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A large pertussis epidemic occurred between 2008 and 2010 in Japan. To investigate epidemic strains, we analyzed 33  Bordetella pertussis  isolates from the epidemic period by sequencing virulence-associated genes ( fim3 ,  ptxP ,  ptxA , and  prn ) and performing multilocus variable-number tandem repeat analysis (MLVA), and compared these results with those of 101 isolates from non-epidemic, earlier and later time periods. DNA sequencing of the  fim3  allele revealed that the frequency of  fim3B  was 4.3%, 12.8%, 30.3%, and 5.1% within isolates in 2002–2004, 2005–2007, 2008–2010, and 2011–2012, respectively. The isolation rate of the  fim3B  strain therefore temporarily increased during the epidemic period 2008–2010. In contrast, the frequencies of the virulence-associated allelic variants,  ptxP3 ,  ptxA1 , and  prn2 , increased with time during overall study period, indicating that these variants were not directly involved in the occurrence of the 2008–2010 epidemic. MLVA genotyping in combination with analysis of allele types showed that the prevalence of an MT27d strain temporarily increased in the epidemic period, and that this strain carried virulence-associated allelic variants ( fim3B ,  ptxP3 ,  ptxA1 , and  prn2 ) also identified in recent epidemic strains of Australia, Europe, and the US. Phenotypic analyses revealed that the serotype Fim3 strain was predominant (≥87%) during all the periods studied, and that the frequency of adhesion pertactin (Prn) non-expressing  B. pertussis  decreased by half in the epidemic period. All MT27d strains expressed Prn and Fim3 proteins, suggesting that  B. pertussis  MT27d strains expressing Prn and Fim3B have the potential to cause large epidemics worldwide.

Genetic Analysis of Bordetella pertussis Isolates from the 2008–2010 Pertussis Epidemic in Japan