A Vanishing Food Infrastructure: The Closure of Food Outlets in Flint in a Pandemic Era

Most food access studies focus on large cities, examine traditional grocery stores, and only consider operational food outlets. This siloed approach exposes a gap in food access literature. Therefore, as a part of our assessment of Flint’s food landscape, we examined closed food outlets in the city and surrounding townships. We investigated the relationship between the racial composition of census tracts and the number and type of defunct food outlets identified. We used Data Axle to collect and verify data on open and closed food outlets between September 2020 and December 2021. We made a final verification of the food outlet closures in June 2022. We used ArcGIS 10.8.1 and SPSS Version 28 to map and analyze the data. We used negative binomial regression models to determine differences in the likelihood of having an additional closed food outlet in census tracts with low and high percentages of Black residents. We also investigated the relationship between a census tract’s median income and the likelihood of having an additional closed food outlet. There were 173 closed food outlets; 81 were in Flint, and 92 were in surrounding townships. The most frequently closed food outlets were restaurants; they accounted for 45.1% of the closures. The mean number of closed food venues in census tracts where less than 40% of the residents were Black was 1.5. The mean was similar in census tracts where 40% or more of the residents were Black; it was 1.6. This difference was not significant. However, the median income of a census tract was a significant predictor of the likelihood of having an additional closed food outlet. Every one-thousand-dollar increase in median income resulted in a 2% less likelihood of having an additional closed food outlet. The results of this study show that there is more to the food landscape of a city than its operational food outlets. Focusing exclusively on active food outlets does not accurately depict a city's food infrastructure.

Community Gardens in Michigan: Demographic Attributes of Managers, Neighborhood Characteristics, and the Impacts of a Pandemic

Community gardens are more popular than ever, yet we know little about how leadership structure and neighborhood characteristics relate to programming. Hence, this paper analyzes how the racial/ethnic backgrounds of the community garden leaders are related to the activities the garden undertakes. What types of initiatives do gardens undertake to reduce food insecurity? The paper analyzes how the location of the garden impacts what it does. The article presents novel findings on the impact of leadership and neighborhood characteristics on community garden operations and outcomes. Hence, the essay examines how the race/ethnicity of garden managers and their sex and neighborhood characteristics, such as poverty rate, household income, and racial composition, are related to garden initiatives. Finally, the paper examines how community gardens responded to increased demands for food and services during the Coronavirus Disease 2019 pandemic. We studied 53 community gardens in Michigan from the summer 2020 through the winter 2021. Whites manage 66% (35) of the gardens, while People of Color manage 34% (18). Roughly half of the gardens are managed by males and the remainder by females. The gardens, which lack paid staff, rely heavily on volunteers. Almost 53% of the gardens are in low-income census tracts (with median income of $40,000 or less). During the pandemic, 31% of the gardens reduced their staff, 51.4% had fewer volunteers than in pre-pandemic times, and 51.9% had increased amounts of people seeking food.

Racial, Gender, and Age Dynamics in Michigan's Urban and Rural Farmers Markets: Reducing Food Insecurity, and the Impacts of a Pandemic

In recent decades, the number of farmers markets has increased dramatically across the country. Though farmers markets have been described as White spaces, they can play important roles in reducing food insecurity. It is particularly true in Michigan, where farmers markets were crucial collaborators in pioneering programs such as Double-Up Food Bucks that help low-income residents and people of color gain access to fresh, healthy, locally grown food. This article examines the questions: (1) What are the demographic characteristics of farmers market managers, vendors, and customers? (2) How do these influence market activities? (3) To what extent do farmers markets participate in programs to reduce food insecurity? (4) To what extent do farmers markets serve low-income residents and people of color? And (5) How has the Coronavirus Pandemic (COVID-19) affected farmers' markets? This article discusses the findings of a 2020 study that examined the extent to which Michigan's farmers markets served low-income customers and people of color, and participated in food assistance programs. The study examined 79 farmers markets and found that 87.3% of the farmers market managers are White. On average, roughly 79% of the markets' vendors are White, and almost 18% are people of color. Most of the vendors in the markets participate in nutrition assistance programs. Market managers estimate that about 76% of their customers are White, and about 23% are people of color. Farmers markets operated by people of color attract more customers and vendors of color than those administered by White market managers. Almost half of the farmers markets started operations later than usual in 2020 because of the pandemic. More than a third of the markets reported that their funding declined during the pandemic. Moreover, the number of vendors fell at two-thirds of the markets; customers dipped by more than 40%. On the other hand, the number of people requesting food assistance during the pandemic increased in more than half of the markets.

