Abstract
Alleles of the vacuolating cytotoxin gene (
vacA
) of
Helicobacter pylori
vary between strains, particularly in the region encoding the signal sequence (which may be type s1 or s2) and the midregion (which may be type m1 or m2). Using a PCR-based typing system developed in the United States, we showed that 36 strains from Asia and South America were all
vacA
signal sequence type s1; 3 were midregion type m1 and 11 were m2, but 22 could not be typed for the
vacA
midregion. All strains possessed
cagA
(cytotoxin-associated gene A), another virulence marker.
vacA
nucleotide sequence analysis showed that midregion typing failure was due to base substitutions at the primer annealing sites. Using the new sequence data, we developed two new PCR-based
vacA
midregion typing systems, both of which correctly typed 41 U.S. strains previously typed by the old system and successfully typed all 36 of the non-U.S. strains. All previously untypeable strains were
vacA
m1, other than one m1/m2 hybrid. In summary, we describe and validate a simple PCR-based system for typing vacuolating cytotoxin (
vacA
) alleles of
H. pylori
and show that this system correctly identifies the signal and midregion types of
vacA
in 77 strains from Asia and North and South America.