Bronchoalveolar Lavage Fluid Culture Research Articles

Clinical analysis of pulmonary nocardiosis associated with bronchiectasis

Objective: To better understand the clinical characteristics of pulmonary nocardiosis associated with bronchiectasis. Methods: Patients diagnosed as bronchiectasis complicated with pulmonary nocardiosis in 9 tertiary general hospitals in China were enrolled from March 2016 to March 2020, with the record of general data, imaging performance and pathogen. The literature was reviewed. Results: Totally 17 patients were included. There were 12 females and 5 males. The ages ranged from 45 to 79 years, with an average of (63±9) years. There were 15 nonsmokers and 2 smokers, all of whom with chronic course. The clinical manifestations were mostly cough, expectoration, hemoptysis, fever, and dyspnea. The imaging manifestation was bronchiectasis in both lungs, with the most common involvement in the left lower lung, right middle lobe and left lingual lobe. Sputum cultures were positive in 10 cases, bronchoalveolar lavage fluid (BALF) cultures were positive in 6 cases, and next generation gene sequencings were positive in 4 cases, including 2 cases of Nocardia gelsenkii, 2 cases of Nocardia abscess, 2 cases of Nocardia stellate, 1 case of Nocardia mexicana, 1 case of Nocardia otitis caviae, and 9 cases of undetermined Nocardia. There were 3 cases of Klebsiella pneumoniae, 2 cases of Pseudomonas aeruginosa and 2 cases of Aspergillus. The symptoms and imaging of all patients were improved after anti Nocardia therapy. Conclusions: Bronchiectasis combined with nocardiosis is more common in middle-aged and elderly women without smoking, which is similar to the clinical manifestations of Lady Windermere syndrome. Bronchiectasis often involves the left lower lobe, right middle lobe and left lingual lobe. Nocardia infection might further precipitate the initiation and progression of bronchiectasis.

Diagnostic Significance of Metagenomic Next-Generation Sequencing for Community-Acquired Pneumonia in Southern China.

BackgroundThe morbidity and mortality of community-acquired pneumonia are relatively high, but many pneumonia pathogens cannot be identified accurately. As a new pathogen detection technology, metagenomic next-generation sequencing (mNGS) has been applied more and more clinically. We aimed to evaluate the diagnostic significance of mNGS for community-acquired pneumonia (CAP) in the south of China.MethodsOur study selected CAP patients who visited the 3rd Xiangya Hospital from May 2019 to April 2021. Pathogens in bronchoalveolar lavage fluid (BALF) specimens were detected using mNGS and traditional microbiological culture. mNGS group: detected by both mNGS and BALF culture; control group: detected only by BALF or sputum culture. The diagnostic performance of pathogens and the antibiotic adjustments were compared within mNGS group.ResultsThe incidence of acute respiratory distress syndrome (ARDS) was 28.3% in the mNGS group and 17.3% in the control group. Within the mNGS group, the positive rate of pathogens detected by mNGS was 64%, thus by BALF culture was only 28%. Pathogens detected by mNGS were consisted of bacteria (55%), fungi (18%), special pathogens (18%), and viruses (9%). The most detected pathogen by mNGS was Chlamydia psittaci. Among the pathogen-positive cases, 26% was not pathogen-covered by empirical antibiotics, so most of which were made an antibiotic adjustment.ConclusionsmNGS can detect pathogens in a more timely and accurate manner and assist clinicians to adjust antibiotics in time. Therefore, we recommend mNGS as the complementary diagnosis of severe pneumonia or complicated infections.

LncRNA MEG3 ameliorates NiO nanoparticles-induced pulmonary inflammatory damage via suppressing the p38 mitogen activated protein kinases pathway.

