Search

Most respiratory microbiome studies use amplicon sequencing due to high host DNA. Metagenomics sequencing offers finer taxonomic resolution, phage assessment, and functional characterization. We evaluated five host DNA depletion methods on frozen nasal swabs from healthy adults, sputum from people with cystic fibrosis (pwCF), and bronchoalveolar lavage (BAL) from critically ill patients. Median sequencing depth was 76.4 million reads per sample. Untreated nasal, sputum, and BAL had 94.1%, 99.2%, and 99.7% host reads, respectively. Host depletion effects varied by sample type, generally increasing microbial reads, species and functional richness; this was mediated by higher effective sequencing depth. Rarefaction curves showed species richness saturation at 0.5-2 million microbial reads. Most methods did not change Morisita-Horn dissimilarity for BAL and nasal samples although the proportion of gram-negative bacteria decreased for sputum from pwCF. Freezing did not affect the viability of Staphylococcus aureus but reduced the viability of Pseudomonas aeruginosa and Enterobacter spp.; this was mitigated by adding a cryoprotectant. QIAamp-based host depletion minimally impacted gram-negative viability even in non-cryoprotected frozen isolates. While some host depletion methods may shift microbial composition, metagenomics sequencing without host depletion severely underestimates microbial diversity of respiratory samples due to shallow effective sequencing depth and is not recommended.

Tools for rapid identification of novel and/or emerging viruses are urgently needed for clinical diagnosis of unexplained infections and pandemic preparedness. Here we developed and clinically validated a largely automated metagenomic next-generation sequencing (mNGS) assay for agnostic detection of respiratory viral pathogens from upper respiratory swab and bronchoalveolar lavage samples in

RATIONALE: Research studies typically quantify acute respiratory exacerbation episodes (AECOPD) among people with chronic obstructive pulmonary disease (COPD) based on self-report elicited by survey questionnaire. However, AECOPD quantification by self-report could be inaccurate, potentially rendering it an imprecise tool for identification of those with exacerbation tendency. OBJECTIVE: Determine the agreement between self-reported and health records-documented quantification of AECOPD and their association with airway inflammation. METHODS: We administered a questionnaire to elicit the incidence and severity of respiratory exacerbations in the three years preceding the survey among current or former heavy smokers with or without diagnosis of COPD. We then examined electronic health records (EHR) of those with COPD and those without (tobacco-exposed persons with preserved spirometry or TEPS) to determine whether the documentation of the three-year incidence of moderate to very severe respiratory exacerbations was consistent with self-report using Kappa Interrater statistic. A subgroup of participants also underwent bronchoalveolar lavage (BAL) to quantify their airway inflammatory cells. We further used multivariable regressions analysis to estimate the association between respiratory exacerbations and BAL inflammatory cell composition with adjustment for covariates including age, sex, height, weight, smoking status (current versus former) and burden (pack-years). RESULTS: Overall, a total of 511 participants completed the questionnaire, from whom 487 had EHR available for review. Among the 222 participants with COPD (70 ± 7 years-old; 96% male; 70 ± 38 pack-years smoking; 42% current smoking), 57 (26%) reported having any moderate to very severe AECOPD (m/s-AECOPD) while 66 (30%) had EHR documentation of m/s-AECOPD. However, 42% of those with EHR-identified m/s-AECOPD had none by self-report, and 33% of those who reported m/s-AECOPD had none by EHR, suggesting only moderate agreement (Cohens Kappa = 0.47 ± 0.07; P

BackgroundPulmonary ischaemia-reperfusion injury (IRI) is a major contributor to poor lung transplant outcomes. We recently demonstrated a central role of airway-centred natural killer (NK) cells in mediating IRI; however, there are no existing effective therapies for directly targeting NK cells in humans.MethodsWe hypothesised that a depleting anti-CD94 monoclonal antibody (mAb) would provide therapeutic benefit in mouse and human models of IRI based on high levels of KLRD1 (CD94) transcripts in bronchoalveolar lavage samples from lung transplant patients.ResultsWe found that CD94 is highly expressed on mouse and human NK cells, with increased expression during IRI. Anti-mouse and anti-human mAbs against CD94 showed effective NK cell depletion in mouse and human models and blunted lung damage and airway epithelial killing, respectively. In two different allogeneic orthotopic lung transplant mouse models, anti-CD94 treatment during induction reduced early lung injury and chronic inflammation relative to control therapies. Anti-CD94 did not increase donor antigen-presenting cells that could alter long-term graft acceptance.ConclusionsLung transplant induction regimens incorporating anti-CD94 treatment may safely improve early clinical outcomes.

Hematopoietic cell transplantation (HCT) uses cytotoxic chemotherapy and/or radiation followed by intravenous infusion of stem cells to cure malignancies, bone marrow failure and inborn errors of immunity, hemoglobin and metabolism. Lung injury is a known complication of the process, due in part to disruption in the pulmonary microenvironment by insults such as infection, alloreactive inflammation and cellular toxicity. How microorganisms, immunity and the respiratory epithelium interact to contribute to lung injury is uncertain, limiting the development of prevention and treatment strategies. Here we used 278 bronchoalveolar lavage (BAL) fluid samples to study the lung microenvironment in 229 pediatric patients who have undergone HCT treated at 32 childrens hospitals between 2014 and 2022. By leveraging paired microbiome and human gene expression data, we identified high-risk BAL compositions associated with in-hospital mortality (P = 0.007). Disadvantageous profiles included bacterial overgrowth with neutrophilic inflammation, microbiome contraction with epithelial fibroproliferation and profound commensal depletion with viral and staphylococcal enrichment, lymphocytic activation and cellular injury, and were replicated in an independent cohort from the Netherlands (P = 0.022). In addition, a broad array of previously occult pathogens was identified, as well as a strong link between antibiotic exposure, commensal bacterial depletion and enrichment of viruses and fungi. Together these lung-immune system-microorganism interactions clarify the important drivers of fatal lung injury in pediatric patients who have undergone HCT. Further investigation is needed to determine how personalized interpretation of heterogeneous pulmonary microenvironments may be used to improve pediatric HCT outcomes.

