The clinical significance of simultaneous detection of pathogens from bronchoalveolar lavage fluid and blood samples by metagenomic next-generation sequencing in patients with severe pneumonia

Introduction. Bloodstream infection is a common complication in patients with severe pneumonia and is regarded as an independent risk factor for prediction of poor outcome. Metagenomic next-generation sequencing (mNGS) has been widely applied for pathogen determination of various clinical specimens from patients with infectious diseases. However, the clinical significance of and necessity for simultaneous pathogen detection of both blood samples and bronchoalveolar lavage fluid (BALF) by mNGS in patients with severe pneumonia remains unclear. Hypothesis/Gap Statement. Simultaneous detection of pathogens from both BALF and blood samples in patients with severe pneumonia helps to determine the complication of the bloodstream infection. Aims. This study aimed to elucidate the clinical significance and necessity of pathogen detection simultaneously in both blood samples and BALF samples with the application of mNGS in patients with severe pneumonia. Methods. In this study, 20 patients with severe pneumonia were enrolled and the potential pathogens in both BALF and blood samples were detected simultaneously by conventional microbial examination and mNGS tests. Moreover, multiple consecutive microbial detections were undertaken to investigate the dynamic variation of pathogens during the course of disease progression in two of the 20 patients. Results. In 85 % (17/20) of the patients with severe pneumonia, various pathogens were determined positively in the BALF by mNGS, including 10 cases with bacterial infection, five cases with viral infection and two cases with fungal infection. By contrast, pathogens in 50 % (10/20) of cases could be detected positively in the BALF by conventional microbial tests. Among 17 severe pneumonia patients with mNGS-positive BALF, pathogens were also identified in 10 cases with mNGS-positive blood samples. By contrast, only one patient complicated with a bloodstream infection could be found by conventional bacterial culture. Moreover, the pathogens from BALF were highly consistent with that from blood samples detected by mNGS in the early stage of the disease. With disease progression and after recurrent antibiotic treatment, significant dynamic changes of the microbial species from the BALF and blood samples could be clearly found by mNGS. Conclusions. This study emphasizes the utility of mNGS in the rapid simultaneous detection of pathogens from both BALF and blood samples in patients with severe pneumonia, and could allow determination of bloodstream infection and guide clinicians regarding antimicrobial treatments.

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Severe pneumonia caused by Parvimonas micra: a case report

BMC Infectious Diseases ◽

10.1186/s12879-021-06058-y ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Qing Yu ◽

Lingling Sun ◽

Zuqing Xu ◽

Lumei Fan ◽

Yunbo Du

Keyword(s):

Bronchoalveolar Lavage Fluid ◽

Case Reports ◽

Severe Pneumonia ◽

Lavage Fluid ◽

Due Date ◽

Case Presentation ◽

Abdominal Abscesses ◽

Parvimonas Micra ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

Abstract Background Parvimonas micra (P. micra) is a gram-positive anaerobic coccus that is detected widely on the skin, in the oral mucosa and in the gastrointestinal tract. In certain circumstances, P. micra can cause abdominal abscesses, bacteraemia and other infections. To the best of our knowledge, there have been no case reports describing the biological characteristics of P. micra-related pneumonia. These bacteria do not always multiply in an aerobic organ, such as the lung, and they could be easily overlooked because of the clinical mindset. Case presentation A 35-year-old pregnant woman was admitted to the emergency department 4 weeks prior to her due date who was exhibiting 5 points on the Glasgow coma scale. A computed tomography (CT) scan showed a massive haemorrhage in her left basal ganglia. She underwent a caesarean section and brain surgery before being admitted to the ICU. She soon developed severe pneumonia and hypoxemia. Given that multiple sputum cultures were negative, the patient’s bronchoalveolar lavage fluid was submitted for next-generation sequencing (NGS) to determine the pathogen responsible for the pneumonia; as a result, P. micra was determined to be the causative pathogen. Accordingly the antibiotic therapy was altered and the pneumonia improved. Conclusion In this case, we demonstrated severe pneumonia caused by the anaerobic organism P. micra, and the patient benefited from receiving the correct antibiotic. NGS was used as a method of quick diagnosis when sputum culture failed to distinguish the pathogen.

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The microbiological diagnostic performance of metagenomic next-generation sequencing in patients with sepsis

BMC Infectious Diseases ◽

10.1186/s12879-021-06934-7 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Di Ren ◽

Chao Ren ◽

Renqi Yao ◽

Lin Zhang ◽

Xiaomin Liang ◽

...

