Genomics of Helicobacter Species 91 6 Genomics of Helicobacter Species Zhongming Ge and David B. Schauer Summary Helicobacter pylori was the first bacterial species to have the genome of two independent strains completely sequenced. Infection with this pathogen, which may be the most frequent bacterial infec- tion of humanity, causes peptic ulcer disease and gastric cancer. Other Helicobacter species are emerging as causes of infection, inflammation, and cancer in the intestine, liver, and biliary tract, although the true prevalence of these enterohepatic Helicobacter species in humans is not yet known. The murine pathogen Helicobacter hepaticus was the first enterohepatic Helicobacter species to have its genome completely sequenced. Here, we consider functional genomics of the genus Helico- bacter, the comparative genomics of the genus Helicobacter, and the related genera Campylobacter and Wolinella. Key Words: Cytotoxin-associated gene; H-Proteobacteria; gastric cancer; genomic evolution; genomic island; hepatobiliary; peptic ulcer disease; type IV secretion system. 1. Introduction The genus Helicobacter belongs to the family Helicobacteriaceae, order Campylo- bacterales, and class H-Proteobacteria, which is also known as the H subdivision of the phylum Proteobacteria. The H-Proteobacteria comprise of a relatively small and recently recognized line of descent within this extremely large and phenotypically diverse phy- lum. Other genera that colonize and/or infect humans and animals include Campylobac- ter, Arcobacter, and Wolinella. These organisms are all microaerophilic, chemoorgano- trophic, nonsaccharolytic, spiral shaped or curved, and motile with a corkscrew-like motion by means of polar flagella. Increasingly, free living H-Proteobacteria are being recognized in a wide range of environmental niches, including seawater, marine sedi- ments, deep-sea hydrothermal vents, and even as symbionts of shrimp and tubeworms in these environments. To date, genome sequencing has been done on only a handful of H-Proteobacteria (Table 1). At the time of writing, six H-Proteobacteria genomes have been completed and six more are in progress (Table 2). 2. Diversity in the Genus Helicobacter 2.1. Helicobacter pylori The genus Helicobacter comprises a remarkable group of bacterial species that thrive in the surface mucus overlaying epithelia in the gastrointestinal tract of humans and animals. Bacteria resembling the Helicobacter species were first observed in gastric From: Bacterial Genomes and Infectious Diseases Edited by: V. L. Chan, P. M. Sherman, and B. Bourke © Humana Press Inc., Totowa, NJ 91 92 GeandSchauer Table 1 Characteristics of H-Proteobacteria With Completed or in Progress Genome Sequences From the NCBI Entrez Genome Projecta Organism Shape Motility Oxygen req. Habitat Disease Campylobacter coli Spiral Yes Microaerophilic Host-associated; intestine Enteritis and septicemia RM2228 (humans and animals) Campylobacter fetus Spiral Yes Microaerophilic Host-associated; intestine, Infertility, abortions, septicemia, reproductive tract, bloodstream meningitis (humans and animals) Campylobacter jejuni Spiral Yes Microaerophilic Host-associated; intestine Enteritis (humans and animals) RM1221 C. jejuni subsp. Spiral Yes Microaerophilic Host-associated; intestine Enteritis (humans and animals) jejuni NCTC 11168 Campylobacter lari Spiral Yes Microaerophilic Host-associated; intestine, Gastroenteritis and diarrhea 92 RM2100 bloodstream (humans and animals) Campylobacter Spiral Yes Microaerophilic Host-associated; intestine, Gastroenteritis and diarrhea upsaliensis RM3195 bloodstream (humans and animals) Helicobacter hepaticus Spiral Yes Microaerophilic Host-associated; intestine, liver, Hepatitis, liver tumors, typhlitis, ATCC 51449 biliary tract intestinal cancer (mice) Helicobacter pylori Spiral Yes Microaerophilic Host-associated; stomach Gastritis, peptic ulcer disease, 26695 gastric cancer (humans) H. pylori J99 Spiral Yes Microaerophilic Host-associated; stomach Gastritis, peptic ulcer disease, gastric cancer (humans) Nautilia sp. Am-H Rod Yes Anaerobic Environmental Not pathogenic Thiomicrospira Spiral No Anaerobic Environmental Not pathogenic denitrificans Wolinella succinogenes “Spiral, Yes Microaerophilic Host-associated; stomach Not pathogenic DSM 1740 curved” (bovine rumen) aBased on prokaryotic genome projects in the NCBI Entrez Genome Project database (http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi). Genomics of Table 2 H-Proteobacteria Genome Sequencing Projects From the NCBI Entrez Genome Projecta Virulence determinants Percent Organism Sizeb GC ORFsc CDTd VacA CagA Ure CiaB T4SS GenBank Released Center Campylobacter 1.78 31% 1838 Yes No No No Yes No f CP000025 1/7/05 TIGR Helicobacter jejuni RM1221 C. jejuni subsp. 