Summary table

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

Database

This protocol uses Abricate v0.5-dev3 for detection of AMR genes in S. aureus (in burn patients across sub-Saharan Africa). Command for installation of Abricate and its dependencies is available via github (https://github.com/tseemann/abricate).

Protocol

• Step 1 Genomic DNA was extracted using the Ultraclean microbial DNA isolation kit

• Step 2 DNA libraries were prepared using the Nextera XT v2 kit and sequenced on the Illumina platform using 2 × 250-bp chemistry

• Step 3 The raw reads were assembled into contigs using spades 3.9.0 and mapped to the fully assembled chromosome of S. aureus COL (ST250) (chromosome: CP000046) using snippy v3.21

• Step 4 Antibiotic resistance detection were undertaken with abricate v0.5-dev3.

Citation

The paper(s) documenting this protocol:

• Amissah NA, Buultjens AH, Ablordey A, et al. Methicillin Resistant Staphylococcus aureus Transmission in a Ghanaian Burn Unit: The Importance of Active Surveillance in Resource-Limited Settings. Front Microbiol. 2017

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