Search Results (260)

Molecular methods allow for a rapid identification of the main causative agents of pneumonia along with the most frequent resistance genes. Prolonged broad-spectrum antibiotic therapy without microbiological evidence of infection drives antimicrobial resistance. We evaluated if the result provided by the molecular method is helpful for antimicrobial de-escalation. All respiratory samples collected and directly processed via Real-Time PCR from patients with suspected pneumonia, of whom clinical data were available, were included in this study. In 82 patients out of a total of 174 (47.1%), antimicrobial therapy was modified after the molecular test, and in 28/82 (34.1%), antimicrobial de-escalation was carried out. Among the 92 patients in whom therapy was not modified, 33 (35.9%) were did not receive any antimicrobial therapy before the molecular test and no antibiotics were prescribed after the test. Therefore, in 61 (28 + 33) out of the 174 (35%) patients, unnecessary antimicrobials were discontinued or avoided. The syndromic panel used at our institution can be of help in better choosing when empiric antibiotic de-escalation therapy could be feasible. Full article

Since 2020, the Gs/Gd H5N1 influenza virus (clade 2.3.4.4b) has established itself within wild bird populations across Asia, Europe, and the Americas, causing outbreaks in wild mammals, commercial poultry, and dairy farms. The impacts on the bird populations and the agricultural industry has been significant, requiring a One Health approach to enhanced surveillance in both humans and animals. To support pandemic preparedness efforts, we evaluated the Cepheid Xpert Xpress CoV-2/Flu/RSV plus kit and the BioFire Respiratory 2.1 Panel for their ability to detect the presence of non-seasonal, zoonotic influenza A viruses, including circulating H5N1 viruses from clade 2.3.4.4b. Both assays effectively detected the presence of influenza virus in clinically-contrived nasal swab and saliva specimens at low concentrations. The results generated using the Cepheid Xpert Xpress CoV-2/Flu/RSV plus kit and the BioFire Respiratory 2.1 Panel, in conjunction with clinical and epidemiological findings provide valuable diagnostic findings that can strengthen pandemic preparedness and surveillance initiatives. Full article

In patients with respiratory diseases, a panel of markers is often used to assess disease severity and progression. Here we test whether the serum lipid signature may surge as a reliable alternative marker to monitor systemic hypoxia, a frequent unfavourable outcome in acute respiratory distress syndrome (ARDS) and chronic obstructive pulmonary diseases (COPD). We recruited 9 healthy controls, 10 COPD patients, and 10 ARDS patients. Various markers related to inflammation, redox imbalance, and iron handling were measured alongside lipid profiles obtained through untargeted lipidomic analysis. The results show that serum lipids were moderately lower in COPD patients and significantly reduced in ARDS patients compared to the controls. Six lipid classes (cholesteryl esters, coenzyme Q, phosphatidylinositol, sterols, hexosylceramides, and phosphatidylethanolamine) exhibited significant changes (ANOVA p < 0.05) and correlated with the Horowitz index (P/F), suggesting their potential as markers of hypoxia severity. While conventional markers also correlated with P/F, the lipid signature was more specific and reliable. This study highlights that hypoxia in pulmonary diseases depresses circulating lipids, with certain lipid classes offering more precise predictions of hypoxia severity. Expanding this research to larger populations could support the lipid signature as a clinical tool. Full article

Climate change poses a significant threat to individuals with chronic illnesses, yet research on the psychological effects of climate change among this population remains scarce. This study’s aim was to compare levels of climate change anxiety among individuals without chronic illnesses, with cardiovascular disease, and with respiratory disease, and to examine the roles of exposure, awareness, and coping strategies in predicting anxiety. A cross-sectional survey was conducted among 522 Israeli adults recruited from a national online panel, including groups with and without chronic illnesses. Participants completed self-report questionnaires assessing climate change exposure, awareness, coping strategies, and anxiety. Analyses revealed that individuals with cardiovascular disease reported higher levels of climate change anxiety than those without a chronic illness or with respiratory disease. Across groups, greater climate change exposure and greater use of problem-focused coping were associated with higher climate change anxiety, whereas meaning-focused coping and awareness were not significant predictors. Additionally, climate change exposure predicted anxiety only among participants with respiratory disease. These findings underscore the differential psychological impact of climate change based on health status, highlighting the need for targeted interventions to address climate change anxiety among vulnerable populations. Full article

The evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its impact on public health continue to demand attention as the virus continues to evolve, demonstrating a remarkable ability to adapt to diverse selective pressures including immune responses, therapeutic treatments, and prophylactic interventions. The SARS-CoV-2 variant landscape remains dynamic, with new subvariants continuously emerging, many harboring spike protein mutations linked to immune evasion. In this study, we characterized a panel of live SARS-CoV-2 strains, including those key subvariants implicated in recent waves of infection. Our findings revealed a significant variability in mutation patterns in the spike protein across the strains analyzed. Commercial antibodies and human convalescent plasma (HCoP) samples from unvaccinated donors were ineffective in neutralizing the most recent Omicron subvariants, particularly after the emergence of JN.1 subvariant. Using human airway epithelial cells derived from healthy bronchiolar tissue (hBAEC), we established both monoinfections and coinfections involving SARS-CoV-2, Influenza A virus H1N1 (IFAV_H1N1) and Respiratory Syncytial Virus (RSV). Assessments were conducted to compare viral infectivity and the production and release of immune mediators in the apical and basolateral compartments. Notably, Omicron KP.3.1.1 subvariant induced a more pronounced cytopathic effect in hBAEC compared to its parental strain JN.1 and even surpassed the impact observed with the ancestral wild-type virus (WA1/2020, Washington strain). Furthermore, the coinfection of KP.3.1.1 subvariant with IFAV_H1N1 or RSV did not attenuate SARS-CoV-2 infectivity; instead, it significantly exacerbated the pathogenic synergy in the lung epithelium. Our study demonstrated that pro-inflammatory cytokines IL-6, IFN-β, and IL-10 were upregulated in hBAEC following SARS-CoV-2 monoinfection with recent Omicron subvariants as well as during coinfection with IFAV_H1N1 and RSV. Taken together, our findings offer new insights into the immune evasion strategies and pathogenic potential of evolving SARS-CoV-2 Omicron subvariants, as well as their interactions with other respiratory viruses, carrying important implications for therapeutic development and public health preparedness. Full article

At least three betacoronaviruses have spilled over from bats to humans and caused severe diseases, highlighting the threat of zoonotic transmission. Thus, it is important to enhance surveillance capabilities by developing tools capable of detecting a broad spectrum of bat-borne betacoronaviruses. Three monoclonal antibodies (mAbs) targeting the nucleocapsid (N) protein were generated using recombinant N proteins from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and Middle East Respiratory Syndrome Coronavirus (MERS-CoV). The cross-reactivities of these mAbs were evaluated against a panel of betacoronaviruses. Sandwich ELISAs (sELISAs) were subsequently developed to detect bat-borne betacoronaviruses that have high zoonotic potential. Among the mAbs, 7A7 demonstrated the broadest cross-reactivity, recognizing betacoronaviruses from the Sarbecovirus, Merbecovirus and Hibecovirus subgenera. The first sELISA, based on mAbs 7A7 and 6G10, successfully detected N protein in all clinical swab samples from COVID-19 patients with cycle threshold (Ct) values < 25, achieving 75% positivity overall (12/16). Using this as a reference, a second sELISA was established by pairing mAb 7A7 with mAb 8E2, which binds to multiple merbecoviruses. This assay detected the N protein of two merbecoviruses, namely the human MERS-CoV and bat-borne HKU5-CoV, at high sensitivity and has a limit of detection (LOD) that is comparable to the first sELISA used successfully to detect COVID-19 infection. These broadly reactive mAbs could be further developed into rapid antigen detection kits for surveillance in high-risk populations with close contact with wild bats to facilitate the early detection of potential zoonotic spillover events. Full article

