Laboratory diagnosis of pneumonia in the molecular age

New Guidelines for Severe Community-acquired Pneumonia

In 2023, the new European guidelines on severe community-acquired pneumonia, providing clinical practice recommendations for the management of this life-threatening infection, characterized by a high burden of mortality, morbidity, and costs for the society. This review article aims to summarize the principal evidence related to eight different questions covered in the guidelines, by also highlighting the future perspectives for research activity.

Viral Pneumonia: From Influenza to COVID-19

Respiratory viruses are increasingly recognized as a cause of community-acquired pneumonia (CAP). The implementation of new diagnostic technologies has facilitated their identification, especially in vulnerable population such as immunocompromised and elderly patients and those with severe cases of pneumonia. In terms of severity and outcomes, viral pneumonia caused by influenza viruses appears similar to that caused by non-influenza viruses. Although several respiratory viruses may cause CAP, antiviral therapy is available only in cases of CAP caused by influenza virus or respiratory syncytial virus. Currently, evidence-based supportive care is key to managing severe viral pneumonia. We discuss the evidence surrounding epidemiology, diagnosis, management, treatment, and prevention of viral pneumonia.

The microbiological diagnostic performance of metagenomic next-generation sequencing in patients with infectious diseases

OBJECTIVE

Metagenomic next-generation sequencing (mNGS) can be used to detect pathogens in clinical infectious diseases through the sequencing analysis of microbial and host nucleic acids in clinical samples. This study aimed to assess the diagnostic performance of mNGS in patients with infections.

METHODS

In this study, 641 patients with infectious diseases were enrolled. These patients simultaneously underwent pathogen detection by both mNGS and microbial culture. Through statistical analysis, we judged the diagnostic performance of mNGS and microbial culture on different pathogens.

RESULTS

Among 641 patients, 276 cases of bacteria and 95 cases of fungi were detected by mNGS, whereas 108 cases of bacteria and 41 cases of fungi were detected by traditional cultures. Among all mixed infections, combined bacterial and viral infections were the highest (51%, 87/169), followed by combined bacterial with fungal infections (16.57%, 28/169) and mixed bacterial, fungal, and viral infections (13.61%, 23/169). Among all sample types, bronchoalveolar lavage fluid (BALF) samples had the highest positive rate (87.8%, 144/164), followed by sputum (85.4%, 76/89) and blood samples (61.2%, 158/258). For the culture method, sputum samples had the highest positive rate (47.2%, 42/89), followed by BALF (37.2%, 61/164). The positive rate of mNGS was 69.89% (448/641), which was significantly higher than that of traditional cultures (22.31% [143/641]) (P < .05).

CONCLUSIONS

Our results show that mNGS is an effective tool for the rapid diagnosis of infectious diseases. Compared with traditional detection methods, mNGS also showed obvious advantages in mixed infections and infections with uncommon pathogens.

Diagnostic Stewardship in Community-Acquired Pneumonia With Syndromic Molecular Testing: A Randomized Clinical Trial

Importance

Lower respiratory tract (LRT) infections, including community-acquired pneumonia (CAP), are a leading cause of hospital admissions and mortality. Molecular tests have the potential to optimize treatment decisions and management of CAP, but limited evidence exists to support their routine use.

Objective

To determine whether the judicious use of a syndromic polymerase chain reaction (PCR)-based panel for rapid testing of CAP in the emergency department (ED) leads to faster, more accurate microbiological test result-based treatment.

Design, Setting, and Participants

This parallel-arm, single-blinded, single-center, randomized clinical superiority trial was conducted between September 25, 2020, and June 21, 2022, in the ED of Haukeland University Hospital, a large tertiary care hospital in Bergen, Norway. Adult patients who presented to the ED with suspected CAP were recruited. Participants were randomized 1:1 to either the intervention arm or standard-of-care arm. The primary outcomes were analyzed according to the intention-to-treat principle.

Intervention

Patients randomized to the intervention arm received rapid syndromic PCR testing (BioFire FilmArray Pneumonia plus Panel; bioMérieux) of LRT samples and standard of care. Patients randomized to the standard-of-care arm received standard microbiological diagnostics alone.

Main Outcomes and Measures

The 2 primary outcomes were the provision of pathogen-directed treatment based on a microbiological test result and the time to provision of pathogen-directed treatment (within 48 hours after randomization).

Results

There were 374 patients (221 males [59.1%]; median (IQR) age, 72 [60-79] years) included in the trial, with 187 in each treatment arm. Analysis of primary outcomes showed that 66 patients (35.3%) in the intervention arm and 25 (13.4%) in the standard-of-care arm received pathogen-directed treatment, corresponding to a reduction in absolute risk of 21.9 (95% CI, 13.5-30.3) percentage points and an odds ratio for the intervention arm of 3.53 (95% CI, 2.13-6.02; P < .001). The median (IQR) time to provision of pathogen-directed treatment within 48 hours was 34.5 (31.6-37.3) hours in the intervention arm and 43.8 (42.0-45.6) hours in the standard-of-care arm (mean difference, -9.4 hours; 95% CI, -12.7 to -6.0 hours; P < .001). The corresponding hazard ratio for intervention compared with standard of care was 3.08 (95% CI, 1.95-4.89). Findings remained significant after adjustment for season.

Conclusions and Relevance

Results of this randomized clinical trial indicated that routine deployment of PCR testing for LRT pathogens led to faster and more targeted microbial treatment for patients with suspected CAP. Rapid molecular testing could complement or replace selected standard, time-consuming, laboratory-based diagnostics.

Trial Registration

ClinicalTrials.gov Identifier: NCT04660084.

Effects of clinically achievable pulmonary antibiotic concentrations on the recovery of bacteria: in vitro comparison of the BioFire FILMARRAY Pneumonia Panel versus conventional culture methods in bronchoalveolar lavage fluid

Empiric antibiotics may affect bacterial pathogen recovery using conventional culture methods (CCMs), while PCR-based diagnostics are likely less affected. Herein, we conducted an in vitro study of bronchoalveolar lavage fluid (BAL) inoculated with bacteria and clinically relevant antibiotic concentrations to compare the recovery between the BioFire FILMARRAY Pneumonia Panel (Pn Panel) and CCMs. Remnant clinical BAL specimens were inoculated to ~105 cfu/mL using 12 clinical isolates. Isolates consisted of one wild-type (WT) and one or more resistant strains of: Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baumannii, and Staphylococcus aureus. Piperacillin-tazobactam, cefepime, meropenem, levofloxacin, or vancomycin was added to achieve pulmonary epithelial lining fluid peak and trough concentrations. Post-exposure cfu/mL was quantified by CCMs and simultaneously tested by the PN Panel for identification and semi-quantitative genetic copies/mL. CCM results were categorized as significant growth (SG) (≥1 × 104), no significant growth (NSG) (≥1 × 103, <1 × 104), or no growth (NG) (<1 × 103). The PN Panel accurately identified all isolates, resistance genes, and reported ≥106 genetic copies/mL regardless of antibiotic exposure. The CCM also identified all S. aureus strains exposed to vancomycin. For WT Gram-negative isolates exposed to antibiotics, SG, NSG, and NG were observed in 7/52 (13%), 18/52 (35%), and 27/52 (52%) of CCM experiments, respectively. For resistant Gram-negatives isolates, SG, NSG, and NG were observed in 62/88 (70%), 17/88 (19%), and 9/88 (10%), respectively. These in vitro data demonstrate that the PN Panel is able to identify Gram-negative pathogens in the presence of clinically significant antibiotic concentrations when CCM may not.

