Diagnosis of pneumonia and monitoring of infection eradication

High specificity of metagenomic next-generation sequencing using protected bronchial brushing sample in diagnosing pneumonia in children

Background

Lower respiratory tract infections are the leading cause of morbidity and mortality in children worldwide. Timely and accurate pathogen detection is crucial for proper clinical diagnosis and therapeutic strategies. The low detection efficiency of conventional methods and low specificity using respiratory samples seriously hindered the accurate detection of pathogens.

Methods

In this study, we retrospectively enrolled 1,032 children to evaluate the performance of metagenomics next-generation sequencing (mNGS) using bronchoalveolar lavage fluid (BALF) sample and protected bronchial brushing (BB) sample in diagnosing pneumonia in children. In addition, conventional tests (CTs) were also performed.

Results

The specificity of BB mNGS [67.3% (95% CI 58.6%-75.9%)] was significantly higher than that of BALF mNGS [38.5% (95% CI 12.0%-64.9%)]. The total coincidence rate of BB mNGS [77.6% (95% CI 74.8%-80.5%)] was slightly higher than that of BALF mNGS [76.5% (95% CI 68.8%-84.1%)] and CTs [38.5% (95% CI 35.2%-41.9%)]. During the epidemics of Mycoplasma pneumoniae, the detection rate of M. pneumoniae in the >6-year group (81.8%) was higher than that in the 3-6-year (78.9%) and <3-year groups (21.5%). The highest detection rates of bacteria, fungi, and viruses were found in the <3-year, >6-year, and 3-6-year groups, respectively. mNGS detection should be performed at the duration of 5-7 days after the start of continuous anti-microbial therapy or at the duration of 6-9 days from onset to mNGS test.

Conclusions

This is the first report to evaluate the performance of BB mNGS in diagnosing pulmonary infections in children on a large scale. Based on our findings, extensive application of BB mNGS could be expected.

Development of a radiomics nomogram to predict the treatment resistance of Chinese MPO-AAV patients with lung involvement: a two-center study

Background

Previous studies from our group and other investigators have shown that lung involvement is one of the independent predictors for treatment resistance in patients with myeloperoxidase (MPO)-anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis (MPO-AAV). However, it is unclear which image features of lung involvement can predict the therapeutic response in MPO-AAV patients, which is vital in decision-making for these patients. Our aim was to develop and validate a radiomics nomogram to predict treatment resistance of Chinese MPO-AAV patients based on low-dose multiple slices computed tomography (MSCT) of the involved lung with cohorts from two centers.

Methods

A total of 151 MPO-AAV patients with lung involvement (MPO-AAV-LI) from two centers were enrolled. Two different models (Model 1: radiomics signature; Model 2: radiomics nomogram) were built based on the clinical and MSCT data to predict the treatment resistance of MPO-AAV with lung involvement in training and test cohorts. The performance of the models was assessed using the area under the curve (AUC). The better model was further validated. A nomogram was constructed and evaluated by DCA and calibration curves, which further tested in all enrolled data and compared with the other model.

Results

Model 2 had a higher predicting ability than Model 1 both in training (AUC: 0.948 vs. 0.824; p = 0.039) and test cohorts (AUC: 0.913 vs. 0.898; p = 0.043). As a better model, Model 2 obtained an excellent predictive performance (AUC: 0.929; 95% CI: 0.827-1.000) in the validation cohort. The DCA curve demonstrated that Model 2 was clinically feasible. The calibration curves of Model 2 closely aligned with the true treatment resistance rate in the training (p = 0.28) and test sets (p = 0.70). In addition, the predictive performance of Model 2 (AUC: 0.929; 95% CI: 0.875-0.964) was superior to Model 1 (AUC: 0.862; 95% CI: 0.796-0.913) and serum creatinine (AUC: 0.867; 95% CI: 0.802-0.917) in all patients (all p< 0.05).

Conclusion

The radiomics nomogram (Model 2) is a useful, non-invasive tool for predicting the treatment resistance of MPO-AAV patients with lung involvement, which might aid in individualizing treatment decisions.

