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

Investigation of species distribution of nontuberculosis mycobacteria isolated from sputum samples in patients with suspected pulmonary tuberculosis

Aims

Rapid and accurate identification of mycobacteria is important for the species-specific treatment of the disease. The aim of this study was the identification at the species level of 34 nontuberculous mycobacteria strains isolated from respiratory tract samples and 14 reference strains as by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method.

Materials and Methods

Isolates derived from clinical specimens were subcultured in the Lowenstein-Jensen medium. Deoxyribonucleic acid isolation was carried out using the boiling method. PCR amplification was performed using primers specific to the hsp65 gene region. The PCR products were digested BstEII and HaEIII enzymes. All samples were studied comparatively by two different centers.

Results

In our study, the most common species were found to be Mycobacterium intracellulare in 23.52% (8/34). The performance of the PCR-RFLP method in detecting mycobacteria was found to be 82.35%.

Conclusions

The PCR-RFLP method is a rapid, cheap, and practical method for the identification of mycobacteria.

Identification of the Mycobacterial Strains Isolated From Clinical Specimens Using hsp65 PCR-RFLP Method

Objectives

It is important to identify mycobacteria at the species level, to distinguish pathogen from non-pathogenic species, to choose the appropriate treatment regimen and to collect epidemiological data. For the identification of mycobacteria, which are time-consuming and laborious with traditional methods, faster, more sensitive and reliable methods are needed. This study aims to investigate the suitability of the hsp65 Polymerase chain reaction-restriction fragment polymorphism (PCR-RFLP) method for routine laboratory use.

Methods

In this study, 141 mycobacterial isolates were obtained from 1632 samples, which were sent to the Medical Microbiology Laboratory.

Results

In the culture, mycobacteria were identified as 138 M. tuberculosis complex (MTBC) and three non-tuberculosis mycobacteria (NTM) by conventional methods. Using the hsp65 PCR-RFLP method, 137 isolates were identified as MTBC, four isolates as NTM. An isolate that was evaluated as MTBC because it was PNB sensitive by the conventional method was determined as NTM with the hsp65 method. In the identification of non-tuberculosis mycobacteria with the hsp65 PCR-RFLP method, one isolate was identified as M. abcessus and three isolates were identified as M. avium complex.

Conclusion

In our study, it was concluded that the hsp65 PCR-RFLP method, which allows identification of mycobacteria, including NTMs, is a method that is cheap, easy and suitable for routine use to provide rapid information to the clinic. The scope of the agar and database used in the method is effective in the definition of the correct species.

Methodological approaches for monitoring opportunistic pathogens in premise plumbing: A review

Opportunistic premise (i.e., building) plumbing pathogens (OPPPs, e.g., Legionella pneumophila, Mycobacterium avium complex, Pseudomonas aeruginosa, Acanthamoeba, and Naegleria fowleri) are a significant and growing source of disease. Because OPPPs establish and grow as part of the native drinking water microbiota, they do not correspond to fecal indicators, presenting a major challenge to standard drinking water monitoring practices. Further, different OPPPs present distinct requirements for sampling, preservation, and analysis, creating an impediment to their parallel detection. The aim of this critical review is to evaluate the state of the science of monitoring OPPPs and identify a path forward for their parallel detection and quantification in a manner commensurate with the need for reliable data that is informative to risk assessment and mitigation. Water and biofilm sampling procedures, as well as factors influencing sample representativeness and detection sensitivity, are critically evaluated with respect to the five representative bacterial and amoebal OPPPs noted above. Available culturing and molecular approaches are discussed in terms of their advantages, limitations, and applicability. Knowledge gaps and research needs towards standardized approaches are identified.

Identification of Species of Nontuberculous Mycobacteria Clinical Isolates from 8 Provinces of China

Pulmonary diseases caused by nontuberculous mycobacteria (NTM) are increasing in incidence and prevalence worldwide. In this study, we identified NTM species of the clinical isolates from 8 provinces in China, in order to preliminarily provide some basic scientific data in the different species and distribution of NTM related to pulmonary disease in China. A total of 523 clinical isolates from patients with tuberculosis (TB) diagnosed clinically from 2005 to 2012 were identified to the species using conventional and molecular methods, including multilocus PCR, rpoB and hsp65 PCR-PRA, hsp65, rpoB, and 16S-23S internal transcribed spacer region sequencing. The isolates were identified into 3 bacterium genera, including NTM, Gordonia bronchialis, and Nocardia farcinica, and, for the 488 NTM isolates, 27 species were identified. For all the 27 species of NTM which were found to cause pulmonary infections in humans, the most prevalent species was M. intracellulare, followed by M. avium and M. abscessus. And seven other species were for the first time identified in patients with TB in China. NTM species identification is very important for distinguishing between tuberculosis and NTM pulmonary diseases, and the species diversity drives the creation of diverse and integrated identification methods with higher accuracy and efficacy.