[Diagnosis and antibiotic therapy of nosocomial pneumonia in adults: from recommendations to real practice. A review]

Nosocomial pneumonia is a healthcare-associated infection with significant consequences for the patient and the healthcare system. The efficacy of treatment significantly depends on the timeliness and adequacy of the antibiotic therapy regimen. The growth of resistance of gram-negative pathogens of nosocomial pneumonia to antimicrobial agents increases the risk of prescribing inadequate empirical therapy, which worsens the results of patient treatment. Identification of risk factors for infection with multidrug-resistant microorganisms, careful local microbiological monitoring with detection of resistance mechanisms, implementation of antimicrobial therapy control strategy and use of rational combinations of antibacterial drugs are of great importance. In addition, the importance of using new drugs with activity against carbapenem-resistant strains, including ceftazidime/aviabactam, must be understood. This review outlines the current data on the etiology, features of diagnosis and antibacterial therapy of nosocomial pneumonia.

Nanofluidic qPCR unable to detect and serotype Streptococcus pneumoniae in urine samples of hospitalized South African patients with community-acquired pneumonia

Pneumonia is a major cause of death among adults living with HIV in South Africa, but the etiology of many cases remains unknown. This study evaluated the utility of a nanofluidic qPCR assay to detect and serotype Streptococcus pneumoniae in urine samples from patients hospitalized with community-acquired pneumonia (CAP). The nanofluidic qPCR assay was optimized to target 13 pneumococcal serotypes and 4 reference genes. Archived urine samples collected from patients > 15 years of age hospitalized with pneumonia between April 2018 and August 2019 were retrospectively tested using the nanofluidic qPCR assay, BinaxNOW urine antigen test, and standard LytA qPCR. Blood culture was undertaken on a subset of the samples at the discretion of the attending physician. Cohens' Kappa statistics were used to determine the concordance between the methods. Of the 828 adults hospitalized for CAP, urine samples were available in 53% (n = 439). Of those, a random subset of 96 (22%) samples underwent testing. Of the participants included in the final analysis, the mean age was 45.8 years (SD 16.2), 49% (n = 47) were female, 98% (n = 94) were black, and 66% (n = 63) were living with HIV infection. The nanofluidic qPCR method was able to detect PCV13 vaccine strains spiked into urine samples; however, the method failed to detect any pneumococcus in clinical samples. In comparison, 19% of the pneumonia cases were attributed to S. pneumoniae using urine antigen testing. Nanofluidic qPCR is unable to detect and serotype Streptococcus pneumoniae in urine samples of South Africans hospitalized with CAP.

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.

Pneumonia-Plus: a deep learning model for the classification of bacterial, fungal, and viral pneumonia based on CT tomography

OBJECTIVES

This study aims to develop a deep learning algorithm, Pneumonia-Plus, based on computed tomography (CT) images for accurate classification of bacterial, fungal, and viral pneumonia.

METHODS

A total of 2763 participants with chest CT images and definite pathogen diagnosis were included to train and validate an algorithm. Pneumonia-Plus was prospectively tested on a nonoverlapping dataset of 173 patients. The algorithm's performance in classifying three types of pneumonia was compared to that of three radiologists using the McNemar test to verify its clinical usefulness.

RESULTS

Among the 173 patients, area under the curve (AUC) values for viral, fungal, and bacterial pneumonia were 0.816, 0.715, and 0.934, respectively. Viral pneumonia was accurately classified with sensitivity, specificity, and accuracy of 0.847, 0.919, and 0.873. Three radiologists also showed good consistency with Pneumonia-Plus. The AUC values of bacterial, fungal, and viral pneumonia were 0.480, 0.541, and 0.580 (radiologist 1: 3-year experience); 0.637, 0.693, and 0.730 (radiologist 2: 7-year experience); and 0.734, 0.757, and 0.847 (radiologist 3: 12-year experience), respectively. The McNemar test results for sensitivity showed that the diagnostic performance of the algorithm was significantly better than that of radiologist 1 and radiologist 2 (p < 0.05) in differentiating bacterial and viral pneumonia. Radiologist 3 had a higher diagnostic accuracy than the algorithm.

CONCLUSIONS

The Pneumonia-Plus algorithm is used to differentiate between bacterial, fungal, and viral pneumonia, which has reached the level of an attending radiologist and reduce the risk of misdiagnosis. The Pneumonia-Plus is important for appropriate treatment and avoiding the use of unnecessary antibiotics, and provide timely information to guide clinical decision-making and improve patient outcomes.

CLINICAL RELEVANCE STATEMENT

Pneumonia-Plus algorithm could assist in the accurate classification of pneumonia based on CT images, which has great clinical value in avoiding the use of unnecessary antibiotics, and providing timely information to guide clinical decision-making and improve patient outcomes.

KEY POINTS

• The Pneumonia-Plus algorithm trained from data collected from multiple centers can accurately identify bacterial, fungal, and viral pneumonia. • The Pneumonia-Plus algorithm was found to have better sensitivity in classifying viral and bacterial pneumonia in comparison to radiologist 1 (5-year experience) and radiologist 2 (7-year experience). • The Pneumonia-Plus algorithm is used to differentiate between bacterial, fungal, and viral pneumonia, which has reached the level of an attending radiologist.

BIChromET: A Chromogenic Culture Medium for Detection of Piperacillin/Tazobactam and Cefepime Resistance in Pseudomonas aeruginosa

OBJECTIVES

The BIChromET selective medium for detecting piperacillin-tazobactam (TZP) and cefepime (FEP) resistant Pseudomonas aeruginosa was developed.

METHODS

The performance of this medium was first evaluated using a collection of 100 P. aeruginosa clinical strains (70 TZP-susceptible, 30 TZP-resistant, 58 FEP-susceptible, and 42 FEP-resistant). Then, we performed clinical validation by testing 173 respiratory clinical samples.

RESULTS

The BIChromET medium showed excellent sensitivity (TZP (avg. 96.7%); FEP (avg. 92.7%)) and specificity (TZP (avg. 98.9%); FEP (avg. 98%)) in distinguishing the detection limit ranging from 104 to 108 CFU/mL. Then, testing the bronchoalveolar lavage (BAL) and tracheobronchial aspirate (TBA) clinical specimens (N = 173) revealed the excellent performance of the medium with P. aeruginosa, showing 100% and 92.6% of categorical agreements with the results obtained via the broth microdilution methods (BMD) for TZP and FEP, respectively.

CONCLUSION

This medium allows for easy and accurate detection of TZP/FEP-resistant isolates regardless of their resistance mechanisms.

Rapid Point-of-Care PCR Testing of Drug-Resistant Strains on Endotracheal Aspirate Samples: A Repurposed Effective Tool in the Stepwise Approach of Healthcare-Acquired Pneumonia-A Pilot Study

Healthcare-associated pneumonia (HCAP) is a common nosocomial infection with high morbidity and mortality. Culture-based detection of the etiologic agent and drug susceptibility is time-consuming, potentially leading to the inadequate use of broad-spectrum empirical antibiotic regimens. The aim was to evaluate the diagnostic capabilities of rapid point-of-care multiplex polymerase chain reaction (PCR) assays from the endotracheal aspirate of critically ill patients with HCAP. A consecutive series of 29 intensive care unit (ICU) patients with HCAP and a control group of 28 patients undergoing elective surgical procedures were enrolled in the study. The results of the PCR assays were compared to the culture-based gold standard. The overall accuracy of the PCR assays was 95.12%, with a sensitivity of 92.31% and a specificity of 97.67%. The median time was 90 min for the rapid PCR tests (p < 0.001), while for the first preliminary results of the cultures, it was 48 h (46-72). The overall accuracy for rapid PCR testing in suggesting an adequate antibiotic adjustment was 82.98% (95% CI 69.19-92.35%), with a specificity of 90% (95% CI 55.50-99.75%), a positive predictive value of 96.77% (95% CI 83.30-99.92%), and a negative predictive value of 56.25 (95% CII 29.88-80.25%). This method of rapid point-of-care PCR could effectively guide antimicrobial stewardship in patients with healthcare-acquired pneumonia.

Interventions to improve outcomes in community-acquired pneumonia

INTRODUCTION

Community-acquired pneumonia (CAP) is a common infection associated with high morbimortality and a highly deleterious impact on patients' quality of life and functionality. We comprehensively review the factors related to the host, the causative microorganism, the therapeutic approach and the organization of health systems (e.g. setting for care and systems for allocation) that might have an impact on CAP-associated outcomes. Our main aims are to discuss the most controversial points and to provide some recommendations that may guide further research and the management of patients with CAP, in order to improve their outcomes, beyond mortality.

