Adaptive nanopore sequencing on miniature flow cell detects extensive antimicrobial resistance

Abstract

Rapid screening of hospital admissions to detect asymptomatic carriers of resistant bacteria can prevent pathogen outbreaks. However, the resulting isolates rarely have their genome sequenced due to cost constraints and long turn-around times to get and process the data, limiting their usefulness to the practitioner. Here we use real-time, on-device target enrichment (“adaptive”) sequencing on a new type of low-cost nanopore flow cell as a highly multiplexed assay covering 1,147 antimicrobial resistance genes. Using this method, we detected three types of carbapenemase in a single isolate of Raoultella ornithinolytica (NDM, KPC, VIM). Further investigation revealed extensive horizontal gene transfer within the underlying microbial consortium, increasing the risk of resistance spreading. From a technical point of view, we identify two important variables that can increase the enrichment of target genes: higher nucleotide identity and shorter read length. Real-time sequencing could thus quickly inform how to monitor this case and its surroundings.