Multiplexed Molecular Diagnostics for Respiratory, Gastrointestinal, and Central Nervous System Infections

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Abstract

Multiplex molecular diagnostic panels represent a paradigm shift for both clinical microbiology and infectious diseases. This review summarizes the advantages and limitations of current US Food and Drug Administration–approved tests for respiratory viruses, diarrheal illness, and meningitis/encephalitis.

abstract

The development and implementation of highly multiplexed molecular diagnostic tests have allowed clinical microbiology laboratories to more rapidly and sensitively detect a variety of pathogens directly in clinical specimens. Current US Food and Drug Administration–approved multiplex panels target multiple different organisms simultaneously and can identify the most common pathogens implicated in respiratory viral, gastrointestinal, or central nervous system infections. This review summarizes the test characteristics of available assays, highlights the advantages and limitations of multiplex technology for infectious diseases, and discusses potential utilization of these new tests in clinical practice.

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Most cited references 29

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Etiology of Community-Acquired Pneumonia: Increased Microbiological Yield with New Diagnostic Methods

Niclas Johansson, Mats Kalin, Annika Tiveljung-Lindell … (2010)

Abstract Background The microbial etiology of community-acquired pneumonia (CAP) is still not well characterized. During the past few years, polymerase chain reaction (PCR)-based methods have been developed for many pathogens causing respiratory tract infections. The aim of this study was to determine the etiology of CAP among adults—especially the occurrence of mixed infections among patients with CAP—by implementing a new diagnostic PCR platform combined with conventional methods. Methods Adults admitted to Karolinska University Hospital were studied prospectively during a 12-month period. Microbiological testing methods included culture from blood, sputum, and nasopharyngeal secretion samples; sputum samples analyzed by real-time quantitative PCR for Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis; nasopharyngeal specimens analyzed by use of PCR; serological testing for Mycoplasma pneumoniae, Chlamydophila pneumoniae, and viruses common in the respiratory tract; and urine antigen assays for detection of pneumococcal and Legionella pneumophila antigens. Results A microbial etiology could be identified for 67% of the patients (n = 124). For patients with complete sampling, a microbiological agent was identified for 89% of the cases. The most frequently detected pathogens were S. pneumoniae (70 patients [38]) and respiratory virus (53 patients [29]). Two or more pathogens were present in 43 (35%) of 124 cases with a determined etiology. Conclusions By supplementing traditional diagnostic methods with new PCR-based methods, a high microbial yield was achieved. This was especially evident for patients with complete sampling. Mixed infections were frequent (most commonly S. pneumoniae together with a respiratory virus).

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Comprehensive Molecular Testing for Respiratory Pathogens in Community-Acquired Pneumonia

Naomi Gadsby, Clark D. Russell, Martin P. McHugh … (2016)

This is the first time a comprehensive, multipathogen, quantitative and qualitative molecular approach for respiratory bacteria and viruses has been compared with traditional diagnostic methods on a large hospitalized pneumonia cohort, with estimation of potential effects on antibiotic prescribing.

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Diagnosis of Clostridium difficile infection: an ongoing conundrum for clinicians and for clinical laboratories.

Carey-Ann D. Burnham, Ronan K Carroll (2013)

Clostridium difficile is a formidable nosocomial and community-acquired pathogen, causing clinical presentations ranging from asymptomatic colonization to self-limiting diarrhea to toxic megacolon and fulminant colitis. Since the early 2000s, the incidence of C. difficile disease has increased dramatically, and this is thought to be due to the emergence of new strain types. For many years, the mainstay of C. difficile disease diagnosis was enzyme immunoassays for detection of the C. difficile toxin(s), although it is now generally accepted that these assays lack sensitivity. A number of molecular assays are commercially available for the detection of C. difficile. This review covers the history and biology of C. difficile and provides an in-depth discussion of the laboratory methods used for the diagnosis of C. difficile infection (CDI). In addition, strain typing methods for C. difficile and the evolving epidemiology of colonization and infection with this organism are discussed. Finally, considerations for diagnosing C. difficile disease in special patient populations, such as children, oncology patients, transplant patients, and patients with inflammatory bowel disease, are described. As detection of C. difficile in clinical specimens does not always equate with disease, the diagnosis of C. difficile infection continues to be a challenge for both laboratories and clinicians.

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Author and article information

Contributors

L. Barth Reller: Role: Section Editor

Melvin P. Weinstein: Role: Section Editor

Journal

Journal ID (nlm-ta): Clin Infect Dis

Journal ID (iso-abbrev): Clin. Infect. Dis

Journal ID (publisher-id): cid

Journal ID (hwp): cid

Title: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America

Publisher: Oxford University Press

ISSN (Print): 1058-4838

ISSN (Electronic): 1537-6591

Publication date (Print): 15 November 2016

Publication date (Electronic): 20 July 2016

Volume: 63

Issue: 10

Pages: 1361-1367

Affiliations

[1 ] Divisions of Infectious Diseases

[2 ] University of Utah and ARUP Laboratories , Salt Lake City

Author notes

Correspondence: K. E. Hanson, School of Medicine, University of Utah, 30 N 1900 E, Rm 4B319, Salt Lake City, UT 84132 ( kim.hanson@ 123456hsc.utah.edu ).

Article

Publisher ID: ciw494

DOI: 10.1093/cid/ciw494

PMC ID: 5091344

PubMed ID: 27444411

SO-VID: 2679d5df-a7ba-4870-aefc-cce4ae3ea817

License:

This article is made available via the PMC Open Access Subset for unrestricted re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the COVID-19 pandemic or until permissions are revoked in writing. Upon expiration of these permissions, PMC is granted a perpetual license to make this article available via PMC and Europe PMC, consistent with existing copyright protections.

History

Date received : 9 March 2016

Date accepted : 11 July 2016

Funding

Funded by: National Institutes of Health

Funded by: BioFire Dignostics, LLC

Award ID: 5R43AI104029-02

Award ID: 5R01AI11703502

Multiplexed Molecular Diagnostics for Respiratory, Gastrointestinal, and Central Nervous System Infections

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European Respiratory Society: COVID-19

Most cited references 29

Etiology of Community-Acquired Pneumonia: Increased Microbiological Yield with New Diagnostic Methods

Comprehensive Molecular Testing for Respiratory Pathogens in Community-Acquired Pneumonia

Diagnosis of Clostridium difficile infection: an ongoing conundrum for clinicians and for clinical laboratories.

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