AREA COVERED

In this review, we aim to provide a critical account of potential measures to improve outcomes of CAP and the supporting evidence from observational studies and clinical trials.

EXPERT OPINION

CAP is associated with high mortality and a highly deleterious impact on patients' quality of life. To improve CAP-associated outcomes, it is important to understand the factors related to the patient, etiology, therapeutics, and the organization of health systems.

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.

Respiratory metagenomics: route to routine service

PURPOSE OF REVIEW

The coronavirus disease 2019 pandemic demonstrated broad utility of pathogen sequencing with rapid methodological progress alongside global distribution of sequencing infrastructure. This review considers implications for now moving clinical metagenomics into routine service, with respiratory metagenomics as the exemplar use-case.

RECENT FINDINGS

Respiratory metagenomic workflows have completed proof-of-concept, providing organism identification and many genotypic antimicrobial resistance determinants from clinical samples in <6 h. This enables rapid escalation or de-escalation of empiric therapy for patient benefit and reducing selection of antimicrobial resistance, with genomic-typing available in the same time-frame. Attention is now focussed on demonstrating clinical, health-economic, accreditation, and regulatory requirements. More fundamentally, pathogen sequencing challenges the traditional culture-orientated time frame of microbiology laboratories, which through automation and centralisation risks becoming increasingly separated from the clinical setting. It presents an alternative future where infection experts are brought together around a single genetic output in an acute timeframe, aligning the microbiology target operating model with the wider human genomic and digital strategy.

SUMMARY

Pathogen sequencing is a transformational proposition for microbiology laboratories and their infectious diseases, infection control, and public health partners. Healthcare systems that link output from routine clinical metagenomic sequencing, with pandemic and antimicrobial resistance surveillance, will create valuable tools for protecting their population against future infectious diseases threats.

Diagnostic performance of an in-house multiplex PCR assay and the retrospective surveillance of bacterial respiratory pathogens at a teaching hospital, Kelantan, Malaysia

Respiratory tract infections (RTIs), including pneumonia and pulmonary tuberculosis, are among the leading causes of death worldwide. The use of accurate diagnostic tests is crucial to initiate proper treatment and therapy to reduce the mortality rates for RTIs. A PCR assay for simultaneous detection of six respiratory bacteria: Haemophilus influenzae, Klebsiella pneumoniae, Mycobacterium tuberculosis, Pseudomonas aeruginosa, Staphylococcus aureus and Streptococcus pneumoniae, was developed in our lab. The current study aimed to evaluate the performance of this assay along with the retrospective surveillance of respiratory pathogens at a teaching hospital in Kelantan, Malaysia. Leftover sputa (n = 200) from clinical laboratories were collected and undergone DNA template preparation for PCR analysis. Sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of the PCR assay were determined in comparison with the gold standard sputum culture. Overall, the accuracy performance of this assay was 94.67% (95% CI: 90.87% to 97.21%) with sensitivity, specificity, PPV and NPV of 100%, 91.67%, 87.1% and 100%, respectively. Based on the organisms detected from sputa, K. pneumoniae ranked as the top isolate (n = 48), followed by P. aeruginosa (n = 13) and H. influenzae (n = 10). Surveillance among the patients showed that the associations of bacterial positive with gender and means of acquisition were found significant (p values = 0.049 and 0.001, respectively). Besides the promising performance of this ready-to-use molecular-based assay for the rapid detection of selected bacteria pathogens, this study also highlighted significant spread of K. pneumoniae RTIs in the community.

Does etiological investigation have an impact on the outcomes of community-acquired pneumonia? - A prospective cohort study

INTRODUCTION

There is lack of evidence that etiological investigation influences outcomes in community-acquired pneumonia (CAP). Guidelines recommend diverse approaches to this matter. Our aim was to find if etiological investigation has an impact on CAP management and outcomes.

METHODS

Prospective cohort study, conducted over a two years' period, in a community-based hospital, including all adult patients with CAP. Univariate and multivariate logistic regression modeling were performed to understand the association of etiological identification with CAP outcomes, particularly hospital mortality.

RESULTS

A total of 660 cases of CAP were included, with a mean±sd age of 74±15 years and 58.9% of males. Etiology was documented in 33% of cases. Antibiotic (ATB) was modified in 148 patients, in 51 (34%) motivated by microbiological results. There was no significant impact on hospital mortality of microbiological documentation (35.5% vs 31.2%, p=0.352), or the fact that ATB was modified due to microbiological findings (27.0% vs 36.9%, p=0.272). When stratified by 3 subgroups of risk for drug-resistant pathogens (zero, one or two risk factors: being bed-ridden and/or ATB use within 90 days), etiology identification still did not influence mortality. When adjusted for CURB-65, Charlson's index, being bed-ridden, having had ATB or hospitalization within 90 days or coming from long-term care facilities, microbial identification was not associated with lower mortality.

CONCLUSION

Etiological investigation of patients with CAP does not have an association with hospital mortality, irrespective of the risk for drug-resistant pathogens.

Respiratory viruses: their importance and lessons learned from COVID-19

Respiratory virus infection can cause severe illnesses capable of inducing acute respiratory failure that can progress rapidly to acute respiratory distress syndrome (ARDS). ARDS is related to poor outcomes, especially in individuals with a higher risk of infection, such as the elderly and those with comorbidities, i.e. obesity, asthma, diabetes mellitus and chronic respiratory or cardiovascular disease. Despite this, effective antiviral treatments available for severe viral lung infections are scarce. The coronavirus disease 2019 (COVID-19) pandemic demonstrated that there is also a need to understand the role of airborne transmission of respiratory viruses. Robust evidence supporting this exists, but better comprehension could help implement adequate measures to mitigate respiratory viral infections. In severe viral lung infections, early diagnosis, risk stratification and prognosis are essential in managing patients. Biomarkers can provide reliable, timely and accessible information possibly helpful for clinicians in managing severe lung viral infections. Although respiratory viruses highly impact global health, more research is needed to improve care and prognosis of severe lung viral infections. In this review, we discuss the epidemiology, diagnosis, clinical characteristics, management and prognosis of patients with severe infections due to respiratory viruses.

Rapid, accurate, and novel diagnostic technique for respiratory pathogens: Clinical application of loop-mediated isothermal amplification assay in older patients with pneumonia, a multicenter prospective observational study

Background

Loop-mediated isothermal amplification (LAMP) is a novel nucleic acid amplification method using only one type of enzyme that can amplify DNA with high specificity, efficiency and rapidity under isothermal conditions. Chips for Complicated Infection Detection (CCID) is based on LAMP. This study translate CCID into clinical application and evaluate its diagnostic value for pneumonia.

Methods

Eighty one older patients with pneumonia were prospectively enrolled from January 1 to July 23, 2021, and 57 sputum/airway secretion and 35 bronchoalveolar lavage fluid samples were collected and analyzed by CCID and conventional microbiological tests (CMTs). Samples were collected, transported, monitored, and managed by a multidisciplinary team using a sample management information system.

Results

CCID turnaround time was 50 min, and the detection limit was 500 copies/reaction. The percentage of positive samples was significantly higher using CCID than CMTs, especially for Klebsiella pneumoniae (odds ratio [OR], 9.0; 95% confidence interval [CI], 1.1-70.5; p < 0.05), Enterococcus faecalis (OR, ∞; p < 0.01), Stenotrophomonas maltophilia (OR, ∞; p < 0.01), fungi (OR, 26.0; 95% CI, 3.6-190.0; p < 0.01), and viruses (CCID only; p < 0.01). In addition, the percentage of positive results was significantly higher using CCID than CMTs in patients who used antibiotics for more than 3 days (91.9% vs. 64.9%; p < 0.01). Analyzing clinical impact, 55 cases (59.8%) benefited from CCID.

