Pathophysiological role of respiratory dysbiosis in hospital-acquired pneumonia

The Respiratory Tract Microbiome and Human Health

The respiratory tract microbiome (RTM) is a multi-kingdom microbial ecosystem that inhabits various niches of the respiratory system. While previously overlooked, there is now sufficient evidence that the RTM plays a crucial role in human health related to immune system training and protection against pathogens. Accordingly, dysbiosis or disequilibrium of the RTM has been linked to several communicable and non-communicable respiratory diseases, highlighting the need to unveil its role in health and disease. Here, we define the RTM and its place in microbiome medicine. Moreover, we outline the challenges of RTM research, emphasising the need for combining methodologies, including multi-omics and computational tools. We also discuss the RTM's potential for diagnosing, preventing and treating respiratory diseases and developing novel microbiome-based therapies to improve pulmonary health.

The pathogenesis of ventilator-associated pneumonia: old and new mechanisms

INTRODUCTION

Ventilator-associated pneumonia (VAP), defined as a lung infection that occurs in patients after 48 hours on mechanical ventilation, is among the most frequently found nosocomial infections in intensive care units around the world and is associated with increased morbidity, mortality, and economic burden.

AREAS COVERED

We review the classical mechanisms of VAP development and explore more recent ones, such as dysbiosis, which has changed our view of the pathogenesis of the disease; whereas in the past the lower respiratory tract was classically considered a sterile organ, the use of new diagnostic techniques has shown that the lungs of healthy humans are inhabited by a large, dynamic ecosystem of microorganisms. Dysbiosis is the disruption of this ecosystem and is a key factor in the development of VAP. Recent findings have demonstrated that host immunity is microbiome-regulated and, consequently, is profoundly affected by dysbiosis. In this paper the significance of the microbiome-immunity crosstalk in the pathophysiology of VAP will be discussed.

EXPERT OPINION

A deeper understanding of mechanisms of VAP pathogenesis should help to devise new preventive, diagnostic and therapeutic strategies for reducing the incidence of this condition and for improving patient prognosis.

Identification and validation of robust hospital-acquired pneumonia subphenotypes associated with all-cause mortality: a multi-cohort derivation and validation

PURPOSE

Despite optimal antimicrobial therapy, the treatment failure rate of hospital-acquired pneumonia (HAP) routinely reaches 40% in critically ill patients. Subphenotypes have been identified within sepsis and acute respiratory distress syndrome with important predictive and possibly therapeutic implications. We derived prognosis subphenotypes for HAP and explored whether they were associated with biological markers and response to treatment.

METHODS

We separately analysed data from four cohorts of critically ill patients in France (PNEUMOCARE, n = 511, ATLANREA, n = 401), Netherlands (MARS, n = 1351) and Europe-South America (ENIRRI, n = 900) to investigate HAP heterogeneity using unsupervised clustering based on clinical and routine biological variables available at HAP diagnosis. Then, we developed a machine learning-based workflow to create a simplified classification model using discovery data sets. This model was validated by applying it to an independent replication data set from an international randomized clinical trial comparing linezolid and tedizolid for the treatment of HAP (VITAL, n = 726 patients). The primary outcome was the association of subphenotypes with 28-day all-cause mortality. Secondary analyses included subphenotype associations with treatment failure at test-of-cure, respiratory microbiome and cytokine profiles in the ATLANREA subgroup, and treatment response in the VITAL trial.

RESULTS

We tested twelve metrics and determined that a two-cluster model best fits all cohorts. HAP subphenotype 2 had greater disease severity, lower body temperature, and worse PaO2/FiO2 ratio than subphenotype 1 patients. Although the prevalence of subphenotype 2 ranged from 26.9 to 66.9% across the four derivation cohorts, the rates of 28-day mortality and treatment failure at test-of-cure were consistently higher to subphenotype 1 (p < 0.01 for all comparisons). Subphenotype 2 was associated with greater respiratory microbiome dysbiosis and higher levels of proinflammatory cytokines in the ATLANREA cohort, as well as with statistically significant tedizolid effect modification in the VITAL trial (Relative Risk of treatment failure with tedizolid = 1.52; 95% CI 1.12-2.06 in subphenotype 1 vs. = 0.98; 95% CI 0.7-1.38 in subphenotype 2).

CONCLUSIONS

We identified two robust clinical subphenotypes by extensively analyzing HAP data sets. Their associations with respiratory microbiome composition, systemic inflammation, and treatment efficacy in independent data sets highlight their potential for prognostic value and predictive enrichment in future clinical trials aimed at personalized therapies.

Development and validation of machine learning models for predicting extubation failure in patients undergoing cardiac surgery: a retrospective study

Patients with multiple comorbidities and those undergoing complex cardiac surgery may experience extubation failure and reintubation. The aim of this study was to establish an extubation prediction model using explainable machine learning and identify the most important predictors of extubation failure in patients undergoing cardiac surgery. Data from 776 adult patients who underwent cardiac surgery and were intubated for more than 24 h were obtained from the Medical Information Mart for Intensive Care (MIMIC)-IV database. The primary endpoint was extubation failure according to the WIND criteria, with 205 patients experiencing extubation failure. The data was split into a training set (80%) and a test set (20%). The performance of the XGBoost algorithm was the highest (AUC 0.793, Mean Precision 0.700, Brier Score0.150), which was better than that of logistic regression (AUC 0.766, Mean Precision 0.553, Brier Score0.173) and random forest (AUC 0.791, Mean Precision 0.510, Brier Score 0.181). The most crucial predictor of extubation failure is the mean value of the anion gap in the 24 h before extubation. The other main features include ventilator parameters and blood gas indicators. By applying machine learning to large datasets, we developed a new method for predicting extubation failure after cardiac surgery in critically ill patients. Based on the predictive factors analyzed, internal environmental indicators and ventilation characteristics were important predictors of extubation failure. Therefore, these predictive factors should be considered when determining extubation readiness.

A nomogram for predicting mortality risk in geriatric patients with hip fractures complicated by pneumonia: A multicenter study

Objectives

Pneumonia is a common perioperative complication in geriatric patients with hip fractures. This study aimed to analyze demographic characteristics, mortality rates, postoperative outcomes, and perioperative comorbidities, identify risk factors for mortality, and develop a nomogram for predicting the prognosis of these patients.

Methods

Data on patients hospitalized for arthroplasty for hip fractures from 2020 to 2023 at three hospitals were retrospectively analyzed. Patients were divided into the P group (patients with hip fractures complicated with pneumonia) and the C group (patients with hip fractures without pneumonia) and demographic characteristics, mortality, postoperative outcomes, and perioperative comorbidities of the patients were analyzed. Multiple logistic regression was then used to identify independent risk factors for inpatient mortality in the P group and a nomogram was constructed to predict inpatient mortality. The predictive performance of the nomogram was assessed using receiver operating characteristic curves, decision curve analysis, and calibration curves.

Results

A total of 311 patients participated in the study. Patients in the P group had longer hospitalization (p = 0.001), higher inpatient mortality (p < 0.001), higher mortality (30 days) (p < 0.001), and a poorer recovery of hip function (p < 0.001). Multiple logistic regression showed that age, BMI, total hip arthroplasty, diabetes, and chronic obstructive pulmonary disease were independent risk factors for inpatient mortality in the P group; these factors were incorporated in the nomogram. The C-index of the nomogram was 0.868 (95% CI: 0.802-0.933), and the C-index of internal bootstrapping validation was 0.851 (95% CI: 0.793-0.908), indicating the effectiveness of the nomogram in predicting patient prognosis.

Conclusions

Coinfection with pneumonia adversely affected both recovery of hip function and survival in geriatric patients with hip fractures. Age, BMI, total hip arthroplasty, diabetes, and chronic obstructive pulmonary disease were found to be independent risk factors for mortality in this patient population.

Diagnostic Performance and Impact on Antimicrobial Treatment of a Multiplex Polymerase Chain Reaction in Critically Ill Patients With Pneumonia: A Multicenter Observational Study (The MORICUP-PCR Study: Morocco ICU Pneumonia-PCR study)

OBJECTIVES

Managing severe pneumonia remains a challenge. Rapid diagnostic tests, such as multiplex polymerase chain reaction (mPCR), facilitate quick microorganism identification and may enable timely and appropriate antimicrobial therapy. However, studies from low-income countries are scarce. This study aimed to evaluate the diagnostic characteristics of mPCR and its impact on antibiotic therapy and outcomes in critically ill patients with pneumonia.

DESIGN

Multicenter observational study.

SETTING

Twelve ICUs across Morocco.

PATIENTS

Adult patients with pneumonia requiring invasive mechanical ventilation, including community-acquired pneumonia (CAP), hospital-acquired pneumonia (HAP), and ventilator-associated pneumonia (VAP).

