Multilocus sequence typing and repetitive element-based polymerase chain reaction analysis of Neisseria meningitidis isolates in Brazil reveal the emergence of 11 new sequence types genetically related to the ST-32 and ST-41/44 complexes and high prevalence of strains related to hypervirulent lineages.

Eighty-four strains of Neisseria meningitidis isolated from patients with meningococcal disease in 4 states of Brazil were analyzed by multilocus sequence typing and repetitive element-based polymerase chain reaction (Rep-PCR). The majority of strains analyzed (82%) belonged to 4 hypervirulent lineages, and 11 of 20 new sequence type (STs) characterized were related to hypervirulent lineages. Sequences of fetA and porA genes were analyzed, and the majority were related to profiles present in the ST-32 complex/electrophoretic type (ET)-5 complex. Rep-PCR analysis showed a unique electrophoretic pattern among strains related to hypervirulent lineages. Considering that 81% of the strains were serogroup B and strains belonging to the ST-32/ET-5 complex are genetically related to the Cuban vaccine strain used in a mass vaccination from 1990 to 1994 in Brazil, we believe that this vaccine did not confer effective herd immunity even among the age group within the vaccine showed higher efficacy. Our results once more raise the question about which strains should be used in the development of a new vaccine against N. meningitidis serogroup B.