Conclusion

CCID allows the rapid and accurate detection of pneumonia in older patients. Moreover, this technique is less affected by previous antibiotic treatment and can improve patient care.

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.

Aetiology of childhood pneumonia in low- and middle-income countries in the era of vaccination: a systematic review

Background

This systematic review aimed to describe common aetiologies of severe and non-severe community acquired pneumonia among children aged 1 month to 9 years in low- and middle-income countries.

Methods

We searched the MEDLINE, EMBASE, and PubMed online databases for studies published from January 2010 to August 30, 2020. We included studies on acute community-acquired pneumonia or acute lower respiratory tract infection with ≥1 year of continuous data collection; clear consistent case definition for pneumonia; >1 specimen type (except empyema studies where only pleural fluid was required); testing for >1 pathogen including both viruses and bacteria. Two researchers reviewed the studies independently. Results were presented as a narrative summary. Quality of evidence was assessed with the Quality Assessment Tool for Quantitative Studies. The study was registered on PROSPERO [CRD42020206830].

Results

We screened 5184 records; 1305 duplicates were removed. The remaining 3879 titles and abstracts were screened. Of these, 557 articles were identified for full-text review, and 55 met the inclusion criteria - 10 case-control studies, three post-mortem studies, 11 surveillance studies, eight cohort studies, five cross-sectional studies, 12 studies with another design and six studies that included patients with pleural effusions or empyema. Studies which described disease by severity showed higher bacterial detection (Streptococcus pneumoniae, Staphylococcus aureus) in severe vs non-severe cases. The most common virus causing severe disease was respiratory syncytial virus (RSV). Pathogens varied by age, with RSV and adenovirus more common in younger children. Influenza and atypical bacteria were more common in children 5-14 years than younger children. Malnourished and HIV-infected children had higher rates of pneumonia due to bacteria or tuberculosis.

Conclusions

Several viral and bacterial pathogens were identified as important targets for prevention and treatment. Bacterial pathogens remain an important cause of moderate to severe disease, particularly in children with comorbidities despite widespread PCV and Hib vaccination.

Raman Spectroscopic Differentiation of Streptococcus pneumoniae From Other Streptococci Using Laboratory Strains and Clinical Isolates

Streptococcus pneumoniae, commonly referred to as pneumococci, can cause severe and invasive infections, which are major causes of communicable disease morbidity and mortality in Europe and globally. The differentiation of S. pneumoniae from other Streptococcus species, especially from other oral streptococci, has proved to be particularly difficult and tedious. In this work, we evaluate if Raman spectroscopy holds potential for a reliable differentiation of S. pneumoniae from other streptococci. Raman spectra of eight different S. pneumoniae strains and four other Streptococcus species (S. sanguinis, S. thermophilus, S. dysgalactiae, S. pyogenes) were recorded and their spectral features analyzed. Together with Raman spectra of 59 Streptococcus patient isolates, they were used to train and optimize binary classification models (PLS-DA). The effect of normalization on the model accuracy was compared, as one example for optimization potential for future modelling. Optimized models were used to identify S. pneumoniae from other streptococci in an independent, previously unknown data set of 28 patient isolates. For this small data set balanced accuracy of around 70% could be achieved. Improvement of the classification rate is expected with optimized model parameters and algorithms as well as with a larger spectral data base for training.

Epidemiology of community-acquired pneumonia among hospitalised children in Indonesia: a multicentre, prospective study

OBJECTIVE

To identify aetiologies of childhood community-acquired pneumonia (CAP) based on a comprehensive diagnostic approach.

DESIGN

'Partnerships for Enhanced Engagement in Research-Pneumonia in Paediatrics (PEER-PePPeS)' study was an observational prospective cohort study conducted from July 2017 to September 2019.

SETTING

Government referral teaching hospitals and satellite sites in three cities in Indonesia: Semarang, Yogyakarta and Tangerang.

PARTICIPANTS

Hospitalised children aged 2-59 months who met the criteria for pneumonia were eligible. Children were excluded if they had been hospitalised for >24 hours; had malignancy or history of malignancy; a history of long-term (>2 months) steroid therapy, or conditions that might interfere with compliance with study procedures.

MAIN OUTCOMES MEASURES

Causative bacterial, viral or mixed pathogen(s) for pneumonia were determined using microbiological, molecular and serological tests from routinely collected specimens (blood, sputum and nasopharyngeal swabs). We applied a previously published algorithm (PEER-PePPeS rules) to determine the causative pathogen(s).

RESULTS

188 subjects were enrolled. Based on our algorithm, 48 (25.5%) had a bacterial infection, 31 (16.5%) had a viral infection, 76 (40.4%) had mixed bacterial and viral infections, and 33 (17.6%) were unable to be classified. The five most common causative pathogens identified were Haemophilus influenzae non-type B (N=73, 38.8%), respiratory syncytial virus (RSV) (N=51, 27.1%), Klebsiella pneumoniae (N=43, 22.9%), Streptococcus pneumoniae (N=29, 15.4%) and Influenza virus (N=25, 13.3%). RSV and influenza virus diagnoses were highly associated with Indonesia's rainy season (November-March). The PCR assays on induced sputum (IS) specimens captured most of the pathogens identified in this study.

CONCLUSIONS

Our study found that H. influenzae non-type B and RSV were the most frequently identified pathogens causing hospitalised CAP among Indonesian children aged 2-59 months old. Our study also highlights the importance of PCR for diagnosis and by extension, appropriate use of antimicrobials.

TRAIL REGISTRATION NUMBER

NCT03366454.

Derivation and Validation of a Predictive Scoring Model of Infections Due to Acinetobacter baumannii in Patients with Hospital Acquired Pneumonia by Gram-Negative Bacilli

Background

The prognosis of ABA-HAP patients is very poor. This study aimed to develop a scoring model to predict ABA-HAP in patients with GNB-HAP.

Methods

A single center retrospective cohort study was performed among patients with HAP caused by GNB in our hospital during January 2019 to June 2019 (the derivation cohort, DC). The variables were assessed on the day when qualified respiratory specimens were obtained. A prediction score was formulated by using independent risk factors obtained from logistic regression analysis. It was prospectively validated with a subsequent cohort of GNB-HAP patients admitted to our hospital during July 2019 to Dec 2019 (the validation cohort, VC).

Results

The final logistic regression model of DC included the following variables: transferred from other hospitals (3 points); blood purification (3 points); risk for aspiration (4 points); immunocompromised (3 points); pulmonary interstitial fibrosis (3 points); pleural effusion (1 points); heart failure (3 points); encephalitis (5 points); increased monocyte count (2 points); and increased neutrophils count (2 points). The AUROC of the scoring model was 0.845 (95% CI, 0.796 ~ 0.895) in DC and 0.807 (95% CI, 0.759 ~ 0.856) in VC. The scoring model clearly differentiated the low-risk patients (the score < 8 points), moderate-risk patients (8 ≤ the score < 12 points) and high-risk patients (the score ≥ 12 points), both in DC (P < 0.001) and in VC (P < 0.001).

Conclusion

This simple scoring model could predict ABA-HAP with high predictive value and help clinicians to choose appropriate empirical antibiotic therapy.

d-Amino Acid-Based Metabolic Labeling Enables a Fast Antibiotic Susceptibility Test of Both Isolated Bacteria and Bronchoalveolar Lavage Fluid

The threat of multidrug-resistant bacteria has escalated rapidly, increasing the demand for accurate antibiotic susceptibility tests (ASTs). Traditional bacterial growth yield-based ASTs often take overnight to report, delaying the timely guidance of antibiotic use. Here, a fluorescent d-amino acid (FDAA) labeling-based AST (FaAST) is reported, which can quickly provide accurate minimum inhibitory concentrations (MICs). The FDAA-labeling signals that reflect the bacterial metabolic status underlie the flow cytometry-based strategy for MIC determination. Resistant bacteria show a reluctant decline in FDAA-labeling (inhibited metabolism) after treatment with the corresponding antibiotics, whereas susceptible bacteria demonstrate quick responses to low doses of drugs. The MICs are determined based on the changing trends in labeling. After testing 23 clinical isolates and laboratory strains of the most critical drug-resistant bacteria against a panel of representative antibiotics, FaAST shows a high susceptibility category with an accuracy of 98.13%. Moreover, FaAST can also make quick and accurate diagnosis against bronchoalveolar lavage fluids collected from hospital-acquired pneumonia patients, saving 2-4 days in guiding antibiotic use for this life-threatening infection. Thus, the speed, accuracy, and broad applicability of FaAST will be valuable in informing antibiotic decisions when treating critical infections caused by drug-resistant bacteria.

