Viral pneumonia

Epidemiology of respiratory viruses according to age group, 2023-24 winter season, Kyoto, Japan

The seasonality and epidemiology of viral acute respiratory infections (ARIs) have changed since the coronavirus disease 2019 pandemic. However, molecular-based ARI surveillance has not been conducted in Japan. We developed a regional surveillance program to define the local epidemiology of ARIs. Between December 2023 and March 2024, 2,992 upper respiratory samples collected from patients suspected of having ARIs at five facilities in Kyoto City, Japan, were tested for SARS-CoV-2, influenza virus, and respiratory syncytial virus (RSV) using RT‒PCR. Samples negative for these viruses were randomly selected for testing with the FilmArray Respiratory Panel, and the detection rates of other viruses were estimated. SARS-CoV-2, influenza virus, and RSV were detected in 598 (20.3%), 165 (5.6%), and 40 (1.4%) of the 2,949 samples with valid RT‒PCR results, respectively. The most prevalent viruses in the < 6, 6-17, 18-64, and ≥ 65 year age groups were rhinovirus/enterovirus, RSV, and SARS-CoV-2; influenza virus, seasonal coronavirus, and rhinovirus/enterovirus; SARS-CoV-2, seasonal coronavirus, and influenza virus; and SARS-CoV-2, seasonal coronavirus, and influenza virus, respectively. Significant differences in the detection rates of these viruses were detected between the age groups. This study highlights the importance of age-stratified molecular-based surveillance for a comprehensive understanding of the epidemiology of ARIs.

Can clinical findings at admission allow withholding of antibiotics in patients hospitalized for community acquired pneumonia when a test for a respiratory virus is positive?

BACKGROUND

Current guidelines recommend empiric antibiotic therapy for patients who require hospitalization for community-acquired pneumonia (CAP). We sought to determine whether clinical, imaging or laboratory features in patients hospitalized for CAP in whom PCR is positive for a respiratory virus enable exclusion of bacterial coinfection so that antibiotics can be withheld.

METHODS

For this prospective study, we selected patients in whom an etiologic diagnosis was likely to be reached, namely those who provided a high-quality sputum sample at or shortly after admission, and in whom PCR was done to test for a respiratory virus. We performed quantitative bacteriologic studies on sputum to determine the presence of bacterial infection or coinfection and reviewed all clinical, imaging and laboratory studies.

RESULTS

Of 122 CAP patients studied, 77 (63.1%) had bacterial infection, 16 (13.1%) viral infection, and 29 (23.8%) bacterial/viral coinfection. Underlying pulmonary disease and a history of smoking were more common in bacterial pneumonia. Upper respiratory symptoms were more common, and mean white blood cell (WBC) counts were lower viral pneumonia. Nevertheless, no clinical, laboratory or imaging findings allowed exclusion of bacterial coinfection in patients who tested positive for a respiratory virus. In fact, patients with bacterial/viral coinfection were sicker than those with bacterial or viral pneumonia; 30% were admitted required transfer to the ICU during their hospital course, compared to 17% and 19% of patients with bacterial or viral infection, respectively (p < .05). In this study, 64.4% of patients who tested positive for a respiratory virus had a bacterial coinfection.

CONCLUSIONS

If a test for a respiratory virus test is positive in a patient hospitalized for CAP, no sufficiently differentiating features exclude bacterial coinfection, thereby supporting the recommendation that empiric antibiotics be administered to all patients who are sufficiently ill to require hospitalization for CAP.

Impact of respiratory pathogens detection by a rapid multiplex polymerase chain reaction assay on the management of community-acquired pneumonia for children at the paediatric emergency department. A randomized controlled trial, the Optimization of Pneumonia Acute Care (OPTIPAC) study

OBJECTIVES

The pathogen of community-acquired pneumonia (CAP) in children is typically uncertain during initial treatment, leading to systematic empiric antibiotic use. This study investigates if having rapid multiplex PCR results in the emergency department (ED) improves empiric treatment.

METHODS

OPTIPAC, a French multicentre study (2016-2018), enrolled patients consulting for CAP at the paediatric ED in 11 centres. Patients were randomized to either receive a multiplex PCR test plus usual care or usual care alone and followed for 15 days. The primary outcome was the appropriateness of initial antimicrobial management, determined by a blinded committee.

RESULTS

Of the 499 randomized patients, 248 were tested with the multiplex PCR. Appropriateness of the antibiotic treatment was higher in the PCR group (168/245, 68.6% vs. 120/249, 48.2%; Relative risk 1.42 [1.22-1.66]; p < 0.0001), chiefly by reducing unnecessary antibiotics in viral pneumonia (RR 3.29 [2.20-4.90]). No adverse events were identified.

DISCUSSION

The multiplex PCR assay result at the ED improves paediatric CAP's antimicrobial stewardship, by both reducing antibiotic prescriptions and enhancing treatment appropriateness.

Severe community-acquired pneumonia compared to severe community-acquired Acinetobacter baumannii pneumonia in Reunion Island: A retrospective study

Acinetobacter baumannii (Ab) has emerged in the last decades as a cause of community-acquired pneumonia (CAP) in tropical and subtropical regions. We previously conducted the first investigation on this topic in France with a case series of severe CAP-Ab in Reunion Island over an eight-year period. In the present work, we aim to highlight the specific aspects of CAP-Ab by comparing our case series with an historical cohort (PAC_RUN), obtained by retrospective chart review (2016-2021) of severe community-acquired pneumonia cases on Reunion Island, in which CAP-Ab was ruled out. During the study period, eight CAP-Ab cases were identified, giving an incidence of 0.1 cases per 100,000 people/year, and an incidence of 16.5 cases per 100,000 people/year for non-Ab-related CAP (n = 761). By comparing with non-Ab-related CAP, patients had more excessive alcohol use (75% vs. 25.6%, p = 0.005) and lower body mass index (21 vs. 24 kg/m2, p = 0.004). Six cases (75%) of CAP-Ab occurred during the rainy season (p = 0.06). Mortality was higher (62.5% vs. 24.3%, p = 0.02) and time to death was shorter (median 2 days vs. 7, p = 0.009) in the CAP-Ab group. Bacteraemic pneumonia was strongly associated with CAP-Ab (62.5% vs. 15.7%, p = 0.004). Significant differences were found in the need for renal replacement therapy (75% vs. 17.2%, p < 0.001), catecholamine use (100% vs. 54.5%, p = 0.01) and use of invasive mechanical ventilation (100% vs. 62.7%, p = 0.03). Also, in the proportion of severe acute respiratory distress syndrome (62.5% vs. 23.2%, p = 0.02), septic shock (100% vs. 40.6%, p < 0.001), and cardiogenic shock (87.5% vs. 15.9%, p < 0.001). Compared to severe non-Ab-related CAP, severe CAP-Ab is characterised by higher mortality, associated with a high frequency of multiple organ failure. Excessive alcohol consumption and malnutrition seem to be risk factors. To improve outcomes, broader spectrum antibiotic therapy must be immediately proposed when CAP-Ab is suspected.

Microfluidic methods for the diagnosis of acute respiratory tract infections

Acute respiratory tract infections (ARTIs) are caused by sporadic or pandemic outbreaks of viral or bacterial pathogens, and continue to be a considerable socioeconomic burden for both developing and industrialized countries alike. Diagnostic methods and technologies serving as the cornerstone for disease management, epidemiological tracking, and public health interventions are evolving continuously to keep up with the demand for higher sensitivity, specificity and analytical throughput. Microfluidics is becoming a key technology in these developments as it allows for integrating, miniaturizing and automating bioanalytical assays at an unprecedented scale, reducing sample and reagent consumption and improving diagnostic performance in terms of sensitivity, throughput and response time. In this article, we describe relevant ARTIs-pneumonia, influenza, severe acute respiratory syndrome, and coronavirus disease 2019-along with their pathogenesis. We provide a summary of established methods for disease diagnosis, involving nucleic acid amplification techniques, antigen detection, serological testing as well as microbial culture. This is followed by a short introduction to microfluidics and how flow is governed at low volume and reduced scale using centrifugation, pneumatic pumping, electrowetting, capillary action, and propagation in porous media through wicking, for each of these principles impacts the design, functioning and performance of diagnostic tools in a particular way. We briefly cover commercial instruments that employ microfluidics for use in both laboratory and point-of-care settings. The main part of the article is dedicated to emerging methods deriving from the use of miniaturized, microfluidic systems for ARTI diagnosis. Finally, we share our thoughts on future perspectives and the challenges associated with validation, approval, and adaptation of microfluidic-based systems.

