Genotyping and whole genome sequencing
Isolates were genotyped by MIRU-VNTR, based on a 24 loci-set described elsewhere (Supply et al., 2006). An additional set of four hypervariable loci was added for the Beijing isolates (Allix-Beguec et al., 2014). WGS on the Illumina MiSeq platform, mapping, and single nucleotide polymorphism (SNP) calling was performed as detailed elsewhere (Dominguez et al., 2019). The median-joining network was constructed from the SNP matrix generated for each case using the NETWORK 5.0.0.1 program Sequences were deposited in EMBL-EBI database (Accession numbers PRJEB39699, PRJEB23681 and PRJEB29408).