Severe Infections Due to Respiratory Viruses

Severe viral infections may result in severe illnesses capable of causing acute respiratory failure that could progress rapidly to acute respiratory distress syndrome (ARDS), related to worse outcomes, especially in individuals with a higher risk of infection, including the elderly and those with comorbidities such as asthma, diabetes mellitus and chronic respiratory or cardiovascular disease. In addition, in cases of severe viral pneumonia, co-infection with bacteria such as Streptococcus pneumoniae and Staphylococcus aureus is related to worse outcomes. Respiratory viruses like influenza, rhinovirus, parainfluenza, adenovirus, metapneumovirus, respiratory syncytial virus, and coronavirus have increasingly been detected. This trend has become more prevalent, especially in critically ill patients, due to the availability and implementation of molecular assays in clinical practice. Respiratory viruses have been diagnosed as a frequent cause of severe pneumonia, including cases of community-acquired pneumonia, hospital-acquired pneumonia, and ventilator-associated pneumonia. In this review, we will discuss the epidemiology, diagnosis, clinical characteristics, management, and prognosis of patients with severe infections due to respiratory viruses, with a focus on influenza viruses, non-influenza viruses, and coronaviruses.

Rapid diagnostic tests in the management of pneumonia

INTRODUCTION

Pneumonia is one of the main causes of mortality associated with infectious diseases worldwide. Several challenges have been identified in the management of patients with pneumonia, ranging from accurate and cost-effective microbiological investigations, prompt and adequate therapeutic management, and optimal treatment duration.

AREAS COVERED

In this review, an updated summary on the current management of pneumonia patients is provided and the epidemiological issues of infectious respiratory diseases, which in the current pandemic situation are of particular concern, are addressed. The clinical and microbiological approaches to pneumonia diagnosis are reviewed, including discussion about the new molecular assays pointing out both their strengths and limitations. Finally, the current recommendations about antibiotic treatment are examined and discussed depending on the epidemiological contexts, including those with high prevalence of multidrug-resistant bacteria.

EXPERT OPINION

We claim that rapid diagnostic tests, if well-positioned in the diagnostic workflow and reserved for the subset of patients who could most benefit from these technologies, may represent an interesting and feasible tool to optimize timing of targeted treatments especially in terms of early de-escalation or discontinuation of antibiotic therapy.

Deep diagnostic agent forest (DDAF): A deep learning pathogen recognition system for pneumonia based on CT

BACKGROUND

Even though antibiotics agents are widely used, pneumonia is still one of the most common causes of death around the world. Some severe, fast-spreading pneumonia can even cause huge influence on global economy and life security. In order to give optimal medication regimens and prevent infectious pneumonia's spreading, recognition of pathogens is important.

METHOD

In this single-institution retrospective study, 2,353 patients with their CT volumes are included, each of whom was infected by one of 12 known kinds of pathogens. We propose Deep Diagnostic Agent Forest (DDAF) to recognize the pathogen of a patient based on ones' CT volume, which is a challenging multiclass classification problem, with large intraclass variations and small interclass variations and very imbalanced data.

RESULTS

The model achieves 0.899 ± 0.004 multi-way area under curves of receiver (AUC) for level-I pathogen recognition, which are five rough groups of pathogens, and 0.851 ± 0.003 AUC for level-II recognition, which are 12 fine-level pathogens. The model also outperforms the average result of seven human readers in level-I recognition and outperforms all readers in level-II recognition, who can only reach an average result of 7.71 ± 4.10% accuracy.

CONCLUSION

Deep learning model can help in recognition pathogens using CTs only, which might help accelerate the process of etiological diagnosis.

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.

LncRNA GAS5 participates in childhood pneumonia by inhibiting cell apoptosis and promoting SHIP-1 expression via downregulating miR-155

Background

LncRNA GAS5 and miR-155 are reported to play opposite roles in lung inflammatory responses. Lung inflammation participates in childhood pneumonia, indicating the involvement of GAS5 and miR-155 in pneumonia. The study aimed to analyze the potential interaction between GAS5 and miR-155 in childhood pneumonia.

Methods

GAS5 and miR-155 levels in plasma samples from pneumonia patients and controls were detected using RT-qPCR. The role of GAS5 in miR-155 RNA gene methylation in human bronchial epithelial cells (HBEpCs) was analyzed by methylation analysis. Flow cytometry and RT-qPCR were applied to analyze cell apoptosis and SHIP-1 expression, respectively.

Results

GAS5 was downregulated in pneumonia, and miR-155 was upregulated in pneumonia. GAS5 and miR-155 were inversely correlated. GAS5 overexpression decreased miR-155 expression in HBEpCs, while miR-155 overexpression showed no significant effects on GAS5 expression. In addition, GAS5 suppressed LPS-induced HBEpC apoptosis, promoted SHIP-1 expression, and reduced the enhancing effect of miR-155 on cell apoptosis and SHIP-1 expression.

Conclusions

GAS5 may participate in childhood pneumonia by inhibiting cell apoptosis and promoting SHIP-1 expression via downregulating miR-155.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12890-021-01724-y.

Future potential of metagenomics in clinical laboratories

INTRODUCTION

Rapid and sensitive diagnostic strategies are necessary for patient care and public health. Most of the current conventional microbiological assays detect only a restricted panel of pathogens at a time or require a microbe to be successfully cultured from a sample. Clinical metagenomics next-generation sequencing (mNGS) has the potential to unbiasedly detect all pathogens in a sample, increasing the sensitivity for detection and enabling the discovery of unknown infectious agents.

AREAS COVERED

High expectations have been built around mNGS; however, this technique is far from widely available. This review highlights the advances and currently available options in terms of costs, turnaround time, sensitivity, specificity, validation, and reproducibility of mNGS as a diagnostic tool in clinical microbiology laboratories.

EXPERT OPINION

The need for a novel diagnostic tool to increase the sensitivity of microbial diagnostics is clear. mNGS has the potential to revolutionise clinical microbiology. However, its role as a diagnostic tool has yet to be widely established, which is crucial for successfully implementing the technique. A clear definition of diagnostic algorithms that include mNGS is vital to show clinical utility. Similarly to real-time PCR, mNGS will one day become a vital tool in any testing algorithm.

The Evolution and Distribution of Pneumococcal Serotypes in Adults Hospitalized With Community-Acquired Pneumonia in Spain Using a Serotype-Specific Urinary Antigen Detection Test: The CAPA Study, 2011-2018

Background

Spain introduced the 13-valent pneumococcal conjugate vaccine (PCV13) in the childhood National Immunization Program in 2015–2016 with coverage of 3 doses of 94.8% in 2018. We assessed the evolution of all pneumococcal, PCV13 vaccine type (VT), and experimental PCV20-VT (PCV13 + serotypes 8, 10A, 11A, 12F, 15B, 22F, 33F) hospitalized community-acquired pneumonia (CAP) in adults in Spain from 2011–2018.

Methods

A prospective observational study of immunocompetent adults (≥18 years) admitted to 4 Spanish hospitals with chest X-ray–confirmed CAP between November 2011 and November 2018. Microbiological confirmation was obtained using the Pfizer serotype-specific urinary antigen detection tests (UAD1/UAD2), BinaxNow test for urine, and conventional cultures of blood, pleural fluid, and high-quality sputum.

