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Speed
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It is important to identify pathogens as quickly as possible to identify appropriate measures for treatment and prevention of spread
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Techniques that require culture can lead to delays, particularly for slow-growing pathogens such as Mycobacterium tuberculosis
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Metagenomic pathogen discovery is increasing in speed and single genomes can now be sequenced in a few hours
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[16, 74, 75]
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Performing multiple tests can delay diagnosis
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Metagenomics comprises a single test
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Cost
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For a technique to be viable in a public health laboratory, it must be economically justifiable
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Performing multiple tests can be very expensive
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Metagenomic approaches are decreasing in cost
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[75–77]
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| | | |
A single metagenomics experiment can now be performed for less than $200
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Identification of pathogens that are present at low levels
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Disease can be caused by pathogens that are present at very low levels. Samples taken may only harbor small numbers of a pathogen
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May not detect pathogens that are present at very low levels
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It is now possible to perform metagenomic studies from a single cell
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[16, 73, 78]
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Biases in culturing and other methods may point to the wrong pathogen
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Genomes have been assembled from organisms with relative nucleic acid abundances as low as 0.1%
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Identification of novel or variant pathogens
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Early identification of novel pathogens is vital to prevent potential outbreaks
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May not identify pathogens that are unknown or too divergent from known organisms
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De novo assembly allows generation of genome sequences from novel pathogens
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[9–11]
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Detection of transmission
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Identification of transmission guides public health practices for containing outbreaks
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Traditional pathogen fingerprinting methods may not have the resolution to detect transmission events
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Whole-genome sequences provide the ultimate resolution required to detect transmission events
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[79]
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Co-infections and complex diseases
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Complex diseases are often caused by a combination of multiple pathogens, host genetics and environmental factors
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Targeted detection of pathogens does not allow identification of multiple pathogens, unless each is specifically investigated
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Can detect multiple pathogens in one test, allowing for inference of interactions
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[79, 80]
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