BACKGROUND: Acute lung allograft dysfunction (ALAD) is an imprecise syndrome denoting concern for the onset of chronic lung allograft dysfunction (CLAD). Mechanistic biomarkers are needed that stratify risk of ALAD progression to CLAD. We hypothesized that single cell investigation of bronchoalveolar lavage (BAL) cells at the time of ALAD would identify immune cells linked to progressive graft dysfunction. METHODS: We prospectively collected BAL from consenting lung transplant recipients for single cell RNA sequencing. ALAD was defined by a ≥10% decrease in FEV1 not caused by infection or acute rejection and samples were matched to BAL from recipients with stable lung function. We examined cell compositional and transcriptional differences across control, ALAD with decline, and ALAD with recovery groups. We also assessed cell-cell communication. RESULTS: BAL was assessed for 17 ALAD cases with subsequent decline (ALAD declined), 13 ALAD cases that resolved (ALAD recovered), and 15 cases with stable lung function. We observed broad differences in frequencies of the 26 unique cell populations across groups (p = 0.02). A CD8 T cell (p = 0.04) and a macrophage cluster (p = 0.01) best identified ALAD declined from the ALAD recovered and stable groups. This macrophage cluster was distinguished by an anti-inflammatory signature and the CD8 T cell cluster resembled a Tissue Resident Memory subset. Anti-inflammatory macrophages signaled to activated CD8 T cells via class I HLA, fibronectin, and galectin pathways (p

UNLABELLED: Invasive mold infections (IMIs) are associated with high morbidity, particularly in immunocompromised patients, with mortality rates between 40% and 80%. Early initiation of appropriate antifungal therapy can substantially improve outcomes, yet early diagnosis remains difficult to establish and often requires multidisciplinary teams evaluating clinical and radiological findings plus supportive mycological findings. Universal digital high-resolution melting (U-dHRM) analysis may enable rapid and robust diagnoses of IMI. A universal fungal assay was developed for U-dHRM and used to generate a database of melt curve signatures for 19 clinically relevant fungal pathogens. A machine learning algorithm (ML) was trained to automatically classify these pathogen curves and detect novel melt curves. Performance was assessed on 73 clinical bronchoalveolar lavage samples from patients suspected of IMI. Novel curves were identified by micropipetting U-dHRM reactions and Sanger sequencing amplicons. U-dHRM achieved 97% overall fungal organism identification accuracy and a turnaround time of ~4 hrs. U-dHRM detected pathogenic molds (Aspergillus, Mucorales, Lomentospora, and Fusarium) in 73% of 30 samples classified as IMI, including mixed infections. Specificity was optimized by requiring the number of pathogenic mold curves detected in a sample to be >8 and a sample volume to be 1 mL, which resulted in 100% specificity in 21 at-risk patients without IMI. U-dHRM showed promise as a separate or combination diagnostic approach to standard mycological tests. U-dHRMs speed, ability to simultaneously identify and quantify clinically relevant mold pathogens in polymicrobial samples, and detect emerging opportunistic pathogens may aid treatment decisions, improving patient outcomes. IMPORTANCE: Improvements in diagnostics for invasive mold infections are urgently needed. This work presents a new molecular detection approach that addresses technical and workflow challenges to provide fast pathogen detection, identification, and quantification that could inform treatment to improve patient outcomes.

Purpose: Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive fibrotic lung disorder characterized by dry cough, fatigue, and exacerbated dyspnea. The prognosis of IPF is notably unfavorable, becoming extremely poor when the disease advances acutely. Effective therapeutic intervention is essential to mitigate disease progression; hence, early diagnosis and treatment are paramount. When high-resolution computed tomography (HRCT) reveals usual interstitial pneumonia (UIP), a diagnosis of IPF can be established. However, when HRCT fails to conclusively confirm IPF, the diagnostic pathway becomes intricate and necessitates a multidisciplinary approach involving clinicians, radiologists, and pathologists. Consequently, the objective of this study was to investigate new diagnostic approaches through bronchoalveolar lavage (BAL) analysis. Methods: BAL is a commonly utilized diagnostic tool for interstitial lung diseases. We review the application of bronchoalveolar lavage (BALF) in idiopathic pulmonary fibrotic disease, emphasizing that the cellular and solute composition of the lower respiratory tract offers valuable insights. Results: This review delineates the advancements in diagnosing IPF cases that remain indeterminate via HRCT, leveraging BALF analysis. In contrast to surgical lung biopsy, BAL is minimally invasive and offers potential diagnostic utility through the identification of specific BALF biomarkers. Conclusion: Augment the clinical diagnostic armamentarium for IPF, particularly in scenarios where HRCT findings are inconclusive. [ABSTRACT FROM AUTHOR]

Background: Severe pulmonary infection is the primary cause of death in children aged < 5 years. The early identification of pathogenic bacteria and targeted anti-infective therapies can significantly improve the prognosis of children with severe infections. This study aims to provide a reference for the rational use of antibiotics at an early stage in children with severe pulmonary infections. Methods: A retrospective, single-center longitudinal study included children with severe pulmonary infections between January 2017 and December 2022 by obtaining their bacterial culture results of bronchoalveolar lavage fluid. Results: This study included 4080 samples. The age of onset for severe pulmonary infection increased annually. The proportion of severe pulmonary infections across the different age groups and years was statistically significant (p < 0.001). Among children with severe pulmonary infections, bacilli were the most prevalent, followed by cocci and fungi. The predominant bacilli were Acinetobacter baumannii and Klebsiella pneumoniae. The predominant cocci identified in this study were Streptococcus pneumoniae and Staphylococcus aureus. The primary fungi included Candida albicans and Aspergillus fumigatus, which showed significant differences (p < 0.05). The incidence of drug-resistant bacteria has gradually declined, with infection rates of multidrug-resistant bacteria and extended-spectrum beta-lactamases consistently decreasing annually. For carbapenem-resistant Acinetobacter baumannii and Pseudomonas aeruginosa, the infection rates peaked in 2018, with statistical significance (p < 0.001). Conclusions: Severe pulmonary infections in children are significantly associated with age and types of infectious pathogens. Gram-negative bacteria are the primary cause of severe pulmonary infections in children. Clinicians should rationally use antibiotics according to the local distribution and drug resistance of pathogens, thereby enhancing therapeutic outcomes. [ABSTRACT FROM AUTHOR]

Background: Although previous studies have reported the dysregulation of respiratory tract microbiota in infectious diseases, insufficient data exist regarding respiratory microbiota imbalances in the lower respiratory tracts of children with pulmonary tuberculosis (PTB). In this study, we assessed the value of mNGS in the pathogen diagnosis and microbiome analysis of PTB patients using bronchoalveolar lavage fluid (BALF) samples. Methods: A total of 64 participants, comprising 43 pediatric PTB and 21 pediatric pneumonia patients were recruited in the present study. BALF samples were collected from the above participants. Parallel comparisons between mNGS and conventional microbial test (CMT) pathogen detection were performed. Moreover, the diversity and structure of all 64 patients' lung BALF microbiomes were explored using the mNGS data. Results: Comparing to the final clinical diagnosis, mNGS in BALF samples produced a sensitivity of 46.51%, which was lower than that of TB-PCR (55.00%) and Xpert (55.00%). The diagnostic efficacy of PTB can be highly enhanced by mNGS combined with TB-PCR (AUC=0.8140, P <0.0001). There were no significant differences in the diversity either between patients with TB and pneumonia. Positive mNGS pathogen results in pediatric PTB patients significantly affect the β-diversity of the pulmonary microbiota. In addition, significant taxonomic differences were found in BALF specimens from patients with PTB and pneumonia, both of which have unique bacterial compositions. Conclusions: mNGS is valuable in the etiological diagnosis of PTB, and can reveal pulmonary microecological characteristics. For pediatric PTB patients, the mNGS should be implemented early and complementary to CMTs. [ABSTRACT FROM AUTHOR]

