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).