Ensuring backwards compatibility: traditional genotyping efforts in the era of whole genome sequencing

S Bletz; A Mellmann; J Rothgänger; D Harmsen

doi:10.1016/j.cmi.2014.11.005

Ensuring backwards compatibility: traditional genotyping efforts in the era of whole genome sequencing

Clin Microbiol Infect. 2015 Apr;21(4):347.e1-4. doi: 10.1016/j.cmi.2014.11.005. Epub 2014 Nov 25.

Authors

S Bletz¹, A Mellmann², J Rothgänger³, D Harmsen⁴

Affiliations

¹ Institute of Hygiene, University Hospital Münster, Münster, Germany.
² Institute of Hygiene, University Hospital Münster, Münster, Germany. Electronic address: mellmann@uni-muenster.de.
³ Ridom GmbH, Münster, Germany.
⁴ Department of Periodontology, University Hospital Münster, Münster, Germany.

PMID: 25658529
DOI: 10.1016/j.cmi.2014.11.005

Abstract

When using next-generation whole genome sequencing (WGS), extraction of spa types from WGS data is essential for backwards compatibility with Sanger sequencing-based spa typing of methicillin-resistant Staphylococcus aureus (MRSA). We evaluated WGS-based spa typing with a 2×250 bp protocol in a diverse collection of 423 MRSA isolates using two pipelines that executed sequence quality-trimming and de novo assembly before spa typing. The SeqSphere(+) pipeline correctly typed 419 isolates (99.1%) whereas the CLCbio pipeline succeeded in 249 isolates (58.9%). In summary, WGS combined with an optimized de novo assembly enables nearly full compatibility with Sanger sequencing-based spa typing data.

Keywords: Backwards compatibility; Staphylococcus aureus; methicillin-resistant Staphylococcus aureus; spa typing; whole genome sequencing.

Publication types

Comparative Study
Research Support, Non-U.S. Gov't

MeSH terms

Genotype*
Genotyping Techniques / methods*
Humans
Methicillin-Resistant Staphylococcus aureus / classification*
Methicillin-Resistant Staphylococcus aureus / genetics*
Molecular Epidemiology / methods
Sequence Analysis, DNA / methods*