The interpretation of nucleic acid amplification tests for tuberculosis: do rapid tests change treatment decisions?

Molecular Diagnostics in Pulmonary Infections

Infection of the lung parenchyma, or pneumonia, accounts for over four million deaths per year worldwide (Ferkol and Schraufnagel, Ann Am Thorac Soc 11:404–406, 2014). The condition is common, but also over-diagnosed, in part due to relatively poor laboratory and radiographic diagnostics. Indeed, we continue to rely on antiquated tools such as sputum culture and chest X-ray – the former of which lacks speed and sensitivity, and the latter specificity (Albaum et al. Chest 110:343–50, 1996). The resulting presumptive diagnoses of pneumonia lead to excessive use of empiric broad spectrum antibiotics; indeed, by some estimates, 30–70% of antibiotic prescriptions for lower respiratory tract infection are inappropriate (Kraus, PLoS One 12(3): e0174584, 2017). This approach begets microbial resistance, exposes patients to medication side effects, and puts patients at risk of potentially life-threatening complications including Clostridium difficile colitis.

To improve diagnostic certainty in patients with suspected pneumonia, we must begin to consider and implement emerging technologies for efficient and accurate characterization of host responses to infection and identification of pathogens. In this chapter, we will discuss precision diagnostics already in common practice and those poised to be, and how these tools may ultimately enable personalization in the diagnosis of pneumonia.

Impact of GeneXpert MTB/RIF on patients and tuberculosis programs in a low-burden setting. a hypothetical trial

RATIONALE

Guidelines recommend routine nucleic-acid amplification testing in patients with presumed tuberculosis (TB), but these tests have not been widely adopted. GeneXpert MTB/RIF (Xpert), a novel, semiautomated TB nucleic-acid amplification test, has renewed interest in this technology, but data from low-burden countries are limited.

OBJECTIVES

We sought to estimate Xpert's potential clinical and public health impact on empiric treatment, contact investigation, and housing in patients undergoing TB evaluation.

METHODS

We performed a prospective, cross-sectional study with 2-month follow-up comparing Xpert with standard strategies for evaluating outpatients for active pulmonary TB at the San Francisco Department of Public Health TB Clinic between May 2010 and June 2011. We calculated the diagnostic accuracy of standard algorithms for initial empiric TB treatment, contact investigation, and housing in reference to three Mycobacterium tuberculosis sputum cultures, as compared with that of a single sputum Xpert test. We estimated the incremental diagnostic value of Xpert, and the hypothetical reductions in unnecessary treatment, contact investigation, and housing if Xpert were adopted to guide management decisions.

MEASUREMENTS AND MAIN RESULTS

A total of 156 patients underwent Xpert testing. Fifty-nine (38%) received empiric TB treatment. Thirteen (8%) had culture-positive TB. Xpert-guided management would have hypothetically decreased overtreatment by 94%, eliminating a median of 44 overtreatment days (interquartile range, 43-47) per patient and 2,169 total overtreatment days (95% confidence interval, 1,938-2,400) annually, without reducing early detection of TB patients. We projected similar benefits for contact investigation and housing.

CONCLUSIONS

Xpert could greatly reduce the frequency and impact of unnecessary empiric treatment, contact investigation, and housing, providing substantial patient and programmatic benefits if used in management decisions.

Impact of GeneXpert MTB/RIF assay on triage of respiratory isolation rooms for inpatients with presumed tuberculosis: a hypothetical trial

BACKGROUND

Placing inpatients with presumed active pulmonary tuberculosis in respiratory isolation pending results of serial sputum acid-fast bacilli (AFB) smear microscopy is standard practice in high-income countries. However, this diagnostic strategy is slow and yields few tuberculosis diagnoses. We sought to determine if replacing microscopy with the GeneXpert MTB/RIF (Xpert) nucleic acid amplification assay could reduce testing time and usage of isolation rooms.

METHODS

We prospectively followed inpatients at San Francisco General Hospital undergoing tuberculosis evaluation. We performed smear microscopy and Xpert testing on concentrated sputum, and calculated diagnostic accuracy for both strategies in reference to serial sputum mycobacterial culture. We measured turnaround time for microscopy and estimated hypothetical turnaround times for Xpert on concentrated and unconcentrated sputum. We compared median and total isolation times for microscopy to those estimated for the 2 Xpert strategies.

RESULTS

Among 139 patients with 142 admissions, median age was 54 years (interquartile range [IQR], 43-60 years); 32 (23%) patients were female, and 42 (30%) were HIV seropositive. Serial sputum smear microscopy and a single concentrated sputum Xpert had identical sensitivity (89%; 95% confidence interval [CI], 52%-100%) and similar specificity (99% [95% CI, 96%-100%] vs 100% [95% CI, 97%-100%]). A single concentrated sputum Xpert could have saved a median of 35 hours (IQR, 24-36 hours) in unnecessary isolation compared with microscopy, and a single unconcentrated sputum Xpert, 45 hours (IQR, 35-46 hours).