Immunothrombosis has emerged as a potential mechanistic link underlying the development and progression of acute respiratory distress syndrome (ARDS), but understanding its specific profile in patients, both locally and systemically, is limited. The objective of this study was to characterize and compare the immunothrombotic signatures in patients diagnosed with pneumonia-related ARDS (p-ARDS) at both the pulmonary and systemic levels and to evaluate their clinical relevance. The study included 23 consecutive patients diagnosed with p-ARDS admitted to the intensive care unit at a tertiary university hospital from July 2022 to May 2023, alongside 40 concurrently hospitalized patients with common pneumonia as controls. Paired bronchoalveolar lavage fluid (BALF) and serum samples were collected from the participants for the analysis of 15 biomarkers to assess and quantify the pulmonary and systemic immunothrombotic signatures. The study results revealed significant pulmonary inflammation and systemic endothelial injury in p-ARDS patients compared to pneumonia controls. These observations were maintained after adjustment for severity of illness (Acute Physiology and Chronic Health Evaluation II scores). In terms of clinical relevance, inflammatory biomarkers (interleukin [IL]-6, IL-8) in BALF were found to correlate with PaO2/FiO2 ratio, while serum levels of a disintegrin and metalloproteinase with thrombospondin type 1 motif 13 (ADAMTS-13) and thrombomodulin showed associations with Sequential Organ Failure Assessment and Disseminated Intravascular Coagulation scores. In conclusion, this preliminary investigation identified compartment-specific variations in the immunothrombotic signature between patients with p-ARDS and those with pneumonia alone, with inflammatory responses predominantly localized in the alveolar compartments and coagulation/endothelial injury biomarkers more pronounced in peripheral blood. [ABSTRACT FROM AUTHOR]

To evaluate the diagnostic value of metagenomic next-generation sequencing (mNGS) and galactomannan (GM) testing in invasive pulmonary aspergillosis (IPA) and to compare mNGS with other diagnostic approaches (serum/bronchoalveolar lavage fluid (BALF)-GM and conventional microbiological tests (CMTs) including sputum smears and culture, BALF fungal culture, and bronchial brushing). In all, 237 patients were enrolled in this retrospective study, including 120 patients with IPA and 117 with non-IPA pulmonary infections treated at Henan Provincial People's Hospital between June 2021 and February 2024. The diagnostic performance of mNGS was compared to conventional diagnostic methods including serum GM, BALF-GM, sputum smear microscopy, sputum culture, bronchial brushings, and BALF culture. The proportion of patients with underlying diseases was significantly higher in the IPA group than in the non-IPA group (P < 0.05). Compared to conventional diagnostic methods for IPA, mNGS showed higher diagnostic efficacy, with a sensitivity of 92.5% and a specificity of 94.02%. The area under the receiver operating characteristic curve (AUC) for BALF-GM for diagnosing IPA was 0.8, with an optimal cutoff value of 0.546, sensitivity of 66.7%, and specificity of 82.1%. The combination of mNGS and BALF-GM testing further improved diagnostic performance (sensitivity of 96.67% and specificity of 78.63%). mNGS testing has excellent diagnostic efficacy for IPA, which is further enhanced by combining it with BALF-GM testing. This approach has considerable potential for the early diagnosis and targeted treatment of IPA. [ABSTRACT FROM AUTHOR]

Objective: We aimed to identify the diagnostic value of next-generation sequencing (NGS) of bronchoalveolar lavage fluid (BALF) from patients with non-small-cell lung cancer (NSCLC). Methods: Forty patients who were initially diagnosed with pulmonary nodules were enrolled. Frozen section histology was used to identify the NSCLC cell types. NGS of collected BALF samples was used for microbial identification. We compared the bacterial and viral distributions in BALF samples from patients with NSCLC with and without obstructive pneumonia as well as their NSCLC drainage times following surgery. Results: Of the 29 patients with NSCLC, eight had obstructive pneumonia. Streptococcus pneumoniae , Streptococcus pseudopneumoniae , and Haemophilus parainfluenzae were the top three bacteria present in almost 50% of patients, both with and without obstructive pneumonia. The viral detection rate was higher in the BALF of patients with NSCLC who did not have obstructive pneumonia. However, in patients with NSCLC and drain times of >5 days, the human herpes virus type 7 detection rate was higher following surgery than it was in patients with NSCLC who had drain times of ≤5 days. Conclusion: Viral imbalance in NSCLC is closely related to the occurrence of obstructive pneumonia and postoperative drainage time. [ABSTRACT FROM AUTHOR]

Bronchial asthma remains a serious medical problem, as approximately 10% of patients fail to achieve adequate symptom control with available treatment options. Macrophages play a pivotal role in the pathophysiology of asthma, as well as in some other respiratory disorders. Typically, they are classified into two major classes, M1 and M2; however, recent findings have indicated that in fact there is a whole range of macrophage polarization and functional diversity beyond this bimodal division. The isolation of individual cell sub-populations and the identification of their role and diagnostic/therapeutic significance is still a challenge. Here, we have attempted to assess the differences between patient-derived macrophage populations from bronchoalveolar lavage fluid (BALF) samples in different pulmonary disease conditions, based on their capability to interact with a range of specific and relatively non-specific carbohydrate-based ligands (containing galactose (linear or cyclic form), mannose, trimannose, etc.). Obviously, the main target of these ligands was CD206; however, other minor receptors, able to bind carbohydrates, have also been reported for macrophages. Trimannose binds most specifically to CD206 macrophage receptors, while monomannose has intermediate affinity, and galactose has low affinity and may involve binding to other receptors. This clearly indicates the ligands were chosen based on their predicted binding strength and specificity for CD206, providing the rationale for the study. In some cases, the activated macrophage affinity to galactose base ligands was higher than that to mannose, indicating that complexes of CD206 or other carbohydrate-binding receptors may contribute substantially to macrophage functional features. In addition, variations in receptor clustering and distribution may substantially affect affinity to the same ligand. Interestingly, with a panel of 6–10 different carbohydrate-based ligands with FTIR or fluorescent marker, we were able not only to distinguish between healthy and disease states but also between closely related diseases such as purulent endobronchitis, obstructive bronchitis, pneumonia, and bronchial asthma. For further investigation, specific sub-populations of macrophages, seen as hallmarks to specific diseases, can be isolated and studied separately, likely giving new insights with diagnostic and therapeutic significance for hard-to-treat patients. The group of patients with resistant disease can also be identified with this approach as a fingerprint method to find a more targeted therapeutic strategy, improving their clinical outcomes. As expected, this will provide a large additional array of data for analysis, compared to the work going on in the world. The dataset used by other researchers mainly for known "antibody" ligands is semi-quantitative and insufficient for the purposes of typing as yet unknown and uncomplicated sub-populations. The analysis of the presented data in combination with personalized information from patients' medical records will be carried out using both traditional methods and machine learning methods. [ABSTRACT FROM AUTHOR]