Keyword(s):

Next Generation Sequencing ◽

Pathogen Detection ◽

Final Analysis ◽

Data Interpretation ◽

Lavage Fluid ◽

Microbial Culture ◽

Next Generation ◽

Multiple Pathogens ◽

Generation Sequencing

Abstract Background In this study, we aimed to perform a comprehensive analysis on the metagenomic next-generation sequencing for the etiological diagnosis of septic patients, and further to establish optimal read values for detecting common pathogens. Methods In this single-center retrospective study, septic patients who underwent pathogen detection by both microbial culture and metagenomic next-generation sequencing in the intensive care unit of the Second People’s Hospital of Shenzhen from June 24, 2015, to October 20, 2019, were included. Results A total of 193 patients with 305 detected specimens were included in the final analysis. The results of metagenomic next-generation sequencing showed significantly higher positive rates in samples from disparate loci, including blood, bronchoalveolar lavage fluid, and cerebrospinal fluid, as well as in the determination of various pathogens. The optimal diagnostic reads were 2893, 1825.5, and 892.5 for Acinetobacter baumannii, Pseudomonas aeruginosa, and Klebsiella pneumoniae, respectively. Conclusions The metagenomic next-generation sequencing is capable of identifying multiple pathogens in specimens from septic patients, and shows significantly higher positive rates than culture-based diagnostics. The optimal diagnostic reads for frequently detected microbes might be useful for the clinical application of metagenomic next-generation sequencing in terms of timely and accurately determining etiological pathogens for suspected and confirmed cases of sepsis due to well-performed data interpretation.

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The Application of Metagenomic Next-Generation Sequencing in Detection of Pathogen in Bronchoalveolar Lavage Fluid and Sputum Samples of Patients with Pulmonary Infection

Computational and Mathematical Methods in Medicine ◽

10.1155/2021/7238495 ◽

2021 ◽

Vol 2021 ◽

pp. 1-6

Author(s):

Wanghui Shi ◽

Shanshan Zhu

Keyword(s):

Next Generation Sequencing ◽

Bronchoalveolar Lavage ◽

Pathogen Detection ◽

Bronchoalveolar Lavage Fluid ◽

Pulmonary Infection ◽

Lavage Fluid ◽

Microbial Culture ◽

Next Generation ◽

Two Samples ◽

Generation Sequencing

Objective. To uncover the application value of metagenomic next-generation sequencing (mNGS) in the detection of pathogen in bronchoalveolar lavage fluid (BALF) and sputum samples. Methods. Totally, 32 patients with pulmonary infection were included. Pathogens in BALF and sputum samples were tested simultaneously by routine microbial culture and mNGS. Main infected pathogens (bacteria, fungi, and viruses) and their distribution in BALF and sputum samples were analyzed. Moreover, the diagnostic performance of mNGS in paired BALF and sputum samples was assessed. Results. The pathogen culture results were positive in 9 patients and negative in 13 patients. No statistical differences were recorded on the sensitivity (78.94% vs. 63.15%, p = 0.283 ) and specificity (62.50% vs. 75.00%, p = 0.375 ) of mNGS diagnosis in bacteria and fungus in two types of samples. As shown in mNGS detection, 10 patients’ two samples were both positive, 13 patients’ two samples were both negative, 7 patients were only positive in BALF samples, and 2 patients’ sputum samples were positive. Main viruses mNGS detected were EB virus, human adenovirus 5, herpes simplex virus type 1, and human cytomegalovirus. Kappa consensus analysis indicated that mNGS showed significant consistency in detecting pathogens in two samples, no matter bacteria ( p < 0.001 ), fungi ( p = 0.026 ), or viruses ( p = 0.008 ). Conclusion. mNGS showed no statistical differences in sensitivity and specificity of pathogen detection in BALF and sputum samples. Under certain conditions, sputum samples might be more suitable for pathogen detection because of invasiveness of BALF samples.

