Universal PCR for bacteria, mycobacteria, and fungi: a 10-year retrospective review of clinical indications and patient outcomes

IMPORTANCE

Our work provides a retrospective analysis of universal PCR orders for bacteria, mycobacteria, and fungi across our institution across a 10-year period. We assessed the positivity rates for this diagnostic tool by test type and specimen type and, critically, studied whether and how the results influenced the outcomes from treatment change, to readmission, to death.

Utility of Broad-Range PCR Sequencing for Infectious Diseases Clinical Decision Making: a Pediatric Center Experience

Broad-range PCR (BRPCR) sequencing is a promising tool for diagnosis of infectious conditions when traditional microbiologic strategies fail to identify a pathogen. Data on the optimal clinical scenarios in which to use this tool are limited.

Clinical Performance of Mycobacterial Immunohistochemistry in Anatomic Pathology Specimens

OBJECTIVES

Diagnosis of mycobacterial infections poses significant challenges in anatomic pathology. We recently described the use of antimycobacteria immunohistochemistry (IHC) as a sensitive, efficient diagnostic tool and now report the clinical performance of this assay among general, noninfectious disease pathology-trained anatomic pathologists.

METHODS

Over a 2-year period, all cases were retrospectively identified in which mycobacterial IHC was performed during routine diagnostic workup.

RESULTS

From October 2017 to September 2019, mycobacterial IHC was evaluated for 267 cases, resulting in 58 (22%) positive stains. Compared with culture and molecular results, the sensitivity and specificity of IHC were 52% and 80%, respectively. IHC performed significantly better than acid-fast bacilli (AFB) staining (Ziehl-Neelsen) (P < .0001; sensitivity 21%, specificity 92%) but similarly to modified AFB staining (mAFB; Fite-Faraco) (P = .9; sensitivity 61%, specificity 84%). In cases with discordant IHC and mAFB staining, there were no differences in rates of culture or polymerase chain reaction-confirmed positivity.

CONCLUSIONS

Mycobacterial IHC was well adopted with superior clinical performance to AFB and comparable performance to mAFB. These results support the use of IHC as an adjunctive tool in the diagnosis of mycobacterial infections and suggests its potential role as a rapid screening test for molecular testing.

Benign Solitary Pulmonary Necrotic Nodules: How Effectively Does Pathological Examination Explain the Cause?

Aims

We investigated the histopathological features of solitary pulmonary necrotic nodules (NNs) of undetermined cause. We combined our findings with those obtained using other methods to determine how well the etiological factors were explained.

Methods

We screened patients who underwent surgery to treat solitary pulmonary granulomatous and nongranulomatous NNs of undetermined cause. The NN sizes and features of both the NNs and adjacent parenchyma were evaluated. Histochemical analyses included Ehrlich-Ziehl-Neelsen (EZN), Grocott, and Gram staining. Polymerase chain reaction (PCR) was used to detect tuberculous and nontuberculous mycobacteria, panfungal DNA, Nocardia, Francisella tularensis types A and B, and actinomycetes.

Results

The NNs were granulomatous in 78.9% and nongranulomatous in 21% of the 114 patients included. EZN staining or PCR was positive for Mycobacterium in 53.5% of all NNs: 62.2% of granulomatous and 20.8% of nongranulomatous NNs. We found a weak but significant correlation between granulomatous NNs and Bacillus positivity and a significant correlation between granulomas surrounding the NNs and the presence of multiple necroses. The NN etiology was determined via histopathological, histochemical, and PCR analyses in 57% of patients but remained undetermined in 42.9%.

Conclusion

The causes of both granulomatous and nongranulomatous NNs can be determined by pathological examination. Granulomatous necrosis and granulomas in the adjacent parenchyma are important for differential diagnosis. When both features are present, they strongly support a diagnosis of tuberculosis, even in the absence of bacilli.

Infectious disease diagnosed by fine needle aspiration biopsy

INTRODUCTION

Fine needle aspiration biopsies (FNABs) have become increasingly important in the assessment of infectious diseases. We assess the ability of cytopathology to predict the presence of a pathogen and review how often neoplasia occurs concurrently with infection.

MATERIALS AND METHODS

A 3-year retrospective review of FNABs with concurrent culture results was performed at the Zuckerberg San Francisco General Hospital and Trauma Center. Rapid onsite evaluation was performed for all cases by a pathologist. The results of the special and immunohistochemical stains and polymerase chain reaction testing were correlated, when available.

RESULTS

A total of 231 samples from 11 different tissue sites were submitted for microbial culture, of which 49 (21%) were positive for pathogenic organisms. Only 2 false-negative cases by cytology were found in immunosuppressed patients. A total of 38 patients had a diagnosis of neoplasia, with 2 (5%) having concurrent infection. Overall, the sensitivity and specificity of cytology in predicting the presence of infection was 96% (95% confidence interval, 86%-100%) and 42% (95% confidence interval, 34%-50%), respectively. Molecular testing was performed in 11 cases, 2 of which were positive for Mycobacterium tuberculosis complex and had cytologic findings of necrosis. Polymerase chain reaction and other ancillary tests were unable to further characterize 2 cases with acid-fast bacilli.