Objective: To address the clinical diagnostic value of CRISPR-Cas13a-based molecular technology for tuberculosis (TB). Methods: The 189 suspected TB patients were simultaneously sent for acid-fast staining smear of bronchoalveolar lavage fluid, MGIT 960 cultures, Xpert MTB/RIF assay, and CRISPR-Cas13a assay. Using the final clinical diagnosis as the gold standard, the TB and non-TB groups were determined, and the diagnostic values of the four assays and the combined test in TB were compared. Using MGIT 960 culture as the gold standard, the diagnostic value of CRISPR-Cas13a assay was explored in TB, and the concordance between the CRISPR-Cas13a assay and MGIT 960 culture was compared. Results: The 189 preliminary diagnosed patients with suspected TB were diagnosed, with 147 in the TB group and 42 in the non-TB group. Taking the final clinical diagnosis as the gold standard, the sensitivity, negative predictive value, and accuracy of CRISPR-Cas13a assay, MGIT 960 culture, and XpertMTB/RIF assay were higher than those of acid-fast staining smear; by comparing the area under the ROC curve, the diagnostic value of the CRISPR-Cas13a assay, MGIT 960 culture, and XpertMTB/RIF assay was superior to that of acid-fast staining smear (all P < 0.05). Using the MGIT 960 culture results as the gold standard, there was a moderate concordance between the CRISPR-Cas13a assay and the MGIT 960 culture (kappa = 0.666). Conclusion: Bronchoalveolar lavage fluid CRISPR-Cas13a assay has high application value in the clinical diagnosis of TB and can be recommended for the initial screening of patients with suspected TB. [ABSTRACT FROM AUTHOR]

The incidence of lower respiratory tract infections (LRTIs) caused by multidrug-resistant organisms (MDRO) has been high in recent years. However, traditional etiological detection methods have not been able to meet the needs for clinical diagnosis and prognosis of LRTIs. The rapid development of metagenomic next-generation sequencing (mNGS) provides new insights for diagnosis and treatment of LRTIs. We conducted a retrospective study on 95 patients with lower respiratory tract infections caused by MDRO admitted to our respiratory department from January 2022 to December 2023. These patients underwent mNGS testing and conventional culture testing. Additionally, 150 patients without lower respiratory tract infections caused by MDRO during the same period were included as the non-MDRO group. General information was collected, and Logistic regression analysis was performed to identify risk factors for MDRO infections in patients with lower respiratory tract infections. Our results show that the time to pathogen detection by mNGS was 50.76 ± 1.730 h, that is significantly shorter than 55.53 ± 2.782 h required for conventional culture testing. The pathogen detection rate by mNGS was 89.47% (85/95), higher than the 67.37% (64/95) identified by conventional testing. In terms of pathogen genus distribution, mNGS detected a total of 279 pathogens, while conventional testing detected 121 pathogens. Logistic multivariate regression analysis identified that the use of more than two antibiotics, invasive procedures, invasive mechanical ventilation for ≥7 days, and stay in the respiratory intensive care unit (RICU) for ≥7 days were the main influencing factors for lower respiratory tract infections caused by MDRO (P < 0.05). [ABSTRACT FROM AUTHOR]

Bronchoalveolar lavage fluid (BALF) is a liquid sample that reflects the biological status of lung tissues, containing a wealth of components such as cells and proteins. These components provide a non-invasive method to obtain pathological information about the lungs, serving as a powerful complement to traditional lung biopsies. However, the similarity in morphology and function of cells in BALF, combined with the diversity of sample processing and analysis methods, can lead to confusion in recognizing and distinguishing these cellular features. This study presents an improved Yolov10 method for the detection and classification of BALF cells, specifically targeting macrophages, lymphocytes, neutrophils, and eosinophils. The backbone network incorporates the PLWA module in place of the PSA module to enhance the acquisition of useful information, and the C2f-DC module replaces the C2f module to improve image feature extraction capabilities. Furthermore, the head network employs the Cross-Attention Fusion module (CAP) to enhance the retrieval of image information. Experimental results demonstrate that the model achieves a mean Average Precision (mAP) of 86.5% and a recall rate of 79.1%, confirming the model’s effectiveness.

Xianning Dai,1 Kai Xu,1 Yu Tong,1 Jing Li,2 Liya Dai,1 Jianyou Shi,1 Haibin Xie,3 Xi Chen3 1Department of Clinical Laboratory, Wenzhou People’s Hospital, Wenzhou Maternal and Child Health Care Hospital, Zhejiang, People’s Republic of China; 2Department of PCCM, Wenzhou People’s Hospital, Wenzhou Maternal and Child Health Care Hospital, Zhejiang, People’s Republic of China; 3Department of Immunization Planning, Prevention and Health Care, Centers for Disease Control of Luchen, Zhejiang, People’s Republic of ChinaCorrespondence: Xi Chen, Department of Immunization Planning, Prevention and health care,Centers for Disease Control of Luchen, No. 3320 Guojing Road, Wenzhou, Zhejiang, 325005, People’s Republic of China, Tel +86 577 56760657, Fax +86 577 56760654, Email cxbrook0577@163.comObjective: This study aims to evaluate the utility of targeted next-generation sequencing (tNGS) in bronchoalveolar lavage fluid (BALF) for hospitalized patients with pulmonary infections.Methods: A cohort of 358 patients who received diagnosis and treatment for respiratory infections in the department of Respiratory Medicine at Wenzhou People’s hospital from January 2023 to April 2024 were selected for this study. The BALF of the patients was analyzed using tNGS, and the diagnostic efficacy of tNGS was subsequently compared with that of conventional testing methods (CTs) for pathogen detection.Results: Through the analysis of tNGS from the cohort, the pathogen detection rate in BALF using tNGS was significantly higher than that of CTs (90.22% VS 57.26%, P=0.001). Among them, Tropheryma Whipplei (6.15%), Bordetella pertussis (2.51%), Non-tuberculous mycobacteria (1.96%), Mycobacteria tuberculosis (1.40%), Chlamydia pneumoniae (1.96%), Chlamydia psittaci (0.56%), Legionella pneumophila (0.28%) were detected using tNGS alone, and the CTs results of these microorganisms were all negative. Among the various types of mixed infections observed, concurrent presence of bacteria and viruses was the most common, accounting for 37.15%. The detection rates of tNGS and CTs have statistical significance (66.87% VS 35.12%, P=0.001). Furthermore, a total of 61 cases of antimicrobial resistance genes were detected, including 34 cases of 23S rRNA A2063G, 6 cases of KPC, 5 cases of OXA, 2 cases of CTX-M, 3 cases of IMP, 1 case of NDM and 13 cases of mecA. Using the clinical diagnosis as references, the positive coincidence rate of the tNGS was significantly higher compared to that of the CTs (P=0.012).Conclusion: Compared to CTs, the application of tNGS enables the identification of a greater diversity of organisms and exhibits superior accuracy, effectively identifying pathogens that are undetectable by CTs, especially fastidious and atypical organisms. Consequently, it holds immense potential in pathogen diagnosis and offers valuable clinical guidance for patients with pulmonary infections.Keywords: bronchoalveolar lavage fluid, targeted next-generation sequencing, pneumonia, pathogen, culture, antimicrobial resistant