CONCLUSIONS

Replacing serial sputum smear microscopy with a single sputum Xpert could eliminate most unnecessary isolation for inpatients with presumed tuberculosis, greatly benefiting patients and hospitals.

Amplified Mycobacterium tuberculosis direct test for diagnosing tuberculous pleurisy--a diagnostic accuracy study

BACKGROUND

The study was designed to investigate the clinical usefulness of Amplified Mycobacterium Tuberculosis Direct (AMTD) tests for diagnosing TB pleurisy.

METHODS

One hundred and fifty-two patients for whom the exclusion of tuberculous pleural effusion was necessary were retrospectively analyzed.

RESULTS

The sensitivity of AMTD in diagnosing pleural TB was 36.4% (20 of 55). Combining sputum and pleural effusion AFB smear, pleural biopsy, and AMTD test of pleural effusion increased sensitivity to 82.5% (33/40). There were significantly higher percentages of neutrophils in the pleural effusion in the positive than in the negative AMTD group (38.0 ± 6.7% vs. 11.1 ± 3.7%, p<0.001). Patients with symptom duration <18 days prior to pleural effusion studies had more positive AMTD tests than those with symptom >18 days (70% vs. 31.4%; OR 5.09; 95% CI 1.54-16.79; p = 0.011).

CONCLUSIONS

Combining AMTD tests with conventional diagnostic methods offer good sensitivity for pleural TB diagnosis. Patients in the early course of the disease are better candidates for AMTD tests.

The limitations of polymerase chain reaction in the setting of possible recurrent tuberculosis: 2 instructional cases

The interpretation of a positive result for Mycobacterium tuberculosis by nucleic acid amplification such as polymerase chain reaction (PCR) can be challenging. We present 2 cases that illustrate the limitations of tuberculosis PCR on respiratory secretions in previously treated patients, even years after the previous disease episode.

Evaluation of a simplified IS6110 PCR for the rapid diagnosis of Mycobacterium tuberculosis in an area with high tuberculosis incidence

PURPOSE

To assess the diagnostic yield of a simplified IS6110-PCR in an area with high tuberculosis incidence.

METHODS

Pulmonary (218) and extrapulmonary (121) samples were collected from 236 patients including smearpositive leprosy patients. All samples were processed to detect acidfast bacilli by microscopy, culture on solid media and PCR. To remove PCR inhibitors, three washing steps of the decontaminated pellet were included before mycobacterial cell lysis by heat treatment. No detergents, enzymes, or chelating agents were used. From the 339 samples, 34 were selected basing on their large volume and were tested by the commercial kit GenoType Mycobacteria Direct (GTMD) (VER 4, Hain Lifescience, Germany) in addition to the tests cited above.

RESULTS

The overall sensitivity and specificity of PCR were 93.8 and 98.6% for pulmonary samples, 63.6 and 100% for extrapulmonary samples, respectively. The assay detected MTC in 94.2% of smear positive samples with a positive predictive value of 100%. No inhibition was found among seven samples that were PCR negative but bacteriological confirmed as containing Mycobacterium tuberculosis. No false positive result occurred with samples from leprosy patients. The sensitivities for PCR and GTMD were 81.8 and 75%, respectively.

CONCLUSION

PCR could efficiently complement conventional bacteriological tools for the rapid diagnosis of tuberculosis but cannot replace them.

A paradigm for the molecular identification of Mycobacterium species in a routine diagnostic laboratory

The aim of this study was to improve the identification ofMycobacteriumspecies in the context of a UK teaching hospital. Real-time PCR assays were established to enable the rapid differentiation betweenMycobacterium tuberculosis(MTB) complex andMycobacteriumspecies other thantuberculosis(MOTT), followed by 16S rRNA gene sequencing for the speciation of MOTT. Real-time PCR assays gave comparable results to those from the reference laboratory. The implementation of these PCR assays using an improved bead extraction method has enhanced the mycobacterial diagnostic service at the Royal Free Hospital by providing a rapid means of differentiating between MTB complex and MOTT, and would be simple to implement in similar laboratories. Sequence analysis successfully identified a range ofMycobacteriumspp. representative of those encountered in the clinical setting of the authors, includingMycobacterium aviumcomplex,Mycobacterium fortuitumgroup,Mycobacterium chelonae–Mycobacterium abscessusgroup,Mycobacterium xenopiandMycobacterium gordonae. It provides a useful tool for the identification of MOTT when clinically indicated.