Accuracy of comprehensive PCR analysis of nasopharyngeal and oropharyngeal swabs for CT-scan-confirmed pneumonia in elderly patients: a prospective cohort study

Impact of FilmArray respiratory panel test for hospitalized pediatric respiratory tract infection in Taiwan: A 3-year single-center cohort study

Respiratory tract infections are prevalent and clinically significant in pediatric populations globally. However, pathogen testing often involves time-consuming processes, resulting in delays in diagnosis. To date, commercial testing machines, such as the FilmArray respiratory panel, have been proposed for hospitals. Therefore, this study aimed to investigate the impact of the FilmArray respiratory panel at a single center. This study utilized the medical records of our hospital to select pediatric inpatients with respiratory tract infections who underwent the FilmArray respiratory panel between September 2020 and April 2021 and those who did not undergo nucleic acid detection (a rapid test group) between September 2019 and April 2020. FilmArray is a polymerase chain reaction-based diagnostic tool. The FilmArray respiratory panel group was scheduled to recruit 150 patients (final 137 patients), whereas the rapid test group was scheduled to recruit 300 patients (final 267 patients). Differences in continuous variables between the 2 groups were analyzed using independent Student t tests. The FilmArray respiratory panel group had a longer length of inpatient days, longer duration of antibiotic use, and higher proportion of pathogens that tested positive, with significant differences than those in the rapid test group. Fever duration showed no significant difference between the 2 groups. For the polymerase chain reaction method, respiratory syncytial virus was the most commonly detected pathogen causing pneumonia, followed by human rhinovirus/enterovirus and parainfluenza virus. Mycoplasma was detected using the rapid test but not with the FilmArray respiratory panel. The FilmArray respiratory panel provides clinicians with a rapid and useful diagnostic tool. The effect was quite good for virus detection, but not for bacteria. Given its limited adoption, the tool may not aid clinicians in the diagnosis of mild cases.

Atypical Pathogens in Adult Community-Acquired Pneumonia and Implications for Empiric Antibiotic Treatment: A Narrative Review

Atypical pathogens are intracellular bacteria causing community-acquired pneumonia (CAP) in a significant minority of patients. Legionella spp., Chlamydia pneumoniae and psittaci, Mycoplasma pneumoniae, and Coxiella burnetii are commonly included in this category. M. pneumoniae is present in 5-8% of CAP, being the second most frequent pathogen after Streptococcus pneumoniae. Legionella pneumophila is found in 3-5% of inpatients. Chlamydia spp. and Coxiella burnetii are present in less than 1% of patients. Legionella longbeachae is relatively frequent in New Zealand and Australia and might also be present in other parts of the world. Uncertainty remains on the prevalence of atypical pathogens, due to limitations in diagnostic means and methodological issues in epidemiological studies. Despite differences between CAP caused by typical and atypical pathogens, the clinical presentation alone does not allow accurate discrimination. Hence, antibiotics active against atypical pathogens (macrolides, tetracyclines and fluoroquinolones) should be included in the empiric antibiotic treatment of all patients with severe CAP. For patients with milder disease, evidence is lacking and recommendations differ between guidelines. Use of clinical prediction rules to identify patients most likely to be infected with atypical pathogens, and strategies of narrowing the antibiotic spectrum according to initial microbiologic investigations, should be the focus of future investigations.

Unmet needs in pneumonia research: a comprehensive approach by the CAPNETZ study group

Introduction

Despite improvements in medical science and public health, mortality of community-acquired pneumonia (CAP) has barely changed throughout the last 15 years. The current SARS-CoV-2 pandemic has once again highlighted the central importance of acute respiratory infections to human health. The “network of excellence on Community Acquired Pneumonia” (CAPNETZ) hosts the most comprehensive CAP database worldwide including more than 12,000 patients. CAPNETZ connects physicians, microbiologists, virologists, epidemiologists, and computer scientists throughout Europe. Our aim was to summarize the current situation in CAP research and identify the most pressing unmet needs in CAP research.

