Search Results (461)

Background/Objectives: Syndromic multiplex PCR assays such as BIOFIRE FilmArray^® Pneumonia (PN) panel enable rapid and simultaneous detection of bacterial and viral pathogens in respiratory specimens, improving diagnostic accuracy and patient management in lower respiratory tract infections (LRTIs). Methods: In this retrospective observational study, PN panel results in 410 bronchoalveolar lavage (BAL) samples from hospitalized patients with suspected pneumonia were analyzed and compared with those obtained using the conventional culture (CC) method. Results: The PN panel showed an overall positivity rate of 54%, detecting bacteria in 39.0% of samples, viruses in 7.1%, and atypical bacteria in 2.2%. Using the conventional culture (CC) method, 33.9% of samples tested positive. Overall, 83 (20.2%) samples that were positive by the PN panel were negative by CC, whereas only 14 specimens (3.4%) were positive by CC and negative by PN panel. The most frequently detected pathogen by both the PN panel and CC was Staphylococcus aureus (n = 67, 16.34% for PN; n = 40, 9.76% for CC). Regarding diagnostic performance, the PN panel demonstrated a sensitivity of 89.02%, a specificity of 97.86%, and an overall accuracy of 97.63%. Lower sensitivity values were observed only for the Enterobacter cloacae complex (57.14%) and the Klebsiella pneumoniae group (75%). Specificity exceeded 92% for all bacterial targets. Conclusions: The PN panel confirms enhanced pathogen detection and a shortened time-to-result. It serves as a valuable adjunct for the timely diagnosis of LRTIs, supporting antimicrobial stewardship through more precise and appropriate antibiotic selection. Full article

Brachycephalic obstructive airway syndrome is a group of abnormalities that primarily affect the upper respiratory tract, particularly in dogs—especially in English and French bulldogs, pugs, and Boston terriers. The description and the consequences of these anomalies are well known. We performed a detailed histopathological analysis of soft palate samples taken from brachycephalic dogs with BOAS III. We examined the impact of the severity and composition of inflammatory infiltrates on individual histological structures, such as mucosal membrane, serosal and mucosal glands, and muscles. The study was conducted on 50 samples of soft palate tissue collected from pugs and French bulldogs. The sections were then stained with haematoxylin and eosin (HE) and Masson–Goldner trichrome. In general, both lymphocytic and plasmocytic inflammation were observed. Plasmacytic inflammation was more commonly associated with more advanced changes, including glandular fibrosis, muscle degeneration, and waxy necrosis of the muscles. Therefore, inflammatory infiltration—particularly plasmocytic infiltration—is associated with more severe clinical symptoms and a poorer prognosis in BOAS III dogs. Full article

Background: Sepsis remains a leading cause of morbidity and mortality, particularly when caused by multidrug-resistant organisms (MDROs). Early identification of colonising or infecting pathogens may inform initial antimicrobial selection. Surveillance cultures, providing microbiological data prior to infection onset, could guide timely and targeted therapy. This retrospective study analysed routine surveillance culture results from patients with bloodstream infection (BSI) episodes, assessing pathogen prevalence, resistance phenotypes, and concordance with specimen type in haemato-oncology (HO) and acute care (AC) settings. Methods: Data were retrieved from the institutional Laboratory Information System of the Department of Clinical Microbiology and ATB Centre, General University Hospital in Prague, covering 1 January to 31 December 2024. All positive blood cultures containing ESCAPE pathogens (excluding Clostridioides difficile) were reviewed. Corresponding surveillance culture records were analysed to evaluate concordance with subsequent BSI episodes. Results: In 2024, 6046 AC and 7267 HO surveillance cultures were performed; MDRO prevalence was 5% and 6.56%, respectively. ESBL-producing Enterobacterales predominated (AC 86.9%, HO 81.6%). In HO, BSI-causing Gram-negative and Gram-positive pathogens were frequently detected in rectal swabs, whereas in AC, concordance was higher with upper and lower respiratory tract samples. Rectal screening detected 100% of E. coli and K. pneumoniae BSI episodes in HO. Other specimen types showed limited concordance. Conclusions: Surveillance culture utility varies by specimen type and clinical setting. In both HO and AC units, these cultures provided valuable insights into colonisation and resistance patterns, supporting early risk stratification and guiding initial therapy in high-risk patients. Full article