Multicenter Evaluation of the QIAstat-Dx and the BioFire Multiplex Panel Tests for the Detection of Respiratory Pathogens

Syndromic multiplex panel testing enables simultaneous detection of multiple respiratory pathogens, but limited data is available on the comparative diagnostic performance of different testing systems. In this multicenter prospective study, we aimed to compare the QIAstat-Dx Respiratory Panel 2.0 (QIAstat-Dx-RP2.0) with the widely used BioFire-RP2.1, using 269 respiratory clinical specimens. Concordant test results were obtained in 232 (86.3%) cases. Discordant test results included 33 BioFire-RP2.1(+)/QIAstat-Dx-RP2.0(-) and 4 BioFire-RP2.1(-)/QIAstat-Dx-RP2.0(+) results. Discordant samples showed significantly lower pathogen loads than concordant ones (p < 0.01). Overall, the QIAstat-Dx-RP2.0 showed an analytical sensitivity of 50%-100% depending on the respiratory target, with an analytical specificity ≥ 99.0%. Most significant differences were found for the detection of adenovirus, human coronaviruses, respiratory syncytial virus, human rhinovirus/enterovirus and SARS-CoV-2 (kappa-score: 0.67-0.91). Co-detections of respiratory pathogens were identified in 47 cases by BioFire-RP2.1 and 29 by QIAstat-Dx-RP2.0. Agreement rates between the two multiplex panel tests decreased from 91.8% for single pathogen detections to 65.0% and 42.9% for co-detecting two and three pathogens, respectively. Pathogen loads were significantly lower in co-detections compared to single pathogen detections (p < 0.01), potentially explaining the lower detection rates with the QIAstat-Dx-RP2.0 in cases of multiple pathogens. In conclusion, our prospective multicenter evaluation showed good diagnostic performance of the QIAstat-Dx-RP2.0 assay, but lower detection rates for some respiratory targets compared to BioFire-RP2.1. As QIAstat-Dx-RP2.0 offers advantages in handling, noise emission, cost effectiveness, and provides semi-quantitative results compared to BioFire-RP2.1 an updated version with enhanced analytical sensitivity would be a viable alternative syndromic testing system for detecting respiratory pathogens.

Impact of antibiotic therapy in patients with respiratory viral infections: a retrospective cohort study

OBJECTIVES

The impact of antibiotics in patients with positive polymerase chain reaction (PCR) for respiratory viruses without evidence of a respiratory bacterial co-infection is largely unknown. The aim of this study was to assess the association of antibiotics on 30-day mortality and length of hospital stay in patients with an acute respiratory infection and PCR documented presence of respiratory viruses.

METHODS

We conducted a retrospective cohort study of adult patients admitted to hospital between 2012 and 2021 with positive PCR for influenza virus (H3N2, H1N1, influenza B), respiratory syncytial virus, human metapneumovirus or severe acute respiratory syndrome coronavirus 2. We used logistic regression, the Kaplan-Meier estimator and Poisson's regression to assess the impact of antibiotic therapy on outcomes.

RESULTS

Among 3979 patients, 67.7% received antibiotics. In adjusted analyses, antibiotics initiated in the emergency department (adjusted OR 1.23, 95% CI 0.77-1.96) and days of antibiotic therapy (adjusted OR per day of therapy 0.98, 95% CI 0.95-1.00) had no significant impact on mortality, whereas antibiotics initiated later during admission (adjusted OR 2.25, 95% CI 1.26-4.02) was associated with increased mortality. Patients prescribed antibiotics had longer duration of hospital admission.

CONCLUSIONS

We observed no protective association between in-hospital antibiotic therapy and outcomes, suggesting overuse of antibiotics in respiratory infections with proven respiratory viruses. A restrictive antibiotic strategy may be warranted.

Systematic review and meta-analysis of the accuracy of lung ultrasound and chest radiography in diagnosing community acquired pneumonia in children

Chest radiography (CXR) is commonly used for diagnosing childhood pneumonia, but concerns about radiation exposure have raised interest in using radiation-free lung ultrasound (LUS) as an alternative imaging modality. Therefore, we designed this meta-analysis to compare the accuracy of LUS and CXR for diagnosing childhood pneumonia. We searched 8 databases and 1 clinical trial registry for studies published from inception to March 2023. Studies assessing lung ultrasound and chest radiography for diagnosing childhood pneumonia were included. Two reviewers independently screened literature, extracted data, and assessed the risk of bias using the QUADAS-2 tool for each study. Meta-analysis was conducted using a random-effects model, and pooled sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, diagnostic odds ratio, and summary receiver operating characteristic (SROC) curve were assessed. Statistical analyses were performed using Meta-Disc 1.4, RevMan 5.4, and Stata 17.0 software. Heterogeneity was examined, and subgroup analysis was conducted to explore the accuracy of lung ultrasound in diagnosing childhood pneumonia. Out of the 4089 screened articles, 30 studies were included, encompassing a total of 4546 children. Of those, 3257 were diagnosed with pneumonia, 3190 through LUS, and 2925 via CXR. The meta-analysis showed that the sensitivity, specificity, positive and negative likelihood ratios, and diagnostic odds ratio of LUS were 0.940 (95% CI 0.930-0.949), 0.855 (95% CI 0.835-0.873), 7.561 (95% CI 4.956-11.536), 0.08 (95% CI 0.056-0.113), and 110.77 (95% CI 62.156-197.40), respectively. The combined area under the SROC curve was 0.9712, Q index = 0.9218. For CXR, the sensitivity, specificity, positive and negative likelihood ratios, and diagnostic odds ratio were 0.893 (95% CI 0.881-0.905), 0.906 (95% CI 0.889-0.921), 18.742 (95% CI 7.551-46.520), 0.105 (95% CI 0.062-0.180), and 237.43 (95% CI 74.080-760.99), respectively. The combined area under the SROC curve was 0.9810, Q index = 0.9391. Subgroup analysis showed that the implementation location, interval between lung ultrasound and chest radiography, and operator experience had no impact on the accuracy of lung ultrasound in diagnosing childhood pneumonia. Existing evidence suggests that lung ultrasound has high accuracy for diagnosing childhood community-acquired pneumonia. Compared with chest radiography, lung ultrasound has higher sensitivity, similar specificity, and advantages such as radiation-free, lower cost, simplicity of operation, and ease of follow-up, making it an important imaging modality for diagnosing childhood pneumonia.

Therapeutic efficacy of JNJ-49214698, an RSV fusion inhibitor, in RSV-infected neonatal lambs

Respiratory syncytial virus (RSV) is a leading cause of respiratory infection, hospitalization and death in infants worldwide. No fully effective RSV therapy using direct antivirals is marketed. Since clinical efficacy data from naturally infected patients for such antivirals are not available yet, animal studies are indispensable to predict therapeutic intervention. Here, we report the impact of an RSV fusion inhibitor, JNJ-49214698, on severe RSV-associated acute lower respiratory tract infection (ALRTI) in neonatal lambs. Randomized animals were treated once daily with 25 mg/kg JNJ-49214698, starting either before RSV infection, 1 day post-infection or as late as peak lung viral load on Day 3 post-infection. Treatment efficacy was assessed by scoring clinical signs of illness, development of RSV-induced gross and microscopic lung lesions and measuring virus titres in the lungs. Treatment with JNJ-49214698 was very effective in all treatment groups. Even in animals for which treatment was delayed until peak viral load was reached, a reduced amount and severity of gross and microscopic lesions, as well as RSV titres and RNA levels, were found. These results strongly suggest that treatment with small-molecule fusion inhibitors is an effective strategy to treat patients who are diagnosed with an RSV-induced ALRTI.

Emergence of infectious diseases and role of advanced nanomaterials in point-of-care diagnostics: a review

Infectious outbreaks are the foremost global public health concern, challenging the current healthcare system, which claims millions of lives annually. The most crucial way to control an infectious outbreak is by early detection through point-of-care (POC) diagnostics. POC diagnostics are highly advantageous owing to the prompt diagnosis, which is economical, simple and highly efficient with remote access capabilities. In particular, utilization of nanomaterials to architect POC devices has enabled highly integrated and portable (compact) devices with enhanced efficiency. As such, this review will detail the factors influencing the emergence of infectious diseases and methods for fast and accurate detection, thus elucidating the underlying factors of these infections. Furthermore, it comprehensively highlights the importance of different nanomaterials in POCs to detect nucleic acid, whole pathogens, proteins and antibody detection systems. Finally, we summarize findings reported on nanomaterials based on advanced POCs such as lab-on-chip, lab-on-disc-devices, point-of-action and hospital-on-chip. To this end, we discuss the challenges, potential solutions, prospects of integrating internet-of-things, artificial intelligence, 5G communications and data clouding to achieve intelligent POCs.