Comparison of metagenomic next-generation sequencing using cell-free DNA and whole-cell DNA for the diagnoses of pulmonary infections

Although the fast-growing metagenomic next-generation sequencing (mNGS) has been used in diagnosing infectious diseases, low detection rate of mNGS in detecting pathogens with low loads limits its extensive application. In this study, 130 patients with suspected pulmonary infections were enrolled, from whom bronchoalveolar lavage fluid (BALF) samples were collected. The conventional tests and mNGS of cell-free DNA (cfDNA) and whole-cell DNA (wcDNA) using BALF were simultaneously performed. mNGS of cfDNA showed higher detection rate (91.5%) and total coincidence rate (73.8%) than mNGS of wcDNA (83.1% and 63.9%) and conventional methods (26.9% and 30.8%). A total of 70 microbes were detected by mNGS of cfDNA, and most of them (60) were also identified by mNGS of wcDNA. The 31.8% (21/66) of fungi, 38.6% (27/70) of viruses, and 26.7% (8/30) of intracellular microbes can be only detected by mNGS of cfDNA, much higher than those [19.7% (13/66), 14.3% (10/70), and 6.7% (2/30)] only detected by mNGS of wcDNA. After in-depth analysis on these microbes with low loads set by reads per million (RPM), we found that more RPM and fungi/viruses/intracellular microbes were detected by mNGS of cfDNA than by mNGS of wcDNA. Besides, the abilities of mNGS using both cfDNA and wcDNA to detect microbes with high loads were similar. We highlighted the advantage of mNGS using cfDNA in detecting fungi, viruses, and intracellular microbes with low loads, and suggested that mNGS of cfDNA could be considered as the first choice for diagnosing pulmonary infections.

Safety and efficacy of human umbilical cord mesenchymal stem cells for the treatment of sepsis induced by pneumonia: study protocol for a single-centre, randomised single-blind parallel group trial

INTRODUCTION

Sepsis is a life-threatening organ disorder caused by a dysregulated inflammatory response to infection with no effective treatment options exist thus far. Therefore, novel therapeutic methods are urgently advocated for decreasing the high mortality rate. Recently, preclinical studies supported the efficacy of mesenchymal stem cells (MSCs) in the treatment of sepsis. In this study, we aim to test the safety, tolerability and efficacy of human umbilical cord MSCs (HUC-MSCs) for the treatment of pneumonia induced sepsis.

METHODS AND ANALYSIS

This study is a single-centre, randomised single-blind parallel group, placebo-controlled trial. Forty eligible participants with pneumonia-induced sepsis will be randomly assigned to the observational cohort and the interventional cohort in a 1:1 ratio. In addition to the standard treatments recommended by the Sepsis 3.0 guidelines, HUC-MSCs will be administered intravenously as adjunctive therapy on day 0 at a dose of 1×10⁶ cells/kg with a total volume of 100 mL diluted with normal saline through 120 mL/hour intravenous central line infusion in the interventional cohort. Placebo (normal saline) will also be administered through 120 mL/hour intravenous central line infusion at the same quantity (total volume of 100 mL) in the observational cohort. The study is approved by Research Ethics Board of East Hospital/Tongji University, which has been registered on Chinese clinical trial registry (chictr.org.cn) and initiated from October 2021. All the participants will be followed at regular intervals for 1 year. Funding is from the 'National Natural Science Foundation, China and top-level clinical discipline project of Shanghai Pudong'. This study is the first trial to assess the safety and efficacy of HUC-MSCs for the treatment of sepsis induced by pneumonia. The results will advance our understanding of the mode of action of HUC-MSCs and will also be critical for the design of future investigation in larger randomised controlled trials in multicentre. These data will offer insight into defining endpoints, key biomarkers and sample size determination.

ETHICS AND DISSEMINATION

This study has been approved by the Research Ethics Board of East Hospital, Tongji University (Shanghai, China), which has accepted responsibility for supervising all aspects of the study (DFSC-2021(CR-04). The results of this study will be presented at both national and international conferences and be considered for publication in a peer-reviewed scientific journal. All the results presented in this study will be of group data, therefore, individual participants will not be identifiable.

TRIAL REGISTRATION NUMBER

ChiCTR2100050544, the trial is now at the stage of pre-results.