Understanding the challenges faced by Michigan's family farmers: race/ethnicity and the impacts of a pandemic

Michigan is a critical agricultural state, and small family farms are a crucial component of the state's food sector. This paper examines how the race/ethnicity of the family farm owners/operators is related to farm characteristics, financing, and impacts of the pandemic. It compares 75 farms owned/operated solely by Whites and 15 with People of Color owners/operators. The essay examines how farmers finance their farm operations and the challenges they face doing so. The article also explores how the Coronavirus-19 (COVID-19) pandemic affected farming operations, the financial viability of farms, and how farmers responded to the challenges posed by the pandemic. The study found that People of Color farm owners/operators were younger than White farm owners/operators. The People of Color farm owners/operators tended to manage smaller farms for shorter periods than White farm owners/operators. Though two-thirds of the Farmers of Color owned their farms, they were more financially vulnerable than White farm owners/operators. The farmers studied had difficulty obtaining loans to finance their farms. Farmers reported increasing requests from people for food assistance during the pandemic. Farmers responded to the pandemic by participating in government programs such as the Farm to Families Food Box Program that purchased their produce. It allowed farmers to supply emergency food assistance programs with products from their farms. The products went to families receiving food assistance from soup kitchens, food banks, and other community-based nonprofits.

College Students and Nature: Differing Thoughts of Fear, Danger, Disconnection, and Loathing

Despite the existence of a robust body of research that investigates human-nature connections, few scholars have examined what people tend to ponder when they think of nature. The objective of the study is to find out how college and university students think about nature. The study also seeks to identify which factors are most significant in influencing students' thoughts about nature. This paper analyzes racial, gender, class, and academic differences in the way college students think about nature. The study of 287 American students found that respondents thought about a wide range of concepts and ideas when they contemplate nature. This article focuses on the demographic differences in thoughts about fear, danger, and loathing. This set of ideas has been the subject of scholarly research, and the findings presented herein contribute to this body of scholarship. The paper discusses both descriptive and multivariate techniques that are used to explore the topic. The study found that white students are less likely than racial/ethnic minorities to think about disconnection, predators, getting lost, loathsome or hateful places, fear, and danger when they think of nature. However, the results also show that it would be inaccurate to describe racial/ethnic minorities as universally fearful of and disconnected from nature. Moreover, the paper demonstrates that race is not the only explanatory variable that has significant impacts in multivariate models-the student's academic interest has significant impacts on thoughts about natural hazards, disconnection, predators, human-made hazards, and loathsome or hateful places. Gender, age, parental education, and first-generation college attendance also has significant impacts on the dependent variables.

H. pylori DNA Transformation by Natural Competence and Electroporation

Helicobacter pylori is an important etiological pathogen of human stomach diseases, such as gastritis, peptic ulcer, and gastric carcinoma (1). In the past few years, great progress has been made in the cloning and characterization of H. pylori genes. Success of these studies stems in part from the finding that chromosomal and recombinant plasmid DNA are able to be efficiently transformed into H. pylori cells by natural competence (2-4) and electroporation (3,5). Such techniques allow the transfer of cloned H. pylori genes, manipulated in vitro, which can then shed light on the structural and functional relationships of the genes of interest. In this chapter, we describe the protocols for the isolation of H. pylori chromosomal and plasmid DNA, natural transformation, and electroporation.

Observations on an outbreak of nutritional steatitis (yellow fat disease) in fitch (Mustella putorius furo)

An outbreak of nutritional steatitis in farmed fitch (Mustella putorius furo) caused by feeding high levels of dietary polyunsaturated fat was investigated. The disease affected mainly 13 to 15 week rapidly growing kits; 793 kits were affected and 183 died. The outbreak was quickly controlled by lowering the level of polyunsaturated fat in the diet and administering high doses of vitamin E. Affected animals had severe generalised steatitis characterised grossly by yellow brown granular fat, which histologically consisted of diffusely necrotic adipose tissue heavily infiltrated with macrophages and neutrophils. There were extensive deposits of PAS-positive, fluorescent lipopigment within macrophages and extracellularly throughout the inflamed fat. Affected fitch had normochromic microcytic anaemia, lowered liver iron levels, increased thrombocytes and acute inflammatory leucograms. Skeletal or cardiac myopathy was not observed grossly or histologically in any of the animals examined. The diet contained high levels of polyunsaturated fat (7.7%DM), a high proportion being docosahexaenoic and eicosapentaenoic acids which were derived from the squid component (40%) of the ration. The livers from affected fitch contained correspondingly high levels of polyunsaturated fatty acids. The diet provided 13 mg Vitamin E per fitch daily, which was clearly inadequate considering the high levels of polyunsaturated fat being fed. Liver selenium levels were extremely high as a result of the high selenium levels in the squid portion of the diet.

Clostridium difficile colitis in lung transplantation

PURPOSE

Clostridium difficile colitis (CDC) is the most common nosocomial infection of the gastrointestinal tract in patients with recent antibiotic use or hospitalization. Lung transplant recipients receive aggressive antimicrobial therapy postoperatively for treatment and prophylaxis of respiratory infections. This report describes the epidemiology of CDC in lung recipients from a single center and explores possible associations with bronchiolitis obliterans syndrome (BOS), a surrogate marker of chronic rejection.