Huihui Zhang,1,&ast; Xiaojing Zhang,2,&ast; Yafeng Zheng,2,&ast; Xiao Gu,1 Zhongming Fu,1 Wei Gai,2 Huaying Wang1 1Department of Respiratory and Critical Care Medicine, The Affiliated People’s Hospital of Ningbo University, Yinzhou People’s Hospital, Ningbo, Zhejiang, 315040, People’s Republic of China; 2WillingMed Technology (Beijing) Co., Ltd, Beijing, People’s Republic of China&ast;These authors contributed equally to this workCorrespondence: Wei Gai, WillingMed Technology (Beijing) Co., Ltd, No. 156 Jinghai 4th Road, Beijing Economic and Technological Development Zone, Beijing, 101103, People’s Republic of China, Email weigai@willingmed.com Huaying Wang, The Affiliated People’s Hospital of Ningbo University, Yinzhou People’s Hospital, No. 251, Baizhang East Road, Ningbo, 315040, People’s Republic of China, Email yingmeire@163.comPurpose: This study aimed to investigate the impact of herpesvirus detection by metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) on lower respiratory tract infections (LRTIs) patients’ lung microbiome composition and prognosis.Patients and methods: We initially enrolled 234 hospitalized patients with LRTIs who underwent BALF mNGS between February 2022 and May 2023. The study analyzed the clinical manifestations and the pulmonary microbial composition between herpesvirus detection (HD) and non-herpesvirus detection (non-HD) group.Results: After exclusions, a total of 201 patients were included, out of which 73 patients had herpesvirus detections (HD). The most frequently detected herpesviruses were Human herpesvirus 7 (HHV-7) (19.4%), Epstein-Barr virus (EBV) (12.4%), and cytomegalovirus (CMV) (10.4%). The HD group had a higher proportion of male patients (78.08% vs 55.04%, P = 0.001) and a greater incidence of hemoptysis and multilobar infiltrates compared non-HD group. Additionally, the HD group tended to have longer hospital stays compared to non-HD group, especially in immunosuppressed patients. Furthermore, in immunocompetent patients, there were significant differences in α diversity and β diversity between the HD group and non-HD group, but such differences were not observed in immunosuppressed patients.Conclusion: The presence of herpesvirus in patients with non-critical LRTI is associated with longer hospital stays and alterations in the lung’s microbial composition. Additionally, the impacts of herpesvirus presence are influenced by the immune status of the patients.Keywords: lower respiratory tract infections, herpesvirus detection, bronchoalveolar lavage fluid, microbial composition, mNGS

BackgroundSilicosis is an occupational disease mainly characterized by pulmonary progressive fibrosis induced by the accumulation of free silica (SiO2) in the lungs due to long-term exposure to SiO2 dust. It has been shown that neutrophil extracellular traps (NETs) are increased in the lung tissues of silicotic mice after 28 d SiO2 exposure, but it is unclear how the levels of NETs change throughout entire progression of silicosis in mice. ObjectiveTo observe the levels of NETs and pathological changes in the lungs of silicotic mice after different duration of SiO2 exposure, and to confirm the possible role and significance of NETsin the development of SiO2-induced pulmonary fibrosis. MethodsA total of 28 SPF male C57BL/6J mice were randomly divided into a control group, and a model group, and the model group was subdivided into, a 2 d model group, a 7 d model group, and a 28 d model group, with 7 mice in each group. The mice in the model groups were given intratracheal instillation with 10 mg SiO2 suspension (50 μL), and the mice in the control group were received same volume of saline. Mice were sacrificed and samples were collected at designed time points. The pathological changes of lung tissues of mice were observed after hematoxylin-eosin (HE) and Van Gieson (VG) staining. Immunofluorescence was used to observe the NETs markers citrullination histone H3 (CitH3) and myeloperoxidase (MPO) in bronchoalveolar lavage fluid (BALF), and the percentage of NETs-positive cells was calculated. PicoGreen fluorescent dye kit was used to detect the content of extracelluar DNA (ex-DNA) in mouse BALF, and the expression levels of fibrosis-related proteins α-smooth muscle actin (α-SMA) and fibronectin (FN) and NETs marker CitH3 in lung tissues of mice were detected by Western blot (WB). ResultsCompared with the control group, inflammatory cells accumulation, alveolar wall thickening, and collagen deposition were obviously observed in the lungs of the silicosis model groups, and a large number of silicone nodules were recorded in the lung tissues in the 28 d group. Compared with the control group, the expressions of α-SMA and FN in the lung tissue of the 28 d group were significantly increased (P

Sha Wen,&ast; Jing-Jing Zeng,&ast; Ying Li Department of Critical Care Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, People’s Republic of China&ast;These authors contributed equally to this workCorrespondence: Ying Li, Email liying20020813@163.comAbstract: Rickettsia felis (R. felis) is a Gram-negative obligate intracellular bacterium with a global presence across various hosts, including mammals, humans, and ectoparasites. Herein, we present a case of R. felis infection in a previously healthy 43-year-old male with a history of Clonorchis sinensis and recent corticosteroid use. The identification of R. felis was accomplished through metagenomic next-generation sequencing (mNGS) of the patient’s bronchoalveolar lavage fluid (BALF). This case represents the first documented pulmonary infection caused by R. felis in China, confirmed by mNGS analysis of bronchoalveolar lavage fluid (BALF) and reported from Shenzhen, China.Keywords: mNGS technology, Rickettsia felis, bronchoalveolar lavage fluid, pulmonary infection

Abstract Reports on the application of metagenomic next-generation sequencing (mNGS) in adult patients with severe pneumonia after cardiac surgery remain limited. This study aimed to evaluate the clinical outcomes of mNGS analysis of bronchoalveolar lavage fluid (BALF) in such patients.A retrospective cohort study was conducted on adult patients with severe pneumonia after cardiac surgery. Samples were collected from patients in the surgical intensive care unit (SICU) of Sichuan Provincial People’s Hospital between January 2019 and March 2024. Upon diagnosis of severe pneumonia, bronchoalveolar lavage fluid was obtained via bronchoscopy within 24 h. The mNGS group was composed of patients tested using mNGS and conventional microbiological tests. BALF was detected only by the conventional microbiological test (CMT) method in the CMT group, which involved examining bacterial and fungal smears and cultures at least. We reviewed a total of 4,064 cardiac surgeries, and based on the inclusion criteria, a total of 113 adult patients with severe pneumonia after cardiac surgery were included in this study. The overall positive rate detected by mNGS was significantly higher than that of the culture method (98% vs. 58%, P

Abstract Background Early targeted antibiotic therapy is crucial for improving the prognosis of immunocompromised patients with severe respiratory infections (SRIs) in the intensive care unit (ICU). Metagenomic next-generation sequencing (mNGS) has shown significant value in pathogen detection, but research on lower respiratory tract microorganisms remains limited. Methods This study enrolled 234 patients with SRIs in the ICU, and individuals were categorized into immunocompromised and immunocompetent groups. We compared the diagnostic performance of mNGS using bronchoalveolar lavage fluid (BALF) with conventional microbiological tests (CMTs) and analyzed the value of mNGS in immunocompromised patients with SRIs in the ICU. Results Among all patients, the pathogenic microorganism detection rate of mNGS was higher than that of CMTs (94.02% vs 66.67%, P 0.05; 42.67% vs 45.83%, P > 0.05). Conclusion mNGS shows significant value in detecting pathogens in immunocompromised patients with SRIs in ICU. For immunocompromised patients who respond poorly to empirical treatment, mNGS can provide an etiological basis, helping adjust antibiotic regimens more precisely and thereby improving patient prognosis.

