Routine use of a simple low-cost genotypic assay for the identification of mycobacteria in a high throughput laboratory

A novel polymerase chain reaction (PCR)-restriction fragment length polymorphism analysis (PRA) of the hsp65 gene was used for the routine identification of mycobacteria in a high throughput clinical laboratory. A total of 2036 clinical isolates were tested by PRA in conjunction with other methods. The PRA identification of M. tuberculosis complex was 100% sensitive and specific, and 74.5% of nontuberculous mycobacteria (NTM) were correctly identified. It gave highly consistent results for Mycobacterium avium complex (MAC) species and for most isolates of M. fortuitum, M. chelonae, and M. kansasii. It had proven to be highly robust and stable despite usage on such a large-scale and is thus particularly suitable for use in high throughput laboratories in areas with a high incidence of tuberculosis.     

Taxonomic and phylogenetic status of non-tuberculous mycobacteria in a Caribbean setting

This report describes detailed taxonomic and phylogenetic analysis of 15 non-tuberculous mycobacteria (NTMs) isolated from human pathological specimens in a Caribbean setting (12 slow-growers and three rapid-growers) that were not identified by cultural and biochemical tests and drug-susceptibility results. These isolates were further studied using PCR restriction fragment length polymorphism analysis (PRA) of a 441bp hsp65 fragment, as well as the sequencing of 16S rDNA and hsp65 DNA, and HPLC of the mycolic acids. Our results showed that taxonomic position of well-defined NTMs was resolved by PRA and sequencing of hsp65, nonetheless, it was not suitable to investigate rarely observed or new strains that required 16S rDNA sequencing and HPLC for a definite response. Unrooted neighbor-joining phylogenetic trees were drawn based upon the 16S rDNA and hsp65 sequences of the 15 NTMs compared with those from described species (73 for 16S rDNA and 45 for hsp65). For most of the NTMs not showing an exactly matching sequence with either hsp65 or 16S rDNA in the GenBank, the phylogenetic tree was able to provide with useful indications about their relatedness to known species. In such a case, a concording HPLC pattern with the sequence data and the place of the strain within the tree could lead to a potential identification. We also identified three identical isolates that define a new mycobacterial species within the group of M. simiae-related mycobacteria. The isolation and characterization of mycobacteria from new settings may lead to identify potential pathogens that may propogate in future because of increased human migration, travels, and climatic and ecological changes of the modern world.     

Comparative evaluation of polymerase chain reaction and restriction enzyme analysis: two amplified targets, hsp65 and rpoB, for identification of cultured mycobacteria

The increasing incidence of tuberculosis and other mycobacterial infections due to AIDS epidemic resulted in the need of rapid and accurate identification of isolated mycobacteria. The correct identification result leads to the selection of an appropriate therapeutic regimen. Polymerase chain reaction and restriction enzyme analysis (PCR-REA) has been developed since 1992 and used as the rapid method for identifying mycobacteria. Several genes or sequences have been used as an amplified target for PCR-REA. The present study aims to evaluate the potential use of PCR-REA of gene-encoding heat shock protein 65 kDa (hsp65) and beta-subunit RNA polymerase (rpoB) for the identification of mycobacteria compared with conventional biochemical identification. Two hundreds clinical isolates, consisting of 50 isolates of Mycobacterium tuberculosis and 150 isolates of nontuberculous mycobacteria (NTM), were submitted for identification using PCR-REA and biochemical method. The results demonstrated that PCR-REA identified 188 isolates of both M. tuberculosis and NTM concordantly with biochemical identification. Discordant identification results obtained from 12 isolates, comprised of 8 M. scrofulaceum, 1 M. avium complex, 1 M. malmoense, 1 M. terrae complex, and 1 M. chelonae/abscessus. Overall, the concordant percentage of results obtained from PCR-REA compared with biochemical method was 100%, 98.8%, and 83.3% for M. tuberculosis complex, rapidly growing, and slowly growing mycobacteria, respectively, and the results of hsp65 PCR-REA was in agreement with those obtained from rpoB PCR-REA. From this study, PCR-REA appears to be a simple, rapid, and reliable method for identifying mycobacteria in a routine microbiology laboratory.     