Detection of Viruses by Multiplex Real-Time Polymerase Chain Reaction in Bronchoalveolar Lavage Fluid of Patients with Nonresponding Community-Acquired Pneumonia

Background

Nonresponding pneumonia is responsible for the most mortality of community-acquired pneumonia (CAP). However, thus far, it is not clear whether viral infection plays an important role in the etiology of nonresponding CAP and whether there is a significant difference in the clinical characteristics between viral and nonviral nonresponding CAP.

Methods

From 2016 to 2019, nonresponding CAP patients were retrospectively enrolled in our study. All patients received bronchoalveolar lavage (BAL) and virus detection in BAL fluid by multiplex real-time polymerase chain reaction (PCR), and clinical, laboratory, and radiographic data were collected.

Results

A total of 43 patients were included. The median age was 62 years, and 65.1% of patients were male. Overall, 20 patients (46.5%) were identified with viral infection. Of these viruses, influenza virus (n = 8) and adenovirus (n = 7) were more frequently detected, and others included herpes simplex virus, human enterovirus, cytomegalovirus, human coronavirus 229E, rhinovirus, and parainfluenza virus. Compared with nonviral nonresponding CAP, only ground-glass opacity combined with consolidation was a more common imaging manifestation in viral nonresponding CAP. However, no obvious differences were found in clinical and laboratory findings between the presence and the absence of viral infections.

Conclusions

Viral infections were particularly frequent in adults with nonresponding CAP. The ground-glass opacity combined with consolidation was a specific imaging manifestation for viral nonresponding CAP, while the clinical and laboratory data showed no obvious differences between viral and nonviral nonresponding CAP.

Simvastatin Improves Neutrophil Function and Clinical Outcomes in Pneumonia. A Pilot Randomized Controlled Clinical Trial

Rationale: Population studies suggest improved sepsis outcomes with statins, but the results of randomized controlled trials in patients with sepsis and organ dysfunction in critical care settings have broadly been negative. In vitro data suggest that statins modulate age-related neutrophil functions, improving neutrophil responses to infection, but only in older patients and at high doses.Objectives: To determine if high-dose simvastatin improves neutrophil functions and is safe and tolerated in hospitalized older adults with community-acquired pneumonia with sepsis (CAP + S) not admitted to critical care.Methods: We conducted a randomized, double-blind, placebo-controlled pilot study of simvastatin 80 mg or placebo for 7 days for patients with CAP + S aged 55 years or older admitted to a secondary care hospital. The Day 4 primary endpoint was change in neutrophil extracellular trap formation (NETosis). Day 4 secondary endpoints included neutrophil chemotaxis, safety and tolerability, Sequential Organ Failure Assessment score, mortality, readmission, and markers of tissue degradation/inflammation.Measurements and Main Results: Four days of simvastatin adjuvant therapy in patients with CAP + S was associated with improvements in systemic neutrophil function (NETosis and chemotaxis), a reduction in systemic neutrophil elastase burden, and improved Sequential Organ Failure Assessment scores compared with placebo. A post hoc analysis demonstrated that simvastatin therapy was associated with improved hospitalization-free survival compared with placebo. Simvastatin was well tolerated in this elderly and multimorbid patient group with common coprescription of macrolide antibiotics.Conclusions: This pilot study supports high-dose simvastatin as an adjuvant therapy for CAP + S in an older and milder disease cohort than assessed previously. A definitive multicenter study is now warranted in this population to assess the likelihood of benefit and harm.Clinical trial registered with EudraCT (2012-00343-29).

Chest radiographs for acute lower respiratory tract infections

BACKGROUND

Acute lower respiratory tract infections (LRTIs) (e.g. pneumonia) are a major cause of morbidity and mortality and management focuses on early treatment. Chest radiographs (X-rays) are one of the commonly used strategies. Although radiological facilities are easily accessible in high-income countries, access can be limited in low-income countries. The efficacy of chest radiographs as a tool in the management of acute LRTIs has not been determined. Although chest radiographs are used for both diagnosis and management, our review focuses only on management.

OBJECTIVES

To assess the effectiveness of chest radiographs in addition to clinical judgement, compared to clinical judgement alone, in the management of acute LRTIs in children and adults.

