RT Journal Article
SR Electronic
T1 Rapid profiling of the preterm infant gut microbiota using nanopore sequencing aids pathogen diagnostics
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 180406
DO 10.1101/180406
A1 Richard M. Leggett
A1 Cristina Alcon-Giner
A1 Darren Heavens
A1 Shabhonam Caim
A1 Thomas C. Brook
A1 Magdalena Kujawska
A1 Samuel Martin
A1 Lesley Hoyles
A1 Paul Clarke
A1 Lindsay J. Hall
A1 Matthew D. Clark
YR 2018
UL http://biorxiv.org/content/early/2018/10/12/180406.abstract
AB The Oxford Nanopore MinION sequencing platform offers near real time analysis of DNA reads as they are generated, which makes the device attractive for in-field or clinical deployment, e.g. rapid diagnostics. We used the MinION platform for shotgun metagenomic sequencing and analysis of gut-associated microbial communities; firstly, we used a 20-species human microbiota mock community to demonstrate how Nanopore metagenomic sequence data can be reliably and rapidly classified. Secondly, we profiled faecal microbiomes from preterm infants at increased risk of necrotising enterocolitis and sepsis. In single patient time course, we captured the diversity of the immature gut microbiota and observed how its complexity changes over time in response to interventions, i.e. probiotic, antibiotics and episodes of suspected sepsis. Finally, we performed ‘real-time’ runs from sample to analysis using faecal samples of critically ill infants and of healthy infants receiving probiotic supplementation. Real-time analysis was facilitated by our new NanoOK RT software package which analysed sequences as they were generated. We reliably identified potentially pathogenic taxa (i.e. Klebsiella pneumoniae and Enterobacter cloacae) and their corresponding antimicrobial resistance (AMR) gene profiles within as little as one hour of sequencing. Antibiotic treatment decisions may be rapidly modified in response to these AMR profiles, which we validated using pathogen isolation, whole genome sequencing and antibiotic susceptibility testing. Our results demonstrate that our pipeline can process clinical samples to a rich dataset able to inform tailored patient antimicrobial treatment in less than 5 hours.