• Genomics and AMR genes of emerging Klebsiella pneumoniae strains using short and long reads

Summary table

Key	Value
category	assembly-based
platform	illumina/ MinION
open source	true
reproducible	true

Database

ARG-Annot database in Kleborate

Protocol

• Step 1

Genomic DNA was sequenced using the MiniSeq or MiSeq (Illumina) and MinION (Oxford Nanopore)

• Step 2

SPAdes v3.8.1 was used for de novo assembly of short reads data
Unicycler v0.4.4 was used for hybrid assembly of short and long reads data

• Step 3

Antimicrobial resistance genes were searched through the database using thresholds of ≥ 90.0% for both nucleotide identity and sequence coverage.

Citation

The paper(s) documenting this protocol:
*Lam M et al. Population genomics of hypervirulent Klebsiella pneumoniae clonal-group 23 reveals early emergence and rapid global dissemination. Nature Communications. 2018
*Wyres KL et al. Emergence and rapid global dissemination of CTX-M-15-associated Klebsiella pneumoniae strain ST307. Journal of Antimicrobial Chemotherapy. 2018

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