Molecular versus culture-based testing for gastrointestinal infection

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Purpose of review

Molecular-based diagnostic methods for the detection of gastrointestinal pathogens are becoming increasingly commonplace in microbiology laboratories. This review aims to summarize recent developments in this field and discuss the clinical application and limitations of implementing these techniques.

Recent findings

Recent evaluations of multiplex PCR assays show increased sensitivity whenever compared with standard microbiological culture-based methods. In addition to shorter turnaround times, assays can detect an increased repertoire of pathogens from a single specimen and provide useful information for infection prevention and control practices. There are many limitations, however, associated with their use, including clinical interpretation of results and lack of concordance between different test panels. Newer technologies, such as metagenomic analysis, can provide comprehensive information useful to both patient management and public health surveillance.


Molecular techniques are capable of replacing culture in the diagnosis of gastrointestinal infections. Whether all positive results, however, represent true infection is still debateable, as is the clinical significance of identifying more than one pathogen. As it currently stands, microbiological culture remains vital for public health surveillance, monitoring antibiotic resistance and managing outbreaks.

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