Typing of Methicillin-Resistant Staphylococcus aureus Based on Whole-Genome Sequencing: the Impact of the Assembler.

Sequencing of the gene of methicillin-resistant Staphylococcus aureus (MRSA) is used for assigning types to e.g., detect transmission and control outbreaks. Traditionally, typing is performed by Sanger sequencing but has in recent years been replaced by whole-genome sequencing (WGS) in some laboratories. typing by WGS involves assembly of millions of short sequencing reads into larger contiguous sequences, from which the type is then determined. The choice of assembly program therefore potentially impacts the typing result. In this study, WGS of 1,754 MRSA isolates was followed by assembly using the assembly programs SPAdes (with two different sets of parameters) and SKESA. The types were assigned and compared to the types obtained by Sanger sequencing, regarding the latter as the correct types. SPAdes with the two different settings resulted in assembly of the correct type for 84.8% and 97.6% of the isolates, respectively, while SKESA assembled the correct type in 98.6% of cases. The misassembled types were generally two repeats shorter than the correct type and mainly included types with repetition of the same repeats. WGS-based typing is thus very accurate compared to Sanger sequencing, when the best assembly program for this purpose is used. typing of methicillin-resistant Staphylococcus aureus (MRSA) is widely used by clinicians, infection control workers, and researchers both in local outbreak investigations and as an easy way to communicate and compare MRSA types between laboratories and countries. Traditionally, types are determined by Sanger sequencing, but in recent years a whole-genome sequencing (WGS)-based approach has become increasingly used. In this study, we compared typing by WGS using different methods for assembling the genome from short sequencing reads and compared to Sanger sequencing as the gold standard. We find substantial differences in correct assembly of types between the assembly methods. Our findings are therefore important for the quality of WGS based typing data being exchanged by clinical microbiology laboratories.