ObjectiveTo explore application value of next-generation sequencing (NGS) technology in diagnosis of pathogenic microorganism infection through two cases report and literature review.MethodsThe NGS technology was used to make clear diagnosis of two cases of suspected pulmonary tuberculosis and pulmonary nontuberculous mycobacterial diseases. Bronchoalveolar lavage fluid of these two patients was collected for gene detection of pathogens using the NGS technology. A systematic literature review was performed for similar published cases in WanFang and CNKI database, using the keywords (next-generation sequencing) OR (NGS) AND (microorganism OR infection) from January 2000 to January 2018, using the PubMed database to retrieve the English literature before January 2018 with the " NGS, infectious diseases, China” as keywords.ResultsOne case of Mycobacterium tuberculosis and one case of non-tuberculous Mycobacteria were detected respectively. A total of 221 Chinese literatures and 3 English literatures were retrieved, excluding dissertations, conferences and newspapers. Finally, 10 articles were published in the infectious diseases and respiratory diseases subjects. The role of NGS technology in the diagnosis and study of related pathogens is proposed.ConclusionThe NGS method is expected to achieve precision medical purposes, such as early diagnosis of infectious diseases, transmission control, accurate treatment, good prognosis and so on.
ObjectiveTo evaluate the accuracy and practicability of matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) in clinical isolates of mycobacteria.MethodsWe collected all tested strains, which were positive for Mycobacterium tuberculosis culture and positive for acid-fast staining, from West China Hospital of Sichuan University from 2014 to 2017, eliminating duplicate strains sent by the same patient at the same time. The traditional method was used with the P-nitrobenzoic acid (PNB)/ 2-Thiophenecarboxylic acid hydrazide (TCH) indicator to initially identify acid-resistant positive strains. Mycobacteria was identified by MALDI-TOF MS; the specificity and sensitivity of the MALDI-TOF MS was analyzed by duplex primer-polymerase chain reaction (Duplex-PCR) method and DNA sequencing method as the "gold standard" for the identification.ResultsA total of 237 anti-acid positive strains were collected; Mycobacterium tuberculosis complex (MTC) and non-tuberculous mycobacteria (NTM) were identified by mycobacterium double primer PCR, and NTM was identified by 16S rRNA gene sequencing. There were 218 cases of MTC and 19 cases of NTM. The results of preliminary identification using the traditional identification method of PNB/TCH indicator showed that there were 209 cases of MTC (with the sensitivity of 95.9%, specificity of 100.0%, positive predictive value of 100.0%, and negative predictive value of 67.9%) and 28 cases of NTM (with the sensitivity of 100.0%, specificity of 95.9%, positive predictive value of 67.9%, and negative predictive value of 100.0%). The results of MALDI-TOF MS method indicated that there were 199 cases of MTC (with the sensitivity of 91.3%, specificity of 100.0%, positive predictive value of 100.0%, and negative predictive value of 50.0%), 32 cases of NTM (with the sensitivity of 68.4%. specificity of 94.0%, positive predictive value of 40.6%, and negative predictive value of 97.1%), and 6 cases of others. There were 168 strains (84.4%) with the identification score>1.9 obtained by MALDI-TOF MS method.ConclusionsMALDI-TOF MS is a better method for identifying mycobacteria, which has the same identification results as the traditional methods, and has low cost and is suitable for routine use in clinical microbiology laboratories.
ObjectiveTo investigate the clinical characteristics of non-tuberculous mycobacterium (NTM) pulmonary disease and pulmonary tuberculosis, as well as the bacterial distribution of NTM pulmonary disease. Methods The bacterial distribution and clinical characteristics of 104 patients with NTM lung disease hospitalized in Jiangxi Provincial People’s Hospital from May 2017 to May 2020 were retrospectively analyzed, as well as the clinicplal characteristics of 155 patients with tuberculosis hospitalized during the same period. Results The age of NTM lung disease group [(60±15) years] was higher than that of tuberculosis group [(55±19) years]. There were statistically significant differences in basic diseases (such as malignant tumor, type 2 diabetes, old tuberculosis, bronchiectasis), laboratory examination (such as blood routine examination, albumin) and chest imaging characteristics between the two groups (P<0.05). There was no significant difference in clinical symptoms (such as cough, sputum or fever) (P>0.05). The common underlying diseases of NTM lung disease were malignant tumor (29%), bronchiectasis (21%), chronic obstructive pulmonary disease (19%), etc. The common clinical symptoms of NTM lung disease included cough, sputum, fever, hemoptysis, chest tightness and shortness of breath, and other non-specific respiratory symptoms. The common manifestations of NTM lung disease on chest high-resolution CT (HRCT) included patchy images (82%), mediastinal lymph node enalargement (35%), pleural thickening (31%), pleural effusion (26%) and other signs. The isolates of NTM included Mycobacterium avium (50%), Mycobacterium intracellulare (21%), Mycobacterium chelonae/abscessus (14%), Mycobacterium fortuitum (5%), Mycobacterium gordonae (4%), Mycobacterium gilvum (3%), and Mycobacterium smegmatis (3%). Multivariate Logistic regression analysis showed that advanced age (OR=1.027) was a risk factor for NTM lung disease. Conclusions The clinical manifestations of NTM lung disease and tuberculosis are similar and difficult to distinguish. For male patients over 60 years old with malignant tumor, old tuberculosis, bronchiectasis and other basic diseases, and the chest HRCT findings are mainly bronchiectasis, NTM lung disease should be actively excluded. There is little difference in clinical manifestations between different strains of NTM lung disease, and the treatment cycle of NTM lung disease is long and easy to be interrupted, requiring enhanced follow-up.