非结核分枝杆菌鉴定方法和病原谱分析

目的分析非结核分枝杆菌（NTM）鉴定方法和病原谱分布情况,为临床NTM的鉴定和病原谱分布提供依据和参考。 方法连续纳入2020年度安徽省胸科医院培养阳性的分枝杆菌培养物进行病原谱分析,采用MPB64抗原和PNB鉴别培养基对培养阳性菌株进行初步鉴定,熔解曲线法进行NTM分子生物学鉴定,并采用微孔板法进行药敏分析。 结果2 563株分枝杆菌培养阳性菌株,最终有207株鉴定为NTM,NTM的分离率为8.08%其中,117例为男性感染者,62.80%的感染者年龄超过60岁。排名前3位的菌种依次为胞内分枝杆菌（76.67%）、堪萨斯分枝杆菌（6.19%）、脓肿分枝杆菌（5.71%）。不同NTM对利奈唑胺、克拉霉素、莫西沙星和阿米卡星的敏感性较高,对多西环素、米诺环素、亚胺培南、磺胺甲唑的耐药率较高。 结论安徽省胸科医院NTM感染以男性和60岁以上感染者居多,胞内分枝杆菌为主要菌种,不同菌种的耐药率有所差异,应提升实验室检测NTM和耐药性的水平,为临床精准诊治NTM提供依据。     

Different molecular methods for the identification of rarely isolated non-tuberculous mycobacteria and description of new hsp65 restriction fragment length polymorphism patterns

Analysis of heat shock protein 65 (hsp65) gene restriction fragment length polymorphism (RFLP) is done frequently to identify non-tuberculous mycobacteria (NTM) on a genetic basis. Here we report the results of analysing the hsp65 patterns of some rarely isolated NTM for which patterns have not been published before (Mycobacterium bohemicum, Mycobacterium hassiacum, Mycobacterium heckeshornense, Mycobacterium monacense, and Mycobacterium triplex). Furthermore new hsp65-variants for Mycobacterium interjectum (type II), Mycobacterium mucogenicum (type V), Mycobacterium gordonae (type VIII) and Mycobacterium paraffinicum (perhaps synonymous to Mycobacterium scrofulaceum) are described. All species were characterised by hsp65-RFLP, sequencing a 441-bp fragment of the hsp65 gene and sequencing the hypervariable region of the 16S rDNA. Additional data for less frequently isolated mycobacteria are provided and the hitherto described data for the Mycobacterium gordonae complex are summarised. Although the hsp65-RFLP analysis turned out to be a useful method a number of restraints (lack of standardisation, slight variability in fragment length) limits its broader use. Reliable identification of NTM needs, however, more than one molecular method. Identification results obtained by applying different methods yielded conflicting results. Confusion may be caused by older data base entries which are not updated and not longer reflect the actual systematic and taxonomy of the genus Mycobacterium.     

不同分子生物学方法快速鉴别非结核分枝杆菌的应用评价

目的 评价3种分子生物学方法快速鉴定非结核分枝杆菌的优缺点.方法 收集41株临床分离的非结核分枝杆菌,以16S rRNA基因测序方法为标准,同时以hsp65基因测序方法及PCR-RFLP方法鉴定菌株,与16S rRNA基因测序结果进行比较.结果 41株非结核分枝杆菌16SrRNA基因测序结果:9株龟分枝杆菌复合群,7株偶发分枝杆菌,7株胞内分枝杆菌,3株鸟分枝杆菌,3株堪萨斯分枝杆菌复合群,3株耻垢分枝杆菌,3株土分枝杆菌,2株草分枝杆菌,2株无色分枝杆菌,1株瘰疬分枝杆菌,1株M.arupense.与16S rRNA基因测序相比较,hs65 PCR-RFLP能鉴定9株龟分枝杆菌复合群至亚种脓肿分枝杆菌,3株堪萨斯分枝杆菌复合群鉴定至亚种堪萨斯分枝杆菌;1株偶发分枝杆菌及1株无色分枝杆菌与其不符;其余菌株鉴定结果一致,符合率为95.1%(39/41).hsp65基因测序结果显示,1株爱尔兰分枝杆菌与16S rRNA测序结果不符,其余菌株鉴定结果与其一致,符合率为97.6%(40/41),并且能进一步将9株龟分枝杆菌复合群鉴定至亚种脓肿分枝杆菌,3株堪萨斯分枝杆菌复合群鉴定至亚种堪萨斯分枝杆菌.结论 3种方法均能快速鉴定非结核分枝杆菌.与16S rRNA基因测序相比,hsp65基因测序及hsp65 PCR-RFLP更容易鉴定临床最常见非结核分枝杆菌(如堪萨斯分枝杆菌和脓肿分枝杆菌),可在临床推广使用.     