METHODS

Patients were divided into those with confirmed disease (CDC+) and those without disease (CDC-) based on positive C. difficile toxin assay. Because of a bimodal distribution in the time to develop CDC, the early postoperative CDC+ group was analyzed separately from the late postoperative CDC+ cohort with respect to BOS development.

RESULTS

Between 1990 and 2005, 202 consecutive patients underwent 208 lung transplantation procedures. Of these, 15 lung recipients developed 23 episodes of CDC with a median follow-up period of 2.7 years (range, 0-13.6). All patients with confirmed disease had at least 1 of the following 3 risk factors: recent antibiotic use, recent hospitalization, or augmentation of steroid dosage. Of the early CDC+ patients, 100% developed BOS, but only 52% of the late CDC+ patients developed BOS, either preceding or following infection.

CONCLUSION

CDC developed in 7.4% of lung transplant patients with identified risk factors, yielding a cumulative incidence of 14.7%. The statistical association of BOS development in early CDC+ patients suggests a relationship between early infections and future chronic lung rejection.

A role for the tet(O) plasmid in maintaining Campylobacter plasticity

Genomic sequencing projects are beginning to reveal regions of extensive DNA homology between bacterial genera. Public fears of the spread of genetically modified organisms into the food chain and the increasing prevalence of multi-drug resistant disease in humans highlight the implications of horizontal gene transfer. The striking DNA sequence similarity between the two uniquely identified tetracycline resistant (Tc(R)) Campylobacter plasmids, pCC31 and pTet, suggests their conserved acquisition and maintenance within Campylobacter [Batchelor, R.A., Pearson, B.M., Friis, L.M., Guerry, P., Wells, J.M. 2004. Nucleotide sequences and comparison of two large conjugative plasmids from different Campylobacter species. Microbiology 150, 3507-3517]. It is thus likely that these and other conjugative plasmids are highly prevalent and broadly distributed across several continents. Microarray technology is now enabling fast and extensive genomic comparisons to be made and allows us to investigate intra- and inter-genetic conservation and variability. This study details the development of a microarray specific for genes from Campylobacter plasmids pCC31, pTet and pVir and its application to the analysis of Campylobacter plasmid gene presence and preservation throughout environmental and clinical isolates. Application of the iterative algorithm GENCOM (freely available at ) is used as a rapid and effective way of comparing the content and conservation of plasmids in bacteria and provides details of the Campylobacter flexible gene pool and its contribution to genomic plasticity.

Multilaboratory comparison of proficiencies in susceptibility testing of Helicobacter pylori and correlation between agar dilution and E test methods

Susceptibility testing was performed at seven Canadian microbiology laboratories and the Helicobacter Reference Laboratory, Halifax, Nova Scotia, Canada, to assess susceptibility testing proficiency and the reproducibility of the results for clarithromycin and metronidazole and to compare the Epsilometer test (E test) method to the agar dilution reference method. Control strain Helicobacter pylori ATCC 43504 (American Type Culture Collection) and 13 clinical isolates (plus duplicates of four of these strains including ATCC 43504) were tested blindly. The National Committee for Clinical Laboratory Standards (NCCLS) guidelines for agar dilution testing were followed, and the same suspension of organisms was used for agar dilution and E test. Antimicrobials and E test strips were provided to the investigators. Methods were provided on a website (www.Helicobactercanada.org). Each center reported MICs within the stated range for strain ATCC 43504. Compared to the average MICs, interlaboratory agreements within 2 log(2) dilutions were 90% (range, 69 to 100%) for clarithromycin by agar dilution, with seven very major errors [VMEs], and 85% (range, 65 to 100%) by E test, with three VMEs. Interlaboratory agreements within 2 log(2) dilutions were 83% (range, 50 to 100%) for metronidazole by agar dilution, with six VMEs and eight major errors (MEs), and 75% (range, 50 to 94%) by E test, with four VMEs and four MEs. At lower and higher concentrations of antibiotic, E test MICs were slightly different from agar dilution MICs, but these differences did not result in errors. When a standardized protocol based on NCCLS guidelines was used, most participants in this study correctly identified clarithromycin- and metronidazole-susceptible and -resistant strains of H. pylori 93% of the time by either the agar dilution or E test method, and the numbers of errors were relatively equivalent by both methods.

