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Table 3 Challenges for traditional pathogen detection in public health

From: Metagenomics for pathogen detection in public health

Challenge Importance Traditional methods Metagenomic approaches Reference(s)
Speed It is important to identify pathogens as quickly as possible to identify appropriate measures for treatment and prevention of spread Techniques that require culture can lead to delays, particularly for slow-growing pathogens such as Mycobacterium tuberculosis Metagenomic pathogen discovery is increasing in speed and single genomes can now be sequenced in a few hours [16, 74, 75]
   Performing multiple tests can delay diagnosis Metagenomics comprises a single test  
Cost For a technique to be viable in a public health laboratory, it must be economically justifiable Performing multiple tests can be very expensive Metagenomic approaches are decreasing in cost [7577]
    A single metagenomics experiment can now be performed for less than $200  
Identification of pathogens that are present at low levels Disease can be caused by pathogens that are present at very low levels. Samples taken may only harbor small numbers of a pathogen May not detect pathogens that are present at very low levels It is now possible to perform metagenomic studies from a single cell [16, 73, 78]
   Biases in culturing and other methods may point to the wrong pathogen Genomes have been assembled from organisms with relative nucleic acid abundances as low as 0.1%  
Identification of novel or variant pathogens Early identification of novel pathogens is vital to prevent potential outbreaks May not identify pathogens that are unknown or too divergent from known organisms De novo assembly allows generation of genome sequences from novel pathogens [911]
Detection of transmission Identification of transmission guides public health practices for containing outbreaks Traditional pathogen fingerprinting methods may not have the resolution to detect transmission events Whole-genome sequences provide the ultimate resolution required to detect transmission events [79]
Co-infections and complex diseases Complex diseases are often caused by a combination of multiple pathogens, host genetics and environmental factors Targeted detection of pathogens does not allow identification of multiple pathogens, unless each is specifically investigated Can detect multiple pathogens in one test, allowing for inference of interactions [79, 80]