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Introduction: As the causative agent of meningitis, Neisseria meningitidis has different serogroups. The purpose of this study was to investigate the molecular properties of N. meningitidis strains among Iranian cases. Methods: 450 samples were collected from children under 5 years of age. Detection of Neisseria genus was done by phenotypic and genotypic methods. Multiplex PCR was used to identify the serogroups of N. meningitides. The sequencing of variable regions of porA gene was performed for detection of the subserogroups. Results: From 137 (30.44%) Neisseria isolates, 4 isolates (0.88%) belonged to N. meningitidis and 133 isolates (29.55%) belonged to other species. Multiplex PCR results showed that one isolate belonged to serogroup A while 3 belonged to serogroup B. The analysis of amplified VR1 and VR2 variable regions of porA showed 100% identity of the serogroup A strain with strain BZ83N and the serogroup B strains with strain 528 of N. meningitidis . In accordance with other findings in Asia, serogroups A and B were the most prevalent serogroups of N. meningitidis. Sequencing of variable regions of porA could identify the subserogroups of the isolates. Conclusion: sequencing of porA could be a valuable method for identification of N. meningitidis strains to be used in epidemiological studies as well as improved vaccine designs.

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