Helicobacter pylori is a human-pathogenic bacterial species that is subdivided geographically, with different genotypes predominating in different parts of the world. Here we test and extend an earlier conclusion that metronidazole (Mtz) resistance is due to mutation in rdxA (HP0954), which encodes a nitroreductase that converts Mtz from prodrug to bactericidal agent. We found that (i) rdxA genes PCR amplified from 50 representative Mtz r strains from previously unstudied populations in Asia, South Africa, Europe, and the Americas could, in each case, transform Mtz s H. pylori to Mtz r ; (ii) Mtz r mutant derivatives of a cultured Mtz s strain resulted from mutation in rdxA; and (iii) transformation of Mtz s strains with rdxA-null alleles usually resulted in moderate level Mtz resistance (16 g/ml). However, resistance to higher Mtz levels was common among clinical isolates, a result that implicates at least one additional gene. Expression in Escherichia coli of frxA (HP0642; flavin oxidoreductase), an rdxA paralog, made this normally resistant species Mtz s , and frxA inactivation enhanced Mtz resistance in rdxA-deficient cells but had little effect on the Mtz susceptibility of rdxA ؉ cells. Strains carrying frxA-null and rdxA-null alleles could mutate to even higher resistance, a result implicating one or more additional genes in residual Mtz susceptibility and hyperresistance. We conclude that most Mtz resistance in H. pylori depends on rdxA inactivation, that mutations in frxA can enhance resistance, and that genes that confer Mtz resistance without rdxA inactivation are rare or nonexistent in H. pylori populations.Helicobacter pylori is a gram-negative microaerophilic bacterium that chronically infects human gastric epithelial cell surfaces and the overlying gastric mucin, a niche that few if any other microbes can occupy. It is carried by more than half of all people worldwide and is an important human pathogen: a major cause of peptic ulcer disease, and a contributor to other illnesses, ranging from childhood malnutrition to gastric cancer, and to increased susceptibility to other food-and waterborne pathogens (7,8,32,38,47). There is great intrinsic and public health interest in fully elucidating H. pylori's metabolic pathways and how H. pylori maintains its redox balance during microaerobic growth. Such knowledge should help us to understand the extraordinary chronicity of H. pylori infection and factors that determine whether a given infection will be benign or virulent, elucidate mechanisms of drug susceptibility and resistance, and identify potential targets for new effective antimicrobial agents.Here we focus on mechanisms of susceptibility and resistance of H. pylori to metronidazole (Mtz), a synthetic nitroimidazole that is a key component of popular and affordable anti-H. pylori therapies worldwide and that is also widely used against various anaerobic and parasitic infections (13,36,45). Resistance to Mtz is common among H. pylori strains, with frequencies among clinical isolates ranging from 10 ...

We developed a microarray hybridization-based method, 'comparative genome sequencing' (CGS), to find mutations in bacterial genomes and used it to study metronidazole resistance in H. pylori. CGS identified mutations in several genes, most likely affecting metronidazole activation, and produced no false positives in analysis of three megabases. We conclude that CGS identifies mutations in bacterial genomes efficiently, should enrich understanding of systems biology and genome evolution, and help track pathogens during outbreaks.

had interpreted that resistance resulted from inactivation either of frxA or rdxA. These two interpretations were tested here. Resistance was defined as efficient colony formation by single cells from diluted cultures rather than as growth responses of more dense inocula on MTZ-containing medium. Tests of three of Kwon's Mtz s strains showed that each was type II, requiring inactivation of both rdxA and frxA to become resistant. In additional tests, derivatives of frxA mutant strains recovered from MTZ-containing medium were found to contain new mutations in rdxA, and frxA inactivation slowed MTZ-induced killing of Mtz s strains. Northern blot analyses indicated that frxA mRNA, and perhaps also rdxA mRNA, were more abundant in type II than in type I strains. We conclude that development of MTZ resistance in H. pylori requires inactivation of rdxA alone or of both rdxA and frxA, depending on bacterial genotype, but rarely, if ever, inactivation of frxA alone, and that H. pylori strains differ in regulation of nitroreductase gene expression. We suggest that such regulatory differences may be significant functionally during human infection.Helicobacter pylori is a genetically diverse bacterial species that chronically infects the stomachs of more than half of all people worldwide. Its long-term carriage is a major cause of chronic gastritis and peptic ulcer disease and is an early risk factor for gastric cancer (for reviews see references 5, 8, 28, and 32). Resistance to metronidazole (MTZ) is common and is important clinically as a primary cause of failure of MTZ-based anti-Helicobacter therapies (for reviews see references 10, 15, and 24). Frequencies of clinical isolates that are MTZ resistant range from only 10% in Japan (25) to 90% or more in India (26), and up to 50% or more of strains in the United States and Western Europe also are resistant (frequency varies among countries) (8, 23). These geographic differences probably reflect frequencies of MTZ use against other, mostly parasitic and anaerobic, infections and thus inadvertent MTZ exposure of resident H. pylori strains. Recent studies have implicated mutations in the chromosomal genes rdxA (HP0954) and frxA (HP0642) in the development of resistance (7,9,14,16,30, 35). These genes encode related nitroreductases that can convert MTZ from a harmless prodrug to products such as hydroxylamine that are both bactericidal and mutagenic (9, 29).There has been disagreement about the quantitative contributions of rdxA and frxA to MTZ susceptibility and resistance. On the one hand, Kwon and associates had concluded that inactivation of either gene by itself could make any typical H. pylori strain resistant to MTZ (Mtz r ) (21), and that following frxA inactivation, growth on MTZ-containing agar was not associated with mutation of rdxA (20). In contrast, we had concluded that rdxA inactivation is usually or always needed for a Mtz s strain to become Mtz r (16,17). Two types of Mtz s strains were distinguished, however, based on relative levels of FrxA nitroreductase...