Inhalable nanocatalytic therapeutics for viral pneumonia

Pneumonia is a ubiquitous disease caused by viral and bacterial infections, characterized by high levels of reactive oxygen species in inflamed areas. Therapeutic strategies targeting reactive oxygen species levels in pneumonia have limited success due to the intricate nature of lung tissues and lung inflammatory responses. Here we describe an inhalable, non-invasive therapeutic platform composed of engineered cerium-based tannic acid nanozymes bound to a self-assembling peptide. In vitro and in vivo studies show that the nanozyme is internalized mostly by activated macrophages and epithelial cells in the inflamed sites. In the oxidative environments of a mouse model of viral pneumonia, nanozyme aggregates into catalytically active structures that reduce reactive oxygen species levels and inflammatory cytokine production and promote macrophage polarization to the prohealing (M2) phenotype. Moreover, the nanozyme attenuates bacterial inflammation and reduces tissue damage in a mouse viral pneumonia model with secondary bacterial infection. Overall, this nanozyme platform is a promising strategy for treating pneumonia and its associated conditions.

Molecular characteristics of organic matters in PM2.5 associated with upregulation of respiratory virus infection in vitro

The extent to which organic matters (OM) in PM2.5 affect virus infections and the key organic molecules involved in this process remain unclear. Herein, this study utilized ultra-high resolution mass spectrometry coupled with in vitro experiments to identify the organic molecules associated with respiratory virus infection for the first time. Water-soluble organic matters (WSOM) and water-insoluble organic matters (WIOM) were separated from PM2.5 samples collected at the urban area of Guangzhou, China. Their molecular compositions were analyzed using Fourier transform ion cyclotron resonance mass spectrometry. Subsequently, in vitro experiments were conducted to explore the impact of WSOM and WIOM exposure on the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pseudo-virus infection in A549 cells. Results revealed that WSOM and WIOM respectively promoted 1.7 to 2.1-fold and 1.9 to 3.5-fold upregulation of SARS-CoV-2 pseudo-virus infection in a concentration-dependent manner (at 25 to 100 μg mL-1) compared to the virus-only control group. Partial least squares model analysis indicated that the increased virus infection was likely related to phthalate ester and nitro-aromatic molecules in WSOM, as well as LipidC molecules with aliphatic and olefinic structures in WIOM. Interestingly, the molecules responsible for upregulating SARS-CoV-2 receptor angiotensin-converting enzyme 2 (ACE2) expression and virus infection differed. Thus, it was concluded that ACE2 upregulation alone may not fully elucidate the mechanisms underlying increased susceptibility to virus infection. The findings highlight the critical importance of aromatic and lipid molecules found in OM in relation to respiratory virus infection.

Burden and Risk Factors for Coinfections in Patients with a Viral Respiratory Tract Infection

Which patients should be monitored for coinfections or should receive empirical antibiotic treatment, in patients with an acute viral respiratory infection, is largely unknown. We evaluated the prevalence, characteristics, outcomes of coinfected patients, and risk factors associated with a coinfection among patients with an acute viral infection. A retrospective, single-center study recruited consecutive patients from October 2022 to March 2023 presenting to the emergency department with signs of a respiratory tract infection. Patients were screened for respiratory viruses and bacterial/fungal secondary infections according to local standard procedures. Outcomes included severe disease, in-hospital complications, all-cause in-hospital and ICU-related mortality, time to death, time to discharge, and time to coinfection. The analysis included 652 patients. A viral infection and a secondary bacterial/fungal infection were detected in 39.1% and 40% of cases. Compared with the rest of the cohort, coinfected patients had more frequently severe disease (88.3%, p < 0.001; 51% in patients with SARS-CoV-2) and higher in-hospital mortality (16.5%, p = 0.010). Nephropathy (OR 3.649, p = 0.007), absence of COVID-19 vaccination (OR 0.160, p < 0.001), SARS-CoV-2 infection (OR 2.390, p = 0.017), and lower blood pressure at admission (OR 0.980, p = 0.007) were independent risk factors for coinfection. Multidrug-resistant pathogens were detected in 30.8% of all coinfections. Patients with a viral infection are at high risk of bacterial coinfections, which carry a significant morbidity and mortality burden.

Dynamic features of virus protein 1 and substitutions in the 3-phenyl ring determine the potency and broad-spectrum activity of capsid-binding pyrazolo[3,4-d]pyrimidines against rhinoviruses

Pyrazolo[3,4-d]pyrimidines represent one potent class of well tolerated and highly active rhinovirus (RV) inhibitors that act as capsid binders. The lead compound OBR-5-340 inhibits a broad-spectrum of RVs. Aiming to improve lead activity, we evaluated the impact of structural modifications in the 3-phenyl ring of OBR-5-340 on its potency and spectrum of anti-RV activity vitro. Our results demonstrate the crucial role of substitution at position 4 for strong, broad-spectrum anti-RV activity. The 4-methyl (RCB23137) and 4-chloro (RCB23138) derivatives outperformed OBR-5-340 in terms of potency and anti-RV activity spectrum. Based on these findings, the compounds were selected for computational binding studies. Molecular dynamic simulations with six RVs differing in OBR-5-340, RCB23137, and RCB23138 sensitivity proved the impact of dynamic features of two VP1 loops enveloping these inhibitors on antiviral potency.

Beneficial effect of sequential treatment with high-dose steroids and short-course oral glucocorticoids in patients with severe influenza virus-associated pneumonia

Accumulating evidence supports that glucocorticoid treatment for viral pneumonia (VPA) can shorten the disease course and improve survival. However, currently, the use of glucocorticoids in treating VPA remains controversial. Moreover, a unified standard for the dosage and duration of glucocorticoid therapy has not been presented in published articles. A retrospective analysis was conducted in patients who were hospitalized for severe influenza virus-associated pneumonia, and they received sequential treatment with high-dose glucocorticoids and short-course oral glucocorticoids. Patients were followed up for 3 months. A total of 11 patients were included in the study (average age 56 years). There was no gender difference, but age and underlying diseases could be risk factors for severe influenza virus-associated pneumonia. The types of viruses causing pneumonia included influenza A/B. The main clinical symptoms of patients were fever, cough, sputum production, and dyspnea. Chest computed tomography showed multiple ground-glass shadows in the lobes, and the presence of bacterial and fungal infections was accompanied by consolidation shadows. After glucocorticoid therapy, the symptoms improved. None of the patients underwent tracheal intubation, and all survived. After a 3-month follow-up, lung CT absorption in all patients had reached more than 80%, and lung imaging absorption in 20% patients was complete. No serious complications occurred in any of the patients. Sequential treatment with high-dose steroids and short-course oral glucocorticoids may be helpful for reducing the tracheal intubation rate and mortality rate in patients with severe influenza virus-associated pneumonia. Additionally, short-course oral glucocorticoids may reduce pulmonary fibrosis in patients with severe influenza virus-associated pneumonia without any serious complications.

Challenges of infectious diseases in older adults: From immunosenescence and inflammaging through antibiotic resistance to management strategies

Infectious diseases in older adults present a significant challenge to the healthcare system, marked by increased morbidity, mortality, and rising costs of care. Age-related changes (ARCs) in the immune system, including immunosenescence and inflammaging, contribute to heightened susceptibility to severe infections and reduced vaccine responsiveness. Additionally, alterations in the normal microbial flora due to aging and factors such as antibiotic therapy predispose older individuals to infections and age-related diseases. Changes in body composition also affect the pharmacokinetics and pharmacodynamics of drugs, complicating the management of antibiotics and leading to potential overdoses, adverse drug reactions, or underdoses that foster antibiotic resistance. The inappropriate use of antibiotics has exacerbated the emergence of multidrug-resistant pathogens, posing a critical global concern. This narrative review provides an overview of immunosenescence and inflammaging and focuses on three major infectious diseases affecting older adults: bacterial pneumonia, urinary tract infections, and Clostridium difficile infections. Through this exploration, we aim to highlight the need for targeted approaches in managing infectious diseases in the aging population.

Natural Binary Herbal Small Molecules Self-Assembled Nanogel for Synergistic Inhibition of Respiratory Syncytial Virus

Respiratory syncytial virus (RSV) is one of the most significant pathogenic infections in childhood, associated with high morbidity and mortality rates. Currently, there is no effective and safe drug or vaccine available for RSV. Glycyrrhizic acid (GA), an active compound derived from the natural herb licorice, has been reported to provide protection against influenza and coronaviruses, exhibiting notable antiviral and anti-inflammatory properties. Ephedrine (EPH) is a commonly prescribed medication for the treatment of cough and asthma, and it also demonstrates certain antiviral effects. In this study, EPH and GA were combined to form an efficient nanomaterial (EPH-GA nanogel). The self-assembly of this nanogel is driven by hydrogen bonding and hydrophobic interactions, allowing it to serve as an antiviral nanomedicine without the need for a dual-component carrier, achieving a 100% drug loading efficiency. Oral administration of the EPH-GA nanogel significantly reduced viral load in the lungs of mice and improved lung lesions and tissue infiltration caused by RSV. Notably, we discovered that the assembled drug may create a "physical barrier" that prevents RSV from adsorbing to host cells, while free GA and EPH may compete with RSV for protein binding sites, thereby enhancing cellular uptake of EPH. Consequently, this prevents RSV infection and proliferation within host cells. Furthermore, the EC50 values changed from 310.83 μM for EPH and 262.88 μM for GA to 68.25 μM for the EPH-GA combination, with a combination index of 0.458. In addition, the in vivo biopharmaceutic process of GA and EPH was investigated, revealing that the oral administration of EPH-GA significantly increased the bioavailability of EPH while maintaining its plasma concentration at a relatively stable level. This enhancement may contribute to a synergistic antiviral effect when combined with GA. Furthermore, the in vivo process of EPH-GA demonstrates the advantage of delivering the drug to the lesion at elevated levels, thereby facilitating its antiviral mechanism at the cellular level. In this study, we identified an effective nanomedicine, EPH-GA nanogel, which can inhibit the proliferation of RSV and mitigate lung lesions resulting from viral infection by influencing the biopharmaceutical process in vivo. This research not only offers a novel strategy for the nanomedicine treatment of RSV but also elucidates, to some extent, the compatibility mechanisms of the multicomponents of traditional Chinese medicine.