Methods

To identify areas of future CAP research, CAPNETZ followed a multiple-step procedure. First, research members of CAPNETZ were individually asked to identify unmet needs. Second, the top 100 experts in the field of CAP research were asked for their insights about the unmet needs in CAP (Delphi approach). Third, internal and external experts discussed unmet needs in CAP at a scientific retreat.

Results

Eleven topics for future CAP research were identified: detection of causative pathogens, next generation sequencing for antimicrobial treatment guidance, imaging diagnostics, biomarkers, risk stratification, antiviral and antibiotic treatment, adjunctive therapy, vaccines and prevention, systemic and local immune response, comorbidities, and long-term cardio-vascular complications.

Conclusion

Pneumonia is a complex disease where the interplay between pathogens, immune system and comorbidities not only impose an immediate risk of mortality but also affect the patients’ risk of developing comorbidities as well as mortality for up to a decade after pneumonia has resolved. Our review of unmet needs in CAP research has shown that there are still major shortcomings in our knowledge of CAP.

Detection of bacteria via multiplex PCR in respiratory samples of critically ill COVID-19 patients with suspected HAP/VAP in the ICU

Background

Critically ill Coronavirus disease 2019 (COVID-19) patients have high rates of bacterial superinfection. Multiplex polymerase chain reaction panels may be able to provide useful information about the incidence and spectrum of bacteria causing superinfections.

Methods

In this retrospective observational study we included all COVID-19 positive patients admitted to our intensive care unit with suspected hospital-acquired pneumonia/ventilator-associated pneumonia (HAP/VAP) in whom the BioFire® Pneumonia Panel (PP) was performed from tracheal aspirate or bronchoalveolar lavage fluid for diagnostic purposes. The aim of our study was to analyze the spectrum of pathogens detected with the PP.

Results

In this study 60 patients with a median age of 62.5 years were included. Suspected VAP was the most frequent (48/60, 80%) indication for performing the PP. Tracheal aspirate was the predominant sample type (50/60, 83.3%).

The PP led to a negative, monomicrobial and polymicrobial result in 36.7%, 35% and 28.3% of the patients, respectively. The three most detected bacteria were Staphylococcus aureus (13/60, 21.7%), Klebsiella pneumoniae (12/60, 20%) and Haemophilus influenzae (9/60, 15%). Neither atypical bacteria nor resistance genes were detected.

Microbiological culture of respiratory specimens was performed in 36 (60%) patients concomitantly. The PP and microbiological culture yielded a non-concordant, partial concordant and completely concordant result in 13.9% (5/36), 30.6% (11/36) and 55.6% (20/36) of the analyzed samples, respectively.

Conclusion

In critically ill COVID-19 patients with suspected HAP/VAP results of the PP and microbiological culture methods were largely consistent. In our cohort, S. aureus and K. pneumoniae were the most frequently detected organisms. A higher diagnostic yield may be achieved if both methods are combined.

Unexpected associations between respiratory viruses and bacteria with Pulmonary Function Testing in children suffering from Cystic Fibrosis (MUCOVIB study)

BACKGROUND

Various bacterial and viral assemblages composing Cystic Fibrosis (CF) lung microbiota contribute to long-term lung function decline over time. Yet, the impact of individual microorganisms on pulmonary functions remains uncertain in children with CF.

METHODS

As part of the 'Mucoviscidosis, respiratory VIruses, intracellular Bacteria and fastidious organisms'' project, children with CF were longitudinally followed in a Swiss multicentric study. Respiratory samples included mainly throat swabs and sputa samples for bacterial culture and 16S rRNA metagenomics and nasopharyngeal swabs for respiratory virus detection by molecular assays. Percentage of predicted Forced Expiratory Volume in one second (FEV1%) and Lung Clearance Index (LCI) were recorded.