The lung inflammatory damage could result from the nickel oxide nanoparticles (NiO NPs), in which the underlying mechanism is still unclear. This article explored the roles of long noncoding RNA maternally expressed gene 3 (lncRNA MEG3) and p38 mitogen activated protein kinases (p38 MAPK) pathway in pulmonary inflammatory injury induced by NiO NPs. Wistar rats were treated with NiO NPs suspensions (0.015, 0.06, and 0.24 mg/kg) by intratracheal instillation twice-weekly for 9 weeks. Meanwhile, A549 cells were treated with NiO NPs suspensions (25, 50, and 100 μg/ml) for 24 h. It can be concluded that the NiO NPs did trigger pulmonary inflammatory damage, which was confirmed by the histopathological examination, abnormal changes of inflammatory cells and inflammatory cytokines (IL-1β, IL-6, TGF-β1, TNF-α, IFN-γ, IL-10, CXCL-1 and CXCL-2) in bronchoalveolar lavage fluid (BALF), pulmonary tissue and cell culture supernatant. Furthermore, NiO NPs activated the p38 MAPK pathway and downregulated MEG3 in vivo and in vitro. However, p38 MAPK pathway inhibitor (10μM SB203580) reversed the alterations in the expression levels of inflammatory cytokines induced by NiO NPs. Meanwhile, over-expressed MEG3 significantly suppressed NiO NPs-induced p38 MAPK pathway activation and inflammatory cytokines changes. Overall, the above results proved that over-expression of lncRNA MEG3 reduced NiO NPs-induced inflammatory damage by preventing the activation of p38 MAPK pathway.

COVID-19-associated pulmonary aspergillosis in a tertiary care center in Shenzhen City

ObjectivesThe severe coronavirus disease 2019 (COVID-19) is characterized by acute respiratory distress syndrome (ARDS) and risk of fungal co-infection, pulmonary aspergillosis in particular. However, COVID-19 associated pulmonary aspergillosis (CAPA) cases remain limited due to the difficulty in diagnosis. MethodsWe describe presumptive invasive aspergillosis in eight patients diagnosed with COVID-19 in a single center in Shenzhen, China. Data collected include underlying conditions, mycological findings, immunodetection results, therapies and outcomes. ResultsFour of the eight patients had tested positive for Aspergillus by either culture or Next-generation sequencing analysis of sputum or bronchoalveolar lavage fluid (BALF), while the rest of patients had only positive results in antigen or antibody detection. Although all patients received antifungal therapies, six of these eight patients (66.7%) died. ConclusionDue to the high mortality rate of CAPA, clinical care in patients with CAPA deserves more attention.

Pulmonary alveolar proteinosis with secondary Aspergillus infection: A case report

Pulmonary alveolar proteinosis (PAP) is a rare disease with mostly due to autoimmune toward granulocyte-macrophage colony-stimulating factor. In some conditions, PAP followed with secondary infection. A 34-year-old woman came with progressive shortness of breath, chronic dry cough, and mild fever. The chest High-Resolution Computed Tomography showed ground-glass opacity with septal reticulation or known as the crazy-paving pattern, and a cavity on the upper lobe of the left lung. The patient underwent bronchoscopy for diagnostic and therapeutic measures and found milky appearance bronchoalveolar lavage fluid (BALF). The serum galactomannan came out positive. Fungal infection detected from the BALF culture, Aspergillus fumigatus, hence fulfilling the diagnosis of PAP with probable invasive pulmonary aspergillosis. The patient showed clinical improvement after undergoing whole lung lavage and given anti-fungal medications.

Bacterial infection in dogs with aspiration pneumonia at 2 tertiary referral practices.

BackgroundIn dogs, antimicrobial drugs are widely prescribed for aspiration pneumonia (AP) despite poor documentation of bacterial infection in AP (b‐AP) using bronchoalveolar lavage fluid (BALF) analysis. Interpretating discordant cytology and culture results is challenging, contributing to lack of a criterion standard, and highlighting differences between veterinary and human medical criteria for b‐AP.ObjectivesDetermine how many dogs with AP had BALF collection and differences in diagnosis of b‐AP using veterinary vs human medical criteria. Report findings of noninvasive markers (e.g. fever, band neutrophilia, radiographic severity score) in dogs with and without b‐AP.AnimalsRetrospective cohort study of client‐owned dogs (n = 429) with AP at 2 university veterinary hospitals. Twenty‐four dogs met enrollment criteria.MethodsInclusion criteria were radiographic diagnosis of AP, ≥1 risk factor, CBC findings, and BALF cytology and culture results. Veterinary medical b‐AP criteria were cytology findings compatible with sepsis with or without positive culture, or cytology findings not consistent with sepsis and positive culture (≥1.7 × 103 cfu/mL). Human medical b‐AP criteria required culture with ≥104 cfu/mL or > 7% cells with intracellular bacteria on cytology.ResultsOnly 24/429 dogs met all enrollment criteria; 379/429 dogs lacked BALF collection. Diagnosis of b‐AP differed using veterinary (79%) vs human (29%) medical criteria. Fever, band neutrophils and high radiographic scores were noted in dogs with and without b‐AP.Conclusions and Clinical ImportanceLack of routine BALF collection hampers definitive recognition of bacterial infection in AP. Differences in dogs meeting veterinary vs human medical definitions for b‐AP and usefulness of noninvasive markers warrant further study to improve understanding of the role of bacteria in AP.

