Abstract: ObjectiveTo analyze genetic characteristics of a Bordetella pertussis strain isolated in Guangdong Province.MethodsBordetella pertussis strain isolated in Guangdong Province in 2017 (BP_GD2017) was analyzed by whole genome sequencing. Four antigenic genes of pertussis toxin Sl subunit(ptxSl)，pertactin (prn), fimbriae 2(fim2) and fimbriae 3(fim3) were compared with those of the isolates in GenBank and the isolate CS which was used in the production of pertussis vaccine in China．The wg-SNPs method was also applied to determine the genetic evolution with 31 strains available from NCBI genome database. ResultsThe genome of BP_GD2017 has a genome size of 3.64 MB, G+C content of 67.74%, and three rRNA operons, 5S, 16S and 23S, 46 tRNAs. The genome structure and characteristics were similar to those of the Bordetella pertussis genome isolated from the vaccine strain CS strain in China and other regions and time. BP_GD2017 belonged to ptxS1A type and prn2 type, different from the CS vaccine strains. Its amino acid sequences of the fim2 and fim3 genes were identical with the CS vaccine strains. The phylogenetic trees showed the BP_GD2017 was clustered into the evolutionary branch with other strains prevalent in recent years, while in different evolutionary branch with the CS vaccine strains. ConclusionThe Bordetella pertussis strain isolated in Guangdong was different from the CS vaccine strains in ptxS1 and prn antigenic genes, and also changed in genetic evolutionary branch, which provide support for molecular epidemiology research and vaccine development of pertussis in China.