Metronidazole resistance in Helicobacter pylori has been attributed to mutations in rdxA or frxA. Insufficient data correlating RdxA and/or FrxA with the resistant phenotype, and the emergence of resistant strains with no mutations in either rdxA or frxA, indicated that the molecular basis of H. pylori resistance to metronidazole required further characterization. The rdxA and frxA genes of four matched pairs of metronidazole-susceptible and -resistant strains were sequenced. The resistant strains had mutations in either rdxA, frxA, neither gene, or both genes. The reduction rates of five substrates suggested that metabolic differences between susceptible and resistant strains cannot be explained only by mutations in rdxA and/or frxA. A more global approach to understanding the resistance phenotype was taken by employing two-dimensional gel electrophoresis combined with tandem mass spectrometry analyses to identify proteins differentially expressed by the matched pair of strains with no mutations in rdxA or frxA. Proteins involved in the oxireduction of ferredoxin were downregulated in the resistant strain. Other redox enzymes, such as thioredoxin reductase, alkyl hydroperoxide reductase, and superoxide dismutase, showed a pI change in the resistant strain. The data suggested that metronidazole resistance involved more complex metabolic changes than specific gene mutations, and they provided evidence of a role for the intracellular redox potential in the development of resistance.Metronidazole (Mtr) is an important component of therapeutic regimens that currently are used to treat many microbial infections. Metronidazole is considered a prodrug whose uptake and activation requires intracellular reduction, resulting in the production of cytotoxic short-lived radicals and other reactive species (29). 5-Nitroimidazole is activated via interactions with redox systems capable of reducing the low-potential (Ϫ415 mV) nitro group in position 5 of the imidazole ring (29). This property makes metronidazole effective against organisms in a low-intracellular-redox state, such as anaerobic bacteria and protozoa, as well as some microaerophiles, such as Campylobacter spp. and Helicobacter pylori (16).Helicobacter pylori is found in the gastric mucous layer or adhering to the epithelial lining of the human stomach and is one of the most prevalent infections in humans (1,19,39). The frequent use of metronidazole has resulted in increased resistance to the antibiotic by H. pylori. The emergence of resistant isolates that do not respond to the drug fostered an interest in understanding the primary causes of resistance to metronidazole in this bacterium. Extensive investigations of H. pylori established that the main causes of metronidazole resistance are mutations in the gene rdxA or frxA (6,7,14,15). However, insufficient data correlating the oxygen-insensitive nitroreductase RdxA and/or the NAD(P)H flavin oxidoreductase FrxA with the resistant phenotype and the fact that a small percentage of resistant strains do not have mutat...