Genome assemblies and pan-genome data for 328 clinical isolates of Klebsiella pneumoniae species complex, representing one year of infections diagnosed in a hospital diagnostic lab

Full description

The Klebsiella Acquisition Surveillance Project at Alfred Health (KASPAH) was conducted from April 1, 2013, to March 31, 2014 in Melbourne, Australia. During this period, all clinical isolates identified as K. pneumoniae or K. variicola infections by the Alfred Hospital microbiological diagnostic laboratory as part of routine care were included in the study. In addition to the Alfred Hospital, the laboratory serves other hospitals in the Alfred Health network, namely Caulfield, Sandringham and Bethlehem Hospitals, and isolates referred from those hospitals are included in the collection.

All isolates were sequenced via Illumina sequencing; reads are available under BioProjects PRJEB6891 (ERP006536) and PRJNA351909 (SRP094663). Subsets of isolates have been additionally sequenced via Oxford Nanopore MinION to generate closed reference-quality genome sequences (assembled sequences available in GenBank, nanopore reads available on request due to large file sizes).

The data included here are:
(i) assemblies generated using Unicycler v0.4.7, from Illumina + ONT reads where available (assembly files labelled as [species]_[strain].fasta) or Illumina reads only (assembly files labelled as [run]_[lane]#[index].fasta); and
(ii) pan-genome data generated from these assemblies using panaroo v1.1.2 (run with default settings).

Also included is spreadsheet Table S1, which lists all isolates and corresponding clinical, sequence and genotype data included in the paper.

An interactive version of the core genome phylogeny for this collection, annotated with Table S1 data, is available at https://microreact.org/project/gVB3ki6iA62RREC1stLLHo-kaspah-clinical-isolates.

All isolates have corresponding antimicrobial susceptibility data (Vitek2) and MALDI-TOF spectra (Bruiker) available on request from the authors (email drkatholt@gmail.com). Resistance calls based on Vitek2 data interpreted with EUCAST breakpoints are included here in Table S1.