Pertussis or whooping cough is a worldwide infection of the upper respiratory tract with some serious clinical symptoms caused by the exclusivelyhuman pathogenic Gram-negative bacterium Bordetella pertussis. BasicallyB. pertussisis described as very monomorphic.However,mutations occurin form of single nucleotide polymorphisms,especially in virulence genes that increase itsadaptability andpathogenicity.A central question in many studiesis, whereby these mutations have arisen and whether it might have come to a vaccine-driven selection, as new identified strains differ genetically from parts of B. pertussisused for vaccine production.Based on a previous characterisation of the virulence genes of Australian B. pertussisisolates the aimof this work was the genotyping of five SNPs within these genes of 86 field isolates, which were collected between 2004 and 2008 in a hospital in Linz (Upper Austria). Specifically, the genotypic affiliation of these isolates to thelaboratory-cultured strain Tohama I and theAustralian strain L517 was investigated. The SNP analysis forthe genes bvgS, fimDand ptxAwas performed usingARMS-qPCR and the SNP in ptxBand tcfAwas determined by PIRA-PCR.Three samples could be genotyped at five loci, and eighty-three samples at least at one locus. In eighty-threesamples a primary affiliation tothe genotype of L517 strain wasfound inthe genesbvgS, fimD, ptxAand ptxBand in foursamples for the tcfAgene the genotype of the Tohama I strainwas demonstrated. Based on the novel combination of the virulence alleles anew haplotype was identified in Austria.Sanger sequencing of a single sample was used to confirm the finding of the novel haplotype termed LINZ09.As a new infection trend emerges in an older section of the population and vaccination appears less effective, because B. pertussisgenetically adapts to its environment and the human host, further research on the shelves typing Bordetellais relevant to adjust antimicrobialtreatments tocirculating strains and to develop possible alternative treatment options to combat antibiotic resistance.