Additional file 2: Figure S1. of Evolution of mobile genetic element composition in an epidemic methicillin-resistant Staphylococcus aureus: temporal changes correlated with frequent loss and gain events JamrozyDorota CollFrancesc MatherAlison HarrisSimon HarrisonEwan MacGowanAlasdair KarasAndreas ElstonTony Estée TörökM. ParkhillJulian PeacockSharon 2017 Prevalence of isolates representing CC5, CC22 and CC30 between 2001 and 2010. Shown as % of S. aureus isolates in each year. Error bars show 95% confidence intervals. Figure S2 (A, B). Unrooted maximum likelihood tree of S. aureus isolates belonging to CC22 (A) or CC30 (B). Both lineages were composed predominantly of EMRSA isolates; red branches show clades representing the EMRSA-15 (A) and EMRSA-16 (B) clones. Figure S3. Relationship between the probability of MGE carriage and the root-to-tip distance in MRSA CC22 isolates. Curve based on prediction from logistic regression model. Figure S4. Annual macrolide prescription items in England between 2001 and 2010. A prescription item refers to a single item prescribed on a prescription form. Copyright NHSBSA 2013. This information is licenced under the terms of the Open Government Licence: http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3 . Figure S5. Prevalence of P1-ermC carriage and erythromycin resistance in MRSA CC22 isolates between 2001 and 2010. Shown as % of MRSA CC22 isolates in each year. Figure S6. Median of pairwise SNP distances between MRSA CC22 isolates each year between 2001 and 2010. (DOCX 1420 kb)