INTERVENTIONS

None.

MEASUREMENTS AND MAIN RESULTS

Respiratory samples were analyzed using both mPCR and conventional microbiological methods. The diagnostic performance of mPCR was evaluated, including its sensitivity and specificity. Additionally, the appropriateness of mPCR-induced modifications in empiric antibiotic therapy and their impact on patient outcomes were assessed. A total of 210 patients were included, with a median age of 50 years (range, 33-67 yr), of whom 66.2% were male. Pneumonia types were distributed as 30% CAP, 58% VAP, and 12% HAP. mPCR demonstrated a sensitivity of 96.9% (95% CI, 92.3-99.2%) and a specificity of 92% (95% CI, 91-93%). Following mPCR, antibiotic therapy modifications were observed in 58% of patients (n = 122), including de-escalation or cessation in 11% (n = 23), escalation in 26.5% (n = 56), adequacy adjustments in 7.5% (n = 16), and initiation of antibiotics in 13% (n = 27). The appropriateness of antibiotic therapy increased significantly from 38.7% (n = 83) to 67% (n = 141; difference, 27.5%; 95% CI, 18.3-36.7; p < 0.0001). Generalized mixed model analysis revealed that appropriate post-mPCR antibiotic therapy was associated with reduced mortality (adjusted odds ratio, 0.37; 95% CI, 0.15-0.93; p = 0.038).

CONCLUSIONS

Our findings suggest that the use of mPCR is associated with a significant improvement in the appropriateness of empiric antibiotic therapy and is also associated with a positive impact on the outcome of patients with pneumonia.

Identification of circulating Tfh/Th subsets as a biomarker of developed hospital-acquired pneumonia

Background

This study aimed to explore the possible value of follicular helper T (Tfh) cells in hospital-acquired pneumonia (HAP).

Methods

Flow cytometry was used to measure circulating Tfh and helper T cell (Th) cells in 62 HAP patients and 16 healthy individuals. HAP patients were further categorized into uncontrolled and controlled groups, in accordance with relevant guidelines. Subgroup analyses were additionally conducted based on the pathogen and the presence of bloodstream infections (BSIs) and the incidence of septic shock. Kaplan-Meier survival analysis and ROC analysis were performed to estimate the prognostic value of the combination of Tfh/Th ratios and PCT levels.

Results

The Tfh/Th ratio was notably higher in uncontrolled HAP patients than in controls (P<0.05). Specifically, either the Klebsiella pneumoniae (K.p) -positive HAP or BSIs subgroups or septic shock subgroups showed significantly increased Tfh/Th ratios (P<0.05). PCT level in BSIs and septic shock subgroups was significantly increased. However, there were no significant differences in PCT level between K.p-infected and non-K.p-infected patients. So, the Tfh/Th ratio is a good supplement to PCT for distinguishing between the K.p and non-K.p groups. The Tfh/Th ratio also demonstrated a strong correlation with procalcitonin (PCT) levels (P<0.05). Accordingly, the combination of Tfh/Th and PCT could serve as a more effective predictive marker for HAP deterioration and survival prediction. HAP patients with a high Tfh/Th ratio along with high PCT levels had a lower 28-day survival rate.

Conclusion

The circulating Tfh/Th ratio, instrumental in gauging the severity of patients with HAP, could be employed as a prognostic biomarker for HAP.

Diagnosis and insight into the unique lung microbiota of pediatric pulmonary tuberculosis patients by bronchoalveolar lavage using metagenomic next-generation sequencing

Background

Although previous studies have reported the dysregulation of respiratory tract microbiota in infectious diseases, insufficient data exist regarding respiratory microbiota imbalances in the lower respiratory tracts of children with pulmonary tuberculosis (PTB). In this study, we assessed the value of mNGS in the pathogen diagnosis and microbiome analysis of PTB patients using bronchoalveolar lavage fluid (BALF) samples.

Methods

A total of 64 participants, comprising 43 pediatric PTB and 21 pediatric pneumonia patients were recruited in the present study. BALF samples were collected from the above participants. Parallel comparisons between mNGS and conventional microbial test (CMT) pathogen detection were performed. Moreover, the diversity and structure of all 64 patients' lung BALF microbiomes were explored using the mNGS data.

Results

Comparing to the final clinical diagnosis, mNGS in BALF samples produced a sensitivity of 46.51%, which was lower than that of TB-PCR (55.00%) and Xpert (55.00%). The diagnostic efficacy of PTB can be highly enhanced by mNGS combined with TB-PCR (AUC=0.8140, P<0.0001). There were no significant differences in the diversity either between patients with TB and pneumonia. Positive mNGS pathogen results in pediatric PTB patients significantly affect the β-diversity of the pulmonary microbiota. In addition, significant taxonomic differences were found in BALF specimens from patients with PTB and pneumonia, both of which have unique bacterial compositions.

Conclusions

mNGS is valuable in the etiological diagnosis of PTB, and can reveal pulmonary microecological characteristics. For pediatric PTB patients, the mNGS should be implemented early and complementary to CMTs.

Synergy between Lactobacillus murinus and anti-PcrV antibody delivered in the airways to boost protection against Pseudomonas aeruginosa

Therapeutic antibodies (Ab) have revolutionized the management of multiple illnesses including respiratory tract infections (RTIs). However, anti-infectious Ab displayed several limitations including antigen restrictiveness, narrowed therapeutic windows, and limited dose in the vicinity of the target when delivered by parenteral routes. Strategies enhancing further Ab-dependent containment of infection are currently needed. Here we showed that a combination of inhaled anti-infectious Ab and probiotics is an efficient formulation to protect against lung infection. Using a mouse model of Pseudomonas aeruginosa-induced pneumonia, we demonstrated a synergistic effect reducing both bacterial burden and pro-inflammatory response affording protection against primary and secondary infections. This is the first study showing that the local combination in the airways of anti-infective Ab and probiotics subverts suboptimal potency of Ab monotherapy and provides protection against respiratory pathogen.

Bacteriology of Aspiration Pneumonia: The Lung Microbiome and the Changing Microbial Etiology

Aspiration pneumonia refers to the process of alveolar inflammation induced by the inhalation of oropharyngeal secretions into the lower respiratory tract. Predisposing factors comprise swallowing dysfunction, impaired cough reflex, and degenerative neurological diseases. Accumulating evidence projects a fading contribution of anaerobic bacteria in aspiration pneumonia at the expense of Gram-negative bacilli, with Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa, becoming the predominant organisms recovered from respiratory specimens. Aspiration of oropharyngeal secretions colonized with respiratory pathogens induces a profound disequilibrium of the lung microbiota resulting in a state of dysbiosis. Understanding this complex temporal variability between microbiome-host associations was only made possible with the introduction of metagenomic sequencing. In this narrative review, we summarize existing knowledge and elaborate on the evolving microbiology of aspiration pneumonia including the link between oral microbiome and pulmonary aspiration. We also highlight the progress and challenges in instituting microbiome-targeted strategies for preventing and treating the sequelae of aspiration pneumonia.

Three-month outcomes and cost-effectiveness of interferon gamma-1b in critically ill patients: a secondary analysis of the PREV-HAP trial

BACKGROUND

Interferon gamma‑1b has been proposed to treat critical illness-induced immunosuppression. We aimed to determine the effects on 90-day outcomes and the cost-effectiveness of interferon gamma‑1b compared to placebo in mechanically ventilated critically ill patients.

METHODS

A cost-effectiveness analysis (CEA) was embedded in the "PREV-HAP trial", a multicenter, placebo‑controlled, randomized trial, which randomly assigned critically ill adults under mechanical ventilation to receive interferon gamma or placebo. The CEA compared interferon-gamma with placebo using a collective perspective at a 90-day time horizon. The primary outcome was the incremental cost-effectiveness ratio (ICER) expressed in terms of adjusted cost per adjusted Quality-Adjusted Life-Years (QALYs) gained. QALYs were estimated from the responses of patients and proxy respondents to the health-related quality of life questionnaire EQ-5D-3L.

RESULTS

The 109 patients in the PREV-HAP trial were included in the CEA. At day 90, all-cause mortality rates were 23.6% in the interferon group and 25% in the placebo group (Odds Ratio (OR) = 0.88 (0.40 -1.93) p = 0.67). The difference in the mean adjusted costs per patient at 90 days was €-1.638 (95%CI €-17.534 to €11.968) in favor of interferon gamma-1b. The mean difference in adjusted QALYs between interferon gamma-1b and the placebo group was + 0.019 (95%CI -0.005 to 0.043). The probability that interferon gamma-1b was cost-effective ranged from 0.60 to 0.71 for a willingness to pay a QALY between €20k and €150k for the base case analysis.