Neutrophils and secondary infections in COVID-19 induced acute respiratory distress syndrome

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus is the cause of the current global pandemic and has affected more than 188 countries worldwide. Infection by the virus can have diverse clinical manifestations, with one of the most severe clinical manifestation being respiratory failure and the development of acute respiratory distress syndrome. Clinical manifestations of acute respiratory distress syndrome secondary to SARS-CoV-2 are also diverse with a lack of diagnostic tools to distinguish between primary viral infection and secondary bacterial infections. This was a single-centre, retrospective case-control study of bronchoalveolar lavage fluid cell counts, flow cytometry and culture results from mechanically ventilated patients with SARS-CoV-2 (COVID-19) pneumonia and acute respiratory distress syndrome. Neutrophils were the predominant cell type in bronchoalveolar fluid samples up to 2 weeks into mechanical ventilation. There also was a strong correlation between positive respiratory cultures and significant elevation in bronchoalveolar fluid neutrophil counts/percentages and serum C-reactive protein levels. Absolute levels of T cell subtypes correlated with reduced lung compliance measurements. Patients with SARS-CoV-2 and severe respiratory disease are at risk for secondary infections. In some COVID-19 patients, serum C-reactive protein and bronchoalveolar fluid neutrophils may be correlated with a secondary infection.

Anisakis pegreffii Extract Induces Airway Inflammation with Airway Remodeling in a Murine Model System.

Exposure of the respiratory system to the Anisakis pegreffii L3 crude extract (AE) induces airway inflammation; however, the mechanism underlying this inflammatory response remains unknown. AE contains allergens that promote allergic inflammation; exposure to AE may potentially lead to asthma. In this study, we aimed to establish a murine model to assess the effects of AE on characteristic features of chronic asthma, including airway hypersensitivity (AHR), airway inflammation, and airway remodeling. Mice were sensitized for five consecutive days each week for 4 weeks. AHR, lung inflammation, and airway remodeling were evaluated 24 h after the last exposure. Lung inflammation and airway remodeling were assessed from the bronchoalveolar lavage fluid (BALF). To confirm the immune response in the lungs, changes in gene expression in the lung tissue were assessed with reverse transcription-quantitative PCR. The levels of IgE, IgG1, and IgG2a in blood and cytokine levels in the BALF, splenocyte, and lung lymph node (LLN) culture supernatant were measured with ELISA. An increase in AHR was prominently observed in AE-exposed mice. Epithelial proliferation and infiltration of inflammatory cells were observed in the BALF and lung tissue sections. Collagen deposition was detected in lung tissues. AE exposure increased IL-4, IL-5, and IL-13 expression in the lung, as well as the levels of antibodies specific to AE. IL-4, IL-5, and IL-13 were upregulated only in LLN. These findings indicate that an increase in IL-4+ CD4+ T cells in the LLN and splenocyte resulted in increased Th2 response to AE exposure. Exposure of the respiratory system to AE resulted in an increased allergen-induced Th2 inflammatory response and AHR through accumulation of inflammatory and IL-4+ CD4+ T cells and collagen deposition. It was confirmed that A. pegreffii plays an essential role in causing asthma in mouse models and has the potential to cause similar effects in humans.

