In the last decade, the incidence of invasive meningococcal disease (IMD) in 
Croatia remained stable at approximately 1 case per 100 000 inhabitants, 
affecting mainly children aged ≤5 years. We report the molecular 
characterization of meningococci causing IMD occurring from June 2009 to January 
2014 in Croatia. Genomic DNA from 50 clinical isolates was analysed for 
serogroup, multilocus sequence typing and allele type of the two outer membrane 
protein genes, porA and the iron-regulated fetA. Furthermore, 22 of them were 
characterized by using whole-genome sequencing to define the meningococcal 
vaccine four-component meningococcal serogroup B (4CMenB) antigen genes factor 
H-binding protein (fHbp), Neisseria heparin-binding antigen (nhba) and Neisseria 
adhesin A (nadA) and the antimicrobial target resistance genes for penicillin 
(penicillin binding protein 2, penA), ciprofloxacin (DNA gyrase subunit A, gyrA) 
and rifampicin (β-subunit of RNA polymerase, rpoB). The Etest was used to 
phenotypically determine the antimicrobial susceptibility of isolated 
meningococci. The main serogroup/clonal complex combinations were MenB cc41/44, 
MenC/cc11, MenW/cc174 and MenY/cc23. PorA P1.7-2, FetA F5-5 and F1-5 were the 
most represented through the serogroups. Meningococci with decreased 
susceptibility to penicillin (38.9 %) and one strain resistant to ciprofloxacin 
were identified. Forty-two percent of MenB showed the presence of at least one 
of the 4CMenB vaccine antigens (fHbp, NHBA, NadA and PorA). Our findings 
highlight the genetic variability of meningococci causing IMD in Croatia, 
especially for the serogroup B. Molecular-based characterization of meningococci 
is crucial to enhance IMD surveillance and to better plan national immunization 
programmes.