Protein and transcriptional biomarker profiling may inform treatment strategies in lower respiratory tract infections by indicating bacterial-viral differentiation

Lower respiratory tract infections (LRTIs) remain a significant global cause of infectious disease-related mortality. Accurate discrimination between acute bacterial and viral LRTIs is crucial for optimal patient care, prevention of unnecessary antibiotic prescriptions, and resource allocation. Plasma samples from LRTI patients with bacterial (n = 36), viral (n = 27; excluding SARS-CoV-2), SARS-CoV-2 (n = 22), and mixed bacterial-viral (n = 38) etiology were analyzed for protein profiling. Whole-blood RNA samples from a subset of patients (bacterial, n = 8; viral, n = 8; and SARS-CoV-2, n = 8) were analyzed for transcriptional profiling. Lasso regression modeling identified a seven-protein signature (CRP, IL4, IL9, IP10, MIP1α, MIP1β, and TNFα) that discriminated between patients with bacterial (n = 36) vs viral (n = 27) infections with an area under the curve (AUC) of 0.98. When comparing patients with bacterial and mixed bacterial-viral infections (antibiotics clinically justified; n = 74) vs patients with viral and SARS-CoV-2 infections (antibiotics clinically not justified; n = 49), a 10-protein signature (CRP, bFGF, eotaxin, IFNγ, IL1β, IL7, IP10, MIP1α, MIP1β, and TNFα) with an AUC of 0.94 was identified. The transcriptional profiling analysis identified 232 differentially expressed genes distinguishing bacterial (n = 8) from viral and SARS-CoV-2 (n = 16) etiology. Protein-protein interaction enrichment analysis identified 20 genes that could be useful in the differentiation between bacterial and viral infections. Finally, we examined the performance of selected published gene signatures for bacterial-viral differentiation in our gene set, yielding promising results. Further validation of both protein and gene signatures in diverse clinical settings is warranted to establish their potential to guide the treatment of acute LRTIs.

IMPORTANCE

Accurate differentiation between bacterial and viral lower respiratory tract infections (LRTIs) is vital for effective patient care and resource allocation. This study investigated specific protein signatures and gene expression patterns in plasma and blood samples from LRTI patients that distinguished bacterial and viral infections. The identified signatures can inform the design of point-of-care tests that can aid healthcare providers in making informed decisions about antibiotic prescriptions in order to reduce unnecessary use, thereby contributing to reduced side effects and antibiotic resistance. Furthermore, the potential for faster and more accurate diagnoses for improved patient management in acute LRTIs is compelling.

Clinical Characteristics of Pediatric Parainfluenza Virus Infections: A Comparative Analysis of Parainfluenza Virus Serotypes 1-4 From April 2021 to October 2023 in Hokkaido, Japan

BACKGROUND

Parainfluenza virus (PIV) is widely known as a causative virus of acute respiratory tract infections in children, and 4 serotypes (PIV-1-PIV-4) have been identified. The purpose of the present study was to clarify the clinical characteristics of the PIV serotypes in pediatric PIV infections in Japan.

METHODS

Between April 2021 and October 2023, 8821 children aged <16 years who presented with respiratory symptoms underwent multiplex polymerase chain reaction analyses at the Department of Pediatrics, NTT Medical Center Sapporo. All 1490 cases in which PIV was detected were analyzed for their clinical characteristics by PIV serotypes.

RESULTS

Of the 1490 cases, 608 were positive for a single PIV serotype: 91 (13.5%) for PIV-1, 54 (4.8%) for PIV-2, 361 (62.1%) for PIV-3 and 102 (19.6%) for PIV-4. The median ages were 3.5 years for PIV-1, 5.4 years for PIV-2, 1.9 years for PIV-3 and 2.2 years for PIV-4, with a significantly older age for PIV-2. Compared with the other serotypes, croup was significantly more common in PIV-1 and lower respiratory tract infection was significantly more common in PIV-4. Of the 608 cases with a single PIV serotype, 114 were hospitalized. The proportion of hospitalized patients was higher for PIV-4 than for the other PIV serotypes, but the difference was not significant.

CONCLUSIONS

Lower respiratory tract infection was more frequent in PIV-4 than in the other PIV serotypes, and PIV-4 infection may increase the risk of hospitalization.

Bacterial co-infection in COVID-19: a call to stay vigilant

Co-infection with diverse bacteria is commonly seen in patients infected with the novel coronavirus, SARS-CoV-2. This type of co-infection significantly impacts the occurrence and development of novel coronavirus infection. Bacterial co-pathogens are typically identified in the respiratory system and blood culture, which complicates the diagnosis, treatment, and prognosis of COVID-19, and even exacerbates the severity of disease symptoms and increases mortality rates. However, the status and impact of bacterial co-infections during the COVID-19 pandemic have not been properly studied. Recently, the amount of literature on the co-infection of SARS-CoV-2 and bacteria has gradually increased, enabling a comprehensive discussion on this type of co-infection. In this study, we focus on bacterial infections in the respiratory system and blood of patients with COVID-19 because these infection types significantly affect the severity and mortality of COVID-19. Furthermore, the progression of COVID-19 has markedly elevated the antimicrobial resistance among specific bacteria, such as Klebsiella pneumoniae, in clinical settings including intensive care units (ICUs). Grasping these resistance patterns is pivotal for the optimal utilization and stewardship of antibiotics, including fluoroquinolones. Our study offers insights into these aspects and serves as a fundamental basis for devising effective therapeutic strategies. We primarily sourced our articles from PubMed, ScienceDirect, Scopus, and Google Scholar. We queried these databases using specific search terms related to COVID-19 and its co-infections with bacteria or fungi, and selectively chose relevant articles for inclusion in our review.

Predictive signature of murine and human host response to typical and atypical pneumonia

BACKGROUND

Pneumonia due to typical bacterial, atypical bacterial and viral pathogens can be difficult to clinically differentiate. Host response-based diagnostics are emerging as a complementary diagnostic strategy to pathogen detection.

METHODS

We used murine models of typical bacterial, atypical bacterial and viral pneumonia to develop diagnostic signatures and understand the host's response to these types of infections. Mice were intranasally inoculated with Streptococcus pneumoniae, Mycoplasma pneumoniae, influenza or saline as a control. Peripheral blood gene expression analysis was performed at multiple time points. Differentially expressed genes were used to perform gene set enrichment analysis and generate diagnostic signatures. These murine-derived signatures were externally validated in silico using human gene expression data. The response to S. pneumoniae was the most rapid and robust.

RESULTS

Mice infected with M. pneumoniae had a delayed response more similar to influenza-infected animals. Diagnostic signatures for the three types of infection had 0.94-1.00 area under the receiver operator curve (auROC). Validation in five human gene expression datasets revealed auROC of 0.82-0.96.

DISCUSSION

This study identified discrete host responses to typical bacterial, atypical bacterial and viral aetiologies of pneumonia in mice. These signatures validated well in humans, highlighting the conserved nature of the host response to these pathogen classes.

Decoding viral and host microRNA signatures in airway-derived biosamples: Insights for biomarker discovery in viral respiratory infections

The global public health crisis caused by the COVID-19 pandemic has intensified the global concern regarding viral respiratory tract infections. Despite their considerable impact on health, society and the economy, effective management of these conditions remains a significant challenge. Integrating high-throughput analyses is pivotal for early detection, prognostication of adverse outcomes, elucidating pathogenetic pathways and developing therapeutic approaches. In recent years, microRNAs (miRNAs), a subset of small noncoding RNAs (ncRNAs), have emerged as promising tools for molecular phenotyping. Current evidence suggests that miRNAs could serve as innovative biological markers, aiding in informed medical decision-making. The cost-effective quantification of miRNAs in standardized samples using techniques routinely employed in clinical laboratories has become feasible. In this context, samples obtained from the airways represent a valuable source of information due to their direct exposure to the infectious agent and host response within the respiratory tract. This review explores viral and host miRNA profiling in airway-derived biosamples as a source of molecular information to guide patient management, with a specific emphasis on SARS-CoV-2 infection.