PCR-RFLP技术用于脓肿分枝杆菌群鉴定的初步研究

目的 探讨PCR-RFLP分子鉴定技术对脓肿分枝杆菌群鉴定的应用价值.方法 收集2009-2010年在福建省肺科医院、北京市朝阳区疾病预防控制中心、北京解放军总医院抗酸染色阳性菌株46株.根据2004年分枝杆菌检验手册临床检验常分离菌鉴定程序,用DNA直接测序方法为对照,以hsp65(441 bp)和rpoB(380 bp)基因的特异片段为分子标识,采用PCR-RFLP对脓肿分枝杆菌群临床分离菌株进行菌种鉴定.结果 接种L-J、PNB和TCH培养基,鉴定为结核分枝杆菌30株,非结核分枝杆菌16株.其中10株非结核分枝杆菌的培养特性和主要生化反应同脓肿分枝杆菌( ATCC 19977)结果一致.经hsp65 PCR-RFLP鉴定,9株菌株的指纹图谱为235和200 bp( BstEⅡ)/145、70、60、55、50和40 bp(HaeⅢ),1株菌株的指纹图谱为235和200 bp(BstEⅡ)/200、70、60和50 bp(HaeⅢ).经rpoB PCR-RFLP鉴定,10株临床菌株的指纹图谱是105、95和80 bp(MspⅠ)/130、100 bp和90 bp( HaeⅢ).DNA测序分析,9株分离株与脓肿分枝杆菌群脓肿亚种hsp65和rpoB基因序列匹配度均为100％;1株分离株与脓肿分枝杆菌群马赛分枝杆菌亚种hsp65和rpoB基因序列匹配度均为100％.结论 PCR-RFLP是一种快速、有效鉴定脓肿分枝杆菌的方法,且hsp65 PCR-RFLP的鉴定效果优于rpoB PCR-RFLP.     

自贡市非结核分枝杆菌临床分离株的菌种鉴定结果分析

目的 对自贡市35株疑似非结核分枝杆菌（NTM）临床分离株进行菌种鉴定。方法 从自贡市各区（县）及市结核病防治获得的临床分枝杆菌分离株,通过罗氏培养基（L-J）、对硝基苯甲酸（PNB）和噻吩-2-羧酸肼（TCH）鉴别培养基初步鉴定为NTM,再经多位点PCR方法确定为NTM后,对rpoB、hsp64及its基因进行测序及分析鉴定。结果 35株疑似NTM临床分离株,通过初步鉴别,多位点PCR,rpoB、hsp64及its基因测序及分析鉴别出32株NTM,分别为脓肿分枝杆菌（M. abscessus）11株、胞内分枝杆菌（M. intracellulare）7株、堪萨斯分枝杆菌（M. kansasii）5株、鸟分枝杆菌（M. avium）3株、脓毒分枝杆菌（M. septicum）1株、马赛分枝杆菌（M. masseillense）1株、戈登分枝杆菌（M. gordonae）2株、副瘰疬分枝杆菌（M. parascrofulaceum）1株和Mycobacterium peregrinum 1株。结论 抗酸染色阳性、PNB/TCH鉴定为NTM的临床分离株中包含不同种类的NTM,自贡市NTM肺病的病原种类较多,以快生长脓肿分枝杆菌为主,其次为慢生长不产色菌的胞内分枝杆菌和缓慢生长光产色菌的堪萨斯分枝杆菌。实验室应开展进一步菌种鉴定,以指导临床正确诊断和合理治疗。     

Differentiation of mycobacteria in sputa by duplex polymerase chain reaction for mycobacterial hsp65 gene