Helicobacter pylori from asymptomatic hosts expressing heptoglycan but lacking Lewis O-chains: Lewis blood-group O-chains may play a role in Helicobacter pylori induced pathology

Helicobacter pylori is a widespread Gram-negative bacterium responsible for the onset of various gastric pathologies and cancers in humans. A familiar trait of H. pylori is the production of cell-surface lipopolysaccharides (LPSs; O-chain --> core --> lipid A) with O-chain structures analogous to some mammalian histo-blood-group antigens, those being the Lewis determinants (Lea, Leb, Lex, sialyl Lex, Ley) and blood groups A and linear B. Some of these LPS antigens have been implicated as autoimmune, adhesion, and colonization components of H. pylori pathogenic mechanisms. This article describes the chemical structures of LPSs from H. pylori isolated from subjects with no overt signs of disease. Experimental data from chemical- and spectroscopic-based studies unanimously showed that these H. pylori manufactured extended heptoglycans composed of 2- and 3-linked D-glycero-alpha-D-manno-heptopyranose units and did not express any blood-group O-antigen chains. The fact that another H. pylori isolate with a similar LPS structure was shown to be capable of colonizing mice indicates that H. pylori histo-blood-group structures are not an absolute prerequisite for colonization in the murine model also. The absence of O-chains with histo-blood groups may cause H. pylori to become inept in exciting an immune response. Additionally, the presence of elongated heptoglycans may impede exposure of disease-causing outer-membrane antigens. These factors may render such H. pylori incapable of creating exogenous contacts essential for pathogenesis of severe gastroduodenal diseases and suggest that histo-blood groups in the LPS may indeed play a role in inducing a more severe H. pylori pathology.

Diversity of silver resistance genes in IncH incompatibility group plasmids

Silver compounds are used as antimicrobial agents in medicine and bacteria that develop resistance to silver cations (Ag(+)) pose problems similar to those of antibiotic-resistant bacteria. The first set of Ag(+) resistance genes (sil) was from plasmid pMG101, now assigned to the IncHI incompatibility group. Questions of whether sil genes are unique to pMG101 or are more widely found, and whether they are associated with a specific incompatibility group or occur in many plasmid groups and on bacterial chromosomes were addressed. sil genes were identified in five IncH plasmids, but not in plasmids of the IncP incompatibility group. Three sil genes (silP, silR and silE) from these plasmids were PCR-amplified, cloned, sequenced and compared to those of pMG101. Differences of 0-50 nt per kb of sequence were found. Predicted gene products were 0-6% different in amino acid sequence, but the differences did not alter residues thought to be involved in protein function (see supplementary data at http://mic.sgmjournals.org or http://www.uic.edu/depts/mcmi/individual/gupta/index.htm). For representative IncH plasmid R476b and pMG101 the effects of Ag(+) exposure on resistance levels were measured by growth. The inducibility of silC, silR and silE gene expression after Ag(+) exposure was studied by reverse transcriptase (RT)-PCR. Silver resistance increased after Ag(+) exposure for strains carrying plasmid R476b. silC and silE expression from R476b was inducible after Ag(+) exposure and was constitutive and high from pMG101. The mRNA levels for the regulatory gene silR was constitutive for both pMG101 and R476b. Close homologues for silABC(ORF96)RS from pMG101 are clustered on the chromosomes of Escherichia coli strains K-12 and O157:H7, without contiguous silP and silE homologues. Insertion deletions of the E. coli K-12 chromosomal homologues for silA and silP gave Ag(+) hypersensitivity for growth. The silA homologue knockout was complemented back to wild-type resistance by the same gene cloned on a plasmid. Homologues of sil genes have also been identified on other enterobacterial genomes.

Cellular location and temperature-dependent assembly of IncHI1 plasmid R27-encoded TrhC-associated conjugative transfer protein complexes

Conjugal transfer of IncHI plasmid DNA between Gram-negative bacteria is temperature sensitive, as mating is optimal between 22 degrees C and 30 degrees C but is inhibited at 37 degrees C. R27, isolated from Salmonella enterica serovar Typhi, is an IncHI1 plasmid of 180 kbp that has been sequenced completely. The gene encoding green fluorescent protein (GFP) was inserted into R27 in frame with trhC. TrhC is a mating pair formation (Mpf) protein that is essential for plasmid transfer and H-pilus production. Fluorescence microscopy allowed visualization of the TrhC-GFP fusion protein, and Escherichia coli cells were examined for the subcellular localization and temperature-dependent production of TrhC-GFP. At 27 degrees C, TrhC-GFP was found at the periphery of cells as discrete foci, indicating an association of TrhC within protein complexes in the bacterial cell membrane, whereas at 37 degrees C, little fluorescence was detected. These foci probably represent the intracellular position of protein complexes involved in conjugative transfer, as the formation of foci was dependent upon the presence of other Mpf proteins. During temperature shift experiments from 37 degrees C to 27 degrees C, a long lag period was required for generation of GFP foci. Conversely, during short shifts from 27 degrees C to 37 degrees C, the GFP foci remained stable. These results suggest that the expression of transfer genes in the Tra2 region of R27 is temperature dependent. Subcellular localization of TrhC was verified by cellular fractionation. Expression patterns of TrhC-GFP were confirmed with immunoblot analysis and reverse transcriptase-polymerase chain reaction (RT-PCR). These results allow us to propose mechanisms to explain the temperature-sensitive transfer of R27.

