Objective To analyze the differences in microbial communities in bronchoalveolar lavage fluid (BALF) from patients with simple pneumonia versus those with chronic obstructive pulmonary disease (COPD) combined with lower respiratory tract infection using metagenomic next-generation sequencing (mNGS). Methods Patients hospitalized for pulmonary infections at the First Affiliated Hospital of Xinjiang Medical University between December 2021 and March 2023 were included. Based on the presence of COPD, the patients were divided into two groups: those with simple pneumonia and those with COPD combined with lower respiratory tract infection. mNGS was employed to detect microbes in BALF, and the microbial community distribution characteristics of the two groups were analyzed. Results A total of 97 patients were included, of whom 80 (81.82%) had positive microbial detection results. The smoking index in COPD group with lower respiratory tract infection was significantly higher than that in the group with simple pneumonia (t= ?3.62, P=0.001). Differences in microbial community distributions were observed between the groups. At the genus level, 19 species of microorganisms were detected in the simple pneumoniapulmonary infection group, including 8 bacteria (42.11%), 2 fungi (10.53%), 3 viruses (15.79%), and 6 other types of microorganisms (31.58%). In contrast, 22 types of microbes were detected in COPD group with lower respiratory tract infection, including 10 bacteria (47.62%), 3 fungi (14.29%), 4 viruses (19.05%), and 4 other types of microorganisms (19.05%). Differences were also noted in reads per million (RPM) values; bacterial RPM values at the genus level were significantly higher in the COPD group during non-severe pneumonia compared to the simple pneumonia group (Z=–2.706, P=0.007). In the patients with severe pneumonia, RPM values at the genus and species levels were significantly higher than those in non-severe pneumonia (Z=?2.202, P=0.028; Z=?2.141, P=0.032). In COPD combined with severe pneumonia, bacterial RPM values were significantly higher at the species level compared to non-severe pneumonia (Z=?2.367, P=0.017). ConclusionsThere are differences in the distribution of microbial communities at the genus and species levels in BALF from patients with COPD combined with lower respiratory tract infection compared to those with simple pulmonary pneumonia. Bacteria are the predominant microbial type in both groups, but the dominant bacterial species differ between them. Simple pneumonia are primarily associated with bacterial, viral, and other types of microbial infections, while COPD combined with lower respiratory tract infection is predominantly associated with fungal and bacterial infections. RPM values may serve as an indicator of the severity of pneumonia.
Objective To explore the clinical characteristics of Chlamydia psittaci pneumonia. Methods From January 2020 to March 2023, 21 cases of Psittacosis from the First Affiliated Hospital of Nanjing Medical University were diagnosed via metagenomic next-generation sequencing (mNGS). They were divided into a severe group (n=10) and a non-severe group (n=11) based on diagnostic criteria for severe pneumonia, and the clinical presentation, secondary examination, treatment, and prognosis of the two groups were analyzed retrospectively. Results Among the 21 patients, there were 11 males and 10 females, with a mean age of (51.7±11.6) years. All patients had an acute onset and 12 had a confirmed history of exposure to poultry. The onset of the disease occurred in the autumn and winter seasons in 18 patients. All the patients were suffering from high fevers. Other symptoms included coughing, phlegm, tightness in the chest and fatigue. Laboratory examinations showed that the levels of leukocytes, neutrophil counts, C-reactive protein, procalcitonin, aminotransferase, creatine kinase, lactic dehydrogenase, brain natriuretic peptide precursors and D-dimer were significantly higher in the severe group than those in the non-severe group. Chest CT scans revealed varying levels of consolidation and spot shadowing with peripheral exudate in all patients. The patients in the severe group were more likely to have bilateral lung involvement, bilateral pleural effusion, cavity and mediastinal lymph node enlargement. Eleven patients received tetracycline alone, three received laudanum alone, two received respiratory quinolones alone, and five received a combination of two drugs including tetracycline. Chest CT at clinical follow-up showed absorption of lung lesions. Conclusions Chlamydia psittaci pneumonia usually occurs in the fall and winter, and most patients have a history of contact with poultry. Clinical presentation and imaging are not specified. The technology of mNGS enables early diagnosis of the disease, and neutrophil lymphocyte ratio, neutrophil-lymphocyte ratio and lactic dehydrogenase levels help assess the risk of severe disease.
