Assessment of long and short-read metagenomics sequencing for detection of gastrointestinal parasites in faeces.


K O'Brien1; M Woubshete1; P Sachs Nique1; J Younger1; V Hunt1
1 University of Bath, UK


The efficient and reliable detection of parasites is crucial for the implementation of effective control measures, leading to growing demands for more accurate diagnostic and detection tools, especially where parasitic load is low. Advances in metagenomics sequencing have revealed its potential in detecting parasites in faecal samples for diagnostic purposes and for wider surveys of parasitic diversity. Here, we evaluate long-read and short-read metagenomics sequencing methods and downstream bioinformatic analysis tools in species-level identification of parasite DNA. We use the gastrointestinal parasite Strongyloides ratti - rat host system to test and compare the accuracy of available approaches. Using short-read sequencing of faecal samples, we find that detection of S. ratti down to the species-level is possible through the use of dedicated bioinformatic techniques. For long-read sequencing, we demonstrate that while the total number of reads are similar, longer reads result in greater depth of coverage for the S. ratti genome compared with short-read sequencing, indicating its use in species-level detection. We also discuss some of the potential issues associated with long-read metagenomics studies on parasites, such as false positive alignments to bacterial contaminants, endosymbionts, or poorly assembled genome regions. Lastly, we discuss the potential for species-specific gene databases in removing these issues in long-read metagenomics sequencing and the implications of these findings for parasite detection in diagnostic versus wildlife population settings.

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