Evaluation of sequence based typing methods (SPA and MSLT) for clonal characterization of staphylococcus aureus

Dmitriy Babenko, Bauyrzhan K. Omarkulov, Ilyaazizov, Tim Sandle, Dan Moraru, Antonella Elisa Chesca

2016

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DOI 10.19193/0393-6384_2016_6_173
Data confidence 70 medium
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Abstract

Staphylococcus aureus is a well-recognized human pathogen that exists in clinical and community settings worldwide. Staphylococcus aureus can asymptomatically colonize the human and is known as responsible for a wide spectrum of illnesses. Many typing methods have been developed to perform subspecies differentiation needed in epidemiological studies. In this context, the aim of the present study was to compare sequence-based typing methods, such as Multilocus sequence typing (MLST) and spa typing, in order to assess their discriminatory power and concordance. Materials and methods: 5290 S. aureus genomes were downloaded and used to determine MLST and spa types in silico. To estimate discriminatory power of typing methods and concordance between them the Simpson, adjusted Rand and adjusted Wallace indices have been calculated. GoeBURST and BURP algorithms were used for grouping MLST and spa types. Results: In 76.6% S.aureus genomes the spa and MLST types have been determined. Discriminatory power of spa typing was higher (89.4%) than MLST typing (80.5%). The overall agreement betwee spa typing and MLST at a type level was 39.2%. This have been proved with directional index of partition relation (adjusted Wallace) indicating no more 60% congruence. Conclusion: Concordance between spa and MLST typing data were no so high at a type level because of difference in their discriminatory power. At the same time, level of agreement between MLST and spa clonal complexes have reached 89.4%. Snp correction of MLST clonal complexes excluding MLST types with 3 and more bases distance from clonal complexes have led to 97.2% concordance. This high concordance was observed regardless of the place and time when Staphylococcus aureus was isolated.