Results

Of 3107 adults hospitalized with CAP, 1943 were ≥65 years. Underlying conditions were present in 87% (n = 2704) of the participants. Among all patients, 895 (28.8%) had pneumococcal CAP and 439 (14.1%) had PCV13-VT CAP, decreasing from 17.9% (n = 77) to 13.2% (n = 68) from 2011–2012 to 2017–2018 (P = .049). PCV20-VT CAP occurred in 243 (23.8%) of those included in 2016–2018. The most identified serotypes were 3 and 8. Serotype 3 accounted for 6.9% (n = 215) of CAP cases, remaining stable during the study period, and was associated with disease severity.

Conclusions

PCV13-VT caused a substantial proportion of CAP in Spanish immunocompetent adults 8 years after introduction of childhood PCV13 immunization. Improving direct PCV13 coverage of targeted adult populations could further reduce PCV13-VT burden, a benefit that could be increased further if PCV20 is licensed and implemented.

Which Biomarkers Can Be Used as Diagnostic Tools for Infection in Suspected Sepsis?

The diagnosis of infection in patients with suspected sepsis is frequently difficult to achieve with a reasonable degree of certainty. Currently, the diagnosis of infection still relies on a combination of systemic manifestations, manifestations of organ dysfunction, and microbiological documentation. In addition, the microbiologic confirmation of infection is obtained only after 2 to 3 days of empiric antibiotic therapy. These criteria are far from perfect being at least in part responsible for the overuse and misuse of antibiotics, in the community and in hospital, and probably the main drive for antibiotic resistance. Biomarkers have been studied and used in several clinical settings as surrogate markers of infection to improve their diagnostic accuracy as well as in the assessment of response to antibiotics and in antibiotic stewardship programs. The aim of this review is to provide a clear overview of the current evidence of usefulness of biomarkers in several clinical scenarios, namely, to diagnose infection to prescribe antibiotics, to exclude infection to withhold antibiotics, and to identify the causative pathogen to target antimicrobial treatment. In recent years, new evidence with "old" biomarkers, like C-reactive protein and procalcitonin, as well as new biomarkers and molecular tests, as breathomics or bacterial DNA identification by polymerase chain reaction, increased markedly in different areas adding useful information for clinical decision making at the bedside when adequately used. The recent evidence shows that the information given by biomarkers can support the suspicion of infection and pathogen identification but also, and not less important, can exclude its diagnosis. Although the ideal biomarker has not yet been found, there are various promising biomarkers that represent true evolutions in the diagnosis of infection in patients with suspected sepsis.

Prediction of ventilator-associated pneumonia outcomes according to the early microbiological response: a retrospective observational study

Ventilator-associated pneumonia is a leading infectious cause of morbidity in critically ill patients; yet current guidelines offer no indications for follow-up cultures.We aimed to evaluate the role of follow-up cultures and microbiological response 3 days after diagnosing ventilator-associated pneumonia as predictors of short- and long-term outcomes.We performed a retrospective analysis of a cohort prospectively collected from 2004 to 2017. Ventilator-associated pneumonia was diagnosed based on clinical, radiographic, and microbiological criteria. For microbiological identification, a tracheobronchial aspirate was performed at diagnosis and repeated after 72 h. We defined three groups when comparing the two tracheobronchial aspirate results: persistence, superinfection, and eradication of causative pathogens.One-hundred-fifty-seven patients were enrolled in the study, among whom microbiological persistence, superinfection, and eradication was present in 67 (48%), 25 (16%), and 65 (41%), respectively, after 72hs. Those with superinfection had the highest mortalities in the intensive care unit (p=0.015) and at 90 days (p=0.036), while also having the fewest ventilation-free days (p=0.024). Multivariable analysis revealed shock at VAP diagnosis (odds ratios [OR] 3.43; 95% confidence interval [CI] 1.25 to 9.40), Staphylococcus aureus isolation at VAP diagnosis (OR 2.87; 95%CI 1.06 to 7.75), and hypothermia at VAP diagnosis (OR 0.67; 95%CI 0.48 to 0.95, per +1°C) to be associated with superinfection.Our retrospective analysis suggests that ventilator-associated pneumonia short-term and long-term outcomes may be associated with superinfection in follow-up cultures. Follow-up cultures may help guiding antibiotic therapy and its duration. Further prospective studies are necessary to verify our findings.

Approach to Identifying Causative Pathogens of Community-Acquired Pneumonia in Children Using Culture, Molecular, and Serology Tests

Determining the causative pathogen(s) of community-acquired pneumonia (CAP) in children remains a challenge despite advances in diagnostic methods. Currently available guidelines generally recommend empiric antimicrobial therapy when the specific etiology is unknown. However, shifts in epidemiology, emergence of new pathogens, and increasing antimicrobial resistance underscore the importance of identifying causative pathogen(s). Although viral CAP among children is increasingly recognized, distinguishing viral from bacterial etiologies remains difficult. Obtaining high quality samples from infected lung tissue is typically the limiting factor. Additionally, interpretation of results from routinely collected specimens (blood, sputum, and nasopharyngeal swabs) is complicated by bacterial colonization and prolonged shedding of incidental respiratory viruses. Using current literature on assessment of CAP causes in children, we developed an approach for identifying the most likely causative pathogen(s) using blood and sputum culture, polymerase chain reaction (PCR), and paired serology. Our proposed rules do not rely on carriage prevalence data from controls. We herein share our perspective in order to help clinicians and researchers classify and manage childhood pneumonia.

Development of a rapid multiplex PCR assay for the detection of common pathogens associated with community-acquired pneumonia

BACKGROUND

Community-acquired pneumonia (CAP) is one of the most common infectious diseases and is a significant cause of mortality and morbidity globally. A microbial cause was not determined in a sizable percentage of patients with CAP; there are increasing data to suggest regional differences in bacterial aetiology. We devised a multiplex real-time PCR assay for detecting four microorganisms (Streptococcus pneumoniae, Haemophilus influenzae, Klebsiella pneumoniae and Burkholderia pseudomallei) of relevance to CAP infections in Asia.

METHODS

Analytical validation was accomplished using bacterial isolates (n=10-33 of each target organism for analytical sensitivity and n=117 for analytical sensitivity) and clinical validation using 58 culture-positive respiratory tract specimens.

RESULTS

The qPCR assay exhibited 100% analytical sensitivity and analytical specificity, and 100% clinical sensitivity and 94-100% clinical specificity. The limit of detection and efficiency for the multiplex PCR assay were 3-33 CFU/mL and 93-110%, respectively. The results showed that the PCR-based method had higher sensitivity than traditional culture-based methods. The assay also demonstrated an ability to semiquantify bacterial loads.

CONCLUSION

We have devised a reliable laboratory-developed multiplex qPCR assay, with a turnaround time of within one working day, for detection of four clinically important CAP-associated microorganisms in Asia. The availability of a test with improved diagnostic capabilities potentially leads to an informed choice of antibiotic usage and appropriate management of the patient to achieve a better treatment outcome and financial savings.

Diagnostic stewardship based on patient profiles: differential approaches in acute versus chronic infectious syndromes

Introduction: New diagnostics may be useful in clinical practice, especially in contexts of high prevalence of multidrug-resistant organisms (MDRO). However, misuse of diagnostic tools may lead to increased costs and worse patient outcome. Conventional and new techniques should be appropriately positioned in diagnostic algorithms to guide an appropriate use of antimicrobial therapy.Areas covered: A panel of experts identified 4 main areas in which the implementation of diagnostic stewardship is needed. Among chronic infections, bone and prosthetic joint infections and subacute-chronic intravascular infections and endocarditis represent common challenges for clinicians. Among acute infections, bloodstream infections and community-acquired pneumonia may be associated with high mortality and require appropriate diagnostic approach.Expert opinion: Diagnostic stewardship aims to improve the appropriate use of microbiological diagnostics to guide therapeutic decisions through appropriate and timely diagnostic testing. Here, diagnostic algorithms based on different patient profiles are proposed for chronic and acute clinical syndromes. In each clinical scenario, combining conventional and new diagnostic techniques is crucial to make a rapid and accurate diagnosis and to guide the selection of antimicrobial therapy. Barriers related to the implementation of new rapid diagnostic tools, such as high initial costs, may be overcome through their rational and structured use.