Cutaneous Mycobacterium haemophilum infections in immunocompromised patients in a tertiary hospital in Bangkok, Thailand: under-reported/under-recognized infection

Introduction:

Mycobacterium haemophilum is one of the non-tuberculous mycobacteria (NTM) that can cause cutaneous infection. As acid-fast staining cannot distinguish NTM from Mycobacterium tuberculosis, and as skin culture for M. haemophilum is not performed routinely, the diagnosis of M. haemophilum infection in Thailand is rarely made.

Case presentation:

Between 2006 and 2009, five patients with M. haemophilum infection were diagnosed in Ramathibodi Hospital, a tertiary care centre in Bangkok, Thailand. The patients were aged 3, 29, 47, 75 and 76 years, and four were immunocompromised. Three patients received immunosuppressive medication. Most patients presented with subacute cutaneous infection. A suboptimal response to conventional antibiotics raised suspicions of M. haemophilum cutaneous infections, which can occur in immunocompromised patients. Diagnoses of these cases were made by skin culture for mycobacteria at an incubating temperature of around 30 °C with iron supplementation, DNA sequencing, or PCR/restriction enzyme analysis. Rifampicin, ofloxacin and clarithromycin were active against all isolates, whereas ethambutol and streptomycin were inactive.

Conclusion:

Skin culture should be performed under special conditions or molecular technique should be used to identify M. haemophilum in susceptible patients.

Development of a real-time qPCR method for detection and enumeration of Mycobacterium spp. in surface water

A real-time quantitative PCR method was developed for the detection and enumeration of Mycobacterium spp. from environmental samples and was compared to two other methods already described. The results showed that our method, targeting 16S rRNA, was more specific than the two previously published real-time quantitative PCR methods targeting another 16S rRNA locus and the hsp65 gene (100% versus 44% and 91%, respectively).

Surveillance of pyrazinamide susceptibility among multidrug-resistant Mycobacterium tuberculosis isolates from Siriraj Hospital, Thailand

Background

Susceptibility testing of pyrazinamide (PZA) against Mycobacterium tuberculosis is difficult to perform because the acidity of culture medium that is required for drug activity also inhibits the growth of bacteria. In Thailand, very limited information has been generated on PZA resistance, particularly among multidrug-resistant tuberculosis (MDR-TB) isolated from Thailand. Only two studies on PZA susceptibility among Thai M. tuberculosis strains have been reported; one used a pyrazinamidase assay, and the other used the BACTEC 460 TB for PZA susceptibility testing. In this study, we determined the percentage of strains possessing pyrazinamide resistance among pan-susceptible M. tuberculosis and MDR-TB isolates by using the pyrazinamidase assay, BACTEC MGIT 960 PZA method and pncA sequencing, and assessed the correlation in the data generated using these methods. The type and frequency of mutations in pncA were also determined.

Results

Overall, 150 M. tuberculosis isolates, consisting of 50 susceptible and 100 MDR-TB isolates, were tested for PZA susceptibility by BACTEC MGIT 960 PZA, the pyrazinamidase assay and pncA sequencing. The study indicated PZA resistance in 6% and 49% of susceptible and MDR-TB isolates, respectively. In comparison to the BACTEC MGIT 960 PZA, the PZase assay showed 65.4% sensitivity and 100% specificity, whereas pncA sequencing showed 75% sensitivity and 89.8% specificity. Twenty-four mutation types were found in this study, with the most frequent mutation (16%) being His71Asp. Of these mutations, eight have not been previously described. The Ile31Ser and Ile31Thr mutations were found both in PZA susceptible and resistant isolates, suggesting that mutation of this codon might not play a role on PZA resistance.

Conclusions

Our findings suggest that phenotypic susceptibility testing is still essential for the detection of PZA resistance, especially for MDR-TB isolates. Some mutations were not associated with resistance and could lead to misinterpretation of the genotypic methods. This information could be helpful for clinicians in managing tuberculosis patients and frequencies, and the types of pncA mutations should offer baseline information on PZA resistance.

Inaccuracy of single-target sequencing for discriminating species of the Mycobacterium abscessus group

We determined nucleotide sequences of rpoB, hsp65, and sodA in 59 clinical isolates (from 58 patients) of the Mycobacterium abscessus group. Identification to the species level, based on three target genes, was concordant for 44 isolates (25 M. abscessus, 13 Mycobacterium massiliense, and 6 Mycobacterium bolletii isolates) and discordant for 15 isolates which had "interspecific composite patterns." Sequence analysis of five housekeeping genes also showed composite patterns in 8 of these 15 isolates.

