Comparison of in-house and commercial 16S rRNA sequencing with high-performance liquid chromatography and genotype AS and CM for identification of nontuberculous mycobacteria

SARS-CoV-2 Supply Shortages and Tuberculosis Diagnostics: Current Issues Requiring Immediate Solutions

The SARS-CoV-2 pandemic has strained manufacturing capacity worldwide, resulting in significant shortages of laboratory supplies both directly and indirectly. Such shortages include probe-based kits for detection of the Mycobacterium tuberculosis complex from positive liquid broth cultures. These shortages and possible loss of this particular assay have consequences for laboratory testing algorithms and public health in the United States. As there are no FDA-approved, commercially available options that currently exist which could immediately fill this gap, laboratories must identify alternatives and plan for modifying current testing algorithms to accommodate this change.

Recent advances in molecular diagnostics and understanding mechanisms of drug resistance in nontuberculous mycobacterial diseases

Accumulating evidence suggests that human infections caused by nontuberculous mycobacteria (NTM) are increasing worldwide, indicating that NTM disease is no longer uncommon in many countries. As a result of an increasing emphasis on the importance of differential identification of NTM species, several molecular tools have recently been introduced in clinical and experimental settings. These advances have led to a much better understanding of the diversity of NTM species with regard to clinical aspects and the potential factors responsible for drug resistance that influence the different outcomes of NTM disease. In this paper, we review currently available molecular diagnostics for identification and differentiation of NTM species by summarizing data from recently applied methods, including commercially available assays, and their relevant strengths and weaknesses. We also highlight drug resistance-associated genes in clinically important NTM species. Understanding the basis for different treatment outcomes with different causative species and drug-resistance mechanisms will eventually improve current treatment regimens and facilitate the development of better control measures for NTM diseases.

Identification of nontuberculous mycobacteria using multilocous sequence analysis of 16S rRNA, hsp65, and rpoB

BACKGROUND

The isolation of nontuberculous mycobacteria (NTM) from clinical specimens has increased, and they now are considered significant opportunistic pathogens. The aims of this study were to develop a database and interpretive criteria for identifying individual species. In addition, using clinical isolates, we evaluated the clinical usefulness of 16S rRNA, hsp65, and rpoB as target genes for this method.

METHODS

The sequences of NTM for 16S rRNA, hsp65, and rpoB were collected from GenBank and checked by manual inspection. Clinical isolates collected between 2005 and 2010 were used for DNA extraction, polymerase chain reaction, and sequencing of these three genes. We constructed a database for the genes and evaluated the clinical utility of multilocus sequence analysis (MLSA) using 109 clinical isolates.

RESULTS

A total 131, 130, and 122 sequences were collected from GenBank for 16S rRNA, hsp65, and rpoB, respectively. The percent similarities of the three genes ranged from 96.57% to 100% for the 16S rRNA gene, 89.27% to 100% for hsp65, and 92.71% to 100% for rpoB. When we compared the sequences of 109 clinical strains with those of the database, the rates of species-level identification were 71.3%, 86.79%, and 81.55% with 16S rRNA, hsp65, and rpoB, respectively. We could identify 97.25% of the isolates to the species level when we used MLSA.

CONCLUSION

There were significant differences among the utilities of the three genes for species identification. The MLSA technique would be helpful for identification of NTM.

Mycobacteria

The immunocompromised host is at increased risk of Mycobacterium tuberculosis complex and nontuberculous mycobacteria infection. Although Mycobacterium tuberculosis complex is a significant mycobacterial pathogen, nontuberculous mycobacteria causes substantial disease in those with suppressed immune responses. Mycobacterial infections can cause significant morbidity and mortality in this patient population, and rapid identification and susceptibility testing of the mycobacterial species is paramount to patient management and outcomes. Mycobacterial diagnostics has undergone some significant advances in the last two decades with immunodiagnostics (interferon gamma release assay), microscopy (light-emitting diode), culture (automated broth-based systems), identification (direct PCR, sequencing and matrix-assisted laser-desorption ionization–time of flight mass spectrometry) and susceptibility testing (molecular detection of drug resistance from direct specimens or positive cultures). Employing the most rapid and sensitive methods in the mycobacterial laboratory will have a tremendous impact on patient care and, in the case of Mycobacterium tuberculosis complex, in the control of tuberculosis.

Direct identification of mycobacteria from clinical specimens by multiplex real-time PCR

AIMS

To directly identify clinically relevant mycobacteria from clinical specimens, we have developed a multiplex real-time PCR assay with hydrolysis probes that can identify 20 mycobacterial species.

METHODS AND RESULTS

The assay was initially evaluated using 248 strains, including both reference strains and clinical isolates. Then, the assay was implemented according to a scheme in our laboratory. The scheme based on the clinical differences between the Mycobacterium tuberculosis complex (MTC) and nontuberculous mycobacteria (NTM) consisted of three stepwise PCRs. MTC and NTM were differentially detected in the step 1 PCR, and the NTM species were identified in the step 2 and step 3 PCRs. During a 2·5-year period, 1877 isolates of MTC (1142 directly recovered from clinical specimens) and 596 isolates of NTM (143 directly recovered from clinical specimens) were detected, and the species of 590 (99·0%) of the 596 NTM isolates were identified.

CONCLUSIONS

Our experience shows that this is a new paradigm for rapidly and accurately identifying clinically relevant mycobacteria, in which a multiplex real-time PCR assay is directly applied to clinical specimens in a stepwise fashion.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study is the first report of a multiplex real-time PCR assay for identifying clinically important mycobacterial species directly from clinical specimens and its application in a clinical microbiology laboratory.

Multiplex real-time PCR assay and melting curve analysis for identifying Mycobacterium tuberculosis complex and nontuberculous mycobacteria

A multiplex real-time PCR assay and melting curve analysis for identifying 23 mycobacterial species was developed and evaluated using 77 reference strains and 369 clinical isolates. Concordant results were obtained for all 189 (100%) isolates of the Mycobacterium tuberculosis complex and 169 (93.9%) isolates of nontuberculous mycobacteria. Our results showed that this multiplex real-time PCR assay is an effective tool for the mycobacterial identification from cultures.

Nontuberculous mycobacterial lung diseases

Nontuberculous mycobacteria (NTM) are generally hardy, ubiquitous environmental bacteria that vary in geographic distribution and pulmonary pathogenicity. Relatively few of the more than 115 species of NTM have been associated with lung disease. Diagnosis of disease due to NTM relies on a combination of clinical, imaging, and microbiologic data. Because NTM may present as acid-fast bacilli in respiratory secretions of patients with clinical and radiologic features that mimic tuberculosis, laboratory discrimination of NTM from Mycobacterium tuberculosis is a priority. This discrimination is now often rapidly achievable using molecular techniques, although some tests have limited sensitivity. NTM species have different antibiotic response patterns, and success with medical treatment alone varies. Macrolides are an essential component of therapy for many species but must be combined with other drugs.

Molecular identification of Mycobacterium chimaera as a cause of infection in a patient with chronic obstructive pulmonary disease

This report describes a case of Mycobacterium chimaera infection in a patient with a history of chronic obstructive pulmonary disease where the organism was identified by using molecular methods. M. chimaera was identified from fresh lung tissue and from an instrument-negative mycobacterial growth indicator tube broth culture. The utility of using sequence analysis of the internal transcribed spacer region for the rapid identification of a slow-growing nontuberculous Mycobacterium spp. where conventional culture methods were not successful was shown.