Objective To analysis and explore the value of metagenomics next-generation sequencing (mNGS) and clinical characteristics of Chlamydia psittaci (C. psittaci) pneumonia. Methods Totally 5 patients who were diagnosed with C. psittaci pneumonia and were treated in the Department of Respiratory and Critical Care Medicine and the Department of Infectious Diseases of Huazhong University of Science and Technology Union Shenzhen Hospital from Febuary 2021 to March 2021 were enrolled in the study. The clinical data of the patients were analyzed, and the clinical characteristics of the disease and treatment experience were summarized. Results The main symptoms of the 5 patients were high fever and cough, 4 of them had a history of raising parrots. The white blood cell and the neutrophils were mostly normal or slightly increased, the C reactive protein and erythrocyte sedimentation rate were significantly increased. The chest CT showed exudation and consolidation of one or several lung lobes. The serious patients might develop respiratory failure, if they were not treated by effective antibiotics. The diagnosis was based on clinical manifestations, contact history and alveolar lavage fluid that were detected by mNGS technology of C. psittaci nucleic acid sequence. The accuracy of detecting pathogens in alveolar lavage fluid by mNGS was high. In addition, mNGS could also identify other bacteria or viruses. After the timely adjustment of treatment, the condition of the patients was improved relied on tetracycline drugs or quinolone drugs, which shortened the diagnosis time and course of C. psittaci pneumnonia and reduced the use of unnecessary antibacterial drugs. Conclusions mNGS is of great significance in diagnosing C. psittaci pneumonia. The timely use of appropriate antibacterial drugs can achieve favorable therapeutic effect.
ObjectiveTo explore the clinical value of metagenomic next-generation sequencing (mNGS) in diagnosis and treatment of periprosthetic joint infection (PJI) after total knee arthroplasty (TKA). MethodsBetween April 2020 and March 2023, 10 patients with PJI after TKA were admitted. There were 3 males and 7 females with an average age of 69.9 years (range, 44-83 years). Infection occurred after 8-35 months of TKA (mean, 19.5 months). The duration of infection ranged from 16 to 128 days (mean, 37 days). The preoperative erythrocyte sedimentation rate (ESR) was 15-85 mm/1 h (mean, 50.2 mm/1 h). The C reactive protein (CRP) was 4.4-410.0 mg/L (mean, 192.8 mg/L). The white blood cell counting was (3.4-23.8)×109/L (mean, 12.3×109/L). The absolute value of neutrophils was (1.1-22.5)×109/L (mean, 9.2×109/L). After admission, the joint fluid was extracted for bacterial culture method and mNGS test, and sensitive antibiotics were chosen according to the results of the test, and the infection was controlled in combination with surgery. Results Seven cases (70%) were detected as positive by bacterial culture method, and 7 types of pathogenic bacteria were detected; the most common pathogenic bacterium was Streptococcus lactis arrestans. Ten cases (100%) were detected as positive by mNGS test, and 11 types of pathogenic bacteria were detected; the most common pathogenic bacterium was Propionibacterium acnes. The difference in the positive rate between the two methods was significant (P=0.211). Three of the 7 patients who were positive for both the bacterial culture method and the mNGS test had the same results for the type of pathogenic bacteria, with a compliance rate of 42.86% (3/7). The testing time (from sample delivery to results) was (4.95±2.14) days for bacterial culture method and (1.60±0.52) days for mNGS test, and the difference was significant (t=4.810, P<0.001). The corresponding sensitive antibiotic treatment was chosen according to the results of bacterial culture method and mNGS test. At 3 days after the one-stage operation, the CRP was 6.8-48.2 mg/L (mean, 23.6 mg/L); the ESR was 17-53 mm/1 h (mean, 35.5 mm/1 h); the white blood cell counting was (4.5-8.1)×109/L (mean, 6.1×109/L); the absolute value of neutrophils was (2.3-5.7)×109/L (mean, 4.1×109/L). All patients were followed up 12-39 months (mean, 23.5 months). One case had recurrence of infection at 6 months after operation, and the remaining 9 cases showed no signs of infection, with an infection control rate of 90%. Conclusion Compared with bacterial culture method, mNGS test can more rapidly and accurately detect pathogenic bacteria for PJI after TKA, which is important for guiding antibiotics combined with surgical treatment of PJI.
