Fig. 3: Population structure, virulence, and antimicrobial resistance gene profiles of IE Streptococcus mitis in context of global isolates.

a Frequency plot of the STs identified across the combined IE and global S. mitis dataset. The plot shows that the UK IE S. mitis belonged to unique STs, however, two isolates isolated in 2014 and 2016 belonged to ST30, and another two isolates collected in 2007 and 2015 were assigned to ST36. Multiple carriage isolates belonging to the same ST were largely from a previous study that sampled multiple isolates from individuals³². ST190 had the highest frequency of 23 isolates and was also likely due to sampling from the same individual. b Frequency plot of the GSCs identified across the combined IE and global S. mitis dataset. The plot shows that the UK IE S. mitis belonged to unique GSCs, however, two isolates isolated in 2014 and 2016 belonged to GSC27, and another two isolates collected in 2007 and 2015 were assigned to lineage GSC28. Multiple carriage isolates belonging to the same GSC were largely from a previous study that sampled multiple isolates from individuals³². GSC1 had the highest frequency of 23 isolates and was also likely due to sampling from the same individual. c Maximum-likelihood phylogeny of IE and global S. mitis is built using 473,175 SNPs out of 1,237,113 core nucleotide bases. The coloured tips of the phylogeny and the first horizontal metadata bar show the isolation condition of the S. mitis isolates. From the second to fifteenth horizontal bars, the isolate metadata shows the IE UK S. mitis isolates, the GSC lineage, and virulence genes. The virulence gene matrix has 7 capsule genes (cps4A – cps4F), autolysins (lytA and lytC), and pneumolysin (ply) genes. The phylogeny shows clustering of capsule genes among isolates in one region of the phylogeny, predominantly UK IE isolates. The last four horizontal bars show antimicrobial resistance (AMR) gene matrices. From the first to fourth matrix bar are the presence or absence of chloramphenicol (cat), macrolide (ermB and mefA), and tetracycline (tetM) genes. Source data are provided as a Source Data file.