CONCLUSION

Early administration of interferon gamma might be cost-effective in critically ill patients supporting the realization of other studies on this treatment. However, the generalization of the findings should be considered cautiously, given the small sample size due to the premature end of PREV-HAP. Trial registration ClinicalTrials.gov Identifier: NCT04793568, Registration date: 2021-02-24.

Respiratory microbiome and clinical course of carbapenem-resistant Acinetobacter baumannii pneumonia in critically Ill patients

Carbapenem-resistant Acinetobacter baumannii (CRAB) pneumonia has been a serious problem in the intensive care unit (ICU). However, defined characteristics of respiratory microbiome in CRAB pneumonia are lacking nowadays. This study aimed to analyze respiratory microbiome of CRAB pneumonia compared to non-CRAB pneumonia and reveal the clinical significance of respiratory microbiome data in these patients. Patients diagnosed with severe pneumonia with mechanical ventilation were enrolled in the ICU of a tertiary care hospital. Respiratory specimens were collected on days 1, 4, 7, and 14 in each participant via tracheal aspiration. Clinical data and outcomes of each enrolled patient were collected via electronic medical records. Microbiome analysis was conducted with collected respiratory specimens undergone by next-generation sequencing of microbial 16S ribosomal DNA. Six CRAB pneumonia, 4 non-CRAB pneumonia and 5 healthy controls were enrolled. In CRAB pneumonia, CRAB was detected in 3 patients by sputum culture at day 1, while it was negative at day 1 and detected later in the others by follow-up sputum culture. Beta diversity plot analysis showed differences between each group. Shannon index was decreased markedly at day 4 in CRAB pneumonia compared to the others. Among CRAB pneumonia cases, 3 respiratory specimens were culture-negative, but positive by microbiome analysis. Lower respiratory microbiome in CRAB pneumonia had distinct characteristics and early loss of diversity compared to non-CRAB pneumonia, which might be related to poor clinical course. Moreover, CRAB acquisition and colonization would be predicted by preemptive microbiome analysis, which will contribute to effective infection control in the ICU.

Clinical challenge of diagnosing non-ventilator hospital-acquired pneumonia and identifying causative pathogens: a narrative review

Non-ventilated hospital-acquired pneumonia (NV-HAP) is associated with a significant healthcare burden, arising from high incidence and associated morbidity and mortality. However, accurate identification of cases remains challenging. At present, there is no gold-standard test for the diagnosis of NV-HAP, requiring instead the blending of non-specific signs and investigations. Causative organisms are only identified in a minority of cases. This has significant implications for surveillance, patient outcomes and antimicrobial stewardship. Much of the existing research in HAP has been conducted among ventilated patients. The paucity of dedicated NV-HAP research means that conclusions regarding diagnostic methods, pathology and interventions must largely be extrapolated from work in other settings. Progress is also limited by the lack of a widely agreed definition for NV-HAP. The diagnosis of NV-HAP has large scope for improvement. Consensus regarding a case definition will allow meaningful research to improve understanding of its aetiology and the heterogeneity of outcomes experienced by patients. There is potential to optimize the role of imaging and to incorporate novel techniques to identify likely causative pathogens. This would facilitate both antimicrobial stewardship and surveillance of an important healthcare-associated infection. This narrative review considers the utility of existing methods to diagnose NV-HAP, with a focus on the significance and challenge of identifying pathogens. It discusses the limitations in current techniques, and explores the potential of emergent molecular techniques to improve microbiological diagnosis and outcomes for patients.

Systemic inflammatory response syndrome triggered by blood-borne pathogens induces prolonged dendritic cell paralysis and immunosuppression

Blood-borne pathogens can cause systemic inflammatory response syndrome (SIRS) followed by protracted, potentially lethal immunosuppression. The mechanisms responsible for impaired immunity post-SIRS remain unclear. We show that SIRS triggered by pathogen mimics or malaria infection leads to functional paralysis of conventional dendritic cells (cDCs). Paralysis affects several generations of cDCs and impairs immunity for 3-4 weeks. Paralyzed cDCs display distinct transcriptomic and phenotypic signatures and show impaired capacity to capture and present antigens in vivo. They also display altered cytokine production patterns upon stimulation. The paralysis program is not initiated in the bone marrow but during final cDC differentiation in peripheral tissues under the influence of local secondary signals that persist after resolution of SIRS. Vaccination with monoclonal antibodies that target cDC receptors or blockade of transforming growth factor β partially overcomes paralysis and immunosuppression. This work provides insights into the mechanisms of paralysis and describes strategies to restore immunocompetence post-SIRS.

Mastering the brain in critical conditions: an update

Acute brain injuries, such as traumatic brain injury and ischemic and hemorragic stroke, are a leading cause of death and disability worldwide. While characterized by clearly distict primary events-vascular damage in strokes and biomechanical damage in traumatic brain injuries-they share common secondary injury mechanisms influencing long-term outcomes. Growing evidence suggests that a more personalized approach to optimize energy substrate delivery to the injured brain and prognosticate towards families could be beneficial. In this context, continuous invasive and/or non-invasive neuromonitoring, together with clinical evaluation and neuroimaging to support strategies that optimize cerebral blood flow and metabolic delivery, as well as approaches to neuroprognostication are gaining interest. Recently, the European Society of Intensive Care Medicine organized a 2-day course focused on a practical case-based clinical approach of acute brain-injured patients in different scenarios and on future perspectives to advance the management of this population. The aim of this manuscript is to update clinicians dealing with acute brain injured patients in the intensive care unit, describing current knowledge and clinical practice based on the insights presented during this course.

Hypercapnia and its relationship with respiratory infections

INTRODUCTION

Hypercapnia is developed in patients with acute and/or chronic respiratory conditions. Clinical data concerning hypercapnia and respiratory infections interaction is limited.

AREAS COVERED

Currently, the relationship between hypercapnia and respiratory infections remains unclear. In this review, we summarize studies on the effects of hypercapnia on models of pulmonary infections to clarify the role of elevated CO2 in these pulmonary pathologies. Hypercapnia affects different cell types in the alveoli, leading to changes in the immune response. In vitro studies show that hypercapnia downregulates the NF-κβ pathway, reduces inflammation and impairs epithelial wound healing. While in vivo models show a dual role between short- and long-term effects of hypercapnia on lung infection. However, it is still controversial whether the effects observed under hypercapnia are pH dependent or not.

EXPERT OPINION

The role of hypercapnia is still a controversial debate. Hypercapnia could play a beneficial role in mechanically ventilated models, by lowering the inflammation produced by the stretch condition. But it could be detrimental in infectious scenarios, causing phagocyte dysfunction and lack of infection control. Further data concerning hypercapnia on respiratory infections is needed to elucidate this interaction.

Evaluation of the BioFire® FilmArray® Pneumonia plus Panel for Detecting Bacterial Etiological Agents of Lower Respiratory Tract Infections in an Oncologic Hospital. Comparison with Conventional Culture Method

Conventional methods used to determine pneumonia pathogens are characterized by low sensitivity and long turnaround times. Introducing new tests with better parameters in patients at higher risk of infections is highly anticipated. The results of the conventional quantitative culture method (CM) in determining the bacterial etiology of pneumonia were compared with the results of the Pneumonia plus Panel test (PNP; BioFire® Diagnostics, USA) in 79 samples of bronchoalveolar lavage (BAL). Materials were collected from 79 patients with suspected pneumonia treated in an oncologic hospital due to solid tumors. Only 16/79 BAL samples (20.3%) were true positive (TP) for bacterial etiology in CM vs. 27/79 samples (34.2%) true positive in the PNP test. The total agreement between methods of interpreting the result (positive or negative) was 84.8%. The most prevalent pathogens in both methods were Staphylococcus aureus, followed by Escherichia coli, Pseudomonas aeruginosa, and Haemophilus influenzae. The PNP test identified several respiratory pathogens that were not grown in culture. The semiquantitative value reported by the PNP test was higher than that reported by culture. The PNP test vs. combined test (PNP test and CM methods) demonstrated positive predictive value (PPV) and negative predictive value (NPV) values of 100.0% and 98.1%, and the sensitivity and specificity were 96.4% and 100.0%. The PNP test is a good tool for determining the etiology of bacterial pneumonia and may support the care of an oncologic patient. However, further large-sample studies are needed to research in strictly defined groups of oncologic patients.