Objective To summarize and explore the clinical features, diagnosis and treatment of severe pulmonary tuberculosis (TB). Methods One death case of pulmonary TB in The First Affiliated Hospital of Soochow University was analyzed, related publications of case reports and articles relevant on the analysis and study of pulmonary tuberculosis deaths from Pubmed between January 2012 and March 2022 were also reviewed. Results A 25-year-old female patient was admitted for "intermittent cough with sputum for more than 1 year, aggravated with chest tightness and shortness of breath for 5 days". She had no underlying disease. Pulmonary TB was diagnosed by TB bacterium smear and next-generation sequencing of bronchoalveolar lavage fluid. The patient was in shock compensation period and developed acute respiratory distress syndrome immediately after admission. Through active anti-tuberculosis, invasive mechanical ventilation, intra-aortic balloon counterpulsation and continuous renal replacement therapy, the disease continued to deteriorate and she died on the third day after admission. A total of 269 pulmonary TB deaths were retrieved. An analysis of 244 patients' past medical history showed that human immunodeficiency virus co-infection was the most common among young people and chronic diseases were the most common among the elderly. All 269 patients died of septic shock, respiratory failure and multiple organ dysfunction syndrome (MODS), among which hyponatremia was also a significant complication. The shortest time from admission to death was 7 days, while the longest average time was only 35 days. Conclusions Pulmonary TB could develop into septic shock and MODS with poor prognosis and high mortality. Health education on TB should be strengthened.
Objective By using metagenomic next-generation sequencing (mNGS), we aimed to analyze the microbes characteristics of lower respiratory tract of patients with pulmonary infection, so as to improve the further understanding of clinical etiological characteristics of patients with pulmonary infection. Methods A total of 840 patients with suspected pulmonary infection were enrolled from August 2020 to October 2021 in West China Hospital of Sichuan University. mNGS was used to detect the microbiome of bronchoalveolar lavage fluid of all patients, and the microbial characteristics of lower respiratory tract of all patients were retrospectively analyzed. Results A total of 840 patients were enrolled, of which 743 were positive for microbiome, with bacterial infection accounting for 35.13% (261/743). Acinetobacter baumannii accounted for 18.98% (141/743), followed by Streptococcus pneumoniae (14.13%, 105/743), Klebsiella pneumoniae (13.46%, 100/743), Enterococcus faecium (12.11%, 90/743) and Mycobacterium tuberculosis complex (11.98%, 89/743). Acinetobacter baumannii had the highest average reads (2607.48). In addition, some specific pathogens were detected, such as 9 cases of Chlamydia psittaci. The main fungal infections were Candida albicans (12.38%, 92/743), Pneumocystis jirovecii (9.02%, 67/743) and Aspergillus fumigatus (7.40%, 55/743), among which the average reads of Pneumocystis jirovecii was higher (141.86) than Candida albicans and Aspergillus fumigatus. In addition, some special pathogens were also detected, such as a case of Talaromyces marneffei. The main viral infections included human β herpevirus 5 (17.90%, 133/743), human γ herpevirus 4 (17.36%, 129/743), human β herpevirus 7 (16.15%, 120/743) and human α herpevirus 1 (13.59%, 101/743), among which the average reads of human herpesvirus type 1 (367.27) was the highest. Parasitic infection was least, with only 2 cases of Echinococcus multilocularis, 2 cases of Angiostrongylus cantonensis, 2 cases of Dermatophagoides pteronyssinus and 1 case of Dermatophagoides farinae, which were mainly infected with bacteria and viruses. In addition, a total of 407 patients were diagnosed with mixed infection, of which virus and bacteria mixed infection was the most (22.61%, 168/743). The distribution of microorganisms in different seasons also has certain characteristics. For example, bacteria (Acinetobacter baumannii) were most frequently detected in autumn and winter, while viruses (human gamma-herpesvirus type 4) were most frequently detected in spring and summer. Conclusions In the lower respiratory tract of patients with pulmonary infection, the main gram-negative bacteria are Acinetobacter baumannii and Klebsiella pneumoniae, while the main gram-positive bacteria are Streptococcus pneumoniae, Enterococcus faecium and Mycobacterium tuberculosis complex; the main fungi are Candida albicans, Pneumocystis jirovecii and Aspergillus fumigatus; the main viruses are human β herpevirus 5, human γ herpevirus 4 and human β herpevirus 7. However, parasites are rarely detected and have no obvious characteristics. Bacterial infection and bacterial virus mixed infection are the main co-infections; the microbial characteristics of autumn and winter are different from those of spring and summer. In addition, attention should be paid to special pathogenic microorganisms, such as Chlamydia psittaci and Talaromyces marneffei. These characteristics could be used as reference and basis for the pathogenic diagnosis of pulmonary infection.