Early differentiation of mycobacteria in sputa is crucial. This study was set to evaluate the usefulness of a newly developed duplex polymerase chain reaction (PCR) for hsp65 gene-based method in differentiating mycobacteria in sputum with a positive acid-fast bacilli (AFB) smear before culturing. One hundred forty-seven sputa with positive AFB smear were included for the analysis. Mycobacterial species were identified using a newly developed duplex PCR for hsp65 gene followed by a nested PCR-direct sequencing and the conventional colony-based method. Final decision of mycobacterial species were made based on 1) results of species identification based on mycobacterial colonies or 2) results of species identification of other sputa from the same patients and clinical findings. The duplex PCR-based method correctly identified 83.2% sputa from tuberculosis patients and 82.2% sputa from nontuberculous mycobacteria patients, whereas the colony-based method correctly identified 86.1% and 77.8%, respectively. Sensitivity and specificity of the colony-based method for Mycobacterium tuberculosis were 86.1% and 100%, respectively, whereas those of the duplex PCR-based method were 83.2% and 95.6%, respectively. The duplex PCR-based method, to differentiate mycobacterial species in sputa, produced comparable results as those of the colony-based identification method.     

2019年北京地区某医院非结核分枝杆菌菌种鉴定结果分析

目的研究该院2019年收治人群检出非结核分枝杆菌(NTM)菌种分布情况,以指导临床诊断。方法收集该院2019年咳出痰、肺泡灌洗液等样本分离出来的NTM,菌种鉴定统一采用16S rRNA和hsp65基因片段测序。同时,收集患者γ-干扰素释放试验(IGRA)结果,对IGRA在不同NTM感染中的水平变化进行分析。结果研究期间检出NTM样本183份,同一患者多次检出同一种NTM按1份统计。患者中男性47.0%(86/183),女性53.0%(97/183);青年组(20~<45岁)19人,中年组(45~<65岁)67人,老年组(≥65岁)97人;菌种鉴定结果显示共检出17种NTM,菌种分布构成比前4位为胞内分枝杆菌54.6%(100/183)、脓肿分枝杆菌12.0%(22/183)、鸟分枝杆菌9.3%(17/183)、堪萨斯分枝杆菌4.4%(8/183)。老年组检出NTM 97人(53.0%),其中男性占43.3%,女性占56.7%。183人中有120人进行IGRA检测,阳性率27.5%(33/120)。快生长分枝杆菌组与慢生长分枝杆菌组的IGRA结果阴、阳性比较,差异无统计学意义(χ2=0.252,P=0.616)。结论NTM所致感染中,以胞内分枝杆菌、脓肿分枝杆菌为主要致病菌,尤其好发于年龄大于或等于65岁的老年人,IGRA检测结果对于NTM感染无明确诊断价值。     

Direct identification of mycobacteria from culture media using a multiplex real-time PCR assay: report on its application in a clinical laboratory in a region of high tuberculosis endemicity

There are few commercial assays that easily and correctly identify the mycobacteria from culture in a clinical laboratory with a high workload. Thus, we developed and evaluated a scheme for the identification of mycobacteria using a multiplex real-time PCR assay and report on its application in our laboratory. The scheme consisted of 3 stepwise PCRs. Mycobacterium tuberculosis complex (MTC) and nontuberculous mycobacteria (NTM) were differentially detected in the step 1 PCR, and the NTM species were identified in the step 2 and 3 PCRs. Over the 1.5-year study period, 1136 isolates of MTC and 618 isolates of NTM were detected, and the species of 608 (98.4%) of the 618 NTM isolates were identified. We conclude that the established scheme is a very useful diagnostic approach for the rapid and accurate identification of MTC and clinically relevant NTM in a clinical laboratory in a region where tuberculosis is endemic.     

多位点PCR技术用于四川267株分枝杆菌临床分离株的鉴定

目的 初步了解四川省肺结核患者分枝杆菌菌种类型。 方法 收集267株分枝杆菌临床菌株,经PNB/TCH鉴别培养基进行培养鉴定后,采用聚合酶链反应(PCR)对16S rRNA、Rv0577、IS1561、Rv1510、Rv1970、Rv3877/8和Rv3120 基因位点进行扩增,鉴定至种,再经PRA-rpoB、hsp65基因测序进行验证。 结果 267株分枝杆菌临床分离株多位点PCR结果显示结核分枝杆菌262株,非洲分枝杆菌Ⅰ型3株,非结核分枝杆菌2株。PNB/TCH鉴别培养基培养鉴定结果为结核分枝杆菌复合群266株,非结核分枝杆菌1株。2株非结核分枝杆菌分别为鸟分枝杆菌(M. avium)和脓毒分枝杆菌(M. septicum)。多位点PCR结果与rpoB-PRA、hsp65基因测序结果一致。 结论 多位点PCR技术鉴定分枝杆菌菌种结果准确可靠,且具有简便和快速等优点,有较大的分子流行病学应用价值,且对于临床诊断和治疗都具有重要意义。     

