Fig. 2. Pangenome Neighbour Identification for Bacterial Populations (PANINI)²⁸ networks on E. faecalis pangenome depict isolates of different origins distributed across the clade structure and embedded within the same, clearly defined extant clusters.

a PANINI network depicts accessory clusters predominantly following the designated Population Partitioning Using Nucleotide K-mers (PopPUNK; PP)¹⁹ clustering, with each node representing a single isolate (n = 2027), each group of attached nodes largely representing a PANINI cluster (n = 70), and each colour indicating a separate PP cluster (n = 173). b Hospitalised patient isolates shown in red and other isolation sources in grey. c Wild bird isolates shown in dark blue and other isolation sources in grey. d Old isolates of human origin shown in black and other isolation sources in grey. The illustration was created using Microreact⁷⁷. Source data are provided as a Source Data file.