Effective classroom ventilation is essential for indoor environmental quality (IEQ), comfort and health of schoolchildren, who spend substantial time indoors. This controlled observational study compared manual window airing (WA) with decentralized mechanical ventilation (DV) in six classrooms of two elementary schools during the winter infection period. Symptoms of upper respiratory tract infections, salivary biomarkers, well-being, perceived comfort, and classroom-level IEQ were assessed through questionnaires, saliva samples and long-term monitoring. Ninety-eight schoolchildren participated (64 WA, 34 DV). Symptom-based outcomes of the WURSS-K questionnaire showed consistently lower illness burden in group DV, with several parameters reaching statistical significance and an absolute risk reduction of 7.8%. Salivary immunoglobulin A (sIgA) concentrations were also significantly lower in group DV (approximately 39–59%, p ≤ 0.01). Sensitivity analyses showed positive associations of CO₂ and PM_2.5 with sIgA and indicated that PM_2.5 exposure accounted for group differences. Comfort perceptions mirrored measured IEQ: DV classrooms exhibited warmer, more stable thermal conditions, lower CO₂ and PM_2.5, and slightly better thermal and draught-related impressions. Overall, decentralized mechanical ventilation supported favorable IEQ and comfort and may influence mucosal immune activity through reduced particulate exposure, complementing the observed reduction in symptom burden. A multidimensional approach integrating medical outcomes with continuous IEQ monitoring proved valuable and should be expanded in larger, balanced cohort studies. Full article

Background/Objectives: Essential oils are liquid natural volatile mixture of compounds with several bioactive properties, which make them useful in a wide range of pharmaceutical applications. The aim of this work is to explore the antimicrobial impact of Cymbopogon martini essential oil against human clinical bacterial isolates from the skin and respiratory tract while also assessing its impact on mammalian cells. Geraniol, its main component according to GC-MS analysis, was evaluated under the same conditions. Methods: The composition of the essential oil was provided by the supplier. To elucidate the antimicrobial activity, the minimum inhibitory concentration (MIC) and the minimum bactericidal concentration (MBC) were determined. The impact on mammalian hepatic cells was determined using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. Results: The essential oil showed activity against Gram-positive bacteria from the Streptococcus and Staphylococcus genera, with MIC values ranging from 125 to 250 µg mL⁻¹ for Streptococcus agalactiae, Streptococcus anginosus, Streptococcus disgalactiae， and Streptococcus pyogenes. It also displayed activity against some of the tested Gram-negative bacteria, namely, Escherichia coli (MIC 350 µg mL⁻¹), Moraxella catarrhalis (MIC 250 µg mL⁻¹), and Morganella morganii (MIC 350 µg mL⁻¹). In most cases, the essential oil showed lower MIC values than geraniol. Additionally, palmarosa oil had a weaker impact than geraniol in HepG2 cells. Conclusions: Both the essential oil and the pure compound exhibited activity against clinical isolates obtained from skin and respiratory tract samples. Full article

We describe RNA-Seq analyses conducted on nasopharyngeal swabs collected from 37 patients admitted to an Australian intensive care unit from October 2022 to August 2023. During this time, the dominant omicron sublineage infections broadly progressed from BA.5 to BA.2-like, to XBB-like, then XBC, consistent with global trends. Viral load and patient metadata correlations indicated this cohort was broadly representative of severe COVID-19 patients. Human gene expression analyses were complicated by the large range (>5 log) and variability in viral reads. Nevertheless, the comparison of XBC and BA.5 samples that had comparable viral read counts, revealed differentially expressed genes and a cellular deconvolution signature that indicated increased targeting of ciliated epithelial cells by XBC. To obtain more evidence for increased targeting of ciliated epithelial cells by the later omicron sublineage viruses, a series of mouse strains were infected with a BA.5 or a XBB isolate. Increased infection of the nasal turbinates and ciliated epithelial cells by XBB was demonstrated by viral titrations and immunohistochemistry, respectively. Compared with previous lineages, the omicron lineage showed increased targeting of ciliated epithelia in the upper respiratory tract, with the data presented herein suggesting this trend continued for the omicron sublineages. Full article