Diagnosis of nontuberculous mycobacterial infections

This section discusses the methods of laboratory diagnosis of nontuberculous mycobacteria (NTM) using conventional biochemical and nutritional requirements, acid-fast smear microscopy, high performance liquid chromatography (HPLC), antibiotic susceptibility testing, and newer genetic methods such as molecular probes, polymerase chain reaction restriction fragment length polymorphism analysis (PRA), and 16S rDNA sequence analysis. This article discusses how laboratory results are applied by clinicians, and some of the difficulties and controversies regarding the diagnosis of NTM disease after the laboratory work is complete.     

Standardization and evaluation of a tetraplex polymerase chain reaction to detect and differentiate Mycobacterium tuberculosis complex and nontuberculous Mycobacteria--a retrospective study on pulmonary TB patients

The clinical presentation of pulmonary tuberculosis by members of Mycobacterium tuberculosis complex (MTC) and nontuberculous mycobacteria (NTM) cannot be differentiated using the available standard diagnostic procedures. A single-tube tetraplex polymerase chain reaction (T-PCR) was designed to simultaneously amplify 4 well-known DNA targets of MTC. Taguchi's protocol was followed for the optimization of the conditions and was then tested on 288 pulmonary TB patient samples. The analytical sensitivity of the T-PCR was 100 fg of purified mycobacterial DNA, and specificity was found to be 100% in being able to distinguish MTC and NTM in all the cases tested. The results correlated well when validated with hsp65 PCR restriction analysis and sequencing of the 16S-23S internal transcribed spacer region, hsp65, and rpoB. The T-PCR described here is a quick, valuable, and cost-effective tool for determining whether the causative organism is MTC or NTM, and thus is useful for disease surveillance.     

Description of a novel Mycobacterium simiae allelic variant isolated from Caribbean AIDS patients by PCR-restriction enzyme analysis and sequencing of hsp65 gene

A sudden upsurge in the isolation of Mycobacterium simiae from terminally ill AIDS patients was recently reported on the Caribbean island of Guadeloupe. Identification of these M. simiae isolates was achieved using biochemical tests and further confirmed by PCR-restriction analysis (PRA) of a 439-bp fragment of hsp65. A novel PRA profile III (three Bst EII fragments of 240/125/80 bp and four Hae III fragments of 145/125/40/25 bp) was observed in four blood isolates from two patients. The 16 S rRNA gene sequencing of the hypervariable A region confirmed that all the pattern III isolates were indeed M. simiae species, and the hsp65 sequencing confirmed the existence of a new hsp65 allele in these caribbean isolates. A hsp65 sequence-based phylogenetic tree was also created for 39 species including M. simiae and related mycobacterial species as well as other rapid and slow growing mycobacteria, and may serve as an useful tool for identification of mycobacteria to species level.     

Direct identification of mycobacteria from smear-positive sputum samples using an improved multiplex polymerase chain reaction assay

The rapid identification of mycobacteria from smear-positive sputum samples is very important. To identify the Mycobacterium tuberculosis complex (MTBC) and frequently isolated nontuberculous mycobacteria strains directly from smear-positive sputum samples, an improved multiplex polymerase chain reaction (PCR) assay was developed. Nine pairs of primers targeting the 16S-23S rDNA internal transcribed spacer-1, hsp65, and the early secretory antigen (ESAT-6) gene sequences were developed, and their efficacy was evaluated in comparison to traditional culturing and 16S rRNA gene sequencing methods. A total of 200 smear- and culture-positive sputum specimens collected between November 2005 and May 2006 were used for the analysis. The results of the assay showed an accurate identification rate for acid-fast bacilli (AFB) 3+, AFB 2+, and AFB rare/1+ samples of 98%, 95%, and 53%, respectively. The improved multiplex PCR method saves time and has advantages for identifying mycobacteria from AFB 2+ and 3+ sputum samples. The method is suitable for use in countries with a high MTBC prevalence rate.     