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Correlation between α-SMA and ß-catenin levels in bronchoalveolar lavage fluid and severity of pneumonia

Pakistan Journal of Medical Sciences ◽

10.12669/pjms.38.3.5329 ◽

2022 ◽

Vol 38 (3) ◽

Author(s):

Xiaoying Li ◽

Zinan Jiang

Keyword(s):

Bronchoalveolar Lavage ◽

Bronchoalveolar Lavage Fluid ◽

Pearson Correlation ◽

Severe Pneumonia ◽

Lavage Fluid ◽

Apache Ii ◽

Apache Ii Score ◽

Creative Commons ◽

Mechanical Ventilation Time ◽

Deterioration Group

Objectives: To assess the association of bronchoalveolar lavage fluid (BALF) α-SMA and ß-catenin levels and the severity of pneumonia. Methods: The records of patients with severe pneumonia treated in our hospital from June 2019 to June 2020 were selected. The clinical outcome was observed within 10 days. For the purpose of analysis, patients were divided into two groups according to the outcome, 47 cases in the improvement group and 39 cases in the deterioration group. The intubation time, mechanical ventilation time and APACHE II score 10 days after admission were compared between the two groups; We assessed pulmonary infections using the clinical pulmonary infection score(CPIS). The levels of α-SMA and ß-catenin in bronchoalveolar lavage fluid at different time points were compared and analyzed, to analyze the association between the levels and the CPIS. Results: The APACHE II score in the improvement group were lower than those in the deterioration group (P<0.05). The expressions of α-SMA and ß-catenin in the BALF of patients in the improvement group were significantly lower than those of patients in the deterioration group on day 1, 3, and 7 (P<0.05); and the expressions of α-SMA and ß-catenin in the BALF of patients in the improvement group decreased with time, while those of patients in the deterioration group increased gradually with time(P<0.05). The expressions of α-SMA and ß-catenin in patients with CPIS>6 was significantly higher than those in patients with CPI≤6(P<0.05). Pearson correlation analysis showed that the levels of α-SMA and ß-catenin in BALF were positively correlated with the CPIS. Conclusion: The levels of α-SMA and ß-catenin in BALF are closely associated with the clinical condition of patients with severe pneumonia; the levels are positively associated with the severity of the disease and they increase with symptomatic worsening. doi: https://doi.org/10.12669/pjms.38.3.5329 How to cite this:Li X, Jiang Z. Correlation between α-SMA and ß-catenin levels in bronchoalveolar lavage fluid and severity of pneumonia. Pak J Med Sci. 2022;38(3):---------. doi: https://doi.org/10.12669/pjms.38.3.5329 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Metagenomic analysis using next-generation sequencing of pathogens in bronchoalveolar lavage fluid from pediatric patients with respiratory failure

Scientific Reports ◽

10.1038/s41598-019-49372-x ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 7

Author(s):

Suguru Takeuchi ◽

Jun-ichi Kawada ◽

Kazuhiro Horiba ◽

Yusuke Okuno ◽

Toshihiko Okumura ◽

...

Keyword(s):

Respiratory Failure ◽

Next Generation Sequencing ◽

Bronchoalveolar Lavage ◽

Bronchoalveolar Lavage Fluid ◽

Pediatric Patients ◽

Respiratory Infections ◽

Sequence Data ◽

Lavage Fluid ◽

Next Generation ◽

Generation Sequencing

Abstract Next-generation sequencing (NGS) has been applied in the field of infectious diseases. Bronchoalveolar lavage fluid (BALF) is considered a sterile type of specimen that is suitable for detecting pathogens of respiratory infections. The aim of this study was to comprehensively identify causative pathogens using NGS in BALF samples from immunocompetent pediatric patients with respiratory failure. Ten patients hospitalized with respiratory failure were included. BALF samples obtained in the acute phase were used to prepare DNA- and RNA-sequencing libraries. The libraries were sequenced on MiSeq, and the sequence data were analyzed using metagenome analysis tools. A mean of 2,041,216 total reads were sequenced for each library. Significant bacterial or viral sequencing reads were detected in eight of the 10 patients. Furthermore, candidate pathogens were detected in three patients in whom etiologic agents were not identified by conventional methods. The complete genome of enterovirus D68 was identified in two patients, and phylogenetic analysis suggested that both strains belong to subclade B3, which is an epidemic strain that has spread worldwide in recent years. Our results suggest that NGS can be applied for comprehensive molecular diagnostics as well as surveillance of pathogens in BALF from patients with respiratory infection.