This study explored the distribution and genetic characteristics of respiratory pathogens in outpatients with acute respiratory infections (ARIs) in Yangon, Myanmar, during the 2023 rainy season. Among 267 patients who tested negative for influenza, RSV, and SARS-CoV-2 using rapid diagnostic tests, 84.6% were positive for at least one pathogen according to a multiplex polymerase chain reaction (PCR) assay, the BioFire^® FilmArray^® Respiratory Panel 2.1. The most common viruses detected were rhinovirus/enterovirus (RV/EV) at 37.8%, respiratory syncytial virus (RSV) at 22.4%, and human metapneumovirus (hMPV) at 10.0%. These pathogens co-circulated mainly from July to September, with RV/EV consistently predominant. Symptom comparison among RV/EV-, RSV-, and hMPV-infected patients showed similar clinical features, though fever was more common in hMPV cases. Among RV/EV-positive patients, 59.3% had single infections, while 40.7% experienced co-infections, especially with RSV and adenovirus. Genotyping identified 28 types from five species, primarily RV-A and RV-C, which were genetically diverse. One EV-D68 case was also found, emphasizing its potential risk. This study underscores the genetic diversity and clinical impact of RV/EV and stresses the importance of ongoing molecular surveillance in Myanmar’s post-COVID-19 context to inform effective public health responses. Full article

Conventional diagnostic methods (CDMs) for lower respiratory infections (LRIs) have limitations in detecting causative pathogens. This study evaluates the utility of shotgun metagenomic sequencing (SMS) as a complementary diagnostic tool using bronchoalveolar lavage (BAL) fluid. Sixteen BAL fluid samples from pneumonia patients with positive CDM results—including bacterial/fungal cultures; PCR for Mycobacterium tuberculosis or cytomegalovirus; and the BioFire^® FilmArray^® Pneumonia Panel (BioFire Diagnostics LLC, Salt Lake City, UT, USA)—underwent 10 Gb SMS on the Illumina NovaSeq 6000 platform (Illumina, San Diego, CA, USA). Reads were aligned to the NCBI RefSeq database; with fungal identification further supported by internal transcribed spacer (ITS) analysis. Antibiotic resistance genes (ARGs) were annotated using the Comprehensive Antibiotic Resistance Database. Microbial reads accounted for 0.00002–0.04971% per sample. SMS detected corresponding bacteria in 63% of cases, increasing to 69% when subdominant taxa were included. Fungal reads were low; however, Candida species were identified in four samples via ITS. No viral reads were detected. ARGs meeting perfect match criteria were found in two cases. This is the first real-world study comparing SMS with CDMs, including semiquantitative PCR, in BAL fluid for LRI. SMS shows promise as a supplementary diagnostic method, with further research needed to optimize its performance and cost-effectiveness. Full article

The aim of the study was to determine the prevalence rates of respiratory pathogens using syndromic tests and also to show which respiratory viruses were detected in suspected cases, especially during and after the pandemic period. A total of 1984 different respiratory tract samples from various departments were included and studied with the QIAstat-Dx device in 2021–2023. The samples were studied with the QIAstat-Dx1 Respiratory SARS-CoV-2 Panel. The kit used was a fully automated, multiplex syndromic test that detected SARS-CoV-2 and 21 other respiratory tract pathogens. As a result of the study, the prevalence of Rhinovirus/Enterovirus (RV/EV) (18.59%), RV/EV-SARS-CoV-2 (42.74%), SARS-CoV-2 (5.04%), and Influenza A Virus (IAV) (5.59%) agents was found to be higher than other agents during the period investigated. Among the 1984 patients examined, 959 (48.33%) had a single viral agent, 156 (7.86%) had double coinfection, 11 (0.55%) had triple coinfection and 1 patient had quadruple coinfection. Nearly half of the patients had a straightforward infection, which helps clinicians in directing specific treatment methods. The study results demonstrate that during the pandemic period, the detection of respiratory pathogens such as SARS-CoV-2 and RV/EV was not only critical for accurate diagnosis but also served as an important indicator of the broader epidemiological trends in respiratory infections. The seasonal distribution showed that while RV/EV was frequently present, its coinfection with SARS-CoV-2 was notably observed only in the first trimester. In light of our findings showing high rates of SARS-CoV-2 and RV/EV detection, along with diverse patterns of coinfection in clinical samples, such comprehensive testing not only assists in rapid diagnosis but also informs public health strategies by reflecting the evolving landscape of respiratory infections in the pandemic and post-pandemic era. Full article