CONCLUSIONS

Our study has shown that FNABs have high sensitivity in detecting infection and that negative cytology findings will correlate with a negative infectious workup. Although infection in the setting of neoplasia is uncommon, it should be considered if clinical data are available to suggest infection.

Molecular and Histologic Diagnosis of Central Nervous System Infections

Infections of the central nervous system cause significant morbidity and mortality in immunocompetent and immunocompromised individuals. A wide variety of microorganisms can cause infections, including bacteria, mycobacteria, fungi, viruses, and parasites. Although less invasive testing is preferred, surgical biopsy may be necessary to collect diagnostic tissue. Histologic findings, including special stains and immunohistochemistry, can provide a morphologic diagnosis in many cases, which can be further classified by molecular testing. Correlation of molecular, culture, and other laboratory results with histologic findings is essential for an accurate diagnosis, and to minimize false positives from microbial contamination.

Broad-range PCR Application in a Large Academic Pediatric Center: Clinical Value and Challenges in Diagnosis of Infectious Diseases

BACKGROUND

Broad-range polymerase chain reaction (BR-PCR) detects infectious pathogens from clinical specimens using targets for bacteria (16S rRNA), fungi (28S rDNA), and mycobacteria (fluorescence resonance energy transfer and heat shock protein 65 gene) with reported diagnostic sensitivity and specificity ranging from 43% to 100% and 100%, respectively. We describe our experience when applying BR-PCR to clinical samples submitted for conventional infectious disease testing [conventional testing (CT)] from pediatric patients with concern for infection.

METHODS

Retrospective analysis of clinical samples obtained from Nationwide Children's Hospital microbiology laboratory from January 2011 to December 2014 and sent for BR-PCR. Medical record review collected data on patient characteristics, clinical manifestations, laboratory results and antimicrobials prescribed, and a determination of clinical value of BR-PCR was assigned.

RESULTS

There were 247 clinical samples from 163 patients identified; 71 (44%) patients were immunocompromised and 192 (78%) samples reflected pretreatment with antimicrobials. A clinically significant putative organism was identified for 59 samples (24%) between all diagnostic modalities. Conventional testing identified organisms in 41 (17%) samples, 17 of which were corroborated by BR-PCR. Broad-range polymerase chain reaction identified an organism in an additional 18 samples with negative CT results and was considered to provide additional important clinical information. Broad-range polymerase chain reaction detected a bacterial or fungal organism more frequently from tissue samples than from bronchoalveolar lavage or other fluid samples (P = 0.0096, χ).

CONCLUSIONS

In our cohort, BR-PCR was an important adjunctive diagnostic in identifying bacteria and fungi in complex clinical situations. Additional data are needed to define the optimal clinical circumstances and specimen type in which BR-PCR can provide the highest diagnostic yield.

Routine Broad-Range Fungal Polymerase Chain Reaction With DNA Sequencing in Patients With Suspected Mycoses Does Not Add Value and Is Not Cost-Effective

Context.—

New molecular diagnostic tests regularly become available, and they may be assumed to be superior to traditional diagnostic studies. The added cost of these studies should be considered in conjunction with the value provided for patient care.

Objective.—

To assess the cost and diagnostic value of broad-range polymerase chain reaction (PCR) and DNA sequencing for the diagnosis of fungal infections compared with traditional studies.

Design.—

We reviewed the cost and clinical impact of broad-range fungal PCR/DNA sequencing for 65 specimens for which this test, a direct fungal examination, fungal culture, and a histopathologic assessment were performed.

Results.—

The sensitivity, specificity, and positive and negative predictive values for each of the assays studied were, respectively: histopathology (83.3%, 100%, 100%, and 98.3%); direct examination (66.7%, 100%, 100%, and 96.7%); fungal culture (83.3%, 100%, 100%, and 98.3%); and broad-range fungal PCR/DNA sequencing (83.3%, 95.0%, 62.5%, and 98.3%). The cost for broad-range fungal PCR/DNA sequencing was $32,500, compared with $8,591.70 for all traditional tests combined, for the 65 specimens included in this review.

Conclusions.—

Broad-range fungal PCR/DNA sequencing did not detect any infecting fungal pathogen that was not detected by at least 1 of the traditional methods, but 3 false-positives occurred. Broad-range fungal PCR/DNA sequencing is not a substitute for traditional laboratory studies and should be used judiciously to promote care affordability.

The Impact of an Electronic Expensive Test Notification

OBJECTIVES

The impact of clinical decision support tools (CDSTs) that display test cost information has been variable.