Tetracycline is useful in combination therapies against the gastric pathogen Helicobacter pylori. We found 6 tetracycline-resistant ( mutants that had acquired mutant rDNA alleles were resistant to tetracycline at levels higher than those to which either parent strain was resistant. Thus, tetracycline resistance in H. pylori results from an accumulation of changes that may affect tetracycline-ribosome affinity and/or other functions (perhaps porins or efflux pumps). We suggest that the rarity of tetracycline resistance among clinical isolates reflects this need for multiple mutations and perhaps also the deleterious effects of such mutations on fitness. Formally equivalent mutations with small but additive effects are postulated to contribute importantly to traits such as host specificity and virulence and to H. pylori's great genetic diversity.

Many Helicobacter pylori genetic studies would benefit from an ability to move DNA sequences easily between strains by transformation and homologous recombination, without needing to leave a conventional drug resistance determinant at the targeted locus. Presented here is a two-gene cassette that can be selected both (i) against, due to a Campylobacter jejuni rpsL gene (dominant streptomycin susceptibility in cells also carrying an rpsL-str r allele), and (ii) for, due to an erm gene (erythromycin resistance). This rpsL,erm cassette's utility was assessed by using it to replace four gene loci (mdaB, frxA, fur, and nikR) in four streptomycin- Genetic studies of the gastric pathogen Helicobacter pylori (21) often entail (i) the construction of cloned DNAs or PCR products containing a drug resistance determinant inserted into or near a gene of interest, (ii) DNA transformation, and (iii) selection for resistant transformants, which arise by homologous recombination and replacement of recipient DNA sequences by corresponding sequences from donor DNA. Although this strategy has been used in hundreds of H. pylori studies, successfully overcoming the rarity of natural transformation events, it becomes seriously limiting or flawed in at least four interesting situations, in each case because transformants retain resistance determinants at targeted loci: (i) if changes at numerous loci in the same strain are needed, e.g., in studies of phenotypes determined by multiple genes with additive or redundant effects (because only a few selectable resistance markers are available for H. pylori); (ii) if donor resistance determinants might affect downstream gene expression, or cellular physiology more generally (e.g., in many cases the resistance enzymes use cellular metabolites to modify antibiotics and thereby confer resistance to them [9]); (iii) if alleles with subtle (e.g., point mutation) differences are to be compared; or (iv) if alleles from many strains are to be studied in a common genetic background. Such limitations can be overcome by using a recipient strain that contains a contraselectable marker at the locus of interest. This allows the desired transformants to be selected by the loss of this recipient marker, thereby bypassing the need for a conventional resistance determinant in donor DNA.Three genes that have been used for contraselection in other systems are thyA (thymidylate requirement; trimethoprim sensitivity) (4, 34), sacB (sucrose sensitivity) (5, 27, 33), and rpsL (streptomycin sensitivity) (25,33). H. pylori is naturally trimethoprim resistant. This could be ascribed to (i) its apparent lack of a thyA gene (based on BLASTP homolog searches [31]); (ii) an intrinsic resistance of its enzyme for reduced folate synthesis, an apparent dihydrofolate reductase-dihydropteroate synthase chimaera (18); and/or (iii) other factors. An early report had indicated that sacB could serve as a contraselectable marker in H. pylori but did not describe the details of efficiency or complications that may have been encounter...