1.64 31% 1654 Yes No No No Yes No f AL111168 2/25/00 Sanger Institute jejuni NCTC 11168 Helicobacter 1.8 36% 1875 Yes No No Yes Yes HHG1 AE017125 6/18/03 University hepaticus of Wuerzburg Species 93 ATCC 51449 Helicobacter 1.67 39% 1590 No Yes Yes Yes No cag AE000511 8/7/97 TIGR pylori 26695 H. pylori J99 1.64 39% 1495 No Yes Yes Yes No cag AE001439 1/29/99 ASTRA Wolinella 2.11 48.5% 2046 No No No No Yes Yes BX571656 9/23/03 Max Planck 93 succinogenes Institute DSM 1740 Campylobacter 1.86e 31.1% – – – – – – – – In progress TIGR coli RM2228 Campylobacter 1.5e 40% – – – – – – – – In progress IIB-UNSAM fetus Campylobacter 1.56e 29.6% – – – – – – – – In progress TIGR lari RM2100 Campylobacter 1.77e 34.3% – – – – – – – – In progress TIGR upsaliensis RM3195 Nautilia sp. Am-H – – – – – – – – – – In progress TIGR Thiomicrospira – 36% – – – – – – – – In progress DOE Joint denitrificans Genome Institute a Based on prokaryotic genome projects in the NCBI Entrez Genome Project database (http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi). b Genome size, MB. c Predicted number of open reading frames. d Cytolethal distending toxin. e Estimated. f Other strains contain a type IV secretion system on the pVir plasmid. 94 Ge and Schauer mucosa around the turn of the last century (for review see ref. 1). These early morpho- logical observations stood in contrast to the widely held belief that the stomach was essentially sterile by virtue of the low pH of gastric acid. Some 100 yr later, Marshall and Warren described spiral-shaped bacteria in biopsy specimens of human gastric mucosa, successfully cultured and isolated the organisms, and speculated (correctly) that the bacteria caused chronic gastritis and peptic ulcer disease (2). Originally believed to be Campylobacter species, these organisms were subsequently recognized to belong to a distinct taxon, and were ultimately named Helicobacter pylori, the type species for the new genus (3). It is now generally accepted that H. pylori infection is the most common bacterial infection worldwide, and that infection is typically acquired during childhood. All infected individuals develop chronic gastritis, and remain persistently infected despite a robust immune response (for reviews see refs. 4 and 5). The intense interest in H. pylori pathogenesis is owing to the fact that it is the major causative fac- tor in peptic ulcer disease (6), and is strongly associated with the development of gas- tric adenocarcinoma (leading to its classification as a definite human carcinogen [7]), as well as mucosa-associated lymphoid tissue (MALT) lymphoma (8). 2.2. Other Gastric Helicobacter Species In addition to H. pylori, there are five named, two proposed, and three uncultured Helicobacter species that have been identified in the stomach of different animal species (for review see ref. 1). Helicobacter mustelae causes gastroduodenal disease in its natu- ral host the ferret (3), and provided the first animal model system that allowed for the study of host-to-host transmission, chronic gastritis, immunity, eradication, and candi- date bacterial virulence determinants (using isogenic mutants) of a gastric Helicobacter species. Helicobacter felis naturally infects dogs and cats (9). It is probably not the most common gastric Helicobacter species in these hosts, and it is not clear how impor- tant it is as a cause of canine and feline gastroduodenal disease, but it was fortuitously found to readily infect the stomach of laboratory mice (for review see ref. 10). The rodent model of H. felis has been extensively utilized to investigate chronic gastritis, gastric atrophy (parietal cell loss), vaccine responses, and immunopathogenesis, as well as gastric neoplasia, including adenocarcinoma in C57BL/6 and hypergastrinemic INS-GAS mice, and MALT lymphoma in BALB/c mice (for review see ref. 11). Helico- bacter bizzozeronni (12) and Helicobacter salomonis (13) have been isolated from the stomach of dogs, and together with H. felis form a cluster of three closely related species. Helicobacter acinonychis (14), formerly known as H. acinonyx, was originally isolated from captive cheetahs, and appears to contribute to clinically significant gastroduodenal disease in these and other big cats. “Helicobacter suncus” isolated from Asian house (musk) shrews (15) and “Helicobacter cetorum” isolated from wild and captive dolphins and a beluga whale (16) are species that have been proposed but not yet validated. Perhaps the most commonly observed bacteria in the stomach of animals with natu- rally occurring Helicobacter species infections are larger than and more tightly coiled than H. pylori. Similar organisms are infrequent causes of human infection. These organisms are uncultured, morphologically indistinguishable,