Identification of nontuberculous mycobacterial infection by IS6110 and hsp65 gene analysis on lung tissues

The clinical, histologic, and radiographic presentations of nontuberculous mycobacterial (NTM) lung disease are usually indistinguishable from those of reactivated pulmonary tuberculosis (TB), so it remains a great challenge for the clinician to make treatment decisions for patients with old TB and a positive culture result for NTM. This study investigated whether the mycobacterial specific heat shock protein 65 (hsp65) and Mycobacterium tuberculosis (MTB)-specific IS6110 gene would present in pulmonary lesions of patients with NTM pulmonary infection. Formalin-fixed and paraffin-embedded (FFPE) tissue blocks of 24 patients with NTM infections treated at the hospital from 1998 to 2008 were included. Mycobacterial hsp65 gene was amplified in 20 of the 24 patients, and the species identified by sequencing was consistent with corresponding culture results in 12 of these patients. MTB-specific IS6110 gene was detected in 3 of the 7 patients who had old TB and a subsequent diagnosis of fibrocavitary NTM lung disease. Polymerase chain reaction (PCR) analysis of hsp65 gene also confirmed the presence of MTB genes in 2 of these 3 patients. Our results indicate that PCR amplification and sequencing of the mycobacterial hsp65 gene is a sensitive assay for identification of NTM species in FFPE materials. However, consistent results of PCR analysis, microbiology study, histologic manifestations, radiology, and clinical presentation are important for correct diagnosis of NTM pulmonary infection. The presence of MTB gene in patients with fibrocavitary NTM lung lesions poses a clinical dilemma for deciding concurrent treatment TB and NTM infection.     

Polymerase chain reaction-restriction fragment length polymorphism of the rpoB gene for identification of Mycobacterium avium subsp. paratuberculosis and differentiation of Mycobacterium avium subspecies

Mycobacterial speciation by polymerase chain reaction (PCR)-restriction fragment length polymorphism analysis (PRA) of the rpoB gene was evaluated for identification of Mycobacterium avium subsp. paratuberculosis (MAP) and other Mycobacterium avium complex (MAC) members to the species or subspecies level by comparison with conventional methods including hsp65 sequencing, high-performance liquid chromatography, and PCR for accepted species- or subspecies-specific genomic targets. A total of 185 type and clinical mycobacterial strains from humans, animals, and environments were tested. A 360-bp PCR product was subsequently digested with MspI, HaeIII, and SmaI restriction enzymes. The PRA using SmaI restriction showed a unique digestion pattern for MAP distinguishing it from other MAC members and other Mycobacterium spp. Moreover, HaeIII and MspI restriction of the rpoB gene enabled MAC-species and -subspecies discrimination. The rpoB-PRA using SmaI or MspI and HaeIII restriction of the rpoB gene is a simple, convenient, and reliable confirmatory assay for simultaneous identification of MAP and other MAC members.     

2011-2018年四川省自贡市分枝杆菌临床分离株鉴定分析

目的了解自贡市肺部感染分枝杆菌的菌种菌型特征,为临床分枝杆菌病的诊断和治疗及制定有效防控策略提供科学依据。方法收集2011－2018年临床疑似结核病患者分离到的抗酸染色阳性培养物,经对硝基苯甲酸（PNB）和噻吩-2-羧酸肼（TCH）鉴别培养和多位点PCR鉴定为结核分枝杆菌和非结核分枝杆菌（NTM）,再经rpoB和hsp65序列分析对NTM进行种的鉴定。结果2 751株分枝杆菌临床分离株经PNB/TCH鉴别培养基和多位点PCR鉴定,结核分枝杆菌2 647株,占96.22%,非洲分枝杆菌Ⅰ型32株,占1.16%,NTM 72株,占2.62%。 72株NTM鉴定出11个种。结论自贡市分枝杆菌肺部感染主要为结核分枝杆菌所致,感染致病的NTM种类较多,以脓肿分枝杆菌、胞内分枝杆菌、堪萨斯分枝杆菌和鸟分枝杆菌为主。 外来分枝杆菌和奥巴涅分枝杆菌在国内为首次报道。