Non-ventilator-associated ICU-acquired pneumonia (NV-ICU-AP) in patients with acute exacerbation of COPD: From the French OUTCOMEREA cohort

BACKGROUND

Non-ventilator-associated ICU-acquired pneumonia (NV-ICU-AP), a nosocomial pneumonia that is not related to invasive mechanical ventilation (IMV), has been less studied than ventilator-associated pneumonia, and never in the context of patients in an ICU for severe acute exacerbation of chronic obstructive pulmonary disease (AECOPD), a common cause of ICU admission. This study aimed to determine the factors associated with NV-ICU-AP occurrence and assess the association between NV-ICU-AP and the outcomes of these patients.

METHODS

Data were extracted from the French ICU database, OutcomeRea™. Using survival analyses with competing risk management, we sought the factors associated with the occurrence of NV-ICU-AP. Then we assessed the association between NV-ICU-AP and mortality, intubation rates, and length of stay in the ICU.

RESULTS

Of the 844 COPD exacerbations managed in ICUs without immediate IMV, NV-ICU-AP occurred in 42 patients (5%) with an incidence density of 10.8 per 1,000 patient-days. In multivariate analysis, prescription of antibiotics at ICU admission (sHR, 0.45 [0.23; 0.86], p = 0.02) and no decrease in consciousness (sHR, 0.35 [0.16; 0.76]; p < 0.01) were associated with a lower risk of NV-ICU-AP. After adjusting for confounders, NV-ICU-AP was associated with increased 28-day mortality (HR = 3.03 [1.36; 6.73]; p < 0.01), an increased risk of intubation (csHR, 5.00 [2.54; 9.85]; p < 0.01) and with a 10-day increase in ICU length of stay (p < 0.01).

CONCLUSION

We found that NV-ICU-AP incidence reached 10.8/1000 patient-days and was associated with increased risks of intubation, 28-day mortality, and longer stay for patients admitted with AECOPD.

Differentiating infection, colonisation, and sterile inflammation in critical illness: the emerging role of host-response profiling

Infection results when a pathogen produces host tissue damage and elicits an immune response. Critically ill patients experience immune activation secondary to both sterile and infectious insults, with overlapping clinical phenotypes and underlying immunological mechanisms. Patients also undergo a shift in microbiota with the emergence of pathogen-dominant microbiomes. Whilst the combination of inflammation and microbial shift has long challenged intensivists in the identification of true infection, the advent of highly sensitive molecular diagnostics has further confounded the diagnostic dilemma as the number of microbial detections increases. Given the key role of the host immune response in the development and definition of infection, profiling the host response offers the potential to help unravel the conundrum of distinguishing colonisation and sterile inflammation from true infection. This narrative review provides an overview of current approaches to distinguishing colonisation from infection using routinely available techniques and proposes matrices to support decision-making in this setting. In searching for new tools to better discriminate these states, the review turns to the understanding of the underlying pathobiology of the host response to infection. It then reviews the techniques available to assess this response in a clinically applicable context. It will cover techniques including profiling of transcriptome, protein expression, and immune functional assays, detailing the current state of knowledge in diagnostics along with the challenges and opportunities. The ultimate infection diagnostic tool will likely combine an assessment of both host immune response and sensitive pathogen detection to improve patient management and facilitate antimicrobial stewardship.

The Impact of Coronavirus Disease 2019 on Viral, Bacterial, and Fungal Respiratory Infections

Although coronavirus disease 2019 (COVID-19) remains an ongoing threat, concerns regarding other respiratory infections remain. Throughout the COVID-19 pandemic various epidemiologic trends have been observed in other respiratory viruses including a reduction in influenza and respiratory syncytial virus infections following onset of the COVID-19 pandemic. Observations suggest that infections with other respiratory viruses were reduced with social distancing, mask wearing, eye protection, and hand hygiene practices. Coinfections with COVID-19 exist not only with other respiratory viruses but also with bacterial pneumonias and other nosocomial and opportunistic infections. Coinfections have been associated with increased severity of illness and other adverse outcomes.

Trends in Molecular Diagnosis of Nosocomial Pneumonia Classic PCR vs. Point-of-Care PCR: A Narrative Review

Nosocomial pneumonia is one of the most frequent hospital-acquired infections. One of the types of nosocomial pneumonia is ventilator-associated pneumonia, which occurs in endotracheally intubated patients in intensive care units (ICU). Ventilator-associated pneumonia may be caused by multidrug-resistant pathogens, which increase the risk of complications due to the difficulty in treating them. Pneumonia is a respiratory disease that requires targeted antimicrobial treatment initiated as early as possible to have a good outcome. For the therapy to be as specific and started sooner, diagnostic methods have evolved rapidly, becoming quicker and simpler to perform. Polymerase chain reaction (PCR) is a rapid diagnostic technique with numerous advantages compared to classic plate culture-based techniques. Researchers continue to improve diagnostic methods; thus, the newest types of PCR can be performed at the bedside, in the ICU, so-called point of care testing-PCR (POC-PCR). The purpose of this review is to highlight the benefits and drawbacks of PCR-based techniques in managing nosocomial pneumonia.

Interferon gamma-1b for the prevention of hospital-acquired pneumonia in critically ill patients: a phase 2, placebo-controlled randomized clinical trial

PURPOSE

We aimed to determine whether interferon gamma-1b prevents hospital-acquired pneumonia in mechanically ventilated patients.

METHODS

In a multicenter, placebo-controlled, randomized trial conducted in 11 European hospitals, we randomly assigned critically ill adults, with one or more acute organ failures, under mechanical ventilation to receive interferon gamma-1b (100 µg every 48 h from day 1 to 9) or placebo (following the same regimen). The primary outcome was a composite of hospital-acquired pneumonia or all-cause mortality on day 28. The planned sample size was 200 with interim safety analyses after enrolling 50 and 100 patients.

RESULTS

The study was discontinued after the second safety analysis for potential harm with interferon gamma-1b, and the follow-up was completed in June 2022. Among 109 randomized patients (median age, 57 (41-66) years; 37 (33.9%) women; all included in France), 108 (99%) completed the trial. Twenty-eight days after inclusion, 26 of 55 participants (47.3%) in the interferon-gamma group and 16 of 53 (30.2%) in the placebo group had hospital-acquired pneumonia or died (adjusted hazard ratio (HR) 1.76, 95% confidence interval (CI) 0.94-3.29; P = 0.08). Serious adverse events were reported in 24 of 55 participants (43.6%) in the interferon-gamma group and 17 of 54 (31.5%) in the placebo group (P = 0.19). In an exploratory analysis, we found that hospital-acquired pneumonia developed in a subgroup of patients with decreased CCL17 response to interferon-gamma treatment.

CONCLUSIONS

Among mechanically ventilated patients with acute organ failure, treatment with interferon gamma-1b compared with placebo did not significantly reduce the incidence of hospital-acquired pneumonia or death on day 28. Furthermore, the trial was discontinued early due to safety concerns about interferon gamma-1b treatment.

Evaluation of the Risk Factors of Nosocomial Pneumonia and the Prevalence of Antibiotic Resistance in Trauma Patients in Need of Immediate Intervention

Background: Pneumonia is the most common nosocomial infection reported worldwide in intensive care units. This study aimed to evaluate the risk factors of nosocomial pneumonia and the frequency of antibiotic resistance in trauma patients who need immediate intervention. Patients and Methods: This prospective cohort study was conducted in Shahid Rajaei Trauma Hospital in Shiraz between 2020 and 2021. All the trauma patients who needed immediate intervention (levels 1 and 2 based on the Canadian Emergency Department Triage and Acuity Scale) and had no symptoms of infection were included. Patients who were discharged or died before 48 hours were excluded. Results: The results demonstrated that major trauma (Injury Severity Score [ISS] ≥16), intubation, and use of invasive mechanical ventilation increase nosocomial pneumonia and death rate. The most common causes of nosocomial infections were Acinetobacter baumannii (23%) and coagulase-negative staphylococcus (18.5%). The highest levels of antibiotic resistance were related to cefoxitin, erythromycin, ciprofloxacin, and trimethoprim-sulfamethoxazole. Conclusions: Major trauma, intubation, and invasive mechanical ventilation were the effective factors in the development of nosocomial pneumonia. Continuous monitoring for mentioned risk factors and strict surveillance of antibiotic prescription can decrease the prevalence of nosocomial infections and subsequent deaths.

Sex differences in factors influencing hospital-acquired pneumonia in schizophrenia patients receiving modified electroconvulsive therapy

BACKGROUND

Sex differences may be presented in the clinical features or symptoms of schizophrenia patients but also affect the occurrence of hospital-acquired pneumonia (HAP). Modified electroconvulsive therapy (mECT) is a common treatment method for schizophrenia, used in combination with antipsychotics. This retrospective research explores the sex difference in HAP affecting patients with schizophrenia who have received mECT treatment during hospitalization.

