Open Access Research

Phylogeographic variation in recombination rates within a global clone of methicillin-resistant Staphylococcus aureus

Santiago Castillo-Ramírez1, Jukka Corander2, Pekka Marttinen34, Mona Aldeljawi1, William P Hanage5, Henrik Westh67, Kit Boye6, Zeynep Gulay8, Stephen D Bentley9, Julian Parkhill9, Matthew T Holden9 and Edward J Feil1*

Author Affiliations

1 Department of Biology and Biochemistry, University of Bath, Claverton Down Bath, Bath and North East Somerset BA2 7AY, UK

2 Department of Mathematics and Statistics, PO Box 68 (Gustaf Hällströmin katu 2b), University of Helsinki, FI-00014 Helsinki, Finland

3 Department of Information and Computer Science, Helsinki Institute for Information Technology HIIT, Aalto University, PO Box 15400 (Konemiehentie 2), FI-00076 Aalto, Finland

4 Department of Biomedical Engineering and Computational Science, Aalto University, PO Box 12200 (Rakentajanaukio 2c), FI-00076 Aalto, Finland

5 Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA

6 Department of Clinical Microbiology 445, Hvidovre Hospital, DK-2650 Hvidovre, Denmark

7 Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark

8 Dokuz Eylul University School of Medicine, Department of Clinical Microbiology, Mithatpaşa cad., Inciralti, Izmir 35340, Turkey

9 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK

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Genome Biology 2012, 13:R126  doi:10.1186/gb-2012-13-12-r126

Published: 27 December 2012

Additional files

Additional file 1:

List of the strains used in this study. This file lists all the strains used as well as their country of origin. The second column states whether the strain was sequenced for this study (newly sequenced) or the strain came from the study by Harris et al. [2] (previously sequenced).

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Additional file 2:

Recombination events detected via BRATNextGen. Details of the recombination events, for every strain the recombination events are listed as well as the boundaries of these events.

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Open Data

Additional file 3:

Neighbor net based on all the SNPs. Tip labels were taken out for the sake of clarity. The network was constructed by means of SplitTree and shows extensive reticulation consistent with the conflicting phylogenetic signals created by recombination. Additionally, we used the Phi test also through SplitTree to further corroborate the presence of recombination. The test was statistically significant with a P-value equal to 0.

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Open Data

Additional file 4:

List of the genes affected by recombination based only on BRATNexGen results. Genes were considered recombinant if more than 100 bp of their sequence have undergone recombination based on the BRATNexGen output. The gene identifier is with respect to the reference genome TW20. The total number of genes affected by recombination according to this criterion was 441.

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Open Data

Additional file 5:

Table showing MGEs used for the r/m analyses. The description and coordinates of the MGEs are with respect to the reference genome TW20.

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Additional file 6:

List of the genes affected by recombination based on BRATNexGen and the method used in[1]. Genes were considered recombinant if more than 100 bp of their sequence have undergone recombination based on the BRATNexGen output and the results from the method used in [1]. The gene identifier is with respect to the reference genome TW20. The number of genes affected by recombination according to this criterion was 312.

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Open Data

Additional file 7:

Functions affected by recombination using BRATNextGen and the method used in[1]. The bars are the most inclusive categories based on an adapted version of Riley's classification. The blue section of the bars represents the percentage of genes of each functional category affected by recombination. The 'extrachromosomal' category was here renamed 'MGE' to avoid confusion as these genes are physically located on the chromosome.

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Open Data

Additional file 8:

Multiple alignment used for constructing the phylogeny in Figure 3. Multiple alignment in phylip format containing all the SNPs not affected by recombination that was used to construct the phylogeny shown in Figure 3 and to conduct the power calculation mentioned in the Discussion.

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Additional file 9:

Groups identified by BAPS. For each group the list of the isolates composing it is given as well as the main geographic location of the group.

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Additional file 10:

Bayesian dated phylogeny constructed via BEAST. For the sake of clarity the Turkish (dark blue triangle), South American (light blue triangle), and Asian (red triangle) groups were collapsed. The violet horizontal bars show the 95% highest posterior density (HPD) intervals for the divergence time estimates.

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Additional file 11:

Description of the populations used for the analysis of the founder events. Three groups were defined and this table gives the list of isolates for each group and the main geographic region.

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Additional file 12:

Domestic flights between the three Turkish cities. Total number of domestic flights between the three Turkish cities during the week 2 to 8 November 2012.

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Additional file 13:

Some clinical details of the newly sequenced Turkish isolates. This file shows the isolation date and the source for most of the newly sequenced Turkish isolates.

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