Use of a novel multiplex probe array for rapid identification of Mycobacterium species from clinical isolates

Phenotypic and molecular characterisation of a novel species, Mycobacterium hubeiense sp., isolated from the sputum of a patient with secondary tuberculosis in Hubei of China

A new fast-growing mycobacterium, designated strain QGD101^T, was isolated from the sputum of an 84-year-old man suspected of tuberculosis in Wuhan Medical Treatment Center, Hubei, China. This strain was a gram-staining-negative, aerobic, non-spore-forming and catalase-positive bacterium, which was further identified as the NTM by PNB and TCH tests. The moxifloxacin and levofloxacin exhibited strong suppressing function against QGD101^T with MIC values of 0.06 and 0.125 µg/ml after drug susceptibility testing of six main antimicrobial agents on mycobacteria. Based on the sequence analysis of 16S rRNA, rpoB, hsp65 and 16S-23S rRNA internal transcribed spacer, the strain QGD101^T could not be identified to a species level. Mycobacterium moriokaense ATCC43059^T that shared the highest 16S rRNA gene sequence similarity (98%) with strain QGD101^T was actually different in genomes average nucleotide identity (78.74%). In addition, the major cellular fatty acids of QGD101^T were determined as C18:1ω9c, C16:0 and C18:2ω6c. The DNA G + C content was 64.9% measured by high performance liquid chromatography. Therefore, the phenotypic and genotypic characterisation of this strain led us to the conclusion that it represents a novel species of mycobacteria, for which the name Mycobacterium hubeiense sp. nov. (type strain QGD101^T = CCTCCAA 2017003^T = KCTC39927^T) was proposed. Thus, the results of this study are very significant for the clinical diagnosis of tuberculosis and future personalised medicine.

Identification and characterization of non-tuberculous mycobacteria isolated from tuberculosis suspects in Southern-central China

The incidence of non-tuberculous mycobacteria (NTM)-related death has increased globally recently. To obtain information of the species and characterization of pathogens involved in NTM pulmonary infection in Southern-central China, we identified 160 non-tuberculous infection cases from 3995 acid-fast bacilli (AFB)-positive tuberculous suspects. We then randomly selected 101 non-tuberculous patients, isolated bacteria from their sputa and genotyped the pathogens using the 16S rRNA gene and 16S-23S rRNA internal transcribed spacer sequences. M. intracellulare (32.67%, 33/101), M. abscessus (32.67%, 33/101) and M. fortuitum (7.92%, 8/101) are identified in these isolates. Surprisingly, non-mycobacteria including Gordonia (8.91%, 9/101), Nocardia (5.94%, 6/101) and Tsukamurella (0.99%, 1/101) are also discovered, and the case of Tsukamurella pulmonis infection is first discovered in Southern-central China. Moreover, species of M. mucogenicum group, M. chubuense, M. kansasii, M. gastri, M. avium, M. porcinum and M. smegmatis are identified. In addition, nine immune compromised cases (8.91%, 9/101), including type two diabetes mellitus and HIV/AIDS are found to be infected with non-tuberculous bacteria. This study revealed the distribution and characteristics of non-tuberculous AFB pathogen infection occurred in Southern-central China, and suggested that physicians should be alert of the emerging of NTM and non-mycobacteria infection in AFB positive cases and take caution when choosing chemotherapy for tuberculosis-like pulmonary infections. Generally, this study may help with the development of new strategy for the diagnosis and treatment of mycobacterial infection.

Immunological evaluation of a novel Mycobacterium tuberculosis antigen, Rv3117, absent in Mycobacterium bovis BCG

Tuberculosis (TB) remains a global infectious disease. To investigate the value of a novel Mycobacterium tuberculosis (M. tuberculosis) region of difference 5 (RD5)-encoded antigen, Rv3117, in the development of effective immuno-diagnostics and vaccines against TB, the immune responses to the antigen were examined in human subjects, as well as in C57BL/6 mice. The results showed that Rv3117 was able to evoke specific humoral and cellular immune responses. Consistent with the results from the RD1-encoded antigens, culture filtrate protein 10 kDa (CFP-10) and early secreted antigenic target 6 kDa (ESAT-6), the immunoglobulin G (IgG), IgM and IgA antibody responses to Rv3117 were able to statistically distinguish between the 65 patients with active pulmonary TB and the 59 healthy controls (P<0.01, respectively). In addition, higher levels of Rv3117‑specific interferon-γ (IFN-γ) were observed in immunized C57BL/6 mice than in the negative control mice (P<0.05). Furthermore, high titers of total IgG, IgG1 and IgG2a antibodies were present in the sera from immunized mice, even six weeks subsequent to the immunization. In conclusion, the present results suggested that Rv3117 may be used as a candidate for the development of TB immunodiagnostics and vaccine design.

Evaluation of a novel fusion protein antigen for rapid serodiagnosis of tuberculosis

The detection of Mycobacterium tuberculosis-specific antibodies in human sera has been a rapid and important diagnostic aid for tuberculosis (TB) control and prevention. However, any single antigen is not enough to be used to cover the antibody profiles of all TB patients. In this study, a novel fusion protein was constructed using gene splicing by overlap extension (SOEing), and then the antibody level against it in 171 TB patients and 86 controls was evaluated by enzyme-linked immunosorbent assay. Compared with the three individual antigen (16 kDa: sensitivity 19.9%, specificity 96.5%; MPT64: sensitivity 75.4%, specificity 34.9%; 38 kDa: sensitivity 33.3%, specificity 83.7%), the fusion protein antigen (sensitivity 42.1%, specificity 89.5%) gave the best diagnostic performance with the largest receiver operating characteristic curve area 0.656 (95% confidence interval [CI], 0.590-0.721; P<0.01). These results suggested that the novel fusion protein antigen successfully constructed by gene SOEing provided the improved diagnostic performance for TB, and other mycobacterial multiepitope fusion proteins may also be worthy of investigation for further enhancing the detection sensitivity.

DNA signature-based approaches for bacterial detection and identification

During the late eighties, environmental microbiologists realized the potential of the polymerase chain reaction (PCR) for the design of innovative approaches to study microbial communities or to detect and identify microorganisms in diverse and complex environments. In contrast to long-established methods of cultivation-based microbial identification, PCR-based techniques allow for the identification of microorganisms regardless of their culturability. A large number of reports have been published that describe PCR-inspired methods, frequently complemented by sequencing or hybridization profiling, to infer taxonomic and clonal microbial diversity or to detect and identify microorganisms using taxa-specific genomic markers. Typing methods have been particularly useful for microbial ecology-driven studies; however, they are not suitable for diagnostic purposes, such as the detection of specific species, strains or clones. Recently, comprehensive reviews have been written describing the panoply of typing methods available and describing their advantages and limitations; however, molecular approaches for bacterial detection and identification were either not considered or only vaguely discussed. This review focuses on DNA-based methods for bacterial detection and identification, highlighting strategies for selecting taxa-specific loci and emphasizing the molecular techniques and emerging technological solutions for increasing the detection specificity and sensitivity. The massive and increasing number of available bacterial sequences in databases, together with already employed bioinformatics tools, hold promise of more reliable, fast and cost-effective methods for bacterial identification in a wide range of samples in coming years. This tendency will foster the validation and certification of these methods and their routine implementation by certified diagnostic laboratories.