Abstract Background The epidemiology of fungi identified via next-generation sequencing in bronchoalveolar lavage fluid among patients with COVID-19 is unknown. Methods De-identified information, including age, SARS-CoV-2 reads and fungi from bronchoalveolar lavage fluid, were used to analysis. Results A total of 960 patients with COVID-19 were included. Gender was unknown in 38 patients, and 648 (70.3%) of the rest patients were male. For 876 patients with information on age, their mean ± standard age was 63.4 ± 21.3 years, with the minimum being 0.2 years and the maximum being 101 years. For all the patients, their median [interquartile range] SARS-CoV-2 reads were 26,038 [4421.5, 44,641.5]. The Aspergilli were identified in 159 (16.6%) patients, with Aspergillus fumigatus, Aspergillus flavus and Aspergillus niger in 103 (10.7%), 81 (8.4%) and 17 (1.8%), respectively. The Mucoraceae were identified in 14 (1.5%) patients. Pneumocystis jirovecii was identified in 65 (6.8%) patients, among whom 12 (18.5%) patients also had Aspergilli. The Cryptococcaceae and the Dematiaceae were also identified in some patients, including Cryptococcus in 11 (1.1%) patients. Conclusions In bronchoalveolar lavage fluid among patients with COVID-19, the Aspergilli were very commonly identified, as were the Mucoraceae, Pneumocystis jirovecii and Cryptococcus via next-generation sequencing.

The number of invasive fungal infections is as high as about 6. 55 million people each year in the world, and it leads to about 3.8 million deaths, among which aspergillus pulmonary infection is the most common. Because the specificity of clinical and imaging manifestations of pulmonary aspergillosis is not obvious, traditional laboratory tests have different degrees of limitations such as long detection period and relatively low sensitivity. Molecular biology detection techniques such as next generation sequencing and Aspergillus polymerase chain reaction have made up for the shortcomings of traditional diagnostic techniques. Molecular biology technology is bound to usher in a broader application prospect. [ABSTRACT FROM AUTHOR]

Objective To elucidate the clinical significance in facilitating timely diagnosis and treatment of RMPP in children by investigating the association between infection caused by macrolide-resistant Mycoplasma pneumoniae (MRMP) and refractory Mycoplasma pneumoniae pneumonia (RMPP) in pediatric patients. Methods The clinical data of 714 hospitalized children with refractory Mycoplasma pneumoniae pneumonia (RMPP) were retrospectively analyzed. Bronchoscopy and bronchoalveolar lavage fluid (BALF) were performed on each subject, and the BALFs were collected to detect mutation sites in the V region of 23S rRNA for Mycoplasma pneumoniae DNA. Based on the gene detection results, children with RMPP were categorized into a macrolide-resistant group and a control group (non-macrolide-resistant group). Results A total of 714 children diagnosed with refractory Mycoplasma pneumoniae pneumonia (RMPP) were enrolled in this study, including 509 cases in the macrolide-resistant group and 205 cases in the control group. Among them, there were 369 males (54. 7%) and 345 females (45. 3%). The macrolide-resistant group exhibited higher average age, fever duration, and hospitalization days compared to the control group. Furthermore, elevated levels of white blood cell count (WBC), neutrophil percentage (NE%), high-sensitivity C-reactive protein (hs-CRP), lactate dehydrogenase (LDH), and interleukin-6 (IL-6) were observed in the macrolide-resistant group when compared to the control group (P ＜ 0. 05 or P ＜ 0. 000 1). Compared to the control group, children with macrolide-resistant Mycoplasma pneumoniae pneumonia (RMPP) exhibited higher incidences of lung consolidation, pleural effusion, necrotic pneumonic lesions, severe MPP (SMPP) /fulminant MPP (FMPP), flocculent and viscous tracheal secretions, severe mucosal lesions (erosion, ulceration or necrosis), bronchial inflammatory stenosis, endo-bronchial plastic phlegm plugs and extra-pulmonary complications (P ＜ 0. 05 or P ＜0. 0001). Conclusions MRMP infection can contribute to the development of RMPP, potentially exacerbating respiratory conditions in affected children. Timely bronchoscopy and collection of BALF samples for accurate evaluation of respiratory tract lesions and detection of MRMP infection have significant implications for guiding precise clinical diagnosis and treatment. [ABSTRACT FROM AUTHOR]

Objective: To evaluate the diagnostic value of metagenomic next-generation sequencing (mNGS) in pulmonary cryptococcosis (PC) using bronchoalveolar lavage fluid (BALF) and lung biopsy tissue specimens. Methods: In this retrospective study, 321 patients diagnosed with lower respiratory tract diseases who underwent mNGS using BALF and LBT samples, between January 2021 and December 2023 were included. Individuals were classified into PC and non-PC groups according to the diagnostic criteria for PC, and conventional fungal cultures were performed. A serum/BALF cryptococcal antigen (CrAg) test was performed in some patients with PC. The diagnostic efficiencies of three methods for PC (mNGS, conventional culture, and CrAg) were compared. Additionally, two mNGS methods were used in this study: original mNGS (OmNGS, testing time from January 2021 to December 2022) and modified mNGS (MmNGS, testing time from January to December 2023). The diagnostic efficiency of the two mNGS methods on PC was simultaneously compared. Results: Among the 321 patients, 23 (7.2%) had PC and 298 (92.8%) did not. Compared with the composite reference standard for PC diagnosis, the sensitivity, specificity, and accuracy of mNGS for PC were 78.3% (95% confidence interval [CI], 55.8%–91.7%), 98.7% (95% CI, 96.4%–99.6%), and 97.2% (95% CI, 94.7%–98.7%), respectively. The sensitivity of mNGS was similar to that of CrAg (80.0%, 12/15) (P > 0.05). The diagnostic sensitivity of both mNGS and CrAg was higher than that of conventional culture (35.0%, 7/20) (P = 0.006, P = 0.016), and the combined detection of mNGS and CrAg further improved the diagnostic sensitivity of PC (93.3%, 14/15). The area under the receiver operating characteristic curve of mNGS was superior to that of conventional culture (0.885 vs. 0.675). In addition, the diagnostic sensitivity of PC was higher than that of OmNGS (P = 0.046). Conclusion: The sensitivity of mNGS is better than that of conventional culture. The combination of mNGS and CrAg improves the testing sensitivity of Cryptococcus. MmNGS could further improve the detection of Cryptococcus. Conventional PC detection methods are indispensable and mNGS can be used as a rapid and accurate auxiliary diagnostic method for PC. [ABSTRACT FROM AUTHOR]