Pyopneumothorax from coinfection by Trichomonas tenax and Geotrichum capitatum in a child from China: a case report

BackgroundTrichomonas tenax may appear in the oral cavity of humans due to poor dentition or oral hygiene. Pyopneumothorax is a serious complication of lower respiratory tract infections that very rarely can be caused by a trichomonad species in predisposed individuals. We report a rare case of pleurisy due to T. tenax with coinfection by a fungus.Case presentationWe describe a 16-year-old patient with cerebral palsy who presented with severe pyopneumothorax. T. tenax was identified by microscopic examination of the pleural effusion and next-generation sequencing. We also identified Geotrichum capitatum in the pleural effusion and bronchoalveolar lavage fluid cultures. Treatment with voriconazole and metronidazole successfully eliminated these pathogens and relieved the clinical symptoms. A literature review indicated this is the first reported case of pleurisy due to T. tenax with coinfection by a fungus.ConclusionThe rarity of pyopneumothorax caused by T. tenax coinfection with a fungus should not be overlooked in the clinic. These patients should be and treated in a timely manner.

Diagnostic Efficacy of Xpert MTB/RIF Assay in Bronchoalveolar Lavage Fluid for Tracheobronchial Tuberculosis: A Retrospective Analysis.

Background: The Xpert Mycobacterium tuberculosis/rifampin (MTB/RIF) assay has shown good diagnostic efficacy in brushing and biopsy tissue samples from patients with tracheobronchial tuberculosis (TBTB). However, its diagnostic value in bronchoalveolar lavage fluid (BALF) is still unclear. Therefore, the present retrospective study aimed to evaluate the diagnostic value of the Xpert MTB/RIF assay in BALF.Methods: The clinical data of 266 patients with suspected TBTB from January 2018 to October 2020 were pooled with complete details of bronchial brush and bronchoalveolar lavage samples. Smears of the bronchial brushings were stained with Auramine O stain to detect acid-fast bacilli (AFB), and BALF samples were used for culturing MTB with the BACTEC MGIT 960 system and the Xpert MTB/RIF assay. The diagnostic performance of these methods was assessed and compared.Results: A total of 266 patients suspected to have TBTB were enrolled in the final analysis. Of these patients, 179 patients were confirmed to have TBTB and 87 patients were non-TBTB. The sensitivity of the Xpert MTB/RIF assay in BALF (87.2%) was significantly higher than that of the brush smear for AFB (35.2%, p < 0.001). No significant difference was observed between the sensitivities of the Xpert MTB/RIF assay in BALF and MTB culture in BALF (87.2 vs. 84.9%, p = 0.542). The specificities of the Xpert MTB/RIF assay in BALF, MTB culture in BALF, and the bronchial brush smear were 97.7, 97.7, and 98.9%, respectively. The positive predictive value (PPV) and negative predictive value (NPV) of the Xpert MTB/RIF assay in BALF, MTB culture in BALF, and the bronchial brush smear were 98.7 and 78.7%, 98.7 and 75.9%, and 98.4 and 42.6%, respectively. Among the MTB culture-positive patients with TBTB detected by the Xpert assay, 27.0% (20/74) were identified to be resistant to RIF.Conclusions: The Xpert MTB/RIF assay in BALF enables a rapid and accurate diagnosis of TBTB and identification of RIF resistance, which is crucial for timely and proper treatment. Moreover, in patients with TBTB, BALF could be used as an alternative to bronchial brushing and biopsy tissues for the Xpert MTB/RIF assay.

Airway obstruction and inflammation on combined bronchoscopy in children with Down syndrome.

To characterize the upper and lower airway findings in children with Down syndrome and chronic respiratory symptoms, based on evaluation by flexible bronchoscopy (FB) with bronchoalveolar lavage and microlaryngoscopy with bronchoscopy (MLB). A retrospective review was conducted of children with Down syndrome aged 1 month to 17 years, who underwent both FB and MLB within a 1-year timeframe between 2010 and 2019 at Children's Hospital Colorado. Anatomic airway findings are reported as frequencies within the cohort. Bronchoalveolar lavage fluid (BALF) culture results, cell differential, and cytopathology are reported as frequencies or mean ± standard deviation. BALF results were compared between children with and without dysphagia documented on a recent swallow evaluation. Overall, 168 children with Down syndrome were included, with median age of 2.1 years (interquartile range: 0.9-5.1 years). At least one abnormal airway finding was recorded in 96% of patients and 46% had at least three abnormal findings. The most common findings included tracheomalacia (39% FB; 37% MLB), subglottic stenosis (35% MLB), pharyngomalacia (32% FB), and laryngomalacia (16% FB; 30% MLB). Comparison of BALF based on dysphagia status showed that children with dysphagia had more frequent cultures positive for mixed upper respiratory flora (76% vs. 47%, p = 0.004) and a higher percentage of neutrophils (20% vs. 7%, p = 0.006). Abnormal findings for FB and MLB are common in children with Down syndrome and chronic respiratory symptoms, and performing the procedures together may increase the diagnostic yield.