Deep Learning for Pneumonia Detection in Chest X-ray Images: A Comprehensive Survey

This paper addresses the significant problem of identifying the relevant background and contextual literature related to deep learning (DL) as an evolving technology in order to provide a comprehensive analysis of the application of DL to the specific problem of pneumonia detection via chest X-ray (CXR) imaging, which is the most common and cost-effective imaging technique available worldwide for pneumonia diagnosis. This paper in particular addresses the key period associated with COVID-19, 2020-2023, to explain, analyze, and systematically evaluate the limitations of approaches and determine their relative levels of effectiveness. The context in which DL is applied as both an aid to and an automated substitute for existing expert radiography professionals, who often have limited availability, is elaborated in detail. The rationale for the undertaken research is provided, along with a justification of the resources adopted and their relevance. This explanatory text and the subsequent analyses are intended to provide sufficient detail of the problem being addressed, existing solutions, and the limitations of these, ranging in detail from the specific to the more general. Indeed, our analysis and evaluation agree with the generally held view that the use of transformers, specifically, vision transformers (ViTs), is the most promising technique for obtaining further effective results in the area of pneumonia detection using CXR images. However, ViTs require extensive further research to address several limitations, specifically the following: biased CXR datasets, data and code availability, the ease with which a model can be explained, systematic methods of accurate model comparison, the notion of class imbalance in CXR datasets, and the possibility of adversarial attacks, the latter of which remains an area of fundamental research.

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

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

Comparison of Real-time Polymerase Chain Reaction and Culture for Targeting Pathogens in Pediatric Severe Community-Acquired Pneumonia

Objective

This study aims to determine the frequency of pathogen detection by real-time polymerase chain reaction (PCR), the frequency of pathogen isolation by culture; and compare the value of real-time PCR and culture of nasopharyngeal aspiration samples in patients with severe community-acquired pneumonia (sCAP).

Materials and Methods

It was a prospective and descriptive study. All pediatric patients diagnosed with sCAP were performed real-time PCR and culture of nasopharyngeal aspiration samples.

Results

A total of 336 patient samples were obtained from children with sCAP. Real-time PCR detected pathogens in 312 patients (92.9%), while culture isolated bacteria in 228 patients (67.9%). Coinfections were reported in 279 cases (83.0%) through real-time PCR. The frequency of agreement between culture and real-time PCR was quite high (P < .001).

Conclusion

Real-time PCR demonstrated more ability for detecting microorganisms than culture. This finding highlighted the value of real-time PCR for targeting pathogens in children with sCAP, particularly in cases involving complex pathogens or those requiring timely identification.

Are Mycoplasma pneumoniae coinfections frequent in COVID-19 patients? A systematic review

Understanding the proportion of SARS-CoV-2 patients with Mycoplasmapneumoniae coinfection is crucial for treating patients suffering from coronavirus disease (COVID-19), help to ensure responsible use of antibiotics and minimize the negative consequences of overuse. In addition, this knowledge could have an impact on empirical antibiotic management guidelines for patients with COVID-19. This systematic review aimed to identify the prevalence of M. pneumoniae in patients with coronavirus disease 2019 (COVID-19). A bibliographic search of studies published in Spanish or English was conducted using the PubMed search engine. Fourteen articles from different continents (America, Asia and Europe) were included, involving a total of 5855 patients in these studies. The mean age of COVID-19 patients with M. pneumoniae was 48 years old (range 1-107), most of whom were male. The detection of laboratory-confirmed M. pneumoniae infection varied between 0 and 33.3%. Most of patients referred fever, cough, and dyspnea, and received empirical antibiotic treatment. Bacterial coinfection was not associated with increased ICU admission and mortality. The prevalence of coinfection showed extremely dissimilar figures according to the population studied and diagnostic criteria. However, it is important to develop Latin American studies, given the heterogeneity observed in the studies conducted in different countries. Standardized definitions should be developed in order to be able to assess the impact of coinfections in patients with a diagnosis of COVID-19.

Differential associations of fine and coarse particulate air pollution with cause-specific pneumonia mortality: A nationwide, individual-level, case-crossover study

BACKGROUND

The connections between fine particulate matter (PM2.5) and coarse particulate matter (PM2.5-10) and daily mortality of viral pneumonia and bacterial pneumonia were unclear.

OBJECTIVES

To distinguish the connections between PM2.5 and PM2.5-10 and daily mortality due to viral pneumonia and bacterial pneumonia.

METHODS

Using a comprehensive national death registry encompassing all areas of mainland China, we conducted a case-crossover investigation from 2013 to 2019 at an individual level. Residential daily particle concentrations were evaluated using satellite-based models with a spatial resolution of 1 km. To analyze the data, we employed the conditional logistic regression model in conjunction with polynomial distributed lag models.

RESULTS

We included 221,507 pneumonia deaths in China. Every interquartile range (IQR) elevation in concentrations of PM2.5 (lag 0-2 d, 37.6 μg/m3) was associated with higher magnitude of mortality for viral pneumonia (3.03%) than bacterial pneumonia (2.14%), whereas the difference was not significant (p-value for difference = 0.38). An IQR increase in concentrations of PM2.5-10 (lag 0-2 d, 28.4 μg/m3) was also linked to higher magnitude of mortality from viral pneumonia (3.06%) compared to bacterial pneumonia (2.31%), whereas the difference was not significant (p-value for difference = 0.52). After controlling for gaseous pollutants, their effects were all stable; however, with mutual adjustment, the associations of PM2.5 remained, and those of PM2.5-10 were no longer statistically significant. Greater magnitude of associations was noted in individuals aged 75 years and above, as well as during the cold season.

CONCLUSION

This nationwide study presents compelling evidence that both PM2.5 and PM2.5-10 exposures could increase pneumonia mortality of viral and bacterial causes, highlighting the more robust effects of PM2.5 and somewhat higher sensitivity of viral pneumonia.

The Role of the Nrf2 Pathway in Airway Tissue Damage Due to Viral Respiratory Infections

Respiratory viruses constitute a significant cause of illness and death worldwide. Respiratory virus-associated injuries include oxidative stress, ferroptosis, inflammation, pyroptosis, apoptosis, fibrosis, autoimmunity, and vascular injury. Several studies have demonstrated the involvement of the nuclear factor erythroid 2-related factor 2 (Nrf2) in the pathophysiology of viral infection and associated complications. It has thus emerged as a pivotal player in cellular defense mechanisms against such damage. Here, we discuss the impact of Nrf2 activation on airway injuries induced by respiratory viruses, including viruses, coronaviruses, rhinoviruses, and respiratory syncytial viruses. The inhibition or deregulation of Nrf2 pathway activation induces airway tissue damage in the presence of viral respiratory infections. In contrast, Nrf2 pathway activation demonstrates protection against tissue and organ injuries. Clinical trials involving Nrf2 agonists are needed to define the effect of Nrf2 therapeutics on airway tissues and organs damaged by viral respiratory infections.

Prevalence and predictors of antibiotic prescription among patients hospitalized with viral lower respiratory tract infections in Southern Province, Sri Lanka

BACKGROUND

Antimicrobial overprescription is common for lower respiratory tract infections (LRTI), as viral and bacterial infections generally present with similar clinical features. Overprescription is associated with downstream antimicrobial resistance. This study aims to identify the prevalence and predictors of antibiotic prescription among patients hospitalized with viral LRTI.

METHODS

A prospective cohort study was conducted among patients aged ≥1 year hospitalized with viral LRTI in a tertiary care hospital in Southern Province, Sri Lanka from 2018-2021. Demographic, clinical, and laboratory data were recorded. Nasopharyngeal and blood samples were collected for multiplex polymerase chain reaction testing for 21 respiratory pathogens and procalcitonin (PCT) detection, respectively. Demographic and clinical features associated with antibiotic prescription were identified using Chi Square and t-tests; significant variables (p<0.05) were further included in multivariable logistic regression models. The potential impact of biomarker testing on antibiotic prescription was simulated using standard c-reactive protein (CRP) and PCT cut-offs.

RESULTS

Of 1217 patients enrolled, 438 (36.0%) had ≥1 respiratory virus detected, with 48.4% of these patients being male and 30.8% children. Influenza A (39.3%) and human rhinovirus/ enterovirus (28.3%) were most commonly detected. A total of 114 (84.4%) children and 266 (87.8%) adults with respiratory viruses were treated with antibiotics. Among children, neutrophil percentage (median 63.6% vs 47.6%, p = 0.04) was positively associated with antibiotic prescription. Among adults, headache (60.6% vs 35.1%, p = 0.003), crepitations/crackles (55.3% vs 21.6%, p<0.001), rhonchi/wheezing (42.9% vs 18.9%, p = 0.005), and chest x-ray opacities (27.4% vs 8.1%, p = 0.01) were associated with antibiotic prescription. Access to CRP and procalcitonin test results could have potentially decreased inappropriate antibiotic prescription in this study by 89.5% and 83.3%, respectively.