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

Pneumonia is a common acute respiratory infection that affects the alveoli and distal airways; it is a major health problem and associated with high morbidity and short-term and long-term mortality in all age groups worldwide. Pneumonia is broadly divided into community-acquired pneumonia or hospital-acquired pneumonia. A large variety of microorganisms can cause pneumonia, including bacteria, respiratory viruses and fungi, and there are great geographical variations in their prevalence. Pneumonia occurs more commonly in susceptible individuals, including children of <5 years of age and older adults with prior chronic conditions. Development of the disease largely depends on the host immune response, with pathogen characteristics having a less prominent role. Individuals with pneumonia often present with respiratory and systemic symptoms, and diagnosis is based on both clinical presentation and radiological findings. It is crucial to identify the causative pathogens, as delayed and inadequate antimicrobial therapy can lead to poor outcomes. New antibiotic and non-antibiotic therapies, in addition to rapid and accurate diagnostic tests that can detect pathogens and antibiotic resistance will improve the management of pneumonia.

Multiresistant Bacterial Pathogens Causing Bacterial Pneumonia and Analyses of Potential Risk Factors from Northeast Ethiopia

BACKGROUND

Pneumonia is the most common cause of morbidity and mortality in developing countries, mostly caused by different species of bacterial pathogens. Hence, patient management needs awareness of the pathogens and antimicrobial susceptibility testing (AST). This study was aimed to assess the type of bacterial isolates and their antimicrobial susceptibility patterns among pneumonia suspected patients at Dessie Referral Hospital, Northeast Ethiopia. Potential risk factors were also assessed to apply preventive measures accordingly.

MATERIALS AND METHODS

A cross-sectional study design was employed among pneumonia suspected patients from February to April 2020 at Dessie Referral Hospital. Sociodemographic characteristics and associated risk factors were collected using a pretested questionnaire, and clinical data were extracted by reviewing medical records. Sputum specimens were collected and inoculated into chocolate agar, blood agar, mannitol salt agar, and MacConkey agar which are then incubated at 35°C or 37°C for 24-48 hours. Bacterial species were identified based on Gram stain, colony characteristics, and biochemical techniques. The data were entered in to Epi-Info version 7.1.5 and analyzed with SPSS software version 20. p value <0.05 at 95% CI was considered as statistically significant.

RESULTS

A total of 406 sputum specimens were collected and cultured, among which 157 (38.7%) were positive for different bacterial pathogens. The predominant pathogens were Klebsiella pneumoniae (28.0%), Streptococcus pneumoniae (24.8%), Staphylococcus aureus (18.5%), and Pseudomonas aeruginosa (14.0%). Majority of the isolates exhibited resistance to ampicillin with 81.5% followed by penicillin with 75.9% and amoxicillin-clavulanate with 61.2%. Multivariable logistic regression showed a significant association of culture positivity with older age (AOR = 2.43, CI: 1.12-5.28, p value = 0.025), cigarette smoking (AOR = 4.67, CI: 2.39-9.20, p value <0.001), and alcohol use (AOR = 5.58, CI: 3.14-9.92, p value <0.001). Resistance to ampicillin and penicillin was associated with repeated prescription and use.

CONCLUSIONS

This study found high prevalence of bacterial pneumonia in the study area, and high rate of bacterial resistance was observed in ampicillin, penicillin, and amoxicillin-clavulanate. Repeated prescriptions and use of antimicrobials were significantly independent factors of bacterial resistance. Therefore, patient management needs identification of bacteria by routine culture with antimicrobial susceptibility testing.

Multicenter Evaluation of the Unyvero Platform for Testing Bronchoalveolar Lavage Fluid

Bronchoalveolar lavage (BAL) culture is a standard, though time-consuming, approach for identifying microorganisms in patients with severe lower respiratory tract (LRT) infections. The sensitivity of BAL culture is relatively low, and prior antimicrobial therapy decreases the sensitivity further, leading to overuse of empirical antibiotics. The Unyvero LRT BAL Application (Curetis GmbH, Germany) is a multiplex molecular panel that detects 19 bacteria, 10 antibiotic resistance markers, and a fungus, Pneumocystis jirovecii, in BAL fluid in ∼4.5 h. Its performance was evaluated using 1,016 prospectively collected and 392 archived specimens from 11 clinical trial sites in the United States. Overall positive and negative percent agreements with culture results for identification of bacteria that grow in routine cultures were 93.4% and 98.3%, respectively, with additional potential pathogens identified by Unyvero in 21.7% of prospectively collected specimens. For detection of P. jirovecii, the positive percent agreement with standard testing was 87.5%. Antibiotic resistance marker results were compared to standard antibiotic susceptibility test results to determine positive predictive values (PPVs). PPVs ranged from 80 to 100%, based on the microorganism and specific resistance marker(s). The Unyvero LRT BAL Application provides accurate detection of common agents of bacterial pneumonia and of P. jirovecii The sensitivity and rapidity of this panel suggest significant clinical value for choosing appropriate antibiotics and for antibiotic stewardship.

Infectious Disease Complications in Patients with Cancer

Critically ill patients with cancer are vulnerable to infections because of the underlying malignancy, tumor-directed therapy, immunosuppression, breaches in mucosa or skin, malnutrition, and other factors. Neutropenia remains the most important risk factor for infection. Infectious complications occurring in critically ill patients with cancer can affect the bloodstream, lungs, gastrointestinal tract, central nervous system, urinary tract, and the skin. Pneumonias are the leading cause of infection in patients with cancer admitted to the intensive care unit. Consideration of opportunistic pathogens in the differential diagnosis is important in patients with impaired cellular and/or humoral immunity or compromised splenic function.

Multicentric evaluation of BioFire FilmArray Pneumonia Panel for rapid bacteriological documentation of pneumonia

OBJECTIVES

To evaluate performances of the rapid multiplex PCR assay BioFire FilmArray Pneumonia Panel (FA-PP) for detection of bacterial pathogens and antibiotic resistance genes in sputum, endotracheal aspirate (ETA) and bronchoalveolar lavage (BAL) specimens.

METHODS

This prospective observational study was conducted in 11 French university hospitals (July to December 2018) and assessed performance of FA-PP by comparison with routine conventional methods.

RESULTS

A total of 515 respiratory specimens were studied, including 58 sputa, 217 ETA and 240 BAL. The FA-PP detected at least one pathogen in 384 specimens, yielding an overall positivity rate of 74.6% (384/515). Of them, 353 (68.5%) specimens were positive for typical bacteria while eight atypical bacteria and 42 resistance genes were found. While identifying most bacterial pathogens isolated by culture (374/396, 94.4%), the FA-PP detected 294 additional species in 37.7% (194/515) of specimens. The FA-PP demonstrated positive percentage agreement and negative percentage agreement values of 94.4% (95% CI 91.7%-96.5%) and 96.0% (95% CI 95.5%-96.4%), respectively, when compared with culture. Of FA-PP false-negative results, 67.6% (46/68) corresponded to bacterial species not included in the panel. At the same semi-quantification level (in DNA copies/mL for FA-PP versus in CFU/mL for culture), the concordance rate was 43.4% (142/327) for culture-positive specimens with FA-PP reporting higher semi-quantification of ≥1 log₁₀ in 48.6% (159/327) of cases. Interestingly, 90.1% of detected bacteria with ≥10⁶ DNA copies/mL grew significantly in culture.

CONCLUSIONS

FA-PP is a simple and rapid molecular test that could complement routine conventional methods for improvement of diagnosis accuracy of pneumonia.

