Objective To investigate the clinical manifestations, diagnosis, treatment and prognosis of psittacosis patients. Methods The clinical features, treatment and prognosis of severe pneumonia caused by Chlamydia psittaci were analyzed and relevant literatures were reviewed. Results An 83-year-old male with a history of type 2 diabetes mellitus was admitted to the hospital for "fever, cough for 5 days and dyspnea for 3 days". Chest CT showed a large mass of increased density in the right lung; CD4+ T lymphocytes had an absolute value of 23 cells/μL; Blood gas analysis showed type Ⅰ respiratory failure; Chlamydia psittaci was detected by metagenomic next-generation sequencing. The patient was diagnosed of severe pneumonia (Chlamydia psittaci), type 2 diabetes mellitus, suspected central nervous system infection. This patient was treated with doxycycline and macrolides antibiotics and discharged from hospital after complete recovery. Literature review showed that patients got infected from contacting sick bird, manifested with multiple system involvement. Respiratory symptoms were common, while central nervous system infection seemed to be rare. The diagnosis of psittacosis depended on serology, nucleic acid detection, pathogen isolation and culture. Metagenomic next-generation sequencing had superiority in the diagnosis of psittacosis. Tetracyclines were the preferable treatment, such as doxycycline or tetracycline, with a duration of at least 10 to 14 days. The prognosis of psittacosis was well, and most of the severe and even life-threatening cases were caused by unclear diagnosis and delayed treatment, and the overall mortality rate was about 1%. Conclusions Psittacosis is one kind of zoonoses. History of poultry exposure is helpful in diagnosis, and metagenomic next-generation sequencing has advantages in diagnosing psittacosis. Tetracyclines are preferred with adequate course of treatment. The overall prognosis is good.
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, due to the extensive usage of immunosuppressant and the rise of patients with cancers and organ transplantation, the incidence rate of invasive fungal infection, especially invasive pulmonary fungal infection, has increased. Besides the clinical manifestations, medical history and imaging, the diagnosis of pulmonary mycosis mainly depends on pathogen detection methods in clinical microbiology laboratory. However, due to the difficulty in fungi culturing and the low sensitivity of smear microscopy, better molecular biology methods are needed. To date, the emergence of metagenomic next-generation sequencing (mNGS) has improved the identification rate of pulmonary fungal infections. mNGS is significantly superior to traditional detection methods in rapid, accurate, and comprehensive determination of fungi from various clinical specimens, especially atypical fungi. However, some problems in mNGS method have to be addressed including sample collection, report interpretation, and its combination with traditional microbiology methods. With the in-depth discussion and solution of the above problems, mNGS will be indispensable to the etiological diagnosis of pulmonary invasive fungal infection.
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 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.
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.
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.
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.
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 analyze the clinical data of patients with Tropheryma whipplei pneumonia, and summarize the clinical characteristics, diagnosis, and treatment methods of Tropheryma whipplei pneumonia. Methods The data of Tropheryma whipplei pneumonia patients from three hospitals in Hunan Province between January 1, 2021 and October 1, 2022 were retrospectively collected. The clinical symptoms, laboratory examination, metagenomics next-generation sequencing (mNGS), CT imaging features, diagnosis and treatments of the included patients were analyzed. Results A total of 4 patients were included. Among them, there were 2 males and 2 females. The main manifestations were cough, expectoration, fever, and shortness of breath. There were 2 cases of diffuse ground glass opacity in both lungs, 1 case of pulmonary nodule, 1 case of pulmonary cavity, 1 case of pleural disease, 2 cases of pulmonary exudative lesions, and 1 case of mediastinal lymphadenectasis. The mNGS results showed that Tropheryma whipplei was detected in all 4 patients, and the median number of serial number (lower quartile, upper quartile) was 1 528 (1 480, 1 576). After anti infection treatment, 3 cases were treated effectively, and 1 case had poor treatment effect. Conclusions mNGS is an effective method to diagnose Tropheryma whipplei pneumonia. The measurement of serum lactate dehydrogenase level is helpful to evaluate the disease and determine the prognosis. Piperacillin tazobactam, meropenem and doxycycline are effective for this disease, while moxifloxacin and trimethoprim / sulfamethoxazole are not recommended because they may be naturally resistant. Without active etiological treatment, the disease may persist in migration and lead to extrapulmonary involvement.