Background: SARS-CoV-2 infection can lead to persistent or newly emerging symptoms lasting for months, a condition known as long COVID (LC). The pathophysiology of LC remains poorly understood, with cytokine dysregulation proposed as a key mechanism, although findings across the studies have been inconsistent. Patients and methods: We conducted a longitudinal study using the Olink^® Target 96 Inflammation Panel to assess cytokines in COVID-19 (COV) patients at three months and six months post-infection. These profiles were compared with those of individuals recovering from other upper respiratory tract infections (non-COV). Additionally, we analyzed differences between individuals with LC and those who recovered from COVID-19. Predictive models for LC at three months and sixth months post-infection were developed using inflammatory markers and relevant clinical cofactors, including gender, age, BMI, hemogram, Β2-microglobulin, D-dimers, LDH, AST, ALT, Ferritin, vitamin D, CRP, and the severity of acute COVID-19 infection as classified by WHO criteria. Results: We observed a general decline in inflammatory biomarkers in post-COVID-19 patients over time, with only a few cytokines elevated (CCL4 at month 3 and CST5 at month 6) compared to non-COV controls. In LC patients, an early phase of low-grade inflammation transitioned into significant reduction in proinflammatory biomarkers compared to recovered individuals. Rather than indicating immune normalization, this pattern suggests a possible suppression or exhaustion of the immune response in the months following acute infection. Importantly, our predictive modeling demonstrated that this specific cytokine signature, in combination with acute disease severity and clinical cofactors, described well the presence of LC. Conclusions: Our findings suggest that inflammation-related biomarker dysregulation following acute SARS-CoV-2 infection evolves dynamically over a six-month period. By the sixth month, compared to the third month, the presence of LC is more accurately predicted by a combination of persistent biomarker alteration and the severity of the initial infection, as defined by WHO criteria. This represents a novel insight, as previous studies have primarily associated LC with elevated proinflammatory markers, whereas our results suggest that immune suppression or exhaustion may play a more prominent role in the later stages. Full article

Background: Children’s interstitial and diffuse lung diseases, commonly referred to as “chILDs”, include around 200 rare conditions that disrupt normal lung function. They are classified, based on etiopathogenesis, into several subgroups, having a varied and multifaceted clinical presentation depending on the type of genetic mutation present. Methods and Results: We describe the case of a late preterm newborn presenting soon after birth with respiratory distress syndrome poorly responsive to surfactant administration, in whom a targeted gene panel analysis for pulmonary congenital diseases, performed using next-generation sequencing (NGS), revealed a novel compound heterozygous variant of the ATP-Binding-Cassette-Subfamily-A-Member-3 (ABCA3) gene. A review of the literature on the subject completes our work. Conclusions: Molecular genetic analysis has become crucial for a more targeted therapeutic treatment, along with the only current curative treatment option that is lung transplantation. Full article

Background: If used in the right clinical context, PCRs carry great potential in rapidly diagnosing various infectious diseases. Objectives: We aimed to evaluate the clinical performance of four novel multiplex real-time PCR (qPCR) assays in the direct detection of pathogens in whole blood, cerebrospinal fluid, respiratory specimens, and stool samples. Methods: Spiked negative clinical specimens were used for the evaluation. Clinical samples for the comparative assessment of culture and molecular analyses were simultaneously examined. RINA^TM robotic nucleic acid isolation system and Bio-Speedy^® multiplex qPCR panels (Bioeksen R&D Technologies, Turkey), and the LightCycler^® 96 Instrument (Roche, USA) were used for the molecular testing. Results: No qPCR assays produced positive results for the samples spiked with the potential cross-reacting pathogens. The limit of detection (LOD) of the assays changed with the use of 10 and 100 pathogens/mL sample based on the target and sample type. The relative sensitivity and specificity of the assays were, respectively, 82% and 94% for blood, 97.1% and 99.3% for blood culture, 94% and 98% for stool, 96% and 97% for CSF, and 97% and 96% for respiratory specimens. Conclusions: The panels evaluated allow the direct molecular analysis of 10 samples from four clinical syndromes on the same run in 3 h with high clinical performance. The number and variety of samples in a single run enable healthcare providers to rapidly and efficiently diagnose and treat various infections. Full article

