All 1,143 strains were tested by MLVA, MLST, and antigen sequence typing.
Both neutral typing methods (MLST and MLVA) provided higher discrimination than antigen sequence typing.
In this work, 466 Bordetella pertussis isolates collected in the period 1998 2012 from 13 European countries were characterised by multi-locus antigen sequence typing (MAST) of the pertussis toxin promoter (ptxP) and of the genes coding for proteins used in the ACVs: pertussis toxin (Ptx), pertactin (Prn), type 2 fimbriae (Fim2) and type 3 fimbriae (Fim3).
Moreover, the higher diversity unveiled by neutral typing techniques compared with antigen sequence typing could suggest positive selection for strains achieving immune escape because of their antigenic profile.
We characterized the isolates by using multilocus variable-number tandem repeat analysis (MLVA) and multiple antigen sequence typing (MAST) to partially sequence the genes encoding pertactin (prn), B. pertussis toxin S1 subunit (ptxA, also designated ptxS1), B. pertussis toxin promoter (ptxP), and tracheal colonization factor A (tcfA).
The combination of antigen sequence typing of PorA and FetA together with MLST seems to provide a robust framework, which can be complemented by sequence typing of other antigens and measurement of their expression.
Nucleotide sequence-based typing, especially MLST and antigen sequence typing (AGST), have established that these genotypes correspond to certain genealogies, known as the 'hyperinvasive lineages' [ 21].
MLST (7 ) and antigen sequence typing of PorA (23 ) and FetA (24 ) were performed according to published protocols.
One method, based on the nucleotide sequence fragments from two gonococcal antigen genes under diversifying immune selection: por and tbpB (N. gonorrhoeae multi antigen sequence typing, NG-MAST) [ 14, 15], provides a high level of discrimination.