METHODS

We included schizophrenia inpatients treated with mECT and antipsychotics between January 2015 and April 2022. Blood-related and demographic data collected on admission were analyzed. Influencing factors of HAP in male and female groups were assessed separately.

RESULTS

A total of 951 schizophrenia patients treated with mECT were enrolled in the study, including 375 males and 576 females, of which 62 patients experienced HAP during hospitalization. The risk period of HAP in these patients was found to be the first day after each mECT treatment and the first three sessions of mECT treatment. Statistically significant differences in the incidence of HAP were identified in male vs. female groups, with an incidence in men about 2.3 times higher than that in women (P < 0.001). Lower total cholesterol (Z = -2.147, P = 0.032) and the use of anti-parkinsonian drugs (χ2 = 17.973, P < 0.001) were found to be independent risk factors of HAP in male patients, while lower lymphocyte count (Z = -2.408, P = 0.016), hypertension (χ2 = 9.096, P = 0.003), and use of sedative-hypnotic drugs (χ2 = 13.636, P < 0.001) were identified in female patients.

CONCLUSION

Influencing factors of HAP in schizophrenia patients treated with mECT have gender differences. The first day after each mECT treatment and the first three sessions of mECT treatment were identified to have the greatest risk for HAP development. Therefore, it would be imperative to monitor clinical management and medications during this period according to these gender differences.

The Role of the Respiratory Microbiome in the Pathogenesis of Aspiration Pneumonia: Implications for Diagnosis and Potential Therapeutic Choices

Although the lungs were considered to be sterile until recently, the advent of molecular biology techniques, such as polymerase chain reaction, 16 S rRNA sequencing and metagenomics has led to our expanding knowledge of the lung microbiome. These methods may be particularly useful for the identification of the causative agent(s) in cases of aspiration pneumonia, in which there is usually prior administration of antibiotics. The most common empirical treatment of aspiration pneumonia is the administration of broad-spectrum antibiotics; however, this may result in negative cultures from specimens taken from the respiratory tract. Therefore, in such cases, polymerase chain reaction or metagenomic next-generation sequencing may be life-saving. Moreover, these modern molecular methods may assist with antimicrobial stewardship. Based upon factors such as age, altered mental consciousness and recent hospitalization, there is a shift towards the predominance of aerobes, especially Gram-negative bacteria, over anaerobes in aspiration pneumonia. Thus, the therapeutic choices should be expanded to cover multi-drug resistant Gram-negative bacteria in selected cases of aspiration pneumonia.

Multisite Evaluation of Toothbrushes and Microbial Growth in the Hospital Setting

DESIGN

This observational, descriptive study was conducted to determine the prevalence of microbial growth on toothbrushes found in hospital patient rooms.

METHODS

Toothbrush sampling was conducted in 136 acute care hospitals and medical centers from November 2018 through February 2022. Inclusion criteria for the units and patient rooms sampled were as follows: general adult medical-surgical units or critical care units; rooms occupied by adults 18 years or older who were capable of (1) mobilizing to the bathroom; (2) using a standard manual, bristled toothbrush; and (3) room did not have signage indicating isolation procedures.

RESULTS

A total of 5340 patient rooms were surveyed. Of the rooms included, 46% (2455) of patients did not have a toothbrush available or had not used a toothbrush (still in package and/or toothpaste not opened). Of the used toothbrushes collected (n = 1817): 48% (872/1817) had at least 1 organism; 14% (251/1817) of the toothbrushes were positive for 3 or more organisms.

CONCLUSIONS

These results identify the lack of availability of toothbrushes for patients and support the need for hospitals to incorporate a rigorous, consistent, and comprehensive oral care program to address the evident risk of microbe exposure in the oral cavity.

Extubation in neurocritical care patients: the ENIO international prospective study

PURPOSE

Neurocritical care patients receive prolonged invasive mechanical ventilation (IMV), but there is poor specific information in this high-risk population about the liberation strategies of invasive mechanical ventilation.

METHODS

ENIO (NCT03400904) is an international, prospective observational study, in 73 intensive care units (ICUs) in 18 countries from 2018 to 2020. Neurocritical care patients with a Glasgow Coma Score (GCS) ≤ 12, receiving IMV ≥ 24 h, undergoing extubation attempt or tracheostomy were included. The primary endpoint was extubation failure by day 5. An extubation success prediction score was created, with 2/3 of patients randomly allocated to the training cohort and 1/3 to the validation cohort. Secondary endpoints were the duration of IMV and in-ICU mortality.

RESULTS

1512 patients were included. Among the 1193 (78.9%) patients who underwent an extubation attempt, 231 (19.4%) failures were recorded. The score for successful extubation prediction retained 20 variables as independent predictors. The area under the curve (AUC) in the training cohort was 0.79 95% confidence interval (CI₉₅) [0.71-0.87] and 0.71 CI₉₅ [0.61-0.81] in the validation cohort. Patients with extubation failure displayed a longer IMV duration (14 [7-21] vs 6 [3-11] days) and a higher in-ICU mortality rate (8.7% vs 2.4%). Three hundred and nineteen (21.1%) patients underwent tracheostomy without extubation attempt. Patients with direct tracheostomy displayed a longer duration of IMV and higher in-ICU mortality than patients with an extubation attempt (success and failure).

CONCLUSIONS

In neurocritical care patients, extubation failure is high and is associated with unfavourable outcomes. A score could predict extubation success in multiple settings. However, it will be mandatory to validate our findings in another prospective independent cohort.

Development and implementation of a customised rapid syndromic diagnostic test for severe pneumonia

Background: The diagnosis of pneumonia has been hampered by a reliance on bacterial cultures which take several days to return a result, and are frequently negative. In critically ill patients this leads to the use of empiric, broad-spectrum antimicrobials and compromises good antimicrobial stewardship. The objective of this study was to establish the performance of a syndromic molecular diagnostic approach, using a custom TaqMan array card (TAC) covering 52 respiratory pathogens, and assess its impact on antimicrobial prescribing. Methods: The TAC was validated against a retrospective multi-centre cohort of broncho-alveolar lavage samples. The TAC was assessed prospectively in patients undergoing investigation for suspected pneumonia, with a comparator cohort formed of patients investigated when the TAC laboratory team were unavailable. Co-primary outcomes were sensitivity compared to conventional microbiology and, for the prospective study, time to result. Metagenomic sequencing was performed to validate findings in prospective samples. Antibiotic free days (AFD) were compared between the study cohort and comparator group. Results: 128 stored samples were tested, with sensitivity of 97% (95% confidence interval (CI) 88-100%). Prospectively, 95 patients were tested by TAC, with 71 forming the comparator group. TAC returned results 51 hours (interquartile range 41-69 hours) faster than culture and with sensitivity of 92% (95% CI 83-98%) compared to conventional microbiology. 94% of organisms identified by sequencing were detected by TAC. There was a significant difference in the distribution of AFDs with more AFDs in the TAC group (p=0.02). TAC group were more likely to experience antimicrobial de-escalation (odds ratio 2.9 (95%1.5-5.5)). Conclusions: Implementation of a syndromic molecular diagnostic approach to pneumonia led to faster results, with high sensitivity and impact on antibiotic prescribing.

Immunomodulatory Effects of Probiotics on COVID-19 Infection by Targeting the Gut-Lung Axis Microbial Cross-Talk

The ecosystem of the human gastrointestinal tract, named gut microbiota, represents the most thoroughly mapped ecosystem. Perturbations on bacterial populations cause dysbiosis, a condition correlated to a wide range of autoimmune, neurological, metabolic, cardiovascular, and respiratory diseases. The lungs have their flora, which are directly related to the gut flora via bidirectional communication allowing the transport of microbial metabolites and toxins produced by intestinal bacteria through the circulation and lymphatic system. This mutual microbial cross-talk communication called the gut-lung axis modulates the immune and inflammatory response to infections. COVID-19 causes dysbiosis, altered intestinal permeability, and bacterial translocation. Dysbiosis, through the gut-lung axis, promotes hyper-inflammation, exacerbates lung damage, and worsens clinical outcomes. Preclinical and clinical studies have shown that probiotics can regulate cytokine secretion, thus affecting both nonspecific and specific immunity. Probiotics act by blocking the virus from invading and proliferating in host cells, by stimulating the immune response, and by suppressing the activation of NLRP3 inflammasome. Herein, we reviewed the evidence from preclinical and clinical studies evaluating the effect of probiotics administration on the immune response to COVID-19 infection by targeting the gut-lung axis microbial cross-talk.

