Rapid MinION profiling of preterm microbiota and antimicrobial-resistant pathogens

• DOI: 10.1038/s41564-019-0626-z
• Publication Date: 2019-12-16T17:03:19Z
• Authors: Richard M. Leggett; Cristina Alcon-Giner; Darren Heavens; Shabhonam Caim; Thomas C. Brook; Magdalena Kujawska; Samuel Martin; Ned Peel; Holly Acford-Palmer; Lesley Hoyles; Paul Clarke; Lindsay J. Hall; Matthew D. Clark
• Keywords: Minion; Profiling (computer programming)

The MinION sequencing platform offers near real-time analysis of DNA sequence; this makes the tool attractive for deployment in fieldwork or clinical settings. We used coupled to NanoOK RT software package perform shotgun metagenomic and profile mock communities faecal samples from healthy ill preterm infants. Using Nanopore data, we reliably classified a 20-species community captured diversity immature gut microbiota over time response interventions such as probiotic supplementation, antibiotic treatment episodes suspected sepsis. also performed rapid runs assess gut-associated microbial critically infants, facilitated by package, which analysed sequences they were generated. Our pipeline identified pathogenic bacteria (that is, Klebsiella pneumoniae Enterobacter cloacae) their corresponding antimicrobial resistance gene profiles within little 1 h sequencing. Results confirmed using pathogen isolation, whole-genome susceptibility testing, well with known genes. results demonstrate that (including cost-effective Flongle flow cells) can process rich dataset < 5 h, creates future studies aimed at developing these tools approaches settings focus on providing tailored patient options.