Lower airway microbiota in children with Down syndrome compared to controls with similar respiratory symptomatology.

BackgroundChildren with Down syndrome (DS) often present with chronic or recurrent respiratory symptoms and generally have a more severe and prolonged disease course in case of infection. This can be caused by anatomical and/or immunological predisposition. With this study, we aim to compare microbial composition in the lower airways of patients with DS versus controls, to see if we can explain the difference in disease course.MethodsAll endoscopic procedures under general anesthesia in patients with DS were reviewed retrospectively. We compared the microbiological data from bronchoalveolar lavage fluid (BALF) cultures (when available) to a cohort of children with chronic respiratory symptoms but without any other relevant medical history.ResultsEndoscopic data were available for 65 DS patients, BAL cultures for 47 out of 65 patients (72%). The “control” group consisted of 150 children without significant underlying disease, who were matched for age and sex. BAL culture results were available for 135 out of 150 patients (90%). Microorganisms were categorized and compared between both groups, with no statistical differences. Among the microorganisms tested, the most frequently reported were typical bacteria such as Haemophilus influenzae, Moraxella catarrhalis, Streptococci and Staphylococci.ConclusionsNo significant differences in lower airways microbial composition of children with DS and chronic respiratory symptoms were found when compared to controls presenting similar symptomatology. A suggestion for future research may be to investigate possible differences in drug sensitivity.

Lower airway microbiota in patients with clinically suspected Mycobacterium avium complex lung disease

The relationship between the lower airway microbiota in humans and respiratory illness has gained attention recently. However, the relationship between nontuberculous mycobacterial lung disease (NTM-LD) and the lower airway microbiota is not fully understood yet. We conducted a study to characterize the lower airway microbiota in Mycobacterium avium complex lung disease (MAC-LD), a representative subclass of the NTM-LD. The subject sample included 25 patients clinically suspected of having mild MAC disease whose condition could not be diagnosed using sputum culture. Upon testing MAC antibodies (anti-glycopeptidolipid (GPL)-core IgA antibodies), mycobacterial culture of bronchoalveolar lavage fluid (BALF), and performing BALF 16S rRNA gene sequencing, we divided the subjects into two groups of patients: those in whom MAC was detected in BALF mycobacterial culture (MAC-LD group) and in whom MAC was not detected in BALF mycobacterial culture (non-MAC-LD group), which was then comparatively examined. BALF mycobacterial culture showed that 9 out of 25 patients were positive for NTM; the detected Mycobacterium was MAC in all. No patients were positive for acid-fast bacteria other than MAC. Eighteen patients were positive for MAC antibodies (anti-glycopeptidolipid (GPL)-core IgA antibodies), including nine patients positive for mycobacterial culture. On BALF 16S rRNA gene sequencing, six patients were positive for the genus Mycobacterium and were culture-positive. Among the 16 patients in the non-MAC-LD group, the genus Pseudomonas was detected by 16S rRNA gene sequencing in 7 patients, 4 among whom were positive for MAC antibodies (anti-GPL-core IgA antibodies). Conversely, the genus Pseudomonas was not detected among the nine patients in the MAC-LD group. Other than the genus Pseudomonas, there was no clear difference in the composition of and no significant difference in the diversity of the bacterial flora between the MAC-LD and non-MAC-LD groups. However, we found that the genus Pseudomonas and MAC tended to exist exclusively.