RESULTS

Sixty-one children, of whom 20 (32.8%) presented with at least one pulmonary exacerbation, were included. Almost half of the 363 nasopharyngeal swabs tested by RT-PCR were positive for a respiratory virus, mainly rhinovirus (26.5%). From linear mixed-effects regression models, P. aeruginosa (-11.35, 95%CI [-17.90; -4.80], p = 0.001) was significantly associated with a decreased FEV1%, whereas rhinovirus was associated with a significantly higher FEV1% (+4.24 95%CI [1.67; 6.81], p = 0.001). Compared to conventional culture, 16S rRNA metagenomics showed a sensitivity and specificity of 80.0% and 85.4%, respectively for detection of typical CF pathogens. However, metagenomics detected a bacteria almost twice more often than culture.

CONCLUSIONS

As expected, P. aeruginosa impacted negatively on FEV1% while rhinovirus was surprisingly associated with better FEV1%. Culture-free assays identifies significantly more pathogens than standard culture, with disputable clinical correlation.

Community-acquired bacterial pneumonia in adults: An update

Community-acquired pneumonia (CAP) is the prominent cause of mortality and morbidity with important clinical impact across the globe. India accounts for 23 per cent of global pneumonia burden with case fatality rates between 14 and 30 per cent, and Streptococcus pneumoniae is considered a major bacterial aetiology. Emerging pathogens like Burkholderia pseudomallei is increasingly recognized as an important cause of CAP in Southeast Asian countries. Initial management in the primary care depends on clinical assessment while the hospitalized patients require combinations of clinical scores, chest radiography and various microbiological and biomarker assays. This comprehensive diagnostic approach together with additional sampling and molecular tests in selected high-risk patients should be practiced. Inappropriate therapy in CAP in hospitalized patients lengthens hospital stay and increases cost and mortality. In addition, emergence of multidrug-resistant organisms poses tough challenges in deciding empirical as well as definitive therapy. Developing local evidence on the cause and management should be a priority to improve health outcomes in CAP.

Pneumonia prevention in the elderly patients: the other sides

Pneumonia is one of the leading causes of morbidity and mortality from infection in elderly patients. The increased frequency of pneumonia among elderly subjects can be explained by the physiological changes linked to the progressive aging of the respiratory tree and the diminished immunological response. A spiral of event leads to frailty, infection and possible death; preventing pneumonia consists of controlling the risk factors. Dysphagia, which is associated with malnutrition and dehydration, is recognized as one of the major pathophysiological mechanism leading to pneumonia and its screening is crucial for the pneumonia risk assessment. The impairment in the oropharyngeal reflexes results in stagnation of foreign material in the lateral cavities of the pharynx which may then get aspirated repeatedly in the lungs and cause pneumonia. Pneumonia prevention starts with lifestyle modifications such as alcohol and tobacco cessation. A careful review of the risk-benefit of the prescribed medication is critical and adaptation may be required in elders with multiple morbidities. Respiratory physiotherapy and mobilization improve the functional status and hence may help reduce the risk of pneumonia. Maintaining teeth and masticatory efficiency is important if malnutrition and its consequences are to be avoided. Daily oral hygiene and regular professional removal of oral biofilm can prevent the onset of periodontitis and can avoid an oral environment favoring the colonization of respiratory pathogens than can then be aspirated into the lungs.

Undetected Causes of Death in Hospitalized Elderly with COVID-19: Lessons from Autopsy

Background: Mechanisms and causes of death in older patients with SARS-CoV-2 infection are still poorly understood. Methods: We conducted in a retrospective monocentric study, a clinical chart review and post-mortem examination of patients aged 75 years and older hospitalized in acute care and positive for SARS-CoV-2. Full body autopsy and correlation with clinical findings and suspected causes of death were done. Results: Autopsies were performed in 12 patients (median age 85 years; median of 4 comorbidities, mainly hypertension and cardiovascular disease). All cases showed exudative or proliferative phases of alveolar damage and/or a pattern of organizing pneumonia. Causes of death were concordant in 6 cases (50%), and undetected diagnoses were found in 6. Five patients died from hypoxemic respiratory failure due to coronavirus disease 2019 (COVID-19), five had another associated diagnosis and two died from alternative causes. Deaths that occurred in the second week were related to SARS-CoV-2 pneumonia whereas those occurring earlier were related mainly to heart failure and those occurring later to complications. Conclusions: Although COVID-19 hypoxemic respiratory failure was the most common cause of death, post-mortem pathological examination revealed that acute decompensation from chronic comorbidities during the first week of COVID-19 and complications in the third week contributed to mortality.