Introduction Deployed military personnel may be at risk for developing acute and chronic lung disease. Prior studies of this patient population have revealed that unexplained exertional dyspnea is the most common diagnosis despite an extensive evaluation. There is a concern that an occult disorder may be affecting this population. This study evaluated the role for bronchoalveolar lavage (BAL) fluid analysis in the evaluation of chronic deployment-associated dyspnea. Materials and Methods Military personnel who reported chronic respiratory symptoms were evaluated as part of the Study of Active Duty Military for Pulmonary Disease Related to Environmental Deployment Exposures III study. Participants underwent bronchoscopy with BAL as part of a standardized evaluation. Results A total of 308 patients with a mean age of 38 ± 8.6 years underwent bronchoscopy with BAL. BAL cell-count percentages of macrophages, lymphocytes, neutrophils, and eosinophils were: 76.2 ± 17.0%, 16.3 ± 13.4%, 6.6 ± 8.9%, and 0.9 ± 3.2%, respectively. There was no clear differentiation between groups based on increases in lymphocyte counts (P  = .640), although lymphocyte values were more elevated (21.4 ± 12.1%) in the interstitial lung disease category. Neutrophil counts (6.6 ± 8.9%) were elevated compared to the reported normal reference values and were increased in the isolated pulmonary function test abnormality (9.4 ± 11.6%), large airway disorder (10.0 ± 7.5%), miscellaneous (10.9 ± 20.2%), and obstructive lung disease (11.0 ± 15.6%) groups. Eosinophil counts were within normal limits (0.9 ± 3.2%) and showed no differences between groups (P  = .545); asthma patients trended higher (1.6 ± 5.7%). BAL counts for the exertional dyspnea group were within normal reference values and showed no differences from the entire cohort. Conclusions The addition of BAL cytology did not help differentiate those patients with unexplained dyspnea from other etiologies. [ABSTRACT FROM AUTHOR]

Background: This study aimed to evaluate the anti-inflammatory effects of a Zephyranthes rosea in an ovalbumin-induced asthma model. Methods: Allergic asthma was induced in mice via intraperitoneal injection, followed by intranasal ovalbumin challenge. Methanolic extract of Z. rosea bulb was orally administered to asthmatic mice for 14 days. Hematological parameters for bronchoalveolar lavage fluid (BALF) and blood were analyzed. The mRNA expression levels of interleukins and transforming growth factor beta (TGF-β1) in lung tissues were determined using reverse transcriptase–polymerase chain reaction (RT–PCR). Network pharmacology analysis was used to find possible Z. rosea targets. After building a protein–protein interaction network to find hub genes, GO and KEGG enrichment analyses were carried out to determine the potential mechanism. In silico analysis was performed by Molecular Operating Environment. Results: GC-MS analysis of Z. rosea extract detected major classes of phytochemicals. Hematological parameters in blood and BALF from Z. rosea extract-treated animals were significantly reduced in a dose-dependent fashion. Histopathology revealed that Z. rosea bulb had an ameliorative effect on lung tissues. Moreover, treatment with Z. rosea bulb extract significantly restored the normal levels of IL-4, IL-6, IL-1β, IL-10, IL-13, and TGF-β1 in allergic asthmatic mice compared to the diseased group. In silico analysis, particularly of the binding affinities of Z. rosea bulb phytoconstituents for IL6, AKT1, and Src, supported in vivo results. Conclusions: These findings indicated that Z. rosea bulb extract significantly ameliorates cellular and molecular biomarkers of bronchial inflammation and could be a potential candidate for treating allergic asthma. [ABSTRACT FROM AUTHOR]

Background: Checkpoint inhibitor pneumonitis (CIP) is a relatively uncommon but potentially life-threatening immune-related adverse event (irAE). Lung biopsies have not been commonly performed for CIP patients. Bronchoalveolar lavage fluid (BALF) analysis is a useful diagnostic approach for interstitial lung disease. However, BALF features were inconsistent across different studies. Methods: We retrospectively reviewed the medical records of 154 patients with pathologically confirmed malignancies and suffering from CIPs between July 2018 and December 2022. Patients who had bronchoalveolar lavage (BAL) data available were enrolled in our study. Patient clinical, laboratory, radiological and follow-up data were reviewed and analyzed. Results: The BALF differential cell count and lymphocyte subset analysis were performed for 42 CIP patients. There were 32 males (76.2%). The mean age at diagnosis of CIP was 62.0 ± 10.4 (range: 31–78) years. The median time to onset of CIP was 98.5 days after the start of immunotherapy. There were 18 patients (42.9%) with low-grade CIPs and 24 patients (57.1%) with high-grade CIPs. The mean lymphocyte percentage was 36.7 ± 22.5%. There were 34 (81%) CIP patients with a lymphocytic cellular pattern. The median ratio of CD3+CD4+/CD3+CD8+ lymphocytes was 0.5 (0.3, 1.0). The ratio was less than 1.0 for 31 CIP patients (73.8%). However, there was no significant difference in the BALF features between patients with low-grade CIPs and those with high-grade CIPs. Conclusions: The CD3+CD8+ lymphocytosis pattern was the main inflammatory profile in the BALF of CIP patients in this cohort. Targeting CD3+CD8+ lymphocytes might be a treatment option for CIPs. [ABSTRACT FROM AUTHOR]

The increasing prevalence of non-tuberculous mycobacterium (NTM) infections alongside tuberculosis (TB) underscores a pressing public health challenge. Yet, the mechanisms governing their infection within the lung remain poorly understood. Here, we integrate metagenomic sequencing, metabolomic sequencing, machine learning classifiers, SparCC, and MetOrigin methods to profile bronchoalveolar lavage fluid (BALF) samples from NTM/TB patients. Our aim is to unravel the intricate interplay between lung microbial communities and NTM/ Mycobacterium tuberculosis infections. Our investigation reveals a discernible reduction in the compositional diversity of the lung microbiota and a diminished degree of mutual interaction concomitant with NTM/TB infections. Notably, NTM patients exhibit a distinct microbial community characterized by marked specialization and notable enrichment of Pseudomonas aeruginosa and Staphylococcus aureus , driving pronounced niche specialization for NTM infection. Simultaneously, these microbial shifts significantly disrupt tryptophan metabolism in NTM infection, leading to an elevation of kynurenine. Mycobacterium intracellulare , Mycobacterium paraintracellulare , Mycobacterium abscessus , and Pseudomonas aeruginosa have been implicated in the metabolic pathways associated with the conversion of indole to tryptophan via tryptophan synthase within NTM patients. Additionally, indoleamine-2,3-dioxygenase converts tryptophan into kynurenine, fostering an immunosuppressive milieu during NTM infection. This strategic modulation supports microbial persistence, enabling evasion from immune surveillance and perpetuating a protracted state of NTM infection. The elucidation of these nuanced microbial and metabolic dynamics provides a profound understanding of the intricate processes underlying NTM and TB infections, offering potential avenues for therapeutic intervention and management. [ABSTRACT FROM AUTHOR]

