Tracking of antibiotic resistance transfer and rapid plasmid evolution in a hospital setting by Nanopore sequencing.. plasmid-evolution-xdr-carbapenemase

We have sequenced extensively multidrug resistant Pseudomonas aeruginosa, Citrobacter freundii and Citrobacter werkmanii isolates from a hospital outbreak, which all harbor the carbapenemase enzyme blaIMP-8. All isolates have been sequenced using short read Illumina sequencing (various instruments) and long read Nanopore sequencing (MinION). Genome sequences (chromosomes and plasmids) were assembled and annotated using the pathoLogic (https://github.com/imgag/pathoLogic) and plasmIDent (https://github.com/imgag/plasmIDent) pipelines. Further details can be found in the main publication of the study (TBA).