome in COVID-19 and relationship disease severity, systemic immunologic features, and outcomes.

Methods And Measurements: We examined 507 oropharyngeal, nasopharyngeal and endotracheal samples from 83 hospitalized COVID-19 patients, along with non-COVID patients and healthy controls.

Upper Respiratory Dysbiosis with a Facultative-dominated Ecotype in Advanced Lung Disease and Dynamic Change after Lung Transplant.

The oropharyngeal microbiome is a primary source of lung microbiota, contributes to lower respiratory infection, and is also a driver of oral health. We sought to understand oropharyngeal microbial communities in advanced lung disease, community dynamics after lung transplantation, and ecological features of dysbiosis. Oropharyngeal wash samples were obtained from individuals with end-stage disease awaiting transplantation ( = 22) and longitudinally from individuals at 6 weeks, 3 months, and 6 months after transplantation ( = 33), along with healthy control subjects ( = 14).

Molecular analysis of the endobronchial stent microbial biofilm reveals bacterial communities that associate with stent material and frequent fungal constituents.

Endobronchial stents are increasingly used to treat airway complications in multiple conditions including lung transplantation but little is known about the biofilms that form on these devices. We applied deep sequencing to profile luminal biofilms of 46 endobronchial stents removed from 20 subjects primarily with lung transplantation-associated airway compromise. Microbial communities were analyzed by bacterial 16S rRNA and fungal ITS marker gene sequencing.

Molecular analysis of bacterial contamination on stethoscopes in an intensive care unit.

Background: Culture-based studies, which focus on individual organisms, have implicated stethoscopes as potential vectors of nosocomial bacterial transmission. However, the full bacterial communities that contaminate in-use stethoscopes have not been investigated.

Methods: We used bacterial 16S rRNA gene deep-sequencing, analysis, and quantification to profile entire bacterial populations on stethoscopes in use in an intensive care unit (ICU), including practitioner stethoscopes, individual-use patient-room stethoscopes, and clean unused individual-use stethoscopes.

Cardiac history and risk of post-cystectomy cardiac complications.

Objectives: To evaluate risk factors for postoperative cardiac complications (POCC). Patients undergoing cystectomy often have significant baseline cardiac disease. Despite preoperative medical optimization, postoperative cardiac complications remain a significant source of morbidity.