FIG. 1.

Genomic differences between paired sequential isolates of H. pylori. The line marked “consensus” represents genes present in both strains. Genes and/or sequences only present in one strain are indicated above and below the consensus lines. Mosaic sequences are indicated in red, the coding sequence is shadowed in dark gray, and the noncoding sequence is shown in light gray. (A) Loss of the complete cag PAI in strains NQ315/1712. The cag PAI was deleted at a 31-bp repeat. The sequences flanking the repeats were identical in both strains. (B) Partial loss of the cag pathogenicity island in the LSU1062 pair. The earlier strain contained an IS606 element at the 3′ end of the cag PAI. The later strain lost half of the 5′ end of gene HP0527, genes HP0528 to -0548, and most of the IS606 element. See the text for details. (C) Uptake or loss of the restriction-modification system HpyAIV in strains LSU1016. The RM system occurs in place of a putative open reading frame of unknown origin (green; the orf gene is indicated by an arrow). The genome alteration was mediated by a recombination event. (D) Incorporation and/or loss of a putative iron binding protein (ceuE) gene in NQ315/1712. The change in copy number of the ceuE gene was mediated by recombination. (E) Partial loss of pseudogenes (marked by asterisks) HP0903/0904 in strains LSU1040. The earlier strain contained a partially deleted gene (HP0903) and a complete gene (HP0904), whereas the deletion of gene HP0903 was longer in the later strain and included part of gene HP0904. The sequence showed a recombination event of at least 600 bp in gene HP0904. The sequence of the later strain was 1,000 bp shorter than for the earlier strain.