Identification of isolated or mixed strains from long reads: a challenge met on Streptococcus thermophilus using a MinION sequencer

Abstract

This study aimed to provide efficient recognition of bacterial strains on personal computers from MinION (Nanopore) long read data. Thanks to the fall in sequencing costs, the identification of bacteria can now proceed by whole genome sequencing. MinION is a fast, but highly error-prone sequencing device and it is a challenge to successfully identify the strain content of unknown simple or complex microbial samples. It is heavily constrained by memory management and fast access to the read and genome fragments. Our strategy involves three steps: indexing of known genomic sequences for a given or several bacterial species; a request process to assign a read to a strain by matching it to the closest reference genomes; and a final step looking for a minimum set of strains that best explains the observed reads. We have applied our method, called ORI, on 77 strains of Streptococcus thermophilus . We worked on several genomic distances and obtained a detailed classification of the strains, together with a criterion that allows merging of what we termed ‘sibling’ strains, only separated by a few mutations. Overall, isolated strains can be safely recognized from MinION data. For mixtures of several non-sibling strains, results depend on strain abundance.

cgMSI: pathogen detection within species from nanopore metagenomic sequencing data

“…Therefore, nanopore sequencing has been considered as a highly potential tool for genomic surveillance of emerging viruses [ 16 – 18 ]. Several tools have been used to analyze nanopore sequencing data, including ORI [ 19 ], Centrifuge, MetaMaps [ 20 ] and Kraken2. ORI identifies strains from whole genome sequencing (WGS) samples.…”

A step forward for Shiga toxin-producing Escherichia coli identification and characterization in raw milk using long-read metagenomics

“…Different long-read sequencing technologies exist, among which the most commonly used were commercialized by Pacific Biosciences (PacBio) and Oxford Nanopore Technology (ONT) [13,14]. The MinION platform, released in 2014 by Oxford Nanopore Technology, known for its portability and its ability to generate very long reads, has been increasingly tested for food-borne pathogen detection [15][16][17][18][19][20].…”