METHODS

We retrospectively analyzed the 3-year impact of a passive CDST that notified providers when the test order cost was $1,000 or more. We determined the most common expensive tests ordered, the frequency with which providers abandoned the order after notification, and the costs saved through this intervention.

RESULTS

The average monthly abandonment rate was 12.5% (2014), 12.9% (2015), and 14.3% (2016). The cost savings from tests not performed for this 3-year period was $696,007. Molecular hematopathology assays were the most frequently ordered tests, with variable abandonment rates.

CONCLUSIONS

Although this CDST was passive (ie, could be overridden at the point of order entry) and was associated with a relatively low abandonment rate, it achieved a considerable cost savings each year since each abandoned test saved the institution $1,000 or more.

Pathology of pulmonary tuberculosis and non-tuberculous mycobacterial lung disease: Facts, misconceptions, and practical tips for pathologists

Most pathologists are familiar with the microscopic features of tuberculosis and the need to examine special stains for acid-fast bacteria (AFB) in cases of granulomatous lung disease. However, misconceptions do exist, including the concept that finding AFB in "caseating granulomas" confirms the diagnosis of tuberculosis. This dogma is attributable to the high prevalence of tuberculosis in many countries, as well as unfamiliarity with the microscopic spectrum of non-tuberculous mycobacterial lung disease. This review aims to provide surgical pathologists with practical tips to identify AFB, illustrate the histologic overlap between pulmonary tuberculosis and non-tuberculous mycobacterial lung disease, and highlight the importance of cultures in this setting. M. tuberculosis and non-tuberculous mycobacteria cannot be reliably differentiated either on the basis of the tissue reaction or by bacterial morphology on acid-fast stains. Although a presumptive clinical diagnosis of tuberculosis can be made without culture-confirmation, the only definitive means to determine the true identity of AFB is by cultures or molecular methods. Making this distinction is most critical when AFB are found in incidentally detected lung nodules in geographic locations where the incidence of tuberculosis is low, because in such settings AFB in necrotizing granulomas of the lung are more likely to be non-tuberculous mycobacteria than M. tuberculosis.

Laboratory Diagnosis and Susceptibility Testing for Mycobacterium tuberculosis

The laboratory, which utilizes some of the most sophisticated and rapidly changing technologies, plays a critical role in the diagnosis of tuberculosis. Some of these tools are being employed in resource-challenged countries for the rapid detection and characterization of Mycobacterium tuberculosis . Foremost, the laboratory defines appropriate specimen criteria for optimal test performance. The direct detection of mycobacteria in the clinical specimen, predominantly done by acid-fast staining, may eventually be replaced by rapid-cycle PCR. The widespread use of the Xpert MTB/RIF (Cepheid) assay, which detects both M. tuberculosis and key genetic determinants of rifampin resistance, is important for the early detection of multidrug-resistant strains. Culture, using both broth and solid media, remains the standard for establishing the laboratory-based diagnosis of tuberculosis. Cultured isolates are identified far less commonly by traditional biochemical profiling and more commonly by molecular methods, such as DNA probes and broad-range PCR with DNA sequencing. Non-nucleic acid-based methods of identification, such as high-performance liquid chromatography and, more recently, matrix-assisted laser desorption/ionization–time of flight mass spectrometry, may also be used for identification. Cultured isolates of M. tuberculosis should be submitted for susceptibility testing according to standard guidelines. The use of broth-based susceptibility testing is recommended to significantly decrease the time to result. Cultured isolates may also be submitted for strain typing for epidemiologic purposes. The use of massive parallel sequencing, also known as next-generation sequencing, promises to continue to this molecular revolution in mycobacteriology, as whole-genome sequencing provides identification, susceptibility, and typing information simultaneously.

Prevalence of Mycobacterium lentiflavum in cystic fibrosis patients, France

Background

Mycobacterium lentiflavum is rarely isolated in respiratory tract samples from cystic fibrosis patients. We herein describe an unusually high prevalence of M. lentiflavum in such patients.

Methods

M. lentiflavum, isolated from the respiratory tract of cystic fibrosis patients, was identified using both rpoB partial sequencing and detected directly in the sputum by using real-time PCR targeting the smpB gene.

Results

M. lentiflavum emerged as the third most prevalent nontuberculous mycobacterial species isolated in cystic fibrosis patients in Marseille, France. Six such patients were all male, and two of them may have fulfilled the American Thoracic Society clinical and microbiological criteria for M. lentiflavum potential lung infection.

Conclusions

M. lentiflavum was the third most common mycobacteria isolated in cystic fibrosis patients, particularly in six male patients. M. lentiflavum outbreaks are emerging particularly in cystic fibrosis patients.

Electronic supplementary material

The online version of this article (doi:10.1186/s12890-015-0123-y) contains supplementary material, which is available to authorized users.