Isolated pulmonary mucormycosis in an immunocompetent patient: a case report and systematic review of the literature

BackgroundPulmonary mucormycosis caused by Mucorales is a highly lethal invasive fungal infection usually found in immunocompromised patients. Isolated pulmonary mucormycosis in immunocompetent patients is very rare. Here, we present a case of a 32-year-old male who developed pulmonary mucormycosis without any known immunodeficiency.Case presentationThe patient presented to our hospital because of cough and chest pain along with blood in the sputum. He was first treated for community-acquired pneumonia until bronchoalveolar lavage fluid culture confirmed the growth of Absidia. His symptoms were relieved with the use of amphotericin B, and he eventually recovered. We also provide a systematic review of relevant literature to summarize the characteristics of pulmonary mucormycosis in immunocompetent patients.ConclusionsPulmonary mucormycosis has variable clinical presentations and is difficult to identify. Due to its high fatality rate, clinicians should make judgements regarding suspected cases correctly and in a timely manner to avoid misdiagnosis and delayed treatment.

Assistant role of manifestations under tracheoscopy in the diagnosis of invasive pulmonary aspergillosis in severe patients

To evaluate the assistant role of manifestations under tracheoscopy in the diagnosis of invasive pulmonary aspergillosis (IPA) in severe patients. A retrospective study was conducted. The patients with suspected IPA admitted to intensive care unit (ICU) of Affiliated Hospital of Binzhou Medical College from January 2015 to December 2019 were enrolled. The diagnosis, clinical diagnosis and suspected diagnosis were made according to the grading criteria of Guidelines for the diagnosis and treatment of invasive fungal infection in severe patients (2007). Those who met the criteria were enrolled in the IPA group, and those who did not meet the criteria or other pathogens were enrolled in the non-IPA group. The general data of the patients were collected, and the changes of tracheal and bronchial mucosa under tracheal microscope before and after treatment were recorded, as well as the results of galactomannan (GM) test and aetiology culture of bronchoalveolar lavage fluid (BALF). The baseline, bronchoscopy and pulmonary CT manifestations and their dynamic changes were compared in each group. A total of 142 patients with suspected IPA were finally enrolled. Among them, 12 were pathologically proven IPA, 77 were probable IPA, 22 were possible IPA, and 31 were undefined IPA. Of the 142 patients, 60 had typical manifestations of mucosal injury under bronchoscopy, including 7 proven IPA patients (58.3%), 52 probable IPA patients (67.5%), and 1 possible IPA patient (4.5%), but none undefined IPA patient. The patients undergoing lung CT scan were 12 proven IPA patients (100%), 73 probable IPA patients (94.8%), and 21 possible IPA patients (95.5%), respectively. Most of the Chest CT showed patchy or strip density increasing and other non-specific manifestations. There were 3 proven IPA patients (25.0%), 7 probable IPA patients (9.0%), and 0 possible IPA patient (0%) who had typical IPA CT manifestations (halo sign and cavity or crescent sign). Among the patients of proven IPA and probable IPA (89 cases), there were a total of 35 cases with endoscopic airway mucosal injury and tracheoscopy reexamination ≥ 3 times. All the 35 patients received anti-aspergillus treatment, among which 16 survived and 19 died. Among the 16 patients who survived, the microscopic appearance of mucosal injury was gradually reduced and the clinical manifestations were gradually improved. Of the 19 patients who died, 16 had deteriorated endoscopic airway mucosal injury. The specific manifestations of severe patients with bronchial mucosal injury are of great significance in the diagnosis of IPA. In the case of severe patients who cannot receive pathological examination or chest CT in time, dynamic observation of the changes of airway mucosal injury is a simple auxiliary method to discover the changes of patients' condition in time, evaluate the effect of antifungal therapy and the prognosis of IPA.

Blood cultures and blood microbiota analysis as surrogates for bronchoalveolar lavage fluid analysis in dogs with bacterial pneumonia