Exploring Virulence Factors and Alternative Therapies against Staphylococcus aureus Pneumonia

Pneumonia is an acute pulmonary infection associated with high mortality and an immense financial burden on healthcare systems. Staphylococcus aureus is an opportunistic pathogen capable of inducing S. aureus pneumonia (SAP), with some lineages also showing multidrug resistance. Given the high level of antibiotic resistance, much research has been focused on targeting S. aureus virulence factors, including toxins and biofilm-associated proteins, in an attempt to develop effective SAP therapeutics. Despite several promising leads, many hurdles still remain for S. aureus vaccine research. Here, we review the state-of-the-art SAP therapeutics, highlight their pitfalls, and discuss alternative approaches of potential significance and future perspectives.

Evaluation of the effect of curcumin on pneumonia: A systematic review of preclinical studies

Pneumonia is a major cause of morbidity and mortality worldwide and causes a significant burden on the healthcare systems. Curcumin is a natural phytochemical with anti-inflammatory and anti-neoplastic characteristics. The aim of this study was to conduct a systematic review of published studies on the effect of curcumin on preclinical models of pneumonia. A comprehensive search was conducted in PubMed/Medline, Scopus, Web of Science and Google Scholar from inception up to March 1, 2020 to recognize experimental or clinical trials assessing the effects of curcumin on pneumonia. We identified 17 primary citations that evaluated the effects of curcumin on pneumonia. Ten (58.8%) studies evaluated the effect of curcumin on mouse models of pneumonia, generated by intranasal inoculation of viruses or bacteria. Seven (41.2%) studies evaluated the inhibitory effects of curcumin on the pneumonia-inducing bacteria. Our results demonstrated that curcumin ameliorated the pneumonia-induced lung injury, mainly through a reduction of the activity and infiltration of neutrophils and the inhibition of inflammatory response in mouse models. Curcumin ameliorates the severity of pneumonia through a reduction in neutrophil infiltration and by amelioration of the exaggerated immune response in preclinical pneumonia models.

Panels and Syndromic Testing in Clinical Microbiology

Syndromic panels have allowed clinical microbiology laboratories to rapidly identify bacteria, viruses, fungi, and parasites and are now fully integrated into the standard testing practices of many clinical laboratories. To maximize the benefit of syndromic testing, laboratories must implement strict measures to ensure that syndromic panels are being used responsibly. This article discusses commercially available syndromic panels, the benefits and limitations of testing, and how diagnostic and laboratory stewardship can be used to optimize testing and improve patient care while keeping costs at a minimum.

Complicated pneumonia in children

Complicated community-acquired pneumonia in a previously well child is a severe illness characterised by combinations of local complications (eg, parapneumonic effusion, empyema, necrotising pneumonia, and lung abscess) and systemic complications (eg, bacteraemia, metastatic infection, multiorgan failure, acute respiratory distress syndrome, disseminated intravascular coagulation, and, rarely, death). Complicated community-acquired pneumonia should be suspected in any child with pneumonia not responding to appropriate antibiotic treatment within 48-72 h. Common causative organisms are Streptococcus pneumoniae and Staphylococcus aureus. Patients have initial imaging with chest radiography and ultrasound, which can also be used to assess the lung parenchyma, to identify pleural fluid; CT scanning is not usually indicated. Complicated pneumonia is treated with a prolonged course of intravenous antibiotics, and then oral antibiotics. The initial choice of antibiotic is guided by local microbiological knowledge and by subsequent positive cultures and molecular testing, including on pleural fluid if a drainage procedure is done. Information from pleural space imaging and drainage should guide the decision on whether to administer intrapleural fibrinolytics. Most patients are treated by drainage and more extensive surgery is rarely needed; in any event, in low-income and middle-income countries, resources for extensive surgeries are scarce. The clinical course of complicated community-acquired pneumonia can be prolonged, especially when patients have necrotising pneumonia, but complete recovery is the usual outcome.

Evaluating the use of a 22-pathogen TaqMan array card for rapid diagnosis of respiratory pathogens in intensive care

Introduction. Pneumonia is highly prevalent in intensive care units (ICUs), with high associated mortality. Empirical treatment prioritizes breadth of coverage while awaiting laboratory diagnosis, often at the expense of antimicrobial stewardship. Microarrays use multiple parallel polymerase chain reactions to enable a rapid syndromic approach to laboratory diagnosis.Aim. To evaluate the clinical and laboratory implications of introducing a bespoke 22-pathogen TaqMan Array Card (TAC) for rapid pathogen detection in deep respiratory samples from adult ICUs.Methodology. TAC results from all ICU patients prospectively tested over a 9-month period at Cambridge's Clinical Microbiology and Public Health Laboratory were compared to those of corresponding conventional microbiological assays (culture-, PCR- or serology-based) in terms of result agreement and time-to-result availability. Clinical impact was assessed by retrospective review of medical records.Results. Seventy-one patients were included [45 (63 %) male, median age 59). Overall result agreement was 94 %, with TAC detecting more pathogens than conventional methods. TAC detected Streptococcus pneumoniae more readily than culture (7 vs 0 cases; P=0.02). TAC did not detect Aspergillus spp. in eight culture- or galactomannan-positive cases. The median turnaround time (1 day) was significantly shorter than that of bacterial/fungal culture, Pneumocystis jirovecii PCR and galactomannan testing (each 3 days; P<0.001), atypical bacteria serology (13 days; P<0.001) and Mycobacterium tuberculosis culture (46 days; P<0.001). Earlier result availability prompted discontinuation of unnecessary antimicrobials in 15/71 (21 %) cases, but had no bearing on patient isolation/deisolation.Conclusion. TAC provided greater overall yield of pathogen detection and faster turnaround times, permitting earlier discontinuation of unnecessary antimicrobials.

A multiplex polymerase chain reaction assay for antibiotic stewardship in suspected pneumonia

Background

Multiplexed molecular rapid diagnostic tests (RDTs) may allow for rapid and accurate diagnosis of the microbial etiology of pneumonia. However, little data are available on multiplexed RDTs in pneumonia and their impact on clinical practice.

Methods

This retrospective study analyzed 659 hospitalized patients for microbiological diagnosis of suspected pneumonia.

Results

The overall sensitivity of the Unyvero LRT Panel was 85.7% (95% CI 82.3–88.7) and the overall specificity was 98.4% (95% CI 98.2–98.7) with a negative predictive value of 97.9% (95% CI 97.6–98.1). The LRT Panel result predicted no change in antibiotics in 12.4% of cases but antibiotic de-escalation in 65.9% (405/615) of patients, of whom 278/405 (69%) had unnecessary MRSA coverage and 259/405 (64%) had unnecessary P. aeruginosa coverage.

Interpretation

In hospitalized adults with suspected pneumonia, use of an RDT on respiratory samples can allow for early adjustment of initial antibiotics, most commonly de-escalation.

Blood and Bronchoalveolar Lavage Fluid Metagenomic Next-Generation Sequencing in Pneumonia

Background

Metagenomic next-generation sequencing (mNGS) has made a revolution in the mode of pathogen identification. We decided to explore the diagnostic value of blood and bronchoalveolar lavage fluid (BALF) as mNGS samples in pneumonia.

Methods

We retrospectively reviewed 467 mNGS results and assessed the diagnostic performance of paired blood and BALF mNGS in 39 patients with pneumonia.

Results

For bacteria and fungi, 16 patients had culture-confirmed pathogen diagnosis, while 13 patients were culture-negative. BALF mNGS was more sensitive than blood mNGS (81.3% vs. 25.0%, p=0.003), and the specificity in BALF and blood mNGS was not statistically significant different (76.9% vs. 84.6%, p=0.317). For 10 patients without culture test, treatments were changed in 2 patients. For viruses, Epstein-Barr virus was positive in blood mNGS in 9 patients. Human adenovirus was detected in both BALF and blood mNGS in 3 patients.

Conclusion

Our study suggests that BALF mNGS is more sensitive than blood mNGS in detecting bacteria and fungi, but blood also has advantages to identify the pathogens of pneumonia, especially for some viruses.