Clinically focused multi-cohort benchmarking as a tool for external validation of artificial intelligence algorithm performance in basic chest radiography analysis

Artificial intelligence (AI) algorithms evaluating [supine] chest radiographs ([S]CXRs) have remarkably increased in number recently. Since training and validation are often performed on subsets of the same overall dataset, external validation is mandatory to reproduce results and reveal potential training errors. We applied a multicohort benchmarking to the publicly accessible (S)CXR analyzing AI algorithm CheXNet, comprising three clinically relevant study cohorts which differ in patient positioning ([S]CXRs), the applied reference standards (CT-/[S]CXR-based) and the possibility to also compare algorithm classification with different medical experts’ reading performance. The study cohorts include [1] a cohort, characterized by 563 CXRs acquired in the emergency unit that were evaluated by 9 readers (radiologists and non-radiologists) in terms of 4 common pathologies, [2] a collection of 6,248 SCXRs annotated by radiologists in terms of pneumothorax presence, its size and presence of inserted thoracic tube material which allowed for subgroup and confounding bias analysis and [3] a cohort consisting of 166 patients with SCXRs that were evaluated by radiologists for underlying causes of basal lung opacities, all of those cases having been correlated to a timely acquired computed tomography scan (SCXR and CT within < 90 min). CheXNet non-significantly exceeded the radiology resident (RR) consensus in the detection of suspicious lung nodules (cohort [1], AUC AI/RR: 0.851/0.839, p = 0.793) and the radiological readers in the detection of basal pneumonia (cohort [3], AUC AI/reader consensus: 0.825/0.782, p = 0.390) and basal pleural effusion (cohort [3], AUC AI/reader consensus: 0.762/0.710, p = 0.336) in SCXR, partly with AUC values higher than originally published (“Nodule”: 0.780, “Infiltration”: 0.735, “Effusion”: 0.864). The classifier “Infiltration” turned out to be very dependent on patient positioning (best in CXR, worst in SCXR). The pneumothorax SCXR cohort [2] revealed poor algorithm performance in CXRs without inserted thoracic material and in the detection of small pneumothoraces, which can be explained by a known systematic confounding error in the algorithm training process. The benefit of clinically relevant external validation is demonstrated by the differences in algorithm performance as compared to the original publication. Our multi-cohort benchmarking finally enables the consideration of confounders, different reference standards and patient positioning as well as the AI performance comparison with differentially qualified medical readers.

The association between accessing dental services and nonventilator hospital-acquired pneumonia among 2019 Medicaid beneficiaries

In this 2019 cross-sectional study, we analyzed hospital records for Medicaid beneficiaries who acquired nonventilator hospital-acquired pneumonia. The results suggest that preventive dental treatment in the 12 months prior or periodontal therapy in the 6 months prior to a hospitalization is associated with a reduced risk of NVHAP.

Nosocomial Pneumonia in the Mechanically Ventilated Patient

Ventilator-associated pneumonia (VAP) is a common complication occurring in critically ill patients who are mechanically ventilated and is the leading cause of nosocomial infection-related death. Etiologic agents for VAP widely differ based on the population of intensive care unit patients, duration of hospital stay, and prior antimicrobial therapy. VAP due to multidrug-resistant pathogens is associated with the highest morbidity and mortality, likely due to delays in appropriate antimicrobial treatment. International guidelines are currently available to guide diagnostic and therapeutic strategies. VAP can be prevented through various pharmacological and non-pharmacological interventions, which are more effective when grouped as bundles. When VAP is clinically suspected, diagnostic strategies should include early collection of respiratory samples to guide antimicrobial therapy. Empirical treatment should be based on the most likely etiologic microorganisms and antibiotics likely to be active against these microorganisms. Response to therapy should be reassessed after 3 to 5 days and antimicrobials adjusted or de-escalated to reduce the burden of the disease. Finally, considering that drug resistance is increasing worldwide, several novel antibiotics are being tested to efficiently treat VAP in the coming decades.

Bacterial and fungal communities in tracheal aspirates of intubated COVID-19 patients: a pilot study

Co-infections with bacterial or fungal pathogens could be associated with severity and outcome of disease in COVID-19 patients. We, therefore, used a 16S and ITS-based sequencing approach to assess the biomass and composition of the bacterial and fungal communities in endotracheal aspirates of intubated COVID-19 patients. Our method combines information on bacterial and fungal biomass with community profiling, anticipating the likelihood of a co-infection is higher with (1) a high bacterial and/or fungal biomass combined with (2) predominance of potentially pathogenic microorganisms. We tested our methods on 42 samples from 30 patients. We observed a clear association between microbial outgrowth (high biomass) and predominance of individual microbial species. Outgrowth of pathogens was in line with the selective pressure of antibiotics received by the patient. We conclude that our approach may help to monitor the presence and predominance of pathogens and therefore the likelihood of co-infections in ventilated patients, which ultimately, may help to guide treatment.

Healthcare-associated infections in adult intensive care unit patients: Changes in epidemiology, diagnosis, prevention and contributions of new technologies

Patients in intensive care units (ICUs) are at high risk for healthcare-acquired infections (HAI) due to the high prevalence of invasive procedures and devices, induced immunosuppression, comorbidity, frailty and increased age. Over the past decade we have seen a successful reduction in the incidence of HAI related to invasive procedures and devices. However, the rate of ICU-acquired infections remains high. Within this context, the ongoing emergence of new pathogens, further complicates treatment and threatens patient outcomes. Additionally, the SARS-CoV-2 (COVID-19) pandemic highlighted the challenge that an emerging pathogen provides in adapting prevention measures regarding both the risk of exposure to caregivers and the need to maintain quality of care. ICU nurses hold a special place in the prevention and management of HAI as they are involved in basic hygienic care, steering and implementing quality improvement initiatives, correct microbiological sampling, and aspects antibiotic stewardship. The emergence of more sensitive microbiological techniques and our increased knowledge about interactions between critically ill patients and their microbiota are leading us to rethink how we define HAIs and best strategies to diagnose, treat and prevent these infections in the ICU. This multidisciplinary expert review, focused on the ICU setting, will summarise the recent epidemiology of ICU-HAI, discuss the place of modern microbiological techniques in their diagnosis, review operational and epidemiological definitions and redefine the place of several controversial preventive measures including antimicrobial-impregnated medical devices, chlorhexidine-impregnated washcloths, catheter dressings and chlorhexidine-based mouthwashes. Finally, general guidance is suggested that may reduce HAI incidence and especially outbreaks in ICUs.

The Microbiome as Part of the Contemporary View of Tuberculosis Disease

The study of the microbiome has changed our overall perspective on health and disease. Although studies of the lung microbiome have lagged behind those on the gastrointestinal microbiome, there is now evidence that the lung microbiome is a rich, dynamic ecosystem. Tuberculosis is one of the oldest human diseases, it is primarily a respiratory infectious disease caused by strains from the Mycobacterium tuberculosis Complex. Even today, during the COVID-19 pandemic, it remains one of the principal causes of morbidity and mortality worldwide. Tuberculosis disease manifests itself as a dynamic spectrum that ranges from asymptomatic latent infection to life-threatening active disease. The review aims to provide an overview of the microbiome in the tuberculosis setting, both in patients’ and animal models. We discuss the relevance of the microbiome and its dysbiosis, and how, probably through its interaction with the immune system, it is a significant factor in tuberculosis’s susceptibility, establishment, and severity.

Inhaled Corticosteroids Selectively Alter the Microbiome and Host Transcriptome in the Small Airways of Patients with Chronic Obstructive Pulmonary Disease

Background: Patients with chronic obstructive pulmonary disease (COPD) are commonly treated with inhaled corticosteroid/long-acting ß2-agonist combination therapy. While previous studies have investigated the host–microbiome interactions in COPD, the effects of specific steroid formulations on this complex cross-talk remain obscure. Methods: We collected and evaluated data from the Study to Investigate the Differential Effects of Inhaled Symbicort and Advair on Lung Microbiota (DISARM), a randomized controlled trial. Bronchoscopy was performed on COPD patients before and after treatment with salmeterol/fluticasone, formoterol/budesonide or formoterol-only. Bronchial brush samples were processed for microbial 16S rRNA gene sequencing and host mRNA sequencing. Longitudinal changes in the microbiome at a community, phylum and genus level were correlated with changes in host gene expression using a Spearman’s rank correlation test. Findings: In COPD patients treated with salmeterol/fluticasone, the expression levels of 676 host genes were significantly correlated to changes in the alpha diversity of the small airways. At a genus level, the expression levels of 122 host genes were significantly related to changes in the relative abundance of Haemophilus. Gene enrichment analyses revealed the enrichment of pathways and biological processes related to innate and adaptive immunity and inflammation. None of these changes were evident in patients treated with formoterol/budesonide or formoterol alone. Interpretation: Changes in the microbiome following salmeterol/fluticasone treatment are related to alterations in the host transcriptome in the small airways of patients with COPD. These data may provide insights into why some COPD patients treated with inhaled corticosteroids may be at an increased risk for airway infection, including pneumonia. Funding: The Canadian Institute of Health Research, the British Columbia Lung Association, and an investigator-initiated grant from AstraZeneca.