BackgroundDiagnosis of canine bacterial pneumonia relies on airway lavage to confirm septic, suppurative inflammation, and a positive bacterial culture. Considering risks of bronchoalveolar lavage fluid (BALF) collection, minimally invasive methods like culture or next generation sequencing of blood would be appealing. In dogs with bacterial pneumonia, our study aims included (1): determining proportion of agreement between cultivable bacteria in BALF and blood (2); characterizing BALF, blood, and oropharyngeal (OP) microbiota and determining if bacteria cultured from BALF were present in these communities; and (3) comparing relatedness of microbial community composition at all three sites. Bacterial cultures were performed on BALF and blood. After DNA extraction of BALF, blood and OP, 16S rRNA amplicon libraries were generated, sequenced, and compared to a bacterial gene sequence database.ResultsDisregarding one false positive, blood cultures were positive in 2/9 dogs (5 total isolates), all 5 isolates were present in BALF cultures (16 total isolates). Based on sequencing data, all sites had rich and diverse microbial communities. Comparing cultured BALF bacterial genera with sequenced taxa, all dogs had ≥1 cultured isolate present in their microbiota: cultured BALF isolates were found in microbiota of BALF (12/16), blood (7/16), and OP (6/11; only 7 dogs had OP swabs). Of 394 distinct taxa detected in BALF, these were present in 75% OP and 45% blood samples. BALF community composition was significantly different than OP (p = 0.0059) and blood (p = 0.0009).ConclusionsBlood cultures are insensitive but specific for cultured BALF bacteria in canine bacterial pneumonia. Cultivable BALF bacteria were present in BALF, blood and OP microbiota to differing degrees.

Pneumonia With Scedosporium apiospermum and Lomentospora prolificans in a Patient After Bilateral Lung Transplantation for Pulmonary Hypertension: A Case Report

Infections caused by the Scedosporium genus have become recognized as a fatal complication after lung transplantation in Europe and Australia, but the reports have been rare from Asian countries including Japan. We present a case of pneumonia caused by a mixed infection of Scedosporium apiospermum (SA) and Lomentospora prolificans (LP) that developed after augmentation of immunosuppression for chronic lung allograft dysfunction (CLAD) after lung transplantation. A 13-year-old man underwent bilateral lung transplantation for pulmonary hypertension. One year after surgery, he was treated with a series of augmented immunosuppressive therapy for severe acute rejection and subsequent CLAD. Three months following the first steroid pulse therapy, his serum β-D-glucan elevated without any sign of fungal infection by other tests. The serum β-D-glucan once returned to a normal level by empirical administration of micafungin; however, the patient's condition worsened again by discontinuation of it. He did not recover by restarting micafungin, and computed tomography (CT) scans eventually demonstrated new infiltrates in his lung field 6 weeks after the elevation of serum β-D-glucan. Microscopic findings of transbronchial lung biopsy specimens showed filamentous fungi, and the culture of bronchoalveolar lavage fluid revealed the growth of SA and LP. Despite subsequent voriconazole administration, he died 14 days after the start of voriconazole. Early and aggressive inspection including bronchoscopy should be performed for the diagnosis of Scedosporium infection in immunocompromised patients, even if CT scans and sputum culture show no evidence of infection.

New clinical algorithm including fungal biomarkers to better diagnose probable invasive pulmonary aspergillosis in ICU

BackgroundThe classification of invasive pulmonary aspergillosis (IPA) issued by the European Organization for the Research and Treatment of Cancer/Mycoses Study Group Education and Research Consortium (EORTC/MSGERC) is used for immunocompromised patients. An alternative algorithm adapted to the intensive care unit (ICU) population has been proposed (AspICU), but this algorithm did not include microbial biomarkers such as the galactomannan antigen and the Aspergillus quantitative PCR. The objective of the present pilot study was to evaluate a new algorithm that includes fungal biomarkers (BM-AspICU) for the diagnosis of probable IPA in an ICU population.Patients and methodsData from 35 patients with pathology-proven IPA according to European Organization for the Research and Treatment of Cancer/Mycosis Study Group (EORTC/MSGERC)-2008 criteria were extracted from the French multicenter database of the Invasive Fungal Infections Surveillance Network (RESSIF). The patients were investigated according to the AspICU algorithm, and the BM-AspICU algorithm in analyzing the clinical, imaging, and biomarker data available in the records, without taking into account the pathology findings.ResultsEight patients had to be excluded because no imaging data were recorded in the database. Among the 27 proven IPAs with complete data, 16 would have been considered as putative IPA with the AspICU algorithm and 24 would have been considered as probable IPA using the new algorithm BM-AspICU. Seven out of the 8 patients with probable BM-AspICU IPA (and not classified with the AspICU algorithm) had no host factors and no Aspergillus-positive broncho-alveolar lavage fluid (BALF) culture. Three patients were non-classifiable with any of the two algorithms, because they did not have any microbial criteria during the course of the infection, and diagnosis of proven aspergillosis was done using autopsy samples.ConclusionInclusion of biomarkers could be effective to identify probable IPA in the ICU population. A prospective study is needed to validate the routine application of the BM-AspICU algorithm in the ICU population.