Lewis antigen expression by Helicobacter pylori

Although Helicobacter pylori express Lewis antigens as a component in the lipopolysaccharide, their role in the infectious process is not well understood. Lewis antigen expression with growth phase was investigated, as well as the distribution of Lewis antigens among isolates from asymptomatic and symptomatic individuals. Lewis antigens are expressed by H. pylori in a growth phase-dependent manner, with the greatest expression occurring in the logarithmic phase of growth. As growth proceeds, an increasing amount of Lewis antigens are shed into the culture supernatant. Lewis antigen expression among H. pylori isolates from asymptomatic individuals is characterized by an absence of type I Lewis antigens, a decrease in Le(x) expression, and an increase in nontypeable H. pylori, as compared with that among H. pylori isolates from symptomatic patients. The data support a role for Lewis antigens in the pathogenesis associated with symptomatic H. pylori infection in colonized individuals.

Antibiotic susceptibility of attached and free-floating Helicobacter pylori

Helicobacter pylori are found attached to mucous cells of the human stomach or under the mucous layer. Models mimicking the in vivo situation may be more suitable for H. pylori MIC determinations than traditional agar dilution methods. Megraud et al. (Antimicrobial Agents and Chemotherapy 1991, 35, 869-72) developed a model for measuring the susceptibility of attached and free-floating H. pylori. We have modified this model so that free-floating and attached H. pylori are treated in a more similar manner, before and after incubation with antibiotic, and performed additional controls to ensure H. pylori and tissue culture cells are not detrimentally affected and maintain their viability during the course of the experiment. We found only 10% of plate-grown H. pylori were competent for attachment to HEp-2 cells; however, all progeny of attached bacteria remained adherent. Killing curves were performed using 0, 0.001, 0.01, 0.1 and 1 mg/L amoxycillin, and 0, 0.0025, 0.0075 and 0.01 mg/L clarithromycin. H. pylori divided at concentrations <or= 0.01 mg/L amoxycillin and <or= 0.0025 mg/L clarithromycin. Contrary to the previous study, using our modified method we found that HEp-2 adherent and freefloating H. pylori are equally susceptible to amoxycillin (strains 26695, CCUG18943, CCUG19104 and CCUG19110) and clarithromycin (strain 26695). Therefore, we find no evidence that attachment of H. pylori to eukaryotic cells increases their resistance to antibiotics compared with non-attached bacteria. Nonetheless, these results confirm confidence in traditional MIC studies when a comparison is made between susceptible and resistant strains.

Localization of the ribosomal protection protein Tet(O) on the ribosome and the mechanism of tetracycline resistance

Tet(O) belongs to a class of ribosomal protection proteins that mediate tetracycline resistance. It is a G protein that shows significant sequence similarity to elongation factor EF-G. Here we present a cryo-electron microscopic reconstruction, at 16 A resolution, of its complex with the E. coli 70S ribosome. Tet(O) was bound in the presence of a noncleavable GTP analog to programmed ribosomal complexes carrying fMet-tRNA in the P site. Tet(O) is directly visible as a mass close to the A-site region, similar in shape and binding position to EF-G. However, there are important differences. One of them is the different location of the tip of domain IV, which in the Tet(O) case, does not overlap with the ribosomal A site but is directly adjacent to the primary tetracycline binding site. Our findings give insights into the mechanism of tetracycline resistance.

Spontaneous mutations that confer antibiotic resistance in Helicobacter pylori

In this study, we systematically examined in vitro frequencies and spectra of the spontaneous mutations in Helicobacter pylori that confer resistance to clarithromycin (Cla(r)), metronidazole (Mtz(r)), amoxicillin (Amx(r)), ciprofloxacin (Cip(r)), and rifampin (Rif(r)). The mutation rate of Rif(r) or Cip(r) determined in a fluctuation assay is 1 x 10(-8) to 2 x 10(-8) per cell per division. In contrast, the mutation rates of Cla(r), Mtz(r), and Amx(r) are much lower (<10(-9)). However, Mtz(r) mutants could be readily selected in vitro by using the serial passage method, suggesting that the mutagenic effect and selective effect of a sublethal dose of metronidazole contribute to the rapid development of Mtz(r). Analysis of spontaneous Rif(r), Cla(r), and Cip(r) mutants confirmed previous results indicating that mutations within the rpoB gene, the 23S rRNA gene, and the gyrA gene, respectively, are responsible; also, several new mutant alleles were identified. Mtz(r) mutants resulted most frequently, but not always, from mutations in the rdxA gene. DNA fragments containing each mutant allele could readily transform susceptible H. pylori strains to resistance, confirming that each mutant allele is responsible for the resistance phenotype.