Background: Early targeted antibiotic therapy is crucial for improving the prognosis of immunocompromised patients with severe respiratory infections (SRIs) in the intensive care unit (ICU). Metagenomic next-generation sequencing (mNGS) has shown significant value in pathogen detection, but research on lower respiratory tract microorganisms remains limited. Methods: This study enrolled 234 patients with SRIs in the ICU, and individuals were categorized into immunocompromised and immunocompetent groups. We compared the diagnostic performance of mNGS using bronchoalveolar lavage fluid (BALF) with conventional microbiological tests (CMTs) and analyzed the value of mNGS in immunocompromised patients with SRIs in the ICU. Results: Among all patients, the pathogenic microorganism detection rate of mNGS was higher than that of CMTs (94.02% vs 66.67%, P < 0.05), both in the immunocompromised group (95.0% vs 58.75%, P < 0.05) and the immunocompetent group (93.51% vs 71.43%, P < 0.05). mNGS detected more pathogens than CMTs did (167 vs 51), identifying 116 organisms that were missed by CMTs. The proportion of antibiotic regimen adjustments based on mNGS results was significantly higher compared to CMTs in both the immunocompromised (70.00% vs 17.50%, P < 0.05) and immunocompetent groups (48.70% vs 15.58%, P < 0.05). In the immunocompromised group, patients who had their antibiotic treatment adjusted on mNGS results had improved prognosis, with significantly lower ICU mortality (8.93% vs 50%, P < 0.05) and 28-day mortality rates (30.36% vs 68.75%, P < 0.05) than CMTs. In the immunocompetent group, no statistically significant differences were observed in ICU mortality or 28-day mortality (20.00% vs 33.33%, P > 0.05; 42.67% vs 45.83%, P > 0.05). Conclusion: mNGS shows significant value in detecting pathogens in immunocompromised patients with SRIs in ICU. For immunocompromised patients who respond poorly to empirical treatment, mNGS can provide an etiological basis, helping adjust antibiotic regimens more precisely and thereby improving patient prognosis. [ABSTRACT FROM AUTHOR]

Sulfur mustard (SM) is an established chemical weapon that can result in severe damage to parts of the body. Currently, there are no effective treatments available for SM-caused damage. We aimed to investigate the therapeutic potential of adipose-derived mesenchymal stromal cells (AD-MSCs) and conditioned medium (CM-MSCs) in acute and chronic pulmonary mouse models caused by 2- chloroethyl ethyl sulfide (CEES), an SM analog. The mice were divided into 4 experimental groups:(1) CEES+AD-MSCs, (2) CEES+CMMSCs, (3) CEES, and (4) control. The model observation time was divided into 7 days for the short and 6 months for the long term. AD-MSCs were injected into mice via intraperitoneal injection 24 hours after CEES exposure. The therapeutic effects of AD-MSCs on pulmonary tissue damage were assessed using a histopathologic assay, measuring the neutrophil count, and bronchial alveolar lavage fluid (BALF) protein level. The levels of inflammatory and anti-inflammatory cytokines were evaluated using the enzyme-linked immunosorbent assay as the outcomes of interest. Lung damage progression was reduced by AD-MSC treatment in mice after CEES injection into the peritoneum. The proportion of CD11b+F4/80+ macrophages in the peritoneum was significantly lowered by AD-MSC treatment following CEES exposure. AD-MSC administration also reduced the level of pro-inflammatory cytokines, BALF protein, and nitric oxide levels in the peritoneal cavity. By reducing inflammation and enhancing tissue healing, AD-MSCs and CM-MSC help prevent acute lung damage caused by CEES. The current study supports the use of a mouse model as a solid experimental foundation and indicates potential use for future cell treatment. [ABSTRACT FROM AUTHOR]

Objective To analyze the clinical value of metagenomic next-generation sequencing (mNGS) in the pathogen detection of elderly patients with community-acquired pneumonia (CAP). Methods A total of 112 elderly CAP patients were included in the study. The detection efficiency of pathogens using mNGS was compared with conventional microbiological tests (CMTs). Statistical analyses were conducted using Fisher′s exact test and ROC curves to evaluate the diagnostic differences between mNGS and CMTs. Results The overall diagnostic rate of mNGS was significantly higher than that of CMTs (94.6% vs. 65.2%, P＜0.001). The detection time for mNGS was significantly shorter than that for CMTs [ (26.3±5.9)h vs. (85.5±6.4)h; t=21.034, P＜0.05]. mNGS detected a higher number of bacterial, viral, fungal, and atypical pathogens compared to CMTs. The detection rate for mixed infections with mNGS was 76.4%, significantly higher than CMTs′ 60.3% (χ²=6.851, P＜0.05). Of the detected pathogens, there were 64 cases of agreement, 35 cases of partial agreement, and 13 cases of complete disagreement between mNGS and CMTs. Conclusion mNGS demonstrates superior capability in detecting a broader spectrum of pathogens in elderly patients with community-acquired pneumonia, highlighting its significant clinical value. [ABSTRACT FROM AUTHOR]

Mycoplasmapneumoniae pneumonia (MPP) is a common respiratory tract infection disease in children. To date, there have been few studies on the relationship between cytological changes in bronchoalveolar lavage fluid (BALF) and clinical features. The objective of this study is to investigate the correlation between changes in the proportion of cell classifications in BALF and the clinical features in children with severe MPP (SMPP). In total, the study included 64 children with SMPP requiring bronchoalveolar lavage who were admitted to our hospital between March and September 2022 (study group) and 11 children with bronchial foreign bodies without co-infection (control group), who were admitted during the same period. The proportion of cell classifications in BALF was determined by microscopic examination after performing Wright-Giemsa staining. Patients were grouped according to different clinical characteristics, and between-group comparisons were made regarding the variations in the proportion of cell classifications in BALF. The levels of blood routine neutrophil percentage (GRA%), C-reactive protein, D-dimer and lactate dehydrogenase in the study group were higher than those in the control group (P < 0.05). There were differences in the GRA% and macrophage percentage in the BALF between the two groups (P < 0.05). The GRA% and blood lymphocyte percentage were associated with pleural effusion. Multiple indicators correlated with extrapulmonary manifestations (P < 0.05). Moreover, the percentage of lymphocytes in the BALF correlated with pleural effusion, extrapulmonary manifestations and refractory MPP (RMPP) (P < 0.05). Logistic regression showed that BALF lymphocytes were protective factors for RMPP, while serum amyloid A and extrapulmonary manifestations were risk factors (P < 0.05). Conclusion: The BALF of children with SMPP is predominantly neutrophilic. A lower percentage of lymphocytes is related to a higher incidence of pleural effusion, extrapulmonary manifestations and progression to RMPP, as well as a longer length of hospitalisation. What Is Known: • Mycoplasma pneumonia in children is relatively common in clinical practice. Bronchoalveolar lavage (BAL) is a routine clinical procedure. What Is New: However, there are relatively few studies focusing on the cytomorphological analysis of cells in BAL fluid. [ABSTRACT FROM AUTHOR]