Molar incisor hypomineralisation (MIH) is a developmental defect affecting permanent first molars and often the incisors too. Hypomineralised second primary molars (HSPM) have been proposed as potential early indicators of MIH. Aim: The aim was to identify potential aetiological factors associated with MIH and assess their relationship with HSPM in a pilot study. Methods: A cross-sectional case–control study was conducted with 120 patients (60 cases and 60 controls), aged 7–15 years, from the Paediatric Dentistry Postgraduate Programme. MIH was diagnosed following European Academy of Paediatric Dentistry (EAPD) guidelines. Parents completed a structured questionnaire on potential aetiological factors. Results: MIH was significantly associated with maternal smoking during pregnancy (p = 0.013), birth hypoxia (p = 0.013) and the use of amoxicillin and inhalation therapy during infancy (p < 0.001). It was also associated with tonsillitis (p = 0.022), bronchiolitis (p = 0.005) and other respiratory disorders (p = 0.049). HSPM was associated with anaemia and hypotension during pregnancy (p = 0.001), bottle-feeding (p = 0.044) and urinary tract infections (p = 0.003). No statistically significant association was found between MIH and HSPM. Conclusions: This pilot study has identified specific prenatal, perinatal, and postnatal factors associated with MIH and HSPM. The findings emphasise the clinical relevance for early diagnosis and management and highlight the need for studies with larger sample sizes to validate these associations. Full article

At the beginning of the COVID-19 pandemic, SARS-CoV-2-positive donors were not considered eligible for organ donation. The Italian National Transplant Centre has gradually introduced measures to prevent donor-to-recipient transmission of SARS-CoV-2 infection through organ transplantation. The current national screening protocol for deceased SARS-CoV-2-positive donors recommends molecular testing of donor lower respiratory tract (LRT) samples, graft biopsies and organ perfusion fluids. The aim of the study is to describe the 3-year experience of protocol application in a northern region of Italy. From 1 January 2022 to 31 January 2025, a total of 132 samples were analyzed (29 liver biopsies, 35 kidney biopsies, 68 perfusion fluids) from 40 organ donors with an active or resolved SARS-CoV-2 infection. SARS-CoV-2 PCR on LRT samples was positive in 26/40 (65%) donors, negative in 11/40 (27.5%) cases and in the remaining 3 (7.5%) the PCR result was unknown. Overall, 65 organs were transplanted into 60 recipients. All processed graft biopsies and organ perfusion fluid samples tested negative for SARS-CoV-2 RNA. Our data suggest that the utilization of non-lung donors with resolved or active SARS-CoV-2 infections who died of other causes appears justified and safe. Full article

Human rhinovirus (HRV) is one of the most common viral causes of respiratory tract infections worldwide. The COVID-19 pandemic and non-pharmaceutical interventions significantly altered the epidemiology of respiratory viruses. This study compared HRV genotypic diversity in Mexican children with pneumonia before and during the pandemic. A total of 1983 children with pneumonia were included: 1404 pre-pandemic (2010–2013) and 579 pandemic (2021–2023). Multiplex RT-PCR was used for HRV detection. Genotyping was conducted on 136 samples with Ct < 30 by sequencing the VP4/VP2 region. Species and genotype assignments were validated using BLAST and maximum-likelihood phylogenetic analysis (MEGA XII). HRV positivity increased from 16% (233/1404) before the pandemic to 60.4% (350/579) during the pandemic period. HRV-A and HRV-C predominated in both periods; HRV-C infection was significantly associated with severe pneumonia in the pre-pandemic period (OR 3.520; p = 0.012), but this association was not observed during the pandemic. A total of 72 genotypes were identified without a dominant type in either period. HRV circulation patterns shifted in the context of the COVID-19 pandemic, with a marked increase in prevalence. The high genotypic diversity observed across both periods underscores the importance of continuous molecular surveillance to better understand HRV circulation and its clinical relevance. Full article