Glutathione is a target in tellurite toxicity and is protected by tellurite resistance determinants in Escherichia coli

Tellurite (TeO3(2-)) is highly toxic to most microorganisms. The mechanisms of toxicity or resistance are poorly understood. It has been shown that tellurite rapidly depletes the reduced thiol content within wild-type Escherichia coli. We have shown that the presence of plasmid-borne tellurite-resistance determinants protects against general thiol oxidation by tellurite. In the present study we observe that the tellurite-dependent depletion of cellular thiols in mutants of the glutathione and thioredoxin thiol:redox system was less than in wild-type cells. To identify the type of low-molecular-weight thiol compounds affected by tellurite exposure, the thiol-containing molecules were analyzed by reverse phase HPLC as their monobromobimane derivatives. Results indicated that reduced glutathione is a major initial target of tellurite reactivity within the cell. Other thiol species are also targeted by tellurite, including reduced coenzyme A. The presence of the tellurite resistance determinants kilA and ter protect against the loss of reduced glutathione by as much as 60% over a 2 h exposure. This protection of glutathione oxidation is likely key to the resistance mechanism of these determinants. Additionally, the thiol oxidation response curves were compared between selenite and tellurite. The loss of thiol compounds within the cell recovered from selenite but not to tellurite.

Quinolone and macrolide resistance in Campylobacter jejuni and C. coli: resistance mechanisms and trends in human isolates

The incidence of human Campylobacter jejuni and C. coli infections has increased markedly in many parts of the world in the last decade as has the number of quinolone-resistant and, to a lesser extent, macrolide-resistant Campylobacter strains causing infections. We review macrolide and quinolone resistance in Campylobacter and track resistance trends in human clinical isolates in relation to use of these agents in food animals. Susceptibility data suggest that erythromycin and other macrolides should remain the drugs of choice in most regions, with systematic surveillance and control measures maintained, but fluoroquinolones may now be of limited use in the empiric treatment of Campylobacter infections in many regions.

Escherichia coli TehB requires S-adenosylmethionine as a cofactor to mediate tellurite resistance

The Escherichia coli chromosomal determinant for tellurite resistance consists of two genes (tehA and tehB) which, when expressed on a multicopy plasmid, confer resistance to K(2)TeO(3) at 128 microg/ml, compared to the MIC of 2 microg/ml for the wild type. TehB is a cytoplasmic protein which possesses three conserved motifs (I, II, and III) found in S-adenosyl-L-methionine (SAM)-dependent non-nucleic acid methyltransferases. Replacement of the conserved aspartate residue in motif I by asparagine or alanine, or of the conserved phenylalanine in motif II by tyrosine or alanine, decreased resistance to background levels. Our results are consistent with motifs I and II in TehB being involved in SAM binding. Additionally, conformational changes in TehB are observed upon binding of both tellurite and SAM. The hydrodynamic radius of TehB measured by dynamic light scattering showed a approximately 20% decrease upon binding of both tellurite and SAM. These data suggest that TehB utilizes a methyltransferase activity in the detoxification of tellurite.

Pathophysiology of antibiotic resistance: clarithromycin

Resistance of Helicobacter pylori to antibiotics ranges from 3% to 10% and may exceed these levels in some countries. The pathophysiology of clarithromycin resistance is reviewed, including the mode of action by which the antibiotic inhibits protein synthesis and the mechanism of resistance, which involves a mutation at position 2142 or 2143 in the V loop domain of the 23SrRNA genes. Mutations of A2142G confer a higher minimum inhibitory concentration than mutations of A2143G. The former demonstrate cross-resistance to macrolide, lincosamide and streptogramin antibiotics, whereas the latter are susceptible to streptogramin B. In vitro mutagenesis combined with natural transformation were used to create several types of clarithromycin-resistant mutants. H pylori strains with A2142G and A2143G mutations had a higher growth rate than those with A2142C, A2143 or A2142T mutations. Data from this study indicate why clarithromycin-resistant clinical isolates of H pylori are more likely to have A2142G or A2143G mutations and only occassionally A2142C mutations.

The role of cysteine residues in tellurite resistance mediated by the TehAB determinant

TehATehB is a tellurite (TeO(2-)(3)) resistance determinant found on the Escherichia coli chromosome. Normally silent, it specifies a minimal inhibitory concentration (MIC) of 2 microg K(2)TeO(3)/ml unless upregulated or present on a multicopy plasmid which results in an MIC of 128 microg/ml. Both TehA and TehB have three cysteine residues. Oligonucleotide site-directed mutagenesis was carried out to systematically replace all six cysteine residues by alaninies. The results showed that cysteine residues in both TehA and TehB play a role in tellurite resistance: A single cysteine change had no effect, however increasing combinations of two or three cysteine substitutions demonstrated strong phenotypic effects with minimal inhibitory concentrations ranging from 16-64 microg K(2)TeO(3)/ml. A cysteine-free mutant in which all six cysteine residues were replaced by alanines maintained a MIC of 16 microg/ml. Further investigations on the role of cysteines in resistance were studied using thiol reactive reagents on the soluble subunit TehB. These studies confirmed that TehB is a dimer and undergoes a conformational change with tellurite and S-adenosyl-l-methionine binding. Studies using native and SDS denaturing PAGE under reducing and oxidizing conditions suggested that a cysteine in TehB is involved in binding tellurite.

