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.
Objective To summarize the clinical characteristics of pneumocystis pneumonia (PCP) secondary to interstitial lung disease (ILD) to improve the prophylaxis and management level of clinicians. Methods The clinical data of 50 patients with PCP secondary to ILD in the Department of Respiratory and Critical Care Medicine of Nanjing Drum Tower Hospital from January 2015 to December 2022 were collected. SPSS 26.0 software was used for statistical analysis. Results A total of 50 patients with PCP secondary to ILD were screened. Among the 50 patients, there were 23 males and 27 females, with a median age of 64 years old. Forty-eight cases (96%) had a history of glucocorticoid therapy with the median duration of 3 months; 31 (77.5%, 31/40) cases developed PCP in the first 6 months after glucocorticoid therapy; 34 cases had a history of glucocorticoid and immunosuppressants at the same time. None of the 50 ILD patients used drugs for PCP prophylaxis before developing PCP. The major clinical manifestations of PCP secondary to ILD were worse cough and shortness of breath or fever. Laboratory results showed 38 cases (76.0%) had peripheral blood total lymphocyte count <200/µL, 27 cases (54.0%) had CD4+ T cell count <200/µL, 34 cases (68.0%) had CD4+ T cell count <300/µL, 37 cases (74.0%) had CD3+ T cell count <750/µL, 34 cases (68.0%) had β-D-glucan test >200 pg/mL, 35 cases (70.0%) had lactic dehydrogenase > 350 U/L and 41 cases (82.0%) had type Ⅰ respiratory failure. High resolution computed tomography showed added ground-glass opacity and consolidation on the basis of the original ILD. Thirty-six cases were detected the Pneumocystis jirovecii by metagenomic next-generation sequencing with broncho-alveolar lavage fluid as the main source, and 2 cases by smear microscopy. All patients were treated with trimethoprim-sulfamethoxazole. After treatment, 29 cases were discharged with a better health condition, 10 cased died, and 11 cases left hospital voluntarily because of treatment failure or disease deterioration. Conclusions After the use of glucocorticoid and immunosuppressants, ILD patients are susceptible to life-threatening PCP. It is particularly important to make an early diagnosis. Attention should be paid to integrate the symptoms, levels of peripheral blood lymphocyte count, β-D-glucan test, lactic dehydrogenase and imaging findings to make an overall consideration. It is suggested to perform next-generation sequencing with broncho-alveolar lavage fluid at an early stage when patients can tolerate fiberoptic bronchoscopy to avoid misdiagnosis and missed diagnosis. ILD patients often develop PCP in the first 6 months after using glucocorticoid and immunosuppressants. During follow-up, peripheral blood CD4+ and CD3+ T cell count should regularly be monitored so as to timely prevent PCP.
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.
ObjectiveTo improve the understanding of psittacosis, the clinical data of 8 cases are reviewed. The application of pathogen metagenomics next-generation sequencing (mNGS) in the diagnosis of nocardiosis is also investigated.MethodsThe clinical data of eight patients with psittacosis diagnosed by mNGS in Nanjing Drum Tower Hospital from January 2018 to May 2020 were reviewed. The clinical characteristics, laboratory examination characteristics and imaging changes were analyzed, and the treatment outcome was followed-up.ResultsAmong the eight cases, there were six males and two females, aged 43～83 years old, with an average age of 64±12 years old. Six of them had a clear history of poultry exposure. The major clinical manifestations were fever, cough, dyspnea, etc. Chest high-resolution computed tomography (HRCT) may have solid shadow, ground glass like shadow. Chlamydia psittaci was detected by mNGS in eight patients’ bronchoalveolar lavage fluid. Minocycline or moxifloxacin were administrated, six patients were discharged after their condition improved, and two patients died.ConclusionsThe incidence of psittacosis is low, and its clinical manifestations lack specificity. In the course of the disease, there may be different degrees of fever, cough, sputum, dyspnea and other symptoms. The lungs can be heard with wet rales, chest HRCT can be seen ground glass shadow, consolidation shadow, accompanied by air bronchogram. Chlamydia psittaci can be detected in alveolar lavage fluid by mNGS. The patients need to be treated for a long time, lasting at least 10 to 14 days. Tetracycline drugs should be the first choice, and can be combined with other antibiotics with activity against gram-positive and gram-negative bacteria in critical patients.
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.
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 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.
ObjectiveTo explore the application and clinical value of metagenomic next-generation sequencing (mNGS) combined with Omadacycline in the treatment of Refractory Mycoplasma pneumoniae pneumonia (RMPP).MethodsThe clinical data, relevant laboratory results, diagnosis and treatment process, and imaging outcomes of four patients diagnosed with Mycoplasma pneumoniae pneumonia through mNGS were analyzed. ResultsThe clinical symptoms at onset in all four patients were consistent with Mycoplasma pneumoniae pneumonia. After conventional treatment with macrolides, tetracyclines, or quinolone antibiotics, the symptoms showed no significant improvement, and there was a trend of radiological worsening. Following the confirmation of Mycoplasma pneumoniae infection through mNGS of bronchoalveolar lavage fluid, and due to various reasons preventing the use of the aforementioned drugs, omadacycline was ultimately chosen for treatment. Radiological improvements were observed in all cases, leading to a good prognosis and discharge. ConclusionsFor pneumonia cases where the infectious pathogen cannot be identified and conventional treatment has failed, mNGS can be utilized for early and accurate diagnosis. In cases of RMPP, Omadacycline can be employed as an alternative treatment to prevent delays in care and reduce the risk of complications.
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.
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.