Resolving structural diversity of Carbapenemase-producing gram-negative bacteria using single molecule sequencing

Carbapenemase-producing bacteria are resistant against almost all commonly used betalactam and cephalosporin antibiotics and represent a growing public health crisis. Carbapenemases reside predominantly in mobile genetic elements and rapidly spread across genetic backgrounds and species boundaries. Here, we report more than one hundred finished, high quality genomes of carbapenemase producing enterobacteriaceae, P. aeruginosa and A. baumannii sequenced with Oxford Nanopore and Illumina technologies. We developed a number of high-throughput criteria to assess the quality of fully assembled genomes for which curated references do not exist. Using this diverse collection of closed genomes and plasmids, we demonstrate rapid movement of carbapenemase between genomic neighborhoods, sequence types, and across species boundaries with distinct patterns for different carbapenemases. Lastly, we present evidence of multiple ancestral recombination events between different Enterobacteriaceae MLSTs. Taken together, our samples suggest a hierarchical picture of genomic variation produced by the evolution of carbapenemase producing bacteria that will require new models to adequately understand and track.