Where is Chlamydophila pneumoniae pneumonia?

BACKGROUND

Molecular diagnostic methods have recently gained widespread use, and consequently, the importance of viral pathogens in community-acquired pneumonia (CAP) has undergone re-evaluation. Under these circumstances, the role of Chlamydophila pneumoniae as a pathogen that causes CAP also needs to be reviewed.

METHODS

We reviewed articles that contained data on the frequency of identification of C. pneumoniae pneumonia as a causative pathogen for CAP. The articles were identified by performing a search in PubMed with the keywords "community-acquired pneumonia" and "pathogen".

RESULTS

Sixty-three articles were identified. The reviewed articles demonstrated that the rates of identification of C. pneumoniae as the causative pathogen for CAP were significantly lower in assessments based on polymerase chain reaction (PCR) methods than in those based on serological methods. In some studies, it was possible to compare both serological and PCR methods directly using the same set of samples.

CONCLUSIONS

The use of PCR methods, including multiplex PCR assays, has revealed that C. pneumoniae may play a limited role as a pathogen for CAP.

Severe influenza/respiratory syncytial virus infections and hospital antimicrobial stewardship opportunities: impact of a 4-year surveillance including molecular diagnosis

OBJECTIVE

To assess the prevalence of influenza and respiratory syncytial virus (RSV) in adults hospitalized for a respiratory infection in the winter months and to evaluate the impact of a viral diagnosis on empirical antimicrobial management (antibiotics and antivirals).

DESIGN

Observational cohort study.

SETTING

Acute-care university hospital.

PATIENTS

The study included 963 adult patients hospitalized over a 4-year surveillance period.

METHODS

Annual surveillance timelines were defined according to epidemiological criteria related to the circulation of RSV and influenza viruses in the general population. Patients were screened following a severe acute respiratory infection (SARI) case definition at the emergency department and were enrolled for molecular assay targeting influenza/RSV viruses after oral informed consent. Epidemiological and clinical data were recorded prospectively, microbiological investigations, antimicrobial management, and outcome data were reviewed retrospectively.

RESULTS

An influenza or RSV virus was documented in 316 of 963 patients (33%). Optimization of antimicrobial management (AM) was achieved in 162 of 265 patients (61%) with a positive viral diagnosis and no bacterial infection at admission (AM treatment not initiated, n = 111; discontinued, n = 51). In contrast, only 128 of 462 patients (28%) with negative microbiological investigations did not have AM treatment initiated (n = 116) or had such treatment discontinued (n = 12). Early, targeted antiviral treatment was prescribed in 235 of 253 patients (93%) confirmed with influenza. Epidemiological, clinical, and outcome data were similar in both groups.

CONCLUSION

Epidemiological surveillance associated with influenza/RSV molecular diagnosis in adults hospitalized for severe winter respiratory infections dramatically enhanced antimicrobial management.

[The new comprehension of pulmonary infections]

Epidemiological data on the distribution of mostly bacterial pathogens are still the basis for empirical treatment recommendations on respiratory infections. Because of the dynamic technological developments in molecular multiplexing and sequencing procedures, the spectrum of potential pathogens is increased and challenges the current dogma of virulence and pathogenicity of certain pathogens. Classical pathogens of the lungs are thereby not questioned but are increasingly placed in a context that reflects co-infections with viruses and changes of the local microbiome in more depth. Recent data indicate that integration of this novel information is required for a better understanding of the seasonal differences in the frequency of particular lung infections and to find new approaches to risk stratification of patients. This becomes most obvious in the subgroup of immunosuppressed patients who are at risk of severe courses of diseases with higher morbidity and mortality from infections with viruses and facultative pathogens, such as nontuberculous mycobacteria (NTM). Based on the fundamental knowledge on the spectrum of pathogens of community-acquired and nosocomial lung infections, novel approaches in pathogen diagnostics and lung microbiome analytics are discussed and the applicability with respect to the current clinical routine is questioned.