CONCLUSIONS

High proportions of viral detection and antibiotic prescription were observed among a large inpatient cohort with LRTI. Increased access to point-of-care biomarker testing may improve antimicrobial prescription.

Determinants of radiological patterns and severity in immunocompromised adults with Metapneumovirus infection

BACKGROUND

Human Metapneumovirus (HMPV) belongs to the Pneumoviridae family and is responsible for respiratory infections. Mild infections are well-recognized in children, while its precise impact in various categories of immunocompromised adults has not been well addressed.

RESEARCH QUESTION

We retrospectively studied HMPV infections in immunocompromised adults followed in two large French university medical centers.

STUDY DESIGN AND METHODS

We identified immunocompromised adults with positive HMPV Polymerase Chain Reaction (PCR) for 36 months and reviewed their medical charts. For lung transplant recipients (LTR), FEV1 was collected at baseline, during and after infection. Imaging was centralized and chest involvement was categorized by dominant CT patterns. We compared severe patients (requiring oxygen or ventilation) and non hypoxemic patients.

RESULTS

Seventy-two patients were included, 27 were LTR, 25 had a hematological malignancy or were hematopoietic stem cell recipients, 20 had another immunocompromised status. Twenty patients (28%) presented a hypoxemic infection, requiring hospitalization and intensive care units transfers in 50/72 (69.4%) and 9/72 (12.5%) respectively, with only one death. Hypoxemia was less pronounced in LTRs (p = 0.014). Finally, age and dyspnea remained independent factors associated with hypoxemia (p < 0.005). The most frequent radiological patterns were bronchopneumonia (34.2%) and bronchiolitis (39.5% and 64.3% in the overall population and in LTRs respectively, p = 0.045). FEV1 improved in LTRs at one month and 85% had recovered their baseline FEV1 within 6 months.

INTERPRETATIONS

In immunocompromised adults, HMPV infections required frequent hospitalizations and ICU transfers, while mortality is low. In LTRs, bronchiolitis pattern was predominant with short and long-term favorable outcome.

A ternary correlation multi-symptom network strategy based on in vivo chemical profile identification and metabolomics to explore the molecular basis of Ephedra herb against viral pneumonia

Ephedra herb (EH), an important medicine prescribed in herbal formulas by Traditional Chinese Medicine practitioners, has been widely used in the treatment of viral pneumonia in China. However, the molecular basis of EH in viral pneumonia remains unclear. In this study, a ternary correlation multi-symptom network strategy was established based on in vivo chemical profile identification and metabolomics to explore the molecular basis of EH against viral pneumonia. Results showed that 143 compounds of EH and 70 prototype components were identified in vivo. EH could reduce alveolar-capillary barrier disruption in rats with viral pneumonia and significantly downregulate the expression of inflammatory factors and bronchoalveolar lavage fluid. Plasma metabolomics revealed that EH may be involved in the regulation of arachidonic acid, tryptophan, tyrosine, nicotinate, and nicotinamide metabolism. The multi-symptom network showed that 12 compounds have an integral function in the treatment of viral pneumonia by intervening in many pathways related to viruses, immunity and inflammation, and lung injury. Further verification demonstrated that sinapic acid and frambinone can regulate the expression of related genes. It has been shown to be a promising representative of the pharmacological constituents of ephedra.

DIAMMONIUM GLYCYRRHIZINATE INHIBITED INFLAMMATORY RESPONSE AND MODULATED SERUM METABOLISM IN POLY(I:C)-INDUCED PNEUMONIA MODEL MICE

ABSTRACT

Currently, the coronavirus disease 2019 (COVID-19) is becoming a serious threat to human health worldwide. Therefore, there is a great need to develop effective drugs against viral pneumonia. Diammonium glycyrrhizinate (DG), derived from Glycyrrhiza glabra L., has been demonstrated with significant anti-inflammatory properties. However, the therapeutic effects and mechanisms of DG on pneumonia require further clarification. In this study, mice received intratracheal injection of polyinosinic-polycytidylic acid (poly(I:C)) to induce pneumonia and were treated with DG. First, we evaluated the therapeutic potential of DG on poly(I:C)-induced pneumonia. Second, the anti-inflammatory and antioxidative activities and the impact of DG on the toll-like receptor 3 (TLR3) pathway were investigated. Third, the mechanism of DG was analyzed through untargeted metabolomics techniques. Our results revealed that DG intervention decreased permeability and reduced abnormal lung alterations in poly(I:C)-induced pneumonia model mice. DG intervention also downregulated cytokine levels in bronchoalveolar lavage fluid. Moreover, DG treatment inhibited the activation of TLR3 pathway. Furthermore, untargeted metabolomics analysis revealed that DG intervention could modulate serum metabolites involved in amino and nucleotide sugar metabolism, fructose and mannose metabolism, tyrosine metabolism, and phenylalanine, tyrosine, and tryptophan biosynthesis pathways. In conclusion, our study showed that DG could ameliorate poly(I:C)-induced pneumonia by inactivating the TLR3 pathway and affecting amino and nucleotide sugar, fructose and mannose metabolism, as well as tryptophan, phenylalanine, and tyrosine biosynthesis.

Detection method of viral pneumonia imaging features based on CT scan images in COVID-19 case study

This study aims to automatically analyze and extract abnormalities in the lung field due to Coronavirus Disease 2019 (COVID-19). Types of abnormalities that can be detected are Ground Glass Opacity (GGO) and consolidation. The proposed method can also identify the location of the abnormality in the lung field, that is, the central and peripheral lung area. The location and type of these abnormalities affect the severity and confidence level of a patient suffering from COVID-19. The detection results using the proposed method are compared with the results of manual detection by radiologists. From the experimental results, the proposed system can provide an average error of 0.059 for the severity score and 0.069 for the confidence level. This method has been implemented in a web-based application for general users.•A method to detect the appearance of viral pneumonia imaging features, namely Ground Glass Opacity (GGO) and consolidation on the chest Computed Tomography (CT) scan images.•This method can separate the lung field to the right lung and the left lung, and it also can identify the detected imaging feature's location in the central or peripheral of the lung field.•Severity level and confidence level of the patient's suffering are measured.

Value of a secretomic approach for distinguishing patients with COVID-19 viral pneumonia among patients with respiratory distress admitted to intensive care unit

In intensive care units, COVID-19 viral pneumonia patients (VPP) present symptoms similar to those of other patients with Nonviral infection (NV-ICU). To better manage VPP, it is therefore interesting to better understand the molecular pathophysiology of viral pneumonia and to search for biomarkers that may clarify the diagnosis. The secretome being a set of proteins secreted by cells in response to stimuli represents an opportunity to discover new biomarkers. The objective of this study is to identify the secretomic signatures of VPP with those of NV-ICU. Plasma samples and clinical data from NV-ICU (n = 104), VPP (n = 30) or healthy donors (HD, n = 20) were collected at Nantes Hospital (France) upon admission. Samples were enriched for the low-abundant proteins and analyzed using nontarget mass spectrometry. Specifically deregulated proteins (DEP) in VPP versus NV-ICU were selected. Combinations of 2 to 4 DEPs were established. The differences in secretome profiles of the VPP and NV-ICU groups were highlighted. Forty-one DEPs were specifically identified in VPP compared to NV-ICU. We describe five of the best combinations of 3 proteins (complement component C9, Ficolin-3, Galectin-3-binding protein, Fibrinogen alpha, gamma and beta chain, Proteoglycan 4, Coagulation factor IX and Cdc42 effector protein 4) that show a characteristic receptor function curve with an area under the curve of 95.0%. This study identifies five combinations of candidate biomarkers in VPP compared to NV-ICU that may help distinguish the underlying causal molecular alterations.

Model-based disease mapping using primary care registry data

BACKGROUND

Spatial modeling of disease risk using primary care registry data is promising for public health surveillance. However, it remains unclear to which extent challenges such as spatially disproportionate sampling and practice-specific reporting variation affect statistical inference.

METHODS

Using lower respiratory tract infection data from the INTEGO registry, modeled with a logistic model incorporating patient characteristics, a spatially structured random effect at municipality level, and an unstructured random effect at practice level, we conducted a case and simulation study to assess the impact of these challenges on spatial trend estimation.

RESULTS

Even with spatial imbalance and practice-specific reporting variation, the model performed well. Performance improved with increasing spatial sample balance and decreasing practice-specific variation.

