Table 3 Challenges for traditional 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 | |
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 | |
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 | |
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 | |
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 |