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Objectives This study sought to determine the genotypes of circulating Bordetella pertussis , the causative agent of pertussis, in Cambodia by direct molecular typing of clinical specimens. Methods DNA extracts from nasopharyngeal swabs obtained from 82 pertussis patients in 2008–2016 were analyzed by multilocus variable-number tandem repeat analysis (MLVA). B. pertussis virulence-associated allelic genes ( ptxA , prn , and fim3 ) and the pertussis toxin promoter ptxP were also investigated by DNA sequence-based typing. Results Forty-four DNA extracts (54%) yielded a complete MLVA profile, and these were sorted into 8 MLVA types (MT18, MT26, MT27, MT29, MT43, MT72, MT95, and MT200). MT27 and MT29, which are common in developed countries, were the predominant strain types (total 73%). The predominant profile of virulence-associated allelic genes was the combination of ptxP3 / ptxA1 / prn2 / fim3A (48%). MT27 strains were detected during the entire study period, whereas MT29 strains were only found in 2014–2016. Conclusions The B. pertussis population in Cambodia, where a whole-cell pertussis vaccine (WCV) has been continuously used, resembled those observed previously in developed countries where acellular pertussis vaccines are used. Circulating B. pertussis strains in Cambodia were distinct from those in other countries using WCVs. [ABSTRACT FROM AUTHOR]