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Determination of ofloxacin in bronchoalveolar lavage fluid by high-performance liquid chromatography and fluorimetric detection

Journal of Chromatography B Biomedical Sciences and Applications ◽

10.1016/s0378-4347(00)82645-6 ◽

1989 ◽

Vol 495 ◽

pp. 354-357 ◽

Cited By ~ 11

Author(s):

Kyuichi Matsubayashi ◽

Tsutomu Une ◽

Yasuaki Osada

Keyword(s):

High Performance Liquid Chromatography ◽

Liquid Chromatography ◽

Bronchoalveolar Lavage ◽

High Performance ◽

Bronchoalveolar Lavage Fluid ◽

Lavage Fluid ◽

Fluorimetric Detection

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Determination of plasma bicarbonate of neonates in intensive care.

Clinical Chemistry ◽

10.1093/clinchem/34.7.1483 ◽

1988 ◽

Vol 34 (7) ◽

pp. 1483-1485 ◽

Cited By ~ 3

Author(s):

P Masters ◽

M E Blackburn ◽

M J Henderson ◽

J F Barrett ◽

P R Dear

Keyword(s):

Intensive Care ◽

Clinical Significance ◽

Systematic Bias ◽

Blood Gas ◽

Laboratory Measurements ◽

Blood Samples ◽

Plasma Bicarbonate ◽

A Value ◽

Hasselbalch Equation

Abstract Most modern blood-gas analyzers are programmed to use the Henderson-Hasselbalch equation to calculate a value for plasma bicarbonate. It has been suggested, however, that among acutely ill patients, including newborns, these calculated values may be at variance with measured total CO2. To assess the clinical significance of such errors, we compared calculated bicarbonate with measured total CO2 in 79 blood samples from 40 babies in intensive care. The calculated bicarbonate values consistently exceeded the measured values by about 1.5 mmol/L. Of the errors, 94% were within the range -10% to +20%. When the systematic bias was removed, calculated and measured bicarbonate values agreed within +/- 3.30 mmol/L in 95% of cases. Because calculated values can be obtained much more quickly and frequently than laboratory measurements, we believe that these limits are clinically acceptable.

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The characteristics and clinical significance of mucin levels in bronchoalveolar lavage fluid of patients with interstitial lung disease

Journal of Investigative Medicine ◽

10.1136/jim-2018-000785 ◽

2018 ◽

Vol 67 (4) ◽

pp. 761-766

Author(s):

Li Wei ◽

Jing Zhao ◽

Jing Bao ◽

Yanliang Ma ◽

Ying Shang ◽

...

Keyword(s):

Lung Cancer ◽

Pleural Effusion ◽

Interstitial Lung Disease ◽

Lung Function ◽

Bronchoalveolar Lavage ◽

Lung Disease ◽

Clinical Significance ◽

Bronchoalveolar Lavage Fluid ◽

Lavage Fluid ◽

Diffusing Capacity

To investigate the expression and clinical significance of secretory mucins in patients with interstitial lung disease (ILD). The bronchoalveolar lavage fluid (BALF) concentrations of mucins (MUCs) from 27 patients with ILD, 6 patients with lung cancer, 8 patients with pleural effusion and 9 patients with bronchiectasis were determined by ELISA. The concentration of MUC5AC was significantly increased in patients with ILD (12.84±15.02 ng/mL) compared with patients with pleural effusion (4.33±2.51 ng/mL), lung cancer (8.02±5.57 ng/mL) or bronchiectasis (6.08±2.40 ng/mL) (p<0.01). The MUC2 level (10.23±9.27 ng/mL) was significantly elevated in patients with ILD than in those with pleural effusion (6.21±3.28 ng/mL) or bronchiectasis (5.73±1.51 ng/mL) (both p<0.05). Patients with ILD (104.64±61.61 ng/mL), lung cancer (148.45±169.24 ng/mL) or bronchiectasis (123.68±63.28 ng/mL) had significantly greater IL-8 levels than in those with pleural effusion (76.46±2.16 ng/mL) (p<0.05). A significant positive correlation was detected between the MUC5AC concentration and the lymphocyte percentage in BALF of patients with ILD (r=0.504, p=0.007). Lung function tests of patients with ILD exhibited various degrees of restrictive ventilation dysfunction and reduced diffusing capacity. The MUC5AC levels in BALF were negatively correlated with forced expiratory volume in 1 second (FEV1)/forced vital capacity (r=−0.761, p=0.000), FEV1 predicted value (FEV1/pred) (r=−0.668, p=0.002), and diffusing capacity (r=−0.606, p=0.006). Secretory mucins MUC5AC, MUC2 and IL-8 were highly expressed in ILD. MUC5AC level was closely correlated with the amount of inflammatory cells in BALF and the lung function parameters.

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