Development and implementation of a customised rapid syndromic diagnostic test for severe pneumonia

Background: The diagnosis of pneumonia has been hampered by a reliance on bacterial cultures which take several days to return a result, and are frequently negative. In critically ill patients this leads to the use of empiric, broad-spectrum antimicrobials and compromises good antimicrobial stewardship. The objective of this study was to establish the performance of a syndromic molecular diagnostic approach, using a custom TaqMan array card (TAC) covering 52 respiratory pathogens, and assess its impact on antimicrobial prescribing. Methods: The TAC was validated against a retrospective multi-centre cohort of broncho-alveolar lavage samples. The TAC was assessed prospectively in patients undergoing investigation for suspected pneumonia, with a comparator cohort formed of patients investigated when the TAC laboratory team were unavailable. Co-primary outcomes were sensitivity compared to conventional microbiology and, for the prospective study, time to result. Metagenomic sequencing was performed to validate findings in prospective samples. Antibiotic free days (AFD) were compared between the study cohort and comparator group. Results: 128 stored samples were tested, with sensitivity of 97% (95% confidence interval (CI) 88-100%). Prospectively, 95 patients were tested by TAC, with 71 forming the comparator group. TAC returned results 51 hours (interquartile range 41-69 hours) faster than culture and with sensitivity of 92% (95% CI 83-98%) compared to conventional microbiology. 94% of organisms identified by sequencing were detected by TAC. There was a significant difference in the distribution of AFDs with more AFDs in the TAC group (p=0.02). TAC group were more likely to experience antimicrobial de-escalation (odds ratio 2.9 (95%1.5-5.5)). Conclusions: Implementation of a syndromic molecular diagnostic approach to pneumonia led to faster results, with high sensitivity and impact on antibiotic prescribing.

Multi-drug resistant gram-negative bacterial pneumonia: etiology, risk factors, and drug resistance patterns

Bacterial pneumonia is one of the most serious public health issues owing to its medical and economic costs, which result in increased morbidity and mortality in people of all ages around the world. Furthermore, antimicrobial resistance has risen over time, and the advent of multi-drug resistance in GNB complicates therapy and has a detrimental impact on patient outcomes. The current review aimed to summarize bacterial pneumonia with an emphasis on gram-negative etiology, pathogenesis, risk factors, resistance mechanisms, treatment updates, and vaccine concerns to tackle the problem before it causes a serious consequence. In conclusion, the global prevalence of GNB in CAP was reported 49.7% to 83.1%, whereas in VAP patients ranged between 76.13% to 95.3%. The most commonly reported MDR-GNB causes of pneumonia were A. baumannii, K. pneumoniae, and P. aeruginosa, with A. baumannii isolated particularly in VAP patients and the elderly. In most studies, ampicillin, tetracyclines, amoxicillin-clavulanic acid, cephalosporins, and carbapenems were shown to be highly resistant. Prior MDR-GNB infection, older age, previous use of broad-spectrum antibiotics, high frequency of local antibiotic resistance, prolonged hospital stays, ICU admission, mechanical ventilation, and immunosuppression are associated with the MDR-GNB colonization. S. maltophilia was reported as a severe cause of HAP/VAP in patients with mechanically ventilated and having hematologic malignancy due to its ability of biofilm formation, site adhesion in respiratory devices, and its intrinsic and acquired drug resistance mechanisms. Effective combination therapies targeting PDR strains and drug-resistant genes, antibiofilm agents, gene-based vaccinations, and pathogen-specific lymphocytes should be developed in the future.

Monocyte Signature Associated with Herpes Simplex Virus Reactivation and Neurological Recovery After Brain Injury

RATIONALE

Brain injury induces systemic immunosuppression increasing the risk of viral reactivations and altering neurological recovery.

OBJECTIVES

To determine if systemic immune alterations and lung replication of Herpesviridae are associated and can help predict outcomes after brain injury.

METHODS

We collected peripheral blood mononuclear cells in severely brain-injured patients requiring invasive mechanical ventilation. We systematically searched for respiratory Herpes Simplex Virus (HSV) replications in tracheal aspirates. We also performed CHiP-sequencing, RNA-sequencing and in vitro functional assays of monocytes and CD4 T cells collected on day 1 to characterize immune response to severe acute brain injury. The primary outcome was the Glasgow outcome scale Extended (GOS-E) at 6 months.

MEASUREMENTS AND MAIN RESULTS

In 344 severe brain-injured patients, lung HSV reactivations were observed in 39% of patients seropositive for HSV, and independently associated with poor neurological recovery at six months (hazard ratio 1.90, 95%CI 1.08-3.57). WGNA analyses of the transcriptomic response of monocytes to brain injury defined a module of 721 genes, including PD-L1 and CD80, enriched for the binding DNA motif of the transcriptional factor Zeb2, and whose ontogenic analyses revealed decreased interferon--mediated and anti-viral response signaling pathways. This monocyte signature was preserved in a validation cohort and predicted the neurological outcome at 6 months with good accuracy (AUC 0.786, 95%CI 0.593-0.978).

CONCLUSIONS

A specific monocyte signature is associated with HSV reactivation and predicts recovery after brain injury. The alterations of the immune control of Herpesviridae replication are understudied and represent a novel therapeutic target.

Bacterial Ventilator-Associated Pneumonia in COVID-19 Patients: Data from the Second and Third Waves of the Pandemic

During the coronavirus disease 2019 (COVID-19) pandemic, many patients requiring invasive mechanical ventilation were admitted to intensive care units (ICU) for COVID-19-related severe respiratory failure. As a matter of fact, ICU admission and invasive ventilation increased the risk of ventilator-associated pneumonia (VAP), which is associated with high mortality rate and a considerable burden on length of ICU stay and healthcare costs. The objective of this review was to evaluate data about VAP in COVID-19 patients admitted to ICU that developed VAP, including their etiology (limiting to bacteria), clinical characteristics, and outcomes. The analysis was limited to the most recent waves of the epidemic. The main conclusions of this review are the following: (i) P. aeruginosa, Enterobacterales, and S. aureus are more frequently involved as etiology of VAP; (ii) obesity is an important risk factor for the development of VAP; and (iii) data are still scarce and increasing efforts should be put in place to optimize the clinical management and preventative strategies for this complex and life-threatening disease.

The liver-gut-axis: initiator and responder to sepsis

PURPOSE OF REVIEW

The 'gut-liver axis' is thought to play an important role in pathogenesis of sepsis. Despite a wealth of experimental data to support the concept of reciprocal crosstalk between gut and liver through bacterial translocation and shaping of the microbiome by liver-derived molecules, for example bile acids, clinical data, and in particular diagnostic and therapeutic options, are limited.

RECENT FINDINGS

Assessment of organ failure in the current definition of sepsis is operationalized by means of the Sequential Organ Failure Assessment (SOFA) score, including exclusively bilirubin to reflect the complex functions of the liver but ignoring the gut. However, our understanding of the intestinal microbiome and how it is affected by critical illness has clearly improved. Microbiota maintain gut-barrier function and modulate the innate and adaptive immune system. The best-defined intervention affecting the gut microbiome, that is selective decontamination of the digestive tract (SDD) is clinically studied regarding prevention of nosocomial lung infection and antibiotic resistance patterns, although its impact on liver function has not been systematically evaluated in critical illness.

SUMMARY

Characterization of liver function beyond bilirubin and the microbiome can be achieved with contemporary sequencing and metabolomic techniques. Such studies are essential to understand how gut-liver crosstalk and 'dysbiosis' affect susceptibility to and outcome of sepsis.

Comparative Respiratory Tract Microbiome Between Carbapenem-Resistant Acinetobacter baumannii Colonization and Ventilator Associated Pneumonia

Background

Carbapenem-resistant Acinetobacter baumannii (CRAB) is a common cause of ventilator-associated pneumonia (VAP) in intensive care unit (ICU) patients, but its infection and colonization state are difficult to distinguish. If the judgment is wrong, it may aggravate the abuse of antibiotics and further accelerate the evolution of drug resistance. We sought to provide new clues for the diagnosis, pathogenesis and treatment of CRAB VAP based on lower respiratory tract (LRT) microbiota.

Methods

A prospective study was conducted on patients with mechanical ventilation from July 2018 to December 2019 in a tertiary hospital. Multi-genomics studies (16S rRNA amplicon, metagenomics, and whole-genome sequencing [WGS]) of endotracheal deep aspirate (ETA) were performed.