SEARCH METHODS

We searched CENTRAL 2013, Issue 1; MEDLINE (1948 to January week 4, 2013); EMBASE (1974 to February 2013); CINAHL (1985 to February 2013) and LILACS (1985 to February 2013). We also searched NHS EED, DARE, ClinicalTrials.gov and WHO ICTRP (up to February 2013).

SELECTION CRITERIA

Randomised controlled trials (RCTs) of chest radiographs versus no chest radiographs in acute LRTIs in children and adults.

DATA COLLECTION AND ANALYSIS

Two review authors independently applied the inclusion criteria, extracted data and assessed risk of bias. A third review author compiled the findings and any discrepancies were discussed among all review authors. We used the standard methodological procedures expected by The Cochrane Collaboration.

MAIN RESULTS

Two RCTs involving 2024 patients (1502 adults and 522 children) were included in this review. Both RCTs excluded patients with suspected severe disease. It was not possible to pool the results due to incomplete data. Both included trials concluded that the use of chest radiographs did not result in a better clinical outcome (duration of illness and of symptoms) for patients with acute LRTIs. In the study involving children in South Africa, the median time to recovery was seven days (95% confidence interval (CI) six to eight days (radiograph group) and six to nine days (control group)), P value = 0.50, log-rank test) and the hazard ratio for recovery was 1.08 (95% CI 0.85 to 1.34). In the study with adult participants in the USA, the average duration of illness was 16.9 days versus 17.0 days (P value > 0.05) in the radiograph and no radiograph groups respectively. This result was not statistically significant and there were no significant differences in patient outcomes between the groups with or without chest radiograph.The study in adults also reports that chest radiographs did not affect the frequencies with which clinicians ordered return visits or antibiotics. However, there was a benefit of chest radiographs in a subgroup of the adult participants with an infiltrate on their radiograph, with a reduction in length of illness (16.2 days in the group allocated to chest radiographs and 22.6 in the non-chest radiograph group, P < 0.05), duration of cough (14.2 versus 21.3 days, P < 0.05) and duration of sputum production (8.5 versus 17.8 days, P < 0.05). The authors mention that this difference in outcome between the intervention and control group in this particular subgroup only was probably a result of "the higher proportion of patients treated with antibiotics when the radiograph was used in patient care".Hospitalisation rates were only reported in the study involving children and it was found that a higher proportion of patients in the radiograph group (4.7%) required hospitalisation compared to the control group (2.3%) with the result not being statistically significant (P = 0.14). None of the trials report the effect on mortality, complications of infection or adverse events from chest radiographs. Overall, the included studies had a low or unclear risk for blinding, attrition bias and reporting bias, but a high risk of selection bias. Both trials had strict exclusion criteria which is important but may limit the clinical practicability of the results as participants may not reflect those presenting in clinical practice.

AUTHORS' CONCLUSIONS

Data from two trials suggest that routine chest radiography does not affect the clinical outcomes in adults and children presenting to a hospital with signs and symptoms suggestive of a LRTI. This conclusion may be weakened by the risk of bias of the studies and the lack of complete data available.

Evaluation of the diagnostic value of fluorescent in situ hybridization in a rat model of bacterial pneumonia

In severe nosocomial pneumonia, the pathogenic responsibility of bacteria isolated from airways is far from certain, and a lung biopsy is sometimes performed. However, detection and identification of pathogens are frequently unachieved. Here, we developed a protocol for direct visualization of bacteria within the lung tissue using fluorescent in situ hybridization (FISH) in a rat model of Acinetobacter baumannii pneumonia. The reference positive diagnosis of bacterial pneumonia was the presence of pathological signs of pneumonia associated with the proof of bacteria or bacterial PCR products into the parenchyma. By analysis of 122 sets of slices from 26 rats and using the eubacterial probe EUB-338, our results show that FISH reached a sensitivity and a diagnostic accuracy higher than that of optic microscopy (sensitivity: 96% versus 55.4% and diagnostic accuracy: 96.7% versus 66.4%), whereas both approaches had 100% specificity. FISH could be useful especially on negative biopsies from patients with suspected infectious pneumonia.