Pneumonia Surveillance in Ugandans with HIV Through the Lens of Culture-Independent Metatranscriptomics: A Cross Sectional Study

Background: Pneumonia is a leading cause of death worldwide and is a major healthcare challenge for HIV-infected persons. Despite this, the etiology of pneumonia in this population remains poorly understood. Methods: We employed a combination of bulk RNA sequencing of bronchoalveolar lavage fluid and standard culture- and PCR-based diagnostics to survey the landscape of transcriptionally active respiratory pathogens in 217 Ugandan patients with HIV who were hospitalized for pneumonia. Findings: A microbiologic diagnosis was obtained in 211 (97.2%) of individuals, with at least one microorganism of established respiratory pathogenicity identified in 113 (52.1%) of patients, and a microbe of possible pathogenicity identified in 94 (47.9%) of patients. Mycobacterium tuberculosis (MTB) was the most commonly identified established pathogen in 35 (16.1%) of the patients and bacterial or viral co-infections were found in 13 (37.2%) of MTB-positive individuals. Streptococcus mitis, not previously reported as a cause of pneumonia in patients with HIV, was the most commonly identified bacterial organism (n=37, 17.1% of patients), and Hemophilus influenzae was the most commonly identified established bacterial pathogen (n=20, 9.2% of patients). Pneumocystis jirovecii, Hemophilus influenza, human rhinovirus, Streptococcus species and Veillonella species were more prevalent in patients with a CD4 T-cell count of <200 cells/mL. Streptococcus species, human herpes virus 4, and Veillonella species were associated with increased 70-day mortality. Interpretation: We advance understanding of the microbiologic landscape of lower respiratory tract infections in the vulnerable demographic of persons living with HIV in a representative and understudied sub-Saharan African region. Funding: This study was funded by NIH U01 HL098964, R01 HL090335, R01 HL143998, R01 HL128156 (LH) and NHLBI K23HL138461-01A1 (CL). Declaration of Interests: L. H. reports NIH grants. S.I. is employed by Second Genome, Inc. from S.L. reports fees from Siolta Therapeutics outside the submitted work. All other authors have nothing to declare. Ethics Approval Statement: This study was approved by the Mulago Hospital Institutional Review Board (IRB) under protocol number 2006-0174, and the University of California San Francisco IRB under protocol number 10-02633.

Antibiotic susceptibility pattern of bacterial isolates from quantitative culture of bronchoalveolar lavage fluid in patients with clinical suspicion of pneumonia

Background: The common bacterial pathogens isolated from bronchoalveolar lavage (BAL) include Klebsiella pneumoniae, Acinetobacter baumanii, Pseudomonas aeruginosa and Coagulase negative Staphylococcus.&#x0D; Objectives: This study was conducted to identify pneumonia causing organisms and to determine their antibiogram.&#x0D; Methodology: A descriptive cross-sectional study was carried out at Kathmandu Medical College Teaching Hospital, Kathmandu, Nepal over a period of one year (Aug 2019-Jul 2020). Ethical approval (Reference Number:1004201810) was taken and convenience samplin g was done using Clinical and Laboratory Standards Institute(CLSI) guidelines. Data were analyzed using Statistical Package for Social Sciences(SPSS) version 19.&#x0D; Results: Out of 32 BAL samples, 14 were culture positive. The commonest bacterial pathogens isolated were Klebsiella Pneumoniae 6(42.85%), followed by Acinetobacter baumanii 5(35.71%), Pseudomonas aeruginosa 2(14.28%) and Coagulase negative Staphylococcus 1(7.14%). The isolates were 100% sensitive to Tigecycline and Polymixin B followed by Colistin(92.85%). Cotrimoxazole was 100% resistant to these isolates followed by Azithromycin (92.85%.&#x0D; Conclusion: Klebsiella pneumomiae, Acinetobacter baumanii were the most common bacterial pathogens isolated from BAL.