Background: Non-cystic fibrosis bronchiectasis (BE) is a chronic lung condition characterized by irreversible bronchial dilation and presented with persistent respiratory symptoms, recurrent respiratory infections, and decreased quality of life. Inhaled corticosteroids (ICSs) are frequently prescribed in patients with bronchiectasis, despite limited evidence supporting their clinical efficacy. Inhaled corticosteroids have been associated with increased risk of respiratory infection with Haemophilus influenzae (H. influenzae) in other groups of lung diseases. We aimed to evaluate the association between ICS use and the risk of isolating H. influenzae from lower respiratory tract samples in patients with bronchiectasis. Methods: A retrospective cohort study was conducted using data from 2010 to 2018, encompassing all patients diagnosed with bronchiectasis in outpatient clinics in Eastern Denmark. ICS use was standardized in budesonide equivalent doses and categorized in tertiles: low (<210 μg/day), moderate (211–625 μg/day), and high (≥626 μg/day) based on cumulative budesonide equivalent doses redeemed in the 12 months before cohort entry. The primary outcome was the first isolation of H. influenzae from lower respiratory tract samples post-cohort entry. Cox proportional hazards models, adjusted for relevant confounders, estimated hazard ratios (HRs), and inverse probability-of-treatment weighting (IPTW) was used in sensitivity analyses. Results: Among 3663 patients (mean age 66 years; 61% female), 2175 (59.4%) did not use ICS, while 484 (13.2%), 508 (13.9%), and 496 (13.5%) were in the low-, moderate-, and high-dose ICS groups, respectively. Furthermore, 594 (16.22%) patients had a lower respiratory tract culture positive for H. influenzae during follow-up. High-dose ICS use was associated with an increased risk of H. influenzae; HR 1.63 (95% Cl, 1.19 to 2.12, p < 0.005) compared with no ICS use. No association for low or moderate ICS use was found: low-dose ICS HR 0.75 (95% Cl, 0.52 to 1.07, p = 0.11) and moderate-dose ICS HR 1.27 (95% Cl, 0.93 to 1.72, p = 0.12). IPTW analysis confirmed the main finding. Conclusions: High-dose ICS use in patients with bronchiectasis was associated with an increased risk of acquiring H. influenzae in the lower respiratory tract. Hence, patients with bronchiectasis should be cautiously prescribed high-dose ICS. Full article

Background and Objectives: Upper respiratory tract infections are one of the most common reasons for outpatient admission. Acute pharyngitis is typically caused by viruses and is self-limiting but in up to 30% of cases, secondary bacterial infection may occur, requiring antibacterial treatment. In the face of growing antibacterial resistance due to inappropriate systemic antibiotic use, different topical therapy would have benefits. The objective of this study was to compare changes in throat and tonsillar mucous membrane bacterial density in patients with acute pharyngitis after a single exposure to a local antibacterial agent presented in different pharmaceutical forms—medicated lozenge, throat spray, or a solution for gargling. Materials and Methods: This was a non-interventional observational study that involved 90 adult outpatients with acute pharyngitis. Patients were prescribed to one of three options: medicated lozenges (containing dequalinium chloride and cinchocaine hydrochloride)—Treatment A; throat spray (containing streptocide soluble and norsulfazol-sodium)—Treatment B; or a powder, Furasol^® 100 mg (containing furagin soluble), for use as an external gargling solution—Treatment C. Throat swab culture was collected before and 20 min after the single exposure to the medication. Microbial testing was performed using a semi-quantitative quadrant streak plate method to assess bacterial density before and after exposure. Results: Four pathogenic agents were isolated from the swabs, with Staphylococcus aureus being the most prevalent. Overall, a reduction in post-exposure bacterial growth intensity was observed in 84.6% of the samples after Treatment C exposure, with a statistically significant difference from both Treatment B (57.1%, p < 0.05) and Treatment A (10%, p < 0.05). The difference was also significant between Treatment A and Treatment B. Conclusions: The findings showed that the throat gargling solution had more impact on mucous bacterial load compared to the throat spray and medicated lozenges in the patients with acute pharyngitis. Further research should address the effects of different pharmaceutical forms of the same antibacterial agent, where available. Full article

Microplastics (MPs), defined as plastic particles < 5 mm diameter, have become a growing public health concern. First identified in the aquatic environment in 2004 and later in air samples in 2015, airborne MPs display wide variations in shape and size, with fibres being the most common. These physical characteristics, together with others such as median aerodynamic diameter, influence how deeply they penetrate and where they deposit within the respiratory tract. Recent studies have confirmed the presence of MPs in nasal lavage fluid, bronchoalveolar lavage fluid, sputum, pleural fluid and lung tissue samples, with higher concentrations observed in older individuals, smokers and those with occupational exposure. Multiple polymer types have been identified, most frequently polypropylene, polyethylene and polyester. Experimental models demonstrate that MPs can induce inflammation, oxidative stress, mitochondrial dysfunction, microbiota alterations, fibrosis and carcinogenic changes, with toxicity generally increasing as particle size decreases. Despite the growing evidence of plastic toxicity, only a limited number of studies have examined MPs’ influence on the respiratory system, focusing mostly on polyester spheres, rather than fibres, which dominate real-world exposure. Current findings suggest MPs contribute to several pathophysiological processes and may play a role in respiratory disease. However, further research is needed to clarify the underlying mechanisms, long-term consequences and clinical relevance of these emerging pollutants. Full article