A European care bundle for management of ventilator-associated pneumonia

BACKGROUND

Although there is a wealth of guidance concerning the management of patients with ventilator-associated pneumonia (VAP), compliance with recommendations concerning optimal treatment practices is highly variable.

METHODS

This document presents a comprehensive care bundle package addressing all aspects of VAP diagnosis and treatment in an attempt to promote guideline-compliant practices. Uniquely, the development of these care bundles used a formalized method to assess the supporting data, based on multicriteria decision analysis.

RESULTS

This system allowed the numerous VAP management parameters identified from recent European guidelines to be ranked according to defined criteria. The resulting VAP care bundles are (a) diagnosis: early chest x-rays within 1 hour, immediate reporting of respiratory secretions Gram staining, and (b) therapy: immediate treatment, empiric therapy based on local pathogens and risk factors, de-escalation, assessment of response within 72 hours, and short therapy duration if feasible.

CONCLUSION

Adoption of these care bundles should rationalize VAP management practices and facilitate the development of consistent and guideline-compliant care processes.

Systemic and bronchoalveolar cytokines as predictors of in-hospital mortality in severe community-acquired pneumonia

OBJECTIVES

The aim of this study was to determine whether cytokine expression (interleukin [IL]-1beta, IL-6, IL-8, IL-10, and tumor necrosis factor [TNF]-alpha), C-reactive protein, and endotoxins on the first day of intensive care unit (ICU) admission are associated with hospital mortality in severe community-acquired pneumonia (CAP).

DESIGN

This was a prospective study with bronchoalveolar lavage (BAL) and blood sampling.

SETTING

This study was carried out in a 44-bed medical ICU of a 1700-bed university hospital.

PATIENTS

Participants included 112 mechanically ventilated patients with severe CAP.

INTERVENTIONS

Serum and BAL fluid IL-1beta, IL-6, IL-8, IL-10, TNF-alpha, C-reactive protein, and endotoxins on the first day of ICU admission were obtained.

MEASUREMENTS AND MAIN RESULTS

The concentrations of TNF-alpha in BALF and IL-6, IL-8, IL-10, and TNF-alpha in serum were higher in nonsurvivors than in survivor patients with CAP. Of these 112 patients with severe CAP (39%), 44 developed acute respiratory distress syndrome (ARDS); these patients seemed to have higher serum IL-6, IL-8, and IL-10 levels than did the non-ARDS group. Furthermore, in the ARDS population, we found that the endotoxin levels in the BAL fluid were higher in the survival than in the nonsurvival group and BAL fluid concentrations of IL-6, IL-8, and IL-1beta and sera levels of IL-6 and IL-10 were lower in the survival than in the nonsurvival group, and they were associated with a high negative predictive value.

CONCLUSIONS

Serum and BAL fluid levels of the studied cytokines on admission may provide valuable prognostic information for patients with severe CAP.

Outcomes of Staphylococcus aureus infection in hemodialysis-dependent patients

BACKGROUND AND OBJECTIVES

Staphylococcus aureus is a leading cause of infection in patients with ESRD. Clinical and economic outcomes associated with S. aureus bacteremia and other S. aureus infections in patients with ESRD were examined.

DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS

Laboratory, clinical, and hospital billing data from a randomized trial of 3359 hemodialysis-dependent patients hospitalized with S. aureus infection in the United States whose vascular access type was fistula or graft and who were hospitalized with S. aureus infection to evaluate inpatient costs, hospital days, and mortality over 12 wk were used. Generalized linear regression was used to identify independent predictors of 12-wk costs, inpatient days, and mortality.

RESULTS

Of the 279 patients (8.3%) who developed S. aureus infection during approximately 1 yr of follow-up, 25.4% were treated as outpatients. Among patients for whom billing data were available, 89 patients hospitalized with S. aureus bacteremia incurred mean 12-wk inpatient costs of $19,454 and 11.9 inpatient days. Among the 70 patients hospitalized with non-bloodstream S. aureus infections, mean inpatient costs were $19,222 and the mean number of inpatient days was 11.3. Twelve-week mortality was 20.2 and 15.7% for patients with S. aureus bloodstream and non-bloodstream infections, respectively. Older age was independently associated with higher risk of death among patients with S. aureus bacteremia and with higher inpatient costs and more hospital days among patients with non-bloodstream infections.

