title: Challenges of the Unknown: Clinical Application of Microbial Metagenomics.
abstract: Availability of fast, high throughput and low cost whole genome sequencing holds great promise within public health microbiology, with applications ranging from outbreak detection and tracking transmission events to understanding the role played by microbial communities in health and disease. Within clinical metagenomics, identifying microorganisms from a complex and host enriched background remains a central computational challenge. As proof of principle, we sequenced two metagenomic samples, a known viral mixture of 25 human pathogens and an unknown complex biological model using benchtop technology. The datasets were then analysed using a bioinformatic pipeline developed around recent fast classification methods. A targeted approach was able to detect 20 of the viruses against a background of host contamination from multiple sources and bacterial contamination. An alternative untargeted identification method was highly correlated with these classifications, and over 1,600 species were identified when applied to the complex biological model, including several species captured at over 50% genome coverage. In summary, this study demonstrates the great potential of applying metagenomics within the clinical laboratory setting and that this can be achieved using infrastructure available to nondedicated sequencing centres.
authors.affiliation: Genomic Research Unit, Public Health England, Microbiology Services, 61 Colindale Avenue, London NW9 5HT, UK.
authors.forename: Graham
authors.initials: G
authors.lastname: Rose
authors.affiliation: Genomic Research Unit, Public Health England, Microbiology Services, 61 Colindale Avenue, London NW9 5HT, UK.
authors.forename: David J
authors.initials: DJ
authors.lastname: Wooldridge
authors.affiliation: Genomic Research Unit, Public Health England, Microbiology Services, 61 Colindale Avenue, London NW9 5HT, UK.
authors.forename: Catherine
authors.initials: C
authors.lastname: Anscombe
authors.affiliation: Division of Virology, National Institute for Biological Standards and Control, Medicines and Healthcare Products Regulatory Agency, South Mimms, Hertfordshire EN6 3QG, UK.
authors.forename: Edward T
authors.initials: ET
authors.lastname: Mee
authors.affiliation: Genomic Research Unit, Public Health England, Microbiology Services, 61 Colindale Avenue, London NW9 5HT, UK.
authors.forename: Raju V
authors.initials: RV
authors.lastname: Misra
authors.affiliation: Genomic Research Unit, Public Health England, Microbiology Services, 61 Colindale Avenue, London NW9 5HT, UK.
authors.forename: Saheer
authors.initials: S
authors.lastname: Gharbia