The ALEX²-test (MacroArray Diagnostics, Vienna, Austria) is a diagnostic multiplex IgE-test for the simultaneous detection of IgE to 178 allergens and 117 extracts, in addition to total IgE. Test results from more than 90 countries are stored on a GDPR-compliant cloud server for backup, customer support, and continuous postmarket surveillance. To improve the coverage of exposomes on a global scale and to further increase the sensitivity of the test, the allergen panel was updated from ALEX² to ALEX³. By mid-2023, when ALEX³ was designed, almost 400,000 real-world ALEX² test results were available. Analysing prevalences and average sIgE-levels of individual allergen preparations, coverage of extracts by components, and co-reactivity of members of the same allergen family provided a rationale for updating the array. In parallel, based on the scientific literature and clinical studies, new allergens were selected. On ALEX³, 218 allergens and 82 extracts will be represented, including 52 new allergens. Allergen preparations with low prevalence and clinical relevance, as well as redundant allergens and extracts, were discontinued. New allergens encompass, e.g., cyclophilins, alpha-gal, and additional markers from respiratory and food allergen sources. Using a large dataset of ALEX² test results exemplifies the targeted, data-driven improvement of a diagnostic IgE-macroarray. Full article

Since the World Health Organization (WHO) issued guidelines for developing a non-sputum test for active tuberculosis (TB) diagnosis that exhibits similar performance characteristics to sputum-based diagnosis, salivary diagnostic techniques have gained prominence as potential screening tools or adjuncts to existing diagnostics. We searched online databases for studies that looked at salivary diagnostic techniques. Afterwards, duplicates were removed, titles and abstracts were screened, and full-text studies were assessed for eligibility based on inclusion and exclusion criteria. The studies chosen for final analysis underwent a rigorous quality assessment following a QUADAS-2 template, and data were extracted. The primary outcome assessed the difference in mean levels of interleukins between TB+ patients and TB-controls (Hedges’ g). We then conducted two subgroup analyses: the first segregated the control group into healthy patients, and those with other respiratory diseases (ORD), and the second addressed three different interleukins separately (IL-6, IL-5, IL-17). The secondary outcome involved comparing salivary molecular diagnostic assays to WHO guidelines. This study is registered with PROSPERO, CRD42024536884. A total of 17 studies, out of an initial 1010, were chosen for the final analysis, but one was then excluded for being of poor quality. Our meta-analyses for the primary outcome revealed minimal diagnostic potential for interleukins. Our first subgroup analysis showed that interleukins were incapable of differentiating active TB patients from both healthy controls and ORD patients. Our second subgroup analysis showed that IL-17 was reduced in active TB patients. Assessment of the secondary outcome revealed that most studies relied on a GeneXpert MTB/RIF assay on saliva, but none fulfilled WHO guidelines for a non-sputum test. Individual biomarkers currently lack sufficient discriminatory power to definitively distinguish active tuberculosis from healthy individuals or those with other respiratory diseases (ORD), reinforcing the need for multi-biomarker panels. Interleukins may be alternatively used as markers for prognosis, severity, or treatment response. Our findings also suggest that assays are unable to meet WHO guidelines. Full article

Respiratory infections are the most common infectious diseases among children, representing a cause of death and generating a significant number of hospitalisations. The aim of the study was to analyse the epidemiological and clinical characteristics of viral pathogens causing respiratory tract infections in newborns and young children admitted to Galati pediatric hospital between October 2022 and December 2023. The diagnosis was performed using multiplex RT-PCR panels, which allowed simultaneous identification of respiratory pathogens (viruses and bacteria). From a total of 803 hospitalised patients with respiratory diseases, 607 (75.6%) children had a positive result for at least one respiratory virus and 96 patients (11.9%) were identified with bacterial infections. Mixed coinfections were found in almost half of the patients (44.5%). Most of RSV positive children had an increased length of stay, more than 7 days. It was shown a decline in severe cases of viral respiratory infections with prolonged hospitalisation as patients age up to 5 years. Full article