CONCLUSION

Our findings indicate that, with correction for reporting efforts, primary care registries are valuable for spatial trend estimation. The diversity of patient locations within practice populations plays an important role.

Pulmonary Infection

Pneumonia is a significant cause of morbidity and mortality in the community and hospital settings. Bacterial, viral, mycobacterial, and fungal pathogens are all potential causative agents of pulmonary infection. Chest radiographs and computed tomography are frequently utilized in the assessment of pneumonia. Learning the imaging patterns of different potential organisms allows the radiologist to formulate an appropriate differential diagnosis. An organism-based approach is used to discuss the imaging findings of different etiologies of pulmonary infection.

Secondary pneumonia from herpes simplex is not so simple: A case report

A 33-year-old female was admitted for community-acquired pneumonia. On presentation, she was tachypneic and tachycardic and leukocytosis at 28,900/µL. Chest imaging showed dense consolidation on the right upper lobe. Due to refractory worsening respiratory failure, she was intubated with mechanical ventilation. Initial bronchoscopy with culture data was negative. Extracorporeal membrane oxygenation was pursued on the fourth day. Repeat bronchoscopy revealed targetoid ulcerative lesions with erythema in the right middle, lower lobes and left lower lobe. We describe a case of herpes simplex virus pneumonia in an immunocompetent patient that occurred in the setting of acute bacterial infection.

Drugs targeting CMPK2 inhibit pyroptosis to alleviate severe pneumonia caused by multiple respiratory viruses

Severe pneumonia caused by respiratory viruses has become a major threat to humans, especially with the SARS-CoV-2 outbreak and epidemic. The aim of this study was to investigate the universal molecular mechanism of severe pneumonia induced by multiple respiratory viruses and to search for therapeutic strategies targeting this universal molecular mechanism. The common differential genes of four respiratory viruses, including respiratory syncytial virus (RSV), rhinovirus, influenza, and SARS-CoV-2, were screened by GEO database, and the hub gene was obtained by Sytohubba in Cytoscape. Then, the effect of hub genes on inflammasome and pyrodeath was investigated in the model of RSV infection in vitro and in vivo. Finally, through virtual screening, drugs targeting the hub gene were obtained, which could alleviate severe viral pneumonia in vitro and in vivo. The results showed that CMPK2 is one of the hub genes after infection by four respiratory viruses. CMPK2 activates the inflammasome by activating NLRP3, and promotes the releases of inflammatory factors interleukin (IL)-1β and IL-18 to induce severe viral pneumonia. Z25 and Z08 can reduce the expression level of CMPK2 mRNA and protein, thereby inhibiting NLRP3 and alleviating the development of severe viral pneumonia. In conclusion, the inflammatory response mediated by CMPK2 is the common molecular mechanism of severe pneumonia induced by viral infection, and Z25 and Z08 can effectively alleviate viral infection and severe pneumonia through this mechanism.

SARS-CoV-2 co-detection with influenza and human respiratory syncytial virus in Ethiopia: Findings from the severe acute respiratory illness (SARI) and influenza-like illness (ILI) sentinel surveillance, January 01, 2021, to June 30, 2022

SARS-CoV-2 co-infection with the influenza virus or human respiratory syncytial virus (RSV) may complicate its progress and clinical outcomes. However, data on the co-detection of SARS-CoV-2 with other respiratory viruses are limited in Ethiopia and other parts of Africa to inform evidence-based response and decision-making. We analyzed 4,989 patients' data captured from the national severe acute respiratory illness (SARI) and influenza-like illness (ILI) sentinel surveillance sites over 18 months period from January 01, 2021, to June 30, 2022. Laboratory specimens were collected from the patients and tested for viral respiratory pathogens by real-time, reverse transcription polymerase chain reaction (RT-PCR) at the national influenza center. The median age of the patients was 14 years (IQR: 1-35 years), with a slight preponderance of them being at the age of 15 to less than 50 years. SARS-CoV-2 was detected among 459 (9.2%, 95% CI: 8.4-10.0) patients, and 64 (1.3%, 95% CI: 1.0-1.6) of SARS-CoV-2 were co-detected either with Influenza virus (54.7%) or RSV (32.8%) and 12.5% were detected with both of the viruses. A substantial proportion (54.7%) of SARS-CoV-2 co-detection with other respiratory viruses was identified among patients in the age group from 15 to less than 50 years. The multivariable analysis found that the odds of SARS-CoV-2 co-detection was higher among individuals with the age category of 20 to 39 years as compared to those less than 20 years old (AOR: 1.98, 95%CI:1.15-3.42) while the odds of SARS-CoV-2 co-detection was lower among cases from other regions of the country as compared to those from Addis Ababa (AOR:0.16 95%CI:0.07-0.34). Although the SARS-CoV-2 co-detection with other respiratory viral pathogens was minimal, the findings of this study underscore that it is critical to continuously monitor the co-infections to reduce transmission and improve patient outcomes, particularly among the youth and patients with ILI.

A neonatal piglet model reveals interactions between nasal microbiota and influenza A virus pathogenesis

While vaccination and therapeutics for prevention/treatment of influenza are available, new strategies are needed to combat influenza disease in susceptible populations, particularly young children and newborns. Host associated microbiota play an important role in modulating the virulence of numerous pathogens, including the influenza A virus. In this study, we examined microbiome-influenza interactions in a neonatal piglet model system. The nasal microbiome of newborn piglets was longitudinally sampled before and after intranasal infection with recombinant viruses expressing hemagglutinins (HAs) derived from distinct zoonotic H1 subtypes. We found that viruses expressing different parental HAs manifested unique patterns of pathogenicity, and varied impacts on microbial community diversity. Despite these virus specific differences, a consistent microbial signature of viral infection was detected. Our results indicate that influenza A virus infection associates with the restructuring of nasal microbiome and such shifts in microbial diversity may contribute to outcomes of viral infection in neonatal piglets.

Clinical Characteristics and Microorganisms Isolated in Community-Acquired Pneumonia in the COVID-19 Period

Introduction

Community-acquired pneumonia is a leading cause of mortality and hospital admissions. The aetiology remains unknown in 30-65% of the cases. Molecular tests are available for multiple pathogen detection and are under research to improve the causal diagnosis.

Methods

We carried out a prospective study to describe the clinical characteristics and aetiology of community-acquired pneumonia during the COVID-19 pandemic and to assess the diagnostic effectivity of the microbiological tests, including a molecular test of respiratory pathogens (FilmArray™ bioMérieux).

Results

From the 1st of February 2021 until the 31st of March 2022, 225 patients were included. Failure in microorganism identification occurred in approximately 70% of patients. Streptococcus pneumoniae was the most common isolate. There were 5 cases of viral pneumonia. The tested FilmArray exhibited a low positivity rate of 7% and mainly aided in the diagnosis of viral coinfections.

Conclusions

Despite our extensive diagnostic protocol, there is still a low rate of microorganism identification. We have observed a reduction in influenza and other viral pneumoniae during the COVID-19 pandemic. Having a high NEWS2 score on arrival at the emergency department, an active oncohematological disease or chronic neurological conditions and a positive microbiological test result were related to worse outcomes. Further research is needed to determine the role of molecular tests in the microbiological diagnosis of pneumonia.

Analysis of viral pneumonia and risk factors associated with severity of influenza virus infection in hospitalized patients from 2012 to 2016

BACKGROUND

Influenza viruses cause pneumonia in approximately one-third of cases, and pneumonia is an important cause of death. The aim was to identify risk factors associated with severity and those that could predict the development of pneumonia.

METHODS

This retrospective, observational study included all adult patients with confirmed influenza virus infection admitted to Son Espases University Hospital during four influenza seasons in Spain (October to May) from to 2012-2016.

RESULTS

Overall, 666 patients with laboratory-confirmed influenza were included, 93 (14%) of which were severe; 73 (10.9%) were admitted to Intensive Care Unit (ICU), 39 (5.8%) died, and 185 (27.7%) developed pneumonia. Compared to less severe cases, patients with severe disease: were less vaccinated (40% vs. 28%, p = 0.021); presented with more confusion (26.9% vs. 6.8%), were more hypoxemic (Horowitz index (PaO2/FiO2) 261 vs. 280), had higher C-reactive protein (CRP) (12.3 vs. 4.0), had more coinfections (26.8% vs. 6.3%) and had more pleural effusion (14% vs. 2.6%) (last six all p < 0.001). Risk factors significantly associated with severity were pneumonia [OR (95% CI) = 4.14 (2.4-7.16)], history of heart disease (1.84, 1.03-3.28), and confusion at admission (4.99, 2.55-9.74). Influenza vaccination was protective (0.53, 0.28-0.98). Compared to those without pneumonia, the pneumonia group had higher CRP (11.3 vs. 4.0, p < 0.001), lower oxygen saturation (92% vs. 94%, p < 0.001), were more hypoxic (PaO2/FiO2 266 vs. 281, p < 0.001), and incurred more mechanical ventilation, septic shock, admission to the ICU, and deaths (all four p < 0.001). Higher CRP and lower oxygen saturation were independent variables for predicting the development of pneumonia.

