design: Pure Bacteria culture were isolated and DNA was extracted using Zybio nucleic acid extraction kit (Chongqing, China) according to the manufactures instruction for bacteria. DNA was quantified using a 1X dsDNA High Sensitivity assay (Invitrogen) in a Qubit fluorometer (ThermoFisher Scientific). The library preparation protocol followed the CDC Standard Operating Procedure (SOP) for PulseNet Nextera XT library preparation.The Sequencing libraries were prepared using the Nextera XT preparation Kit (Illumina, USA). Libraries quality was accertained using the Qubit fluorometer (ThermoFisher Scientific) and the Bioanalyzer (Agilent 2100, Germany) for fragment size estimation. Libraries were subsequently pooled and sequenced on the Illumina NextSeq 1000/2000 platforms.