Results

Fifty-two ICU patients were enrolled, including 24 with CRAB VAP (CRAB-I), 22 with CRAB colonization (CRAB-C), and six CRAB-negative patients (infection-free) (CRAB-N). Diversity of pulmonary microbiota was significantly lower in CRAB-I than in CRAB-C or CRAB-N (mean Shannon index, 1.79 vs. 2.73 vs. 4.81, P < 0.05). Abundances of 11 key genera differed between the groups. Acinetobacter was most abundant in CRAB-I (76.19%), moderately abundant in CRAB-C (59.14%), and least abundant in CRAB-N (11.25%), but its interactions with other genera increased in turn. Metagenomics and WGS analysis showed that virulence genes were more abundant in CRAB-I than in CRAB-C. Multi-locus sequence typing (MLST) of 46 CRAB isolates revealed that the main types were ST208 (30.43%) and ST938 (15.22%), with no difference between CRAB-I and CRAB-C.

Conclusion

Lower respiratory tract microbiota dysbiosis including elevated relative abundance of Acinetobacter and reduced bacterial interactions, and virulence enrichment may lead to CRAB VAP.

Spatiotemporal Adaptations of Macrophage and Dendritic Cell Development and Function

Macrophages and conventional dendritic cells (cDCs) are distributed throughout the body, maintaining tissue homeostasis and tolerance to self and orchestrating innate and adaptive immunity against infection and cancer. As they complement each other, it is important to understand how they cooperate and the mechanisms that integrate their functions. Both are exposed to commensal microbes, pathogens, and other environmental challenges that differ widely among anatomical locations and over time. To adjust to these varying conditions, macrophages and cDCs acquire spatiotemporal adaptations (STAs) at different stages of their life cycle that determine how they respond to infection. The STAs acquired in response to previous infections can result in increased responsiveness to infection, termed training, or in reduced responses, termed paralysis, which in extreme cases can cause immunosuppression. Understanding the developmental stage and location where macrophages and cDCs acquire their STAs, and the molecular and cellular players involved in their induction, may afford opportunities to harness their beneficial outcomes and avoid or reverse their deleterious effects. Here we review our current understanding of macrophage and cDC development, life cycle, function, and STA acquisition before, during, and after infection. We propose a unified framework to explain how these two cell types adjust their activities to changing conditions over space and time to coordinate their immunosurveillance functions. Expected final online publication date for the Annual Review of Immunology, Volume 40 is April 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Empiric antimicrobial therapy for early-onset pneumonia in severe trauma patients

PURPOSE

The bacterial ecology involved in early pneumonia of severe trauma patients is mostly commensal and would allow wide use of narrow-spectrum antibiotics. We describe risk factors for treatment failure of severe trauma patients' pneumonia with the use of narrow-spectrum antimicrobial therapy in order to develop a score that could help clinicians to determine which patients might be treated with narrow-spectrum antibiotics.

METHODS

A retrospective, observational, monocentric cohort study was conducted of severe trauma patients requiring mechanical ventilation for > 48 h and developing a first episode of microbiologically confirmed pneumonia occurring within the first 10 days after admission.

RESULTS

Overall, 370 patients were included. The resistance rate against narrow-spectrum antibiotics (amoxicillin/clavulanic acid) was 22.7% (84 pneumonia). In a multivariate analysis, two independent risk factors were associated with this resistance: prior antimicrobial therapy ≥ 48 h (OR 4.00; 95 CI [2.39; 6.75]) and age ≥ 30y (OR 2.10; 95 CI [1.21; 3.78]). We created a prediction score that defined patient with one or two risk factors at high risk of resistance. This score presented a sensitivity of 0.92 [0.88; 0.94], a specificity of 0.33 [0.28; 0.38], a positive predictive value of 0.29 [0.24; 0.33] and a negative predictive value of 0.93 [0.90; 0.95].

CONCLUSION

Simple risk factors may help clinicians to identify severe trauma patients at high risk of pneumonia treatment failure with the use of narrow-spectrum antimicrobial therapy and, thus, use better tailored empiric therapy and limit the use of unnecessary broad-spectrum antimicrobial therapy.

Rapid identification of pathogens associated with ventilator-associated pneumonia by Nanopore sequencing

BACKGROUND

Aetiology detection is crucial in the diagnosis and treatment of ventilator-associated pneumonia (VAP). However, the detection method needs improvement. In this study, we used Nanopore sequencing to build a quick detection protocol and compared the efficiency of different methods for detecting 7 VAP pathogens.

METHODS

The endotracheal aspirate (ETA) of 83 patients with suspected VAP from Peking University Third Hospital (PUTH) was collected, saponins were used to deplete host genomes, and PCR- or non-PCR-amplified library construction methods were used and compared. Sequence was performed with MinION equipment and local data analysis methods were used for sequencing and data analysis.

RESULTS

Saponin depletion effectively removed 11 of 12 human genomes, while most pathogenic bacterial genome results showed no significant difference except for S. pneumoniae. Moreover, the average sequence time decreased from 19.6 h to 3.62 h. The non-PCR amplification method and PCR amplification method for library build has a similar average sensitivity (85.8% vs. 86.35%), but the non-PCR amplification method has a better average specificity (100% VS 91.15%), and required less time. The whole method takes 5-6 h from ETA extraction to pathogen classification. After analysing the 7 pathogens enrolled in our study, the average sensitivity of metagenomic sequencing was approximately 2.4 times higher than that of clinical culture (89.15% vs. 37.77%), and the average specificity was 98.8%.

CONCLUSIONS

Using saponins to remove the human genome and a non-PCR amplification method to build libraries can be used for the identification of pathogens in the ETA of VAP patients within 6 h by MinION, which provides a new approach for the rapid identification of pathogens in clinical departments.

Management of pneumonia in critically ill patients

Severe pneumonia is associated with high mortality (short and long term), as well as pulmonary and extrapulmonary complications. Appropriate diagnosis and early initiation of adequate antimicrobial treatment for severe pneumonia are crucial in improving survival among critically ill patients. Identifying the underlying causative pathogen is also critical for antimicrobial stewardship. However, establishing an etiological diagnosis is challenging in most patients, especially in those with chronic underlying disease; those who received previous antibiotic treatment; and those treated with mechanical ventilation. Furthermore, as antimicrobial therapy must be empiric, national and international guidelines recommend initial antimicrobial treatment according to the location's epidemiology; for patients admitted to the intensive care unit, specific recommendations on disease management are available. Adherence to pneumonia guidelines is associated with better outcomes in severe pneumonia. Yet, the continuing and necessary research on severe pneumonia is expansive, inviting different perspectives on host immunological responses, assessment of illness severity, microbial causes, risk factors for multidrug resistant pathogens, diagnostic tests, and therapeutic options.

Alveolar Macrophages: Adaptation to Their Anatomic Niche during and after Inflammation

At the early stages of life development, alveoli are colonized by embryonic macrophages, which become resident alveolar macrophages (ResAM) and self-sustain by local division. Genetic and epigenetic signatures and, to some extent, the functions of ResAM are dictated by the lung microenvironment, which uses cytokines, ligand-receptor interactions, and stroma cells to orchestrate lung homeostasis. In resting conditions, the lung microenvironment induces in ResAM a tolerogenic programming that prevents unnecessary and potentially harmful inflammation responses to the foreign bodies, which continuously challenge the airways. Throughout life, any episode of acute inflammation, pneumonia being likely the most frequent cause, depletes the pool of ResAM, leaving space for the recruitment of inflammatory monocytes that locally develop in monocyte-derived alveolar macrophages (InfAM). During lung infection, the local microenvironment induces a temporary inflammatory signature to the recruited InfAM to handle the tissue injury and eliminate the pathogens. After a few days, the recruited InfAM, which locally self-sustain and develop as new ResAM, gain profibrotic functions required for tissue healing. After the complete resolution of the infectious episode, the functional programming of both embryonic and monocyte-derived ResAM remains altered for months and possibly for the entire life. Adult lungs thus contain a wide diversity of ResAM since every infection brings new waves of InfAM which fill the room left open by the inflammatory process. The memory of these innate cells called trained immunity constitutes an immunologic scar left by inflammation, notably pneumonia. This memory of ResAM has advantages and drawbacks. In some cases, lung-trained immunity offers better defense capacities against autoimmune disorders and the long-term risk of infection. At the opposite, it can perpetuate a harmful process and lead to a pathological state, as is the case among critically ill patients who have immune paralysis and are highly susceptible to hospital-acquired pneumonia and acute respiratory distress syndrome. The progress in understanding the kinetics of response of alveolar macrophages (AM) to lung inflammation is paving the way to new treatments of pneumonia and lung inflammatory process.