Antimicrobial resistance is a rigorous health issue around the world. Because of the short turn-around-time and broad pathogen spectrum, culture-independent metagenomic next-generation sequencing (mNGS) is a powerful and highly efficient tool for clinical pathogen detection. The increasing question is whether mNGS is practical in the prediction of antimicrobial susceptibility. This review summarizes the current mNGS-based antimicrobial susceptibility testing technologies. The critical determinants of mNGS-based antibacterial resistance prediction have been comprehensively analyzed, including antimicrobial resistance databases, sequence alignment tools, detection tools for genomic antimicrobial resistance determinants, as well as resistance prediction models. The clinical challenges for mNGS-based antibacterial resistance prediction have also been reviewed and discussed.
In recent years, with the wide application of metagenomics next-generation sequencing, more and more rare pathogens have been detected in our clinical work, including non-tuberculous Mycobacterium, Corynebacterium, Fusarium, Cryptococcus pneumoniae, human herpes virus, torque teno virus, parvovirus, Tropheryma whipplei, Bartonella, Chlamydia psittaci, etc. It is difficult to determine whether these rare pathogens are clinically significant and need treatment. This article puts forward some suggestions and discussions on the diagnosis and treatment of pulmonary infections with some rare pathogens.
Objective To explore the application value of metagenomic next-generation sequencing (mNGS) based on human sequencing in the clinical early diagnosis of lung cancer. Methods Four patients hospitalized with suspected lung infection were retrospectively analyzed, and the test results of bronchoalveolar lavage fluid (BALF) on mNGS of tumor metagenome, the routine clinical test results, and their clinical diagnosis and treatment information in between August 26, 2021, and December 18, 2021. Results Patient 1 was preliminarily diagnosed with lung cancer by referring to chest computed tomography (CT) imaging. Chest radiograph or CT in the other three patients showed bilateral lung CT and lamellar hyperintensities (patient 2), bilateral lung mass-like and lamellar hyperintensities (patient 3), and lung masses (patient 4), respectively. BALF samples from all 4 patients were detected with mNGS based on human tumor sequences, indicating tumor. In addition, the result in patient 3 also indicated white pseudofilamentous yeast infection consistent with clinical culture, and the result in patient 4 also showed infection of rhinovirus type A. Conclusion The second generation genome sequencing technology based on human sequence can not only assist clinical diagnosis of infection, but also provide detection datUM support for tumor early warning.
The morbidity and mortality of pulmonary infection are high among infectious diseases worldwide. Rapid and accurate etiological diagnosis is the key to timely and effective treatment. Metagenomic next-generation sequencing (mNGS) technology has brokenthrough the limitations of traditional pathogenic microorganism detection methods and improved the detection rate of pathogens. In this paper, the application and advantages of mNGS technology in the diagnosis of bacteria, fungi, viruses and mixed infections in the lungs are analyzed, and the challenges and breakthroughs in RNA detection, wall breaking of firmicutes and host DNA clearance are described, in order to achieve targeted and accurate etiological diagnosis through mNGS, so as to effectively treat pulmonary infections.