Monday, 9 January 2017

Clonal characterization of Staphylococcus aureus


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.

This is the subject of a new paper.

For the study, 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 were calculated. GoeBURST and BURP algorithms were used for grouping MLST and spa types.

It was found that in 76.6% S.aureus genomes the spa and MLST types were determined. Discriminatory power of spa typing was higher (89.4%) than MLST typing (80.5%). The overall agreement between spa typing and MLST at a type level was 39.2%. This has been proved with directional index of partition relation (adjusted Wallace) indicating no more 60% congruence.


Concordance between spa and MLST typing data were not 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 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.

The reference is:

Babenko, D., Omarkulov, B., Azizov, I., Sandle, T., Moraru, D. and Chesca, A. (2016) Evaluation of sequence based typing methods (SPA and MSLT) for clonal characterization of Staphylococcus aureus, Acta Medica Mediterranea, 32: 1851-1856

For further details see: Typing methods, or contact Tim Sandle

Posted by Dr. Tim Sandle