CONCLUSIONS

Pneumonia, history of heart disease, confusion and no influenza vaccination were independent variables to present complications in patients admitted with influenza infection.

Clinical epidemiology of adenovirus pneumonia among Chinese hospitalized children

Adenovirus pneumonia is a prevalent form of community-acquired pneumonia among children. Research on the epidemiology and economic burden of this disease is crucial for public health, yet comprehensive data remains scarce, making it crucial to highlight on this topic. In this study, the data were extracted from the face sheet of discharge medical records collected from 26 tertiary children's hospitals from January 2016 to December 2021. In total, 1854 children with laboratory-confirmed adenovirus pneumonia were hospitalized, accounting for 0.13% of the total number of hospitalized for pneumonia in the database during the period. In addition, this figure represents a meager 0.027% when compared to the total number of hospitalized children. The male-to-female ratio was 1.78:1. The 1-3-year age group had the highest number of inpatients for adenoviral pneumonia and the largest proportion of the total hospitalizations in the same age group. Overall, winter is the primary season for the prevalence of adenovirus pneumonia, however, in southern China, there are two peak seasons, winter and summer. Although patients with 3/4 adenovirus pneumonia had no significant complications, some patients had complications such as respiratory failure, diarrhea, and myocardial damage. The median length of stay of adenovirus pneumonia was 8 d [interquartile range (IQR) 6-11], and the median hospitalization cost was 1293.83 United States dollars (IQR 811.81-2472.51). These valuable epidemiological insights into adenovirus pneumonia in Chinese children can help direct the development of targeted prevention and control strategies and surveillance measures for HAdV infections in this demographic.

Interferon lambda in respiratory viral infection: immunomodulatory functions and antiviral effects in epithelium

Type III interferon (IFN-λ), a new member of the IFN family, was initially considered to possess antiviral functions similar to those of type I interferon, both of which are induced via the JAK/STAT pathway. Nevertheless, recent findings demonstrated that IFN-λ exerts a nonredundant antiviral function at the mucosal surface, preferentially produced in epithelial cells in contrast to type I interferon, and its function cannot be replaced by type I interferon. This review summarizes recent studies showing that IFN-λ inhibits the spread of viruses from the cell surface to the body. Further studies have found that the role of IFN-λ is not only limited to the abovementioned functions, but it can also can exert direct and/or indirect effects on immune cells in virus-induced inflammation. This review focuses on the antiviral activity of IFN-λ in the mucosal epithelial cells and its action on immune cells and summarizes the pathways by which IFN-λ exerts its action and differentiates it from other interferons in terms of mechanism. Finally, we conclude that IFN-λ is a potent epidermal antiviral factor that enhances the respiratory mucosal immune response and has excellent therapeutic potential in combating respiratory viral infections.

Label correlation guided discriminative label feature learning for multi-label chest image classification

BACKGROUND AND OBJECTIVE

Multi-label Chest X-ray (CXR) images often contain rich label relationship information, which is beneficial to improve classification performance. However, because of the intricate relationships among labels, most existing works fail to effectively learn and make full use of the label correlations, resulting in limited classification performance. In this study, we propose a multi-label learning framework that learns and leverages the label correlations to improve multi-label CXR image classification.

METHODS

In this paper, we capture the global label correlations through the self-attention mechanism. Meanwhile, to better utilize label correlations for guiding feature learning, we decompose the image-level features into label-level features. Furthermore, we enhance label-level feature learning in an end-to-end manner by a consistency constraint between global and local label correlations, and a label correlation guided multi-label supervised contrastive loss.

RESULTS

To demonstrate the superior performance of our proposed approach, we conduct three times 5-fold cross-validation experiments on the CheXpert dataset. Our approach obtains an average F1 score of 44.6% and an AUC of 76.5%, achieving a 7.7% and 1.3% improvement compared to the state-of-the-art results.

CONCLUSION

More accurate label correlations and full utilization of the learned label correlations help learn more discriminative label-level features. Experimental results demonstrate that our approach achieves exceptionally competitive performance compared to the state-of-the-art algorithms.

Multiplex PCR and Antibiotic Use in Children with Community-Acquired Pneumonia

Antibiotics are frequently prescribed to children with pneumonia, although viruses are responsible for most cases. We aimed to evaluate the impact of multiplex polymerase chain reaction (mPCR) on antibiotic use. We conducted a prospective study of children under 14 years of age admitted for suspected viral pneumonia, from October 2019 to June 2022 (except March-November 2020). A mPCR respiratory panel (FilmArray® 2plus, bioMérieux, Marcy-l'Étoile, France) was performed within 72 h of admission. Patients with positive reverse transcription PCR for respiratory syncytial virus, influenza, or SARS-CoV-2 were excluded. We compared the patients with historical controls (2017-2018) who had suspected viral pneumonia but did not undergo an aetiological study. We included 64 patients and 50 controls, with a median age of 26 months. The respiratory panel detected viral pathogens in 55 patients (88%), including 17 (31%) with co-infections. Rhinovirus/enterovirus (n = 26) and human metapneumovirus (n = 22) were the most common pathogens, followed by adenovirus and parainfluenza (n = 10). There were no statistically significant differences in the total antibiotic consumption (83% of cases and 86% of controls) or antibiotics given for ≥72 h (58% vs. 66%). Antibiotics were prescribed in 41% of the cases and 72% of the controls at discharge (p = 0.001). Ampicillin was the most commonly prescribed antibiotic among the patients (44% vs. 18% for controls, p = 0.004), while azithromycin was the most commonly prescribed among the controls (19% vs. 48% for patients and controls, respectively; p = 0.001). Our findings underscore the need for additional interventions alongside molecular diagnosis to reduce antibiotic usage in paediatric community-acquired pneumonia.

Molecular mechanism of rhinovirus escape from the Pyrazolo[3,4-d]pyrimidine capsid-binding inhibitor OBR-5-340 via mutations distant from the binding pocket: Derivatives that brake resistance

Rhinoviruses (RVs) cause the common cold. Attempts at discovering small molecule inhibitors have mainly concentrated on compounds supplanting the medium chain fatty acids residing in the sixty icosahedral symmetry-related hydrophobic pockets of the viral capsid of the Rhinovirus-A and -B species. High-affinity binding to these pockets stabilizes the capsid against structural changes necessary for the release of the ss(+) RNA genome into the cytosol of the host cell. However, single-point mutations may abolish this binding. RV-B5 is one of several RVs that are naturally resistant against the well-established antiviral agent pleconaril. However, RV-B5 is strongly inhibited by the pyrazolopyrimidine OBR-5-340. Here, we report on isolation and characterization of RV-B5 mutants escaping OBR-5-340 inhibition and show that substitution of amino acid residues not only within the binding pocket but also remote from the binding pocket hamper inhibition. Molecular dynamics network analysis revealed that strong inhibition occurs when an ensemble of several sequence stretches of the capsid proteins enveloping OBR-5-340 move together with OBR-5-340. Mutations abrogating this dynamic, regardless of whether being localized within the binding pocket or distant from it result in escape from inhibition. Pyrazolo [3,4-d]pyrimidine derivatives overcoming OBR-5-340 escape of various RV-B5 mutants were identified. Our work contributes to the understanding of the properties of capsid-binding inhibitors necessary for potent and broad-spectrum inhibition of RVs.

Dynamics of platelet parameters in children with severe community-acquired pneumonia between viral and bacterial infections

Background

Changes in platelet parameters may vary according to the different pathogens. However, little is known about the differences in platelet parameters in children with severe community-acquired pneumonia (CAP) children of viral and bacterial infections.

Methods

This was a single-center retrospective study that included 156 children with severe CAP. Dynamic changes in platelet parameters, including platelet count (PLT), mean platelet volume (MPV), platelet distribution width (PDW) and plateletcrit (PCT), were recorded at 24 h, 48 h, 72 h, and day 7 of admission, as well as at discharge.

Results

At 72 h of admission, PLT in the viral infection group was significantly lower than that in the bacterial infection and bacterial and viral coinfections group. Meanwhile, the curve of changes in PLT (ΔPLT) in the viral infection group was clearly separated from the other two groups at this time point. Receiver operating characteristic (ROC) analysis showed that PLT at 72 h of admission could assist in distinguishing bacterial and viral infections in severe pneumonia children with the area under curve (AUC) value of 0.683 [95% confidence interval (CI): 0.561-0.805, P=0.007]. However, its sensitivity and specificity were not high, at 68% and 65%, respectively.

Conclusions

Although the diagnostic value of platelet parameters in bacterial and viral infection in children with severe CAP is limited, they are still expected to be combined with other indicators to provide a reference for timely treatment.