Mycobacterium tuberculosis is the causative agent of human tuberculosis. Through the genotyping of Mycobacterium tuberculosis, we can find the epidemic situation and characteristics of tuberculosis in time, analyze the transmission chain between patients in different jurisdictions, and formulate effective intervention measures in time, to provide a strong basis for clinical diagnosis and treatment. At present, several genotyping techniques for Mycobacterium tuberculosis have their advantages and disadvantages in application. This article reviews the genotyping technology, population genetics and genotyping naming rules of Mycobacterium tuberculosis.
【摘要】 目的 分析成都市近年一线抗结核药的耐药状况，为耐药结核病预防控制提供依据。 方法 对成都市2007年1月-2009年12月就诊的结核患者，临床分离株培养鉴定为结核分枝杆菌的菌株采用绝对浓度法进行一线抗结核药:链霉素（SM）、异烟肼（INH）、利福平（RF）、乙胺丁醇（EMB）耐药性检测，分析结核分枝杆菌的耐药情况。 结果 1 235例结核患者中，总耐药率和总耐多药率分别为28.83%、14.01%，初始耐药率和获得性耐药率分别为12.82%、61.27%。近3年耐多药率有下降趋势，但获得性耐药率呈逐年上升趋势。 结论 成都市结核耐药状况仍然比较严重，进一步加强耐药结核的监测和控制非常重要。【Abstract】 Objective To analyze the drug resistant treating mycobacterium tuberculosis (MTB) in Chengdu in recent three years, and to provide the evidence for tuberculosis controlling. Methods The patients with MTB diagnosed from January 2007 to December 2009 in Chengdu were enrolled. Absolute concentration method was used to test the drug-resistance of streptomycin (SM), isoniazide (INH), rifampicin (RFP), and ethambutol (EMB). Results The total rate of drug resistance and multi-drug resistance were 28.83% and 14.01% respectively. The rates of initial drug resistance and the acquired drug resistance were 12.88% and 61.27% respectively. Multi-drug resistance rate showed a downward trend, but the rate of acquired drug resistance increased gradually. Conclusion The situation of drug resistance of tuberculosis in Chengdu is still serious, and it′s very important to further monitor and control the drug resistance treating tuberculosis.
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 systematically review the diagnostic value of PCR-single-strand conformational polymorphism (PCR-SSCP) method for detecting rpoB gene mutation of rifampin-resistant mycobacterium tuberculosis. MethodsSuch databases as PubMed, Web of Science, The Cochrane Library (Issue 2, 2014), CBM, VIP and WanFang Data were electronically and comprehensively searched for relevant studies on the diagnostic value of PCR-SSCP method for detecting rpoB gene mutation of rifampin-resistant mycobacterium tuberculosis from inception to January 1st, 2014. Literature screening according to the inclusion and exclusion criteria, data extraction and methodological quality assessment were completed by two reviewers independently. Meta-analysis was then conducted using Meta-Disc 1.4 and Stata 12.0. ResultsA total of 10 studies were included involving 1 299 cases. The results of meta-analysis showed SEN=0.92 (95%CI 0.90 to 0.94, P=0.019 3), SPE=0.97 (95%CI 0.95 to 0.98, P < 0.000 1), +LR=23.68 (95%CI 8.71 to 64.37, P < 0.000 1), -LR=0.10 (95%CI 0.06 to 0.15, P=0.023 1), DOR=257.16 (95%CI 96.82 to 683.02, P=0.020 0), and SROC area under the curve (AUC) was 0.971 5, and Q* was 0.922 3. The results of sensitivity analysis (after removing studies with sample size less than 100, Chinese studies and QUADAS more than 10 studies) showed that, the results were stable with reliable conclusion. ConclusionPCR-SSCP method has a fairly high value in the diagnosis of rpoB gene mutation of rifampinresistant mycobacterium tuberculosis.
Objective To investigate a suspected outbreak of hospital-acquired infections caused by Mycobacterium chelonae related to flexible bronchoscope (hereinafter referred to as “bronchofibroscope”) and apply targeted high-throughput sequencing (tNGS) technology for etiological analysis, providing references for controlling hospital infection outbreaks. Methods A retrospective survey of patients who were detected with Mycobacterium chelonae through tNGS testing of bronchoalveolar lavage fluid (BALF) after bronchofibroscopy at the Zhengdong District, People’s Hospital of Henan University of Chinese Medicine, People’s Hospital of Zhengzhou between May 1, 2018 and March 18, 2024. The causes were investigated through comprehensive measures including on-site epidemiological surveys and environmental health assessments, and intervention measures were developed and evaluated for effectiveness. Results A total of 52 patients were included. Mycobacterium chelonae was detected in 30 patients, nosocomial infection was excluded in all cases. The suspicious contaminated bronchofibroscope lavage fluid and its cleaning and disinfection equipment, environment and other samples were collected. The traditional microbial culture results were negative. The tNGS results showed that Mycobacterium chelonae was detected in bronchofibroscope lavage fluid (sequence number 156), and all the patients with Mycobacterium chelonae detected in BALF used the bronchofibroscope. It was judged that this event was a pseudo-outbreak of nosocomial infection caused by the contamination of bronchofibroscope with the patient’s BALF. After three months of continuous follow-up after the comprehensive control measures were taken, Mycobacterium chelonae was not detected by tNGS in bronchofibroscope lavage fluid or patients’ BALF. All patients in the hospital improved and discharged without any new cases. The pseudo-outbreak of nosocomial infection was effectively controlled. Conclusions There are many links in the reprocessing of bronchofibroscope, which is easy to cause pollution, and the management needs to be strengthened. tNGS detection has the characteristics of high efficiency, few background bacteria and clear pathogen spectrum, which can be used as a supplementary means for the investigation of nosocomial infection outbreaks, and is of great significance for identifying the source of infection and determining the transmission route.