CONCLUSIONS

Hemodialysis-dependent patients with fistula or graft access incur high costs and long inpatient stays when hospitalized for S. aureus infection.

Acute bronchitis: state of the art diagnosis and therapy

In managing acute bronchitis, pneumonia or an exacerbation of underlying chronic bronchitis should be excluded. Simple bronchitis is best treated symptomatically while an exacerbation of chronic bronchitis can be treated with antibiotics. Broad spectrum antibiotics are appropriate in selected patients.

Impact of introducing quality control/quality assurance (QC/QA) guidelines in respiratory specimen processing

OBJECTIVES

To assess the impact of the introduction of a new quality control/quality assurance (QA/QC) protocol on the processing and reporting of respiratory specimens.

METHODS

After implementation of guidelines for processing respiratory specimens, an investigation was carried out over a six-month period on 200 specimens, 105 sputa, and 95 deep tracheal aspirates (DTAs), assessed blindly by two independent investigators. Data regarding disagreement were arranged into two subgroups. A minor disagreement was defined as a difference in the two assessments of < 10 or 10-25 for white blood cell (WBC) or squamous epithelial cell (SEC) counts. A major disagreement was defined as one assessor reporting < 10 and the other > 25 for either WBC count or SEC count, or one assessor reporting the specimen as non-assessable, or both assessors having a minor disagreement in both the WBC count and the SEC count.

RESULTS

Agreement was obtained on 111 samples. For 45 specimens, a major disagreement was documented, and in 44 cases, a minor disagreement was recorded, WBC being the most common cause of divergence. Data for sputa and DTAs were examined separately: of 45 major disagreements, 64.4% were observed for DTAs, while minor disagreements were recorded mostly for sputa. The role of the settings in which samples were taken in affecting quality was studied. Among the 105 sputa, 27 were from Community Health Centers (CHCs) and 78 from hospitalized patients. Agreement between the two observers was obtained in 48.1% of CHC cases versus 60.2% of hospital samples. To investigate how many of the rejected samples presented WBC > 25 suggestive of infection, we looked at the 107 samples rejected during the six-month period, grouped according to the suspected diagnosis. The highest number of rejected samples falls in the category of unrelated (non-respiratory) diagnosis, and clinical suspicion is not helpful in Gram stain interpretation. The annual saving (not culturing, not testing, and not treating) derived from this simple QC procedure totals about 5000 Euro.

CONCLUSIONS

Standardization in microscopic screening of respiratory samples is difficult to achieve. Criteria for rejection must be adapted to local conditions after discussion with clinicians to increase their compliance with the newly introduced guidelines and to avoid sending unnecessary specimens. The effects on patient management and cost control are significant.

Hospital-acquired pneumonia: challenges and options for diagnosis and treatment

The management of hospital-acquired pneumonia (HAP) presents a major challenge for the clinician. The insensitivity of current diagnostic methods and the increasing prevalence of nosocomial pathogens with multiple antibiotic resistance complicate the issue. Use of mechanical ventilation and broad-spectrum antimicrobials in the intensive care setting predipose patients to acquire HAP more frequently with antimicrobial-resistant pathogens. Controversy exists regarding the patients in which invasive diagnostic testing is indicated; the timing of these procedures is another subject of debate. Proper empirical therapy is fundamental to a favourable outcome, and the selection of inappropriate agents to which pathogens are resistant contributes significantly to morbidity and mortality. In general, there is agreement on the requirement for a thorough knowledge of the local causative organisms and the pathogens' resistance profiles. A wide variety of antimicrobials can be used either as monotherapy or in combinations.

Ventilator-associated pneumonia

Ventilator-associated pneumonia is the most serious infectious complication in critically ill patients, associated with increased length of intensive care unit treatment and high mortality rates. Investigations focused on outcome variables have improved the database to estimate diagnostic and therapeutic management strategies. This knowledge has diminished the importance of the discussion on how to diagnose the pneumonia. This review summarizes recent data on epidemiology and mortality, risk factors and prevention, diagnosis, microbiology and antimicrobial treatment of ventilator-associated pneumonia.