Synthesis of mono- and di-fucosylated type I Lewis blood group antigens by Helicobacter pylori

The identification of Helicobacter pylori isolates that expresses exclusively type I Lewis antigens is necessary to determine the biosynthetic pathway of these antigens. Fast-atom bombardment MS provides evidence that the H. pylori isolate UA1111 expresses predominantly Leb, with H type I and Lea in lesser amounts. Cloning and expression of the H. pylori fucosyltransferases (FucTs) allow comparisons with previously identified H. pylori enzymes and determination of the enzyme specificities. Although all FucTs, one alpha(1,2) FucT and two alpha(1,3/4) FucTs, appear to be functional in this isolate, their activities are lower and enzyme specificities are different to other H. pylori FucTs previously characterized. Studies of the cloned enzyme activities and mutational analysis indicate that Lea acts as the substrate for the synthesis of Leb. This is different from the human Leb biosynthetic pathway, but analogous to the biosynthetic pathway utilized by H. pylori for the production of Ley.

Lewis antigens in Helicobacter pylori: biosynthesis and phase variation

The lipopolysaccharides (LPS) of most Helicobacter pylori strains contain complex carbohydrates known as Lewis antigens that are structurally related to the human blood group antigens. Investigations on the genetic determinants involved in the biosynthesis of Lewis antigens have led to the identification of the fucosyltransferases of H. pylori, which have substrate specificities distinct from the mammalian fucosyltransferases. Compared with its human host, H. pylori utilizes a different pathway to synthesize the difucosylated Lewis antigens, Lewis y. and Lewis b. Unique features in the H. pylori fucosyltransferase genes, including homopolymeric tracts mediating slipped-strand mispairing and the elements regulating translational frameshifting, enable H. pylori to produce variable LPS epitopes on its surface. These new findings have provided us with a basis to further examine the roles of molecular mimicry and phase variation of H. pylori Lewis antigen expression in both persistent infection and pathogenesis of this important human gastric pathogen.

The complete DNA sequence and analysis of R27, a large IncHI plasmid from Salmonella typhi that is temperature sensitive for transfer

Salmonella typhi, the causative agent of typhoid fever, annually infects 16 million people and kills 600 000 world wide. Plasmid-encoded multiple drug resistance in S. typhi is always encoded by plasmids of incompatibility group H (IncH). The complete DNA sequence of the large temperature-sensitive conjugative plasmid R27, the prototype for the IncHI1 family of plasmids, has been compiled and analyzed. This 180 kb plasmid contains 210 open reading frames (ORFs), of which 14 have been previously identified and 56 exhibit similarity to other plasmid and prokaryotic ORFs. A number of insertion elements were found, including the full Tn 10 transposon, which carries tetracycline resistance genes. Two transfer regions, Tra1 and Tra2, are present, which are separated by a minimum of 64 kb. Homologs of the DNA-binding proteins TlpA and H-NS that act as temperature-regulated repressors in other systems have been located in R27. Sequence analysis of transfer and replication regions supports a mosaic-like structure for R27. The genes responsible for conjugation and plasmid maintenance have been identified and mechanisms responsible for thermosensitive transfer are discussed.

Colonization and immune responses in mice to Helicobacter pylori expressing different Lewis antigens

BACKGROUND AND AIMS

A mouse model was established to compare colonization by the H. pylori Sydney strain SS1 with several clinical isolates expressing different Lewis antigens on their surface. In addition, both humoral and cell mediated immune responses were determined for different H. pylori strains.

METHODS

Mice were inoculated intragastrically separately with the Sydney strain as well as with five clinical isolates of H. pylori expressing different Lewis (Le) antigen phenotypes. Colonization of the mouse stomach by the bacteria was monitored from two to fourteen weeks post inoculation by four independent methods namely, urease, PCR (using CagA primers), bacterial culture and histology. Antibody titers and cellular immune responses were monitored by ELISA and antigen stimulation test respectively.

RESULTS

Different degrees of colonization were observed in C57, CD1 and Balb/c mice inoculated with H. pylori strain SS1 (Le(x), Le(y)) and clinical isolates UA948 (Le(a), Le(x)), UA861 (alpha-glucosyl polyLacNAc), UA1258 (Le(y)), UA802 (Le(y)) and UA1264 (no Le antigen) starting from week two post inoculation. All three mice strains mounted high immune responses against different H. pylori antigens. Treatment of mice with vancomycin prior to inoculation has no effect either on colonization of the stomach or the immune response of the mice. Histological evaluation established colonization after 10 weeks post inoculation but not gastritis.

