Resolving complex mobile genetic elements with nanopore sequencing

Abstract

Sequence-based surveillance of antimicrobial resistance (AMR) is becoming increasingly prevalent – with the emergence of low-capital investment long-read technology in the form of Oxford Nanopore Technologies (ONT) MinION enabling such surveillance in infrastructure poor low-middle income countries. In such settings, the surveillance of mobile genetic elements, which can facilitate the rapid spread of beneficial AMR genotypes horizontally throughout bacterial populations, and across species boundaries may provide a relatively low-cost target for surveillance. In this study we used an ONT MinION to whole genome sequence E. coli isolates from Nairobi, Kenya for which Illumina data had previously been generated alongside producing whole genome sequences for novel isolates collected for a model surveillance project in Busia, Kenya. The Illumina sequenced isolates had been found to carry a consistently co-occurring set of antibiotic resistance genes (tetA, strAB, sul1, bla-TEM, and dfrA7), conferring resistance to five antibiotic classes. The exact genomic context of which could not be determined with Illumina sequence data alone. Whilst those isolates collected in Busia demonstrated phenotypic resistance to those classes. Initially suspected to be borne on regionally disseminated plasmids; the long-reads generated by the MinION allowed the full resolution of these genes across several closely associated transposable elements, which were further found to be integrated chromosomally, across these geographically independent isolates. This study demonstrates that value of long-read sequencing in the resolution of regionally important mobile genetic elements, simultaneously allowing further value to be added to previously produced long-read data.