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Journal of Clinical Microbiology, September 1999, p. 2979-2982, Vol. 37, No. 9
0095-1137/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.

Simple and Accurate PCR-Based System for Typing Vacuolating Cytotoxin Alleles of Helicobacter pylori

J. C. Atherton,1,2,* T. L. Cover,3 R. J. Twells,2 M. R. Morales,3,dagger C. J. Hawkey,1 and M. J. Blaser3

Department of Medicine, Division of Gastroenterology, University Hospital,1 and Institute of Infections and Immunity,2 University of Nottingham, Nottingham, United Kingdom, and Department of Medicine, Division of Infectious Diseases, Vanderbilt University School of Medicine, and Veterans Affairs Medical Center, Nashville, Tennessee3

Received 30 December 1998/Returned for modification 19 March 1999/Accepted 4 June 1999

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.

* Corresponding author. Mailing address: Department of Medicine, Division of Gastroenterology, University Hospital, Nottingham NG7 2UH, United Kingdom. Phone: 44 115 9249924. Fax: 44 115 9422232. E-mail: John.Atherton{at}nottingham.ac.uk.

dagger Present address: Facultad de Medicina, Universidad Nacional Autonoma de Mexico, Mexico City, Mexico.

Journal of Clinical Microbiology, September 1999, p. 2979-2982, Vol. 37, No. 9
0095-1137/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.


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