ObjectiveTo evaluate the relationship between the genes involved in regulating iron uptake and maintaining iron homeostasis in Klebsiella pneumoniae from different sources and pathogenicity.MethodsThe genomic DNA sequences of two strains of Klebsiella pneumoniae from different sources were sequenced, stitched together, annotated and analyzed by second generation sequencing technique. The transversal comparison between different types of Klebsiella pneumoniae in NCBI database of iron carrier gene cluster iroB/C/D.ResultsIn these two Klebsiella pneumoniae clinical strains, the strain isolated from liver abscess patient carried 11 different iron acquisition and transportation system specific genes, which were not found in the non-liver abscess patient strain. Combined with the analysis of this sequence, in the NCBI database, six different strains of Klebsiella pneumoniae showed iroB/C/D triple positive.ConclusionIron acquisition and transportation system in Klebsiella pneumoniae may be an important pathogenic factor, which is closely related to hepatic abscess.
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 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 study the application of non-real-time ultrasound bronchoscopy combined with Metagenomic Next-Generation Sequencing (mNGS) for diagnosis in focal pulmonary infectious diseases. MethodsProspective inclusion of patients with focal pulmonary infection were randomly divided into two groups, the experimental group used non-real-time ultrasound bronchoscopy positioning to collect bronchial alveolar lavage fluid (BALF), while the control group used chest CT position. BALF was subjected to mNGS and traditional microbial detection including traditional culture, the fungal GM test and Xpert (MTB/RIF). ResultThe positive rate of traditional culture (39.58% vs. 16.67%, P=0.013) and mNGS (89.58% vs. 72.92%, P=0.036) in experimental group was higher. The positive rate of Xpert MTB/RIF (4.17% vs. 2.08%, P=1) and fungal GM test (6.25% vs. 4.17%, P=0.765) was similar. The positive rate of bacteria and fungi detected by mNGS was higher than traditional culture (61.46% vs. 28.13%, P<0.001). Mycobacterium tuberculosis was similar to Xpert MTB/RIF (8.33% vs. 3.13%, P=0.21). Aspergillus was similar to GM test (7.29% vs. 5.21%, P=0.77). The total positive rate of traditional microbial methods was 36.46%, but 81.25% in mNGS (P<0.001). mNGS showed that 35 cases were positive and 13 kinds of pathogens were detected in control group, but 43 patients and 17 kinds of pathogens were detected in experimental group. The average hospitalization time [(12.92±3.54) days vs. (16.35±7.49) days] and the cost [CNY (12209.17±3956.17) vs. CNY (19044.10±17350.85)] of experimental group was less (P<0.001). ConclusionsNon-real-time ultrasound bronchoscopy combined with mNGS can improve the diagnostic rate of focal pulmonary infectious diseases which is worthy of popularization and application in clinical practice.
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 clinical value of next-generation sequencing (NGS) in the diagnosis of Pneumocystis jirovecii pneumonia (PCP).MethodsTwo patients with Pneumocystis jirovecii pneumonia after lung transplantation were detected by NGS in the sputum and bronchoalveolar lavage fluid. The clinical data, imaging features, laboratory examination and treatment of the two patients were reported. A systematic literature review was performed for similar published cases in PubMed database, using the keywords "lung transplantation/solid organ transplantation" and "Pneumocystis jirovecii".ResultsThere were six references based on the keywords of "lung transplantation " and " Pneumocystis jirovecii ", of which three were case report. Sixty-six lung transplant patients were complicated with Pneumocystis jirovecii in total. The clinical manifestations of Pneumocystis jirovecii pneumonia were fever and dyspnea of different degrees. The diffuse "ground glass" infiltration could be shown on imaging. Computer tomography scan of chest was a sensitive method to detect PCP. Combined immunofluorescence microscope/PCR/serum 3-β-D-glucan could effectively improve the accuracy of microbiology detection. In addition, NGS could quickly and accurately identify pathogenic bacteria, give guidance for treatment and improve prognosis so as to benefit patients well. Trimethoprim/sulfamethoxazole (TMP/SMZ) was the preferred choice for the treatment of PCP patients.ConclusionsPneumocystis jirovecii pneumonia is more common in patients with immunodeficiency or immunosuppression. NGS can help rapid and accurate diagnosis, and the treatment should be early and sufficient.
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.