Feline herpesvirus type-1 (FHV-1), a double-stranded DNA virus, which is a highly infectious upper respiratory tract infection of felids, particularly in kittens. Droplet digital PCR (ddPCR) provides an absolute quantification method with high sensitivity and accuracy. This study aimed to develop a highly sensitive and accurate ddPCR assay for the detection of FHV-1. We designed primers and a probe targeting the FHV-1 glycoprotein D (gD) gene and evaluated the assay’s limit of detection (LOD), sensitivity, repeatability, and specificity in comparison to quantitative real-time PCR (qPCR). The developed ddPCR assay demonstrated a strong linear dynamic range (R² ≥ 0.99) and an exceptionally low LOD of 0.18 copies/μL, which was significantly more sensitive than the method qPCR (LOD ~10 copies/μL). Additionally, the assay exhibited high specificity with no cross-reactivity against other common feline pathogens (feline calicivirus, FCV; feline panleukopenia virus, FPV; feline infectious peritonitis virus, FIPV; Bordetella bronchiseptica and Chlamydia felis) and displayed outstanding repeatability (inter-run CV < 1.35). When applied to 118 clinical samples, the ddPCR assay achieved a significantly higher positive detection rate (27.4%) compared to qPCR (14.8%). In conclusion, we have successfully established a reliable ddPCR assay for the absolute quantification of FHV-1, providing a superior tool for laboratory diagnosis and research. Full article

Feline calicivirus (FCV) is widespread in multi-cat environments and typically causes acute upper respiratory tract disease (URTD). FCV also causes outbreaks of virulent systemic disease (VSD), mainly in adults, with multiple organ involvement. In this study, an FCV-VSD infection was described in a less-one-month-old Maine Coon kitten originating from a cattery where an outbreak of FCV-URTD had previously been reported. After spontaneous death, post-mortem examination as well as histopathological, immunohistochemical, bacteriological and virological investigations were carried out. Pathological findings were consistent with severe pneumonia and cutaneous oedema of the footpads. No concomitant bacterial infection was detected. FCV RNA was detected in several organs and the highest amount of viral RNA was observed in the lung sample, in which the presence of the FCV antigen was confirmed by immunohistochemistry. With the same immunohistochemical technique, the IBA-1 antibody detected sparse alveolar macrophages, the main viral target cell and pulmonary replication site. The nucleotide sequences of the viral ORF2 gene amplified from all positive tissues were identical with each other and phylogeny confirms that highly virulent FCV strains are not distinguishable from FCV-URTD phenotypes. Our findings reinforce the hypothesis that VSD outbreaks can occur even in small populations, due to the high genetic variability of FCV. Full article

Acinetobacter baumanni (A. baumannii) is a well-known pathogen associated with antimicrobial-resistant infections. It is a major cause of nosocomial infections and is frequently associated with polymicrobial and antibiotic-resistant infections. This study investigates the frequency of A. baumannii infections, its antimicrobial resistance profile and the main co-pathogens isolated in respiratory samples at the San Giovanni di Dio e Ruggi d’Aragona Hospital in 2015–2019 (pre-COVID-19 pandemic) and 2020–2023 (during/post-COVID-19 pandemic). Bacterial identification and antibiotic susceptibility testing were performed using the VITEK^® 2 system (2015–2019), while identification was carried out with MALDI-TOF MS starting from 2020. A total of 1679 strains were isolated between 2015 and 2019, and 1186 between 2020 and 2023, with significantly higher frequencies in males 61–80 and females 71–80. A. baumannii was isolated predominantly from respiratory specimens, derived predominantly in intensive care units (ICUs). The antimicrobial resistance rates of A. baumannii were above 90% for gentamicin, trimethoprim/sulfamethoxazole, imipenem and ciprofloxacin, while colistin resistance was less than 1% (0.95%) in pre-pandemic and alarmingly increased during/post pandemic period (6.1%). A. baumannii was most frequently associated with Klebsiella pneumoniae, Staphylococcus aureus and Pseudomonas aeruginosa in respiratory tract infections. A. baumannii represents a serious global health threat due to its extensive antimicrobial resistance, highlighting the need for continuous surveillance, detailed strain characterization, and development of new antimicrobial agents. Full article