Open Access Research

The multidrug-resistant PMEN1 pneumococcus is a paradigm for genetic success

Kelly L Wyres1, Lotte M Lambertsen2, Nicholas J Croucher3, Lesley McGee4, Anne von Gottberg5, Josefina Liñares6, Michael R Jacobs7, Karl G Kristinsson8, Bernard W Beall4, Keith P Klugman9, Julian Parkhill3, Regine Hakenbeck10, Stephen D Bentley3 and Angela B Brueggemann1*

Author Affiliations

1 Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK

2 Department of Microbiology Surveillance and Research, Statens Serum Institut, 5 Artillerivej, DK 2300 Copenhagen S, Denmark

3 Pathogen Genomics Team, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK

4 Streptococcus Laboratory, Centers for Disease Control and Prevention, 1600 Clifton Rd, Atlanta, Georgia, 30333, USA

5 Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Sandringham, Johannesburg 2131, South Africa

6 Department of Microbiology, Bellvitge Hospital-CIBERes-IDIBELL-UB, Feixa Llarga s/n, 08907 Barcelona, Spain

7 Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA

8 Clinical Microbiology Department, Landspitali University Hospital and University of Iceland, 101 Reykjavik, Iceland

9 Hubert Department of Global Health Epidemiology, Rollins School of Public Health, 1518 Clifton Road NE, Atlanta, GA 30322, USA

10 Department of Microbiology, University Kaiserslautern, Paul-Ehrlich-Straße, 67663 Kaiserslautern, Germany

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Genome Biology 2012, 13:R103  doi:10.1186/gb-2012-13-11-r103

Published: 16 November 2012

Additional files

Additional file 1:

Tables S1 to S3. Lists of the pbp allele sequence regions that were identical or highly similar to those of the PMEN1 reference strain.

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Additional file 2:

Tables S4 and S5. Details of the regions of the CGSP14 and PMEN3 genomes, respectively, that were identified as putatively recombinogenic and acquired from PMEN1.

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Additional file 3:

Table S6. More information (for example, serotype and penicillin susceptibility) about the isolates for which whole-genome sequences were analyzed in this study.

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Additional file 4:

Supporting Results and Methods. More information about MLST and pbp diversity, the imported regions of CGSP14 and PMEN3, coding sequences found in both PMEN1 and isolates of CC66, outlier isolates highlighted in Figure 4 and methodological details related to whole-genome sequence assemblies.

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Additional file 5:

Figure S2. Depiction of the results of a Genome Comparator analysis of 104 pneumococcal genomes compared to the TIGR4 reference genome.

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Additional file 6:

Table S7. Summary of the 442 isolates included in this study, stratified by era of isolation.

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Additional file 7:

Table S8. Details of the primers used for PCR and conventional sequencing of regions of pbp2x, pbp1a and pbp2b.

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Additional file 8:

Table S9. Details of the metadata for the 442 isolates included in this study.

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Additional file 9:

Figure S3. A variable site map of one PMEN3 putative imported region and flanking regions.

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