Comparison of bacterial genome assembly software for MinION data and their applicability to medical microbiology

Translating the Oxford Nanopore MinION sequencing technology into medical microbiology requires on-going analysis that keeps pace with technological improvements to the instrument and release of associated analysis software. Here, we use a multidrug resistant Enterobacter kobei isolate as a model organism to compare open source software for the assembly of genome data, and relate this to the time taken to generate actionable information.

Three software tools (PBcR, Canu and miniasm) were used to assemble MinION data, and a fourth (SPAdes) was used to combine MinION and Illumina data to produce a hybrid assembly. All four had a similar number of contigs and were more contiguous than the assembly using Illumina data alone, with SPAdes producing a single chromosomal contig. Evaluation of the four assemblies to represent the genome structure revealed a single large inversion for the SPAdes assembly, which also incorrectly integrated a plasmid into the chromosomal contig. Almost 50%, 80% and 90% of MinION pass reads were generated in the first 6, 9 and 12 hours, respectively. Using data from the first 6 hours alone led to a less accurate, fragmented assembly, but data from the first 9 or 12 hours generated comparable assemblies to that from 48-hour sequencing. Assemblies were generated in two hours using Canu, indicating that isolate to assembled data is possible in less than 48 hours.

MinION data identified that genes responsible for resistance were carried by two different plasmids encoding resistance to carbapenem, and to sulphonamides, rifampicin and aminoglycosides, respectively.