Drug resistance and genotypic analysis of Mycobacterium tuberculosis strains from Thai tuberculosis patients

The aim of this study was the molecular characterization of primary drug-resistant Mycobacterium tuberculosis strains in Thailand. We examined a group of M. tuberculosis isolates from newly registered tuberculosis (TB) cases, collected at the largest university hospital, the Siriraj Hospital, in Thailand. Of 76 selected drug-resistant M. tuberculosis strains recovered from previously untreated pulmonary TB patients whose sputum samples were sent to this hospital, 29 (38%) were single-drug resistant, 26(34%) multidrug resistant and two (2.6%) extensively drug resistant. Fifty (66%) strains belonged to Beijing genotype. The study demonstrated a severe problem of drug resistance among recently detected TB patients, and two large clusters of genetically similar strains indicated ongoing transmission of drug-resistant TB.

Distribution of rpoB mutations among multidrug-resistant Mycobacterium tuberculosis (MDRTB) strains from Thailand and development of a rapid method for mutation detection

Since rifampicin resistance is a surrogate marker for multidrug-resistant Mycobacterium tuberculosis (MDRTB), the present study aimed to investigate rpoB mutations conferring rifampicin resistance in M. tuberculosis strains from Thailand, and to develop a rapid, inexpensive and simple PCR-based method for rapid detection of MDRTB. Overall, 267 M. tuberculosis isolates, including 143 MDRTB isolates, were investigated. Isolates of the Beijing strain predominated among the MDRTB isolates (79.1%), but accounted for only 45.5% of the susceptible isolates. Mutations in the rpoB gene were found most commonly at codons 531, 526 and 516 (58%, 25.2% and 9.1%, respectively). A multiplex allele-specific PCR was developed and tested with 216 clinical isolates. In comparison with the proportion method, the method showed 94.2% sensitivity and 100% specificity, and had a 100% positive predictive value and a 95% negative predictive value, which suggested that this method could be useful for screening for MDRTB, particularly in resource-limited countries.

Rapid diagnostic testing for mycobacterial infections

Tests based on nucleic acid amplification can rapidly detect mycobacteria in clinical samples. These appear to be promising and may change how mycobacterial diseases are diagnosed in the future. Utilization of nucleic acid hybridization and DNA sequencing has enabled the identification of mycobacteria to the species level and detection of mutations associated with antimicrobial resistance. Combining nucleic acid amplification with genotypic identification methods allows detection and identification of mycobacteria directly in clinical samples and, to a limited extent, detection of antimicrobial resistance. IFN-gamma-based assays provide results faster than the tuberculin skin test and address many of its shortcomings, and are thus poised to replace the latter in the coming years.

Case of pyomyositis due to Mycobacterium haemophilum in a renal transplant recipient

We report a case of pyomyositis due to Mycobacterium haemophilum in a renal transplant recipient. M. haemophilum was identified by PCR-mediated sequence analysis of the heat shock protein gene in the DNA of the specimen. The patient was successfully treated with repeated surgical debridement and prolonged antimycobacterial therapy.

The evolving story of Mycobacterium tuberculosis clade members detected in fish

Advances in molecular analyses have permitted documentation of an increasing spectrum of mycobacteria infecting fish. Although some of these mycobacteria are not closely related, several species belong to the Mycobacterium tuberculosis clade. One member of the clade, M. marinum, is well known as an agent of piscine mycobacteriosis. Three other clade species, M. shottsii, M. pseudoshottsii and M. 'chesapeaki', have recently been identified as predominant disease agents in a widespread, continuing epizootic in wild striped bass of the Chesapeake Bay. A fifth clade member, M. ulcerans, has recently been indirectly detected in wild, African cichlid fish. As M. ulcerans is the third most common human mycobacterial infection worldwide, even such indirect evidence of M. ulcerans in fish must be more thoroughly investigated. Complicating the differentiation of these clade members is the growing recognition of intraspecies and interspecies variation in phenotypes, genes and virulence. Thus, researchers must be aware of the variety of piscine isolates within the M. tuberculosis clade. This review summarizes the methods of detection and differentiation for this important group of mycobacteria.

Distribution of hsp65 PCR-restriction enzyme analysis patterns among Mycobacterium avium complex isolates in Thailand

A total of 227 clinical Mycobacterium avium complex isolates from Thailand were differentiated into species and types by using PCR-restriction enzyme analysis of hsp65. The distribution of types showed the predominance of M. avium I (77%) in blood specimens, whereas M. intracellulare I was more commonly found in pulmonary specimens (44.2%). In addition, infections with M. avium were more likely to be found in younger adults (20 to 39 years old), while infections with M. intracellulare were more likely to be found in older adults (> or =60 years old). Our results provide the useful epidemiological information that some particular types have more invasive and virulent characters than others.