Fig. 1

Synapomorphic polymorphisms by functional category and isolate subgroup. a Virulence and adaptation, b Regulatory and information pathways, c Conserved proteins without known function, d Cell wall and lipid metabolism, e Intermediary metabolism and respiration. L4 includes all (n = 47) Lineage 4 isolates included in this study, NYC-NJ (N = 32) includes L4 isolates collected in New York City or New Jersey, USA, including the S75 outbreak cluster, and S75 (N = 9) includes isolates belonging the New Jersey outbreak cluster described in the text. Genes carrying diagnostic SNPs with known functions in virulence, growth, and/or adaptation are listed above each column, and of these genes, those with non-synonymous polymorphisms are highlighted in yellow. The number of total diagnostic SNPs unique to S75 (which includes those unique to L4 and NYC-NJ) are listed in the third column