PT  - JOURNAL ARTICLE
AU  - Adrian Viehweger
AU  - Mike Marquet
AU  - Martin Hölzer
AU  - Nadine Dietze
AU  - Mathias Pletz
AU  - Christian Brandt
TI  - Adaptive nanopore sequencing on miniature flow cell detects extensive antimicrobial resistence
AID  - 10.1101/2021.08.29.458107
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.08.29.458107
4099  - http://biorxiv.org/content/early/2021/09/10/2021.08.29.458107.short
4100  - http://biorxiv.org/content/early/2021/09/10/2021.08.29.458107.full
AB  - 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 four types of carbapenemase in a single isolate of Raoultella ornithinolytica (NDM, KPC, VIM, OXA). Further investigation revealed extensive horizontal gene transfer within the underlying microbial consortium, increasing the risk of resistance spreading. Real-time sequencing could thus quickly inform how to monitor this case and its surroundings.Competing Interest StatementThe authors have declared no competing interest.