Objective To evaluate the diagnostic value of all diagnostic tests detecting the ethambutol resistance in Mycobacterium tuberculosis. Methods PubMed, EMbase, Chinese Biomedical Database (CBM), Chinese Scientific Journals Full-Text Database (CSJD), and Chinese Journal Full-text Database (CJFD) were searched, and QUADAS items were used to evaluate the quality of included studies. Meta-disc software was used to handle data from included studies. Such index as sensitivity, specificity, and SROC were applied to assess the diagnostic value of individual diagnostic test. Results Nine studies were included. The results of meta-analyses showed that compared with proportion method, the summary sensitivity, summary specificity, positive likelihood ratio, negative likelihood ratio, and SROC area under curve of a nitrate reductase assay were 92%, 99%, 30.50, 0.13, and 0.975 2, respectively, while compared with BACTEC 460 TB, the above mentioned indexes of BACTEC MGIT 960 System were 92%, 99%, 6.27, 0.11, and 0.9, respectively. Bacteriophage biological amplification method revealed relative good analysis effectiveness on MB/BacT. Conclusion According to the results, it is recommended that nitrate reductase assay can replace proportion method as screening test of ethambutol resistance in Mycobacterium tuberculosis, and BACTEC MGIT 960 System can replace BACTEC 460 as final diagnostic test of ethambutol resistance in Mycobacterium tuberculosis.
ObjectiveTo summarize the clinical manifestations, basic diseases, imaging features, drug sensitivity results and recovery of Mycobacterium Kansasii pulmonary disease patients to enhance understanding of the disease. Methods The clinical data of 116 patients with Mycobacterium Kansas pulmonary disease diagnosed in Guangzhou chest hospital from January 2019 to September 2024 were analyzed retrospectively. Results The 116 patients with Mycobacterium kansasensei lung disease were 67 males and 49 females, aged 27 to 92 years, with clinical manifestations of cough and sputum (102 cases) and hemoptysis (48 cases) as the predominant symptoms. There were 98 cases with history of bronchiectasis, 8 cases with cancer,18 cases with cardiovascular disease, 22 cases with chronic obstructive pulmonary disease, 10 cases with diabetes mellitus, 9 cases with rheumatoid immune system disease, 5 cases with pulmonary aspergillus infection, 2 cases with asthma, and 10 cases without underlying disease. All of them had lung shadows on imaging, including 30 cases with simple bronchodilatation manifestation, 48 cases with bronchodilatation combined with cavitation, 10 cases with patchy streak shadow, 18 cases with patchy streak shadow combined with cavitation, and 10 cases with nodules combined with cavitation. The results of drug sensitivity showed that the resistance rate of more than 50% was isoniazid (89.66%), streptomycin (75.87%), amikacin (72.41%), and isoniazid para-aminosalicylate (Likely Lung Disease) (56.90%); while the sensitivity rate of more than 50% was rifabutin (100%), moxifloxacin (94.83%), rifampicin (93.10%), prothioisonicotinamide ( 91.38%), levofloxacin (89.66%), ethambutol (84.48%), and linezolid (79.31%). 76 of the remaining 98 of 116 patients had negative sputum cultures within 1 year, with the exception of 12 who were left untreated and 6 who did not complete treatment. The 116 patients with Mycobacterium kansasensei lung disease presented with chronic cough, sputum, and hemoptysis, and most of them were combined with structural lung diseases such as bronchiectasis, or with underlying diseases such as chronic obstructive pulmonary disease and diabetes mellitus. Imaging features show pulmonary shadows. Moreover, Mycobacterium kansasii shows high sensitivity to most conventional antituberculosis drugs, which may result in a higher cure rate compared with other types of nontuberculous mycobacterial lung disease. Therefore, timely and well-conducted strain identification and drug sensitivity testing are essential for the development of a targeted treatment program that can significantly improve patient outcomes. Conclusions Clinical manifestations of 116 patients with Mycobacterium kansasense lung disease were characterized by chronic cough, sputum and hemoptysis, which were mostly combined with structural lung diseases such as bronchiectasis. The imaging features show pulmonary shadows. Mycobacterium kansasii exhibits a higher sensitivity rate to most conventional anti-tuberculosis drugs, which may result in a higher cure rate in treatment compared to other types of nontuberculous mycobacterial lung diseases. Therefore, timely and comprehensive species identification and drug susceptibility testing are crucial for formulating targeted treatment regimens, which can significantly improve patients' treatment outcomes.
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.