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Opinion

Culture-Independence for Surveillance and Epidemiology

1
Department of Wound Infections, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
2
Uniformed Services University of the Health Sciences, Bethesda, MD 20914, USA 
Pathogens 2013, 2(3), 556-570; https://doi.org/10.3390/pathogens2030556
Received: 1 August 2013 / Revised: 3 September 2013 / Accepted: 5 September 2013 / Published: 24 September 2013
(This article belongs to the Special Issue Bacterial Pathogenomics: From Technology to Application)
Culture-independent methods in microbiology (quantitative PCR (qPCR), sequencing, microarrays, direct from sample matrix assisted laser desorption/ionization time of flight mass spectroscopy (MALDI-TOF MS), etc.) are disruptive technology. Rather than providing the same results as culture-based methods more quickly, more cheaply or with improved accuracy, they reveal an unexpected diversity of microbes and illuminate dark corners of undiagnosed disease. At times, they overturn existing definitions of presumably well-understood infections, generating new requirements for clinical diagnosis, surveillance and epidemiology. However, current diagnostic microbiology, infection control and epidemiology rest principally on culture methods elegantly optimized by clinical laboratorians. The clinical significance is interwoven; the new methods are out of context, difficult to interpret and impossible to act upon. Culture-independent diagnostics and surveillance methods will not be deployed unless the reported results can be used to select specific therapeutics or infection control measures. To cut the knots surrounding the adoption of culture-independent methods in medical microbiology, culture-dependent methods should be supported by consistent culture-independent methods providing the microbial context. This will temper existing biases and motivate appropriate scrutiny of the older methods and results. View Full-Text
Keywords: culture-independence; next generation sequencing; diagnostics culture-independence; next generation sequencing; diagnostics
MDPI and ACS Style

Kirkup, B.C., Jr. Culture-Independence for Surveillance and Epidemiology. Pathogens 2013, 2, 556-570. https://doi.org/10.3390/pathogens2030556

AMA Style

Kirkup BC Jr.. Culture-Independence for Surveillance and Epidemiology. Pathogens. 2013; 2(3):556-570. https://doi.org/10.3390/pathogens2030556

Chicago/Turabian Style

Kirkup, Benjamin C., Jr. 2013. "Culture-Independence for Surveillance and Epidemiology" Pathogens 2, no. 3: 556-570. https://doi.org/10.3390/pathogens2030556

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