CONCLUSIONS

Stomach of mice can be colonized consistently, with H. pylori strain SS1, and colonization was also achieved with all clinical isolates that were not mouse adapted. These strains could be detected more consistently by PCR in the early stages, then by culture only after 8 - 10 weeks. In our study, Lewis(x) expressing bacterial strain (UA948) failed to colonize Balb/c mice, whereas the Le(y) expressing strain (UA1258) did not colonize C57/BL6 mice.

Analysis of the complete nucleotide sequence of the tetracycline-resistance transposon Tn10

An analysis of the complete nucleotide sequence of the composite tetracycline-resistance transposon Tn10 (9147 bp) from the Salmonella typhi conjugative plasmid R27 is presented. A comparison of the protein sequences from IS10-right and IS10-left transposases has identified four amino acid differences. These residues appear to play an important role in normal transposase function and may account for the differences in exhibited transposition activities. The tetracycline determinants encoded by this version of Tn10 share >99% identity with those of Tn10(R100), demonstrating the conservation that exists between these transposons. A previously uncharacterized approximately 3000-bp region of Tn10 contains four putative open reading frames. One of these open reading frames shares 55% identity with the glutamate permease protein sequence from Haemophilus influenzae although it was unable to complement an Escherichia coli glutamate permease mutant, with which it shares 51% identity. The three remaining putative open reading frames are arranged as a discrete genetic unit adjacent to the glutamate permease homolog and are transcribed in the opposite direction. Two of these open reading frames are homologous with Bacillus subtilis proteins of unknown functions while the other has no homologs in the database. The presence of an aminoacyl-tRNA synthetase class II motif in one of these open reading frames in combination with the glutamate permease homolog allows us to postulate that this region of Tn10 could once have played a role in amino acid metabolism.

Lewis antigen expression and stability in Helicobacter pylori isolated from serial gastric biopsies

The expression of Lewis antigens by the gastric pathogen Helicobacter pylori in serial biopsy isolates was investigated to assess antigen distribution and stability. A total of 26 asymptomatic subjects were given various doses of 3' sialyllactose for up to 56 days. Gastric biopsies were performed during the dosing period, as well as 30 days after dosing, which provided 127 H. pylori isolates that were examined by use of ELISA and immunoblot. A large proportion of subjects (14/26) yielded sequential H. pylori isolates, which appeared genetically identical but had variable Lewis antigen expression. The proportion of subjects with H. pylori isolates not expressing any Lewis antigens was greater than that previously reported (10/26). Thus, the expression of the Lewis antigens by H. pylori does not appear to be a requirement for colonization, whereas the antigen expression after human infection is more variable than the previously reported rate observed with in vitro cultures.

Quantification of Hyphomicrobium populations in activated sludge from an industrial wastewater treatment system as determined by 16S rRNA analysis

The bacterial community structure of the activated sludge from a 25 million-gal-per-day industrial wastewater treatment plant was investigated using rRNA analysis. 16S ribosomal DNA (rDNA) libraries were created from three sludge samples taken on different dates. Partial rRNA gene sequences were obtained for 46 rDNA clones, and nearly complete 16S rRNA sequences were obtained for 18 clones. Seventeen of these clones were members of the beta subdivision, and their sequences showed high homology to sequences of known bacterial species as well as published 16S rDNA sequences from other activated sludge sources. Sixteen clones belonged to the alpha subdivision, 7 of which showed similarity to Hyphomicrobium species. This cluster was chosen for further studies due to earlier work on Hyphomicrobium sp. strain M3 isolated from this treatment plant. A nearly full-length 16S rDNA sequence was obtained from Hyphomicrobium sp. strain M3. Phylogenetic analysis revealed that Hyphomicrobium sp. strain M3 was 99% similar to Hyphomicrobium denitrificans DSM 1869(T) in Hyphomicrobium cluster II. Three of the cloned sequences from the activated sludge samples also grouped with those of Hyphomicrobium cluster II, with a 96% sequence similarity to that of Hyphomicrobium sp. strain M3. The other four cloned sequences from the activated sludge sample were more closely related to those of the Hyphomicrobium cluster I organisms (95 to 97% similarity). Whole-cell fluorescence hybridization of microorganisms in the activated sludge with genus-specific Hyphomicrobium probe S-G-Hypho-1241-a-A-19 enhanced the visualization of Hyphomicrobium and revealed that Hyphomicrobium appears to be abundant both on the outside of flocs and within the floc structure. Dot blot hybridization of activated sludge samples from 1995 with probes designed for Hyphomicrobium cluster I and Hyphomicrobium cluster II indicated that Hyphomicrobium cluster II-positive 16S rRNA dominated over Hyphomicrobium cluster I-positive 16S rRNA by 3- to 12-fold. Hyphomicrobium 16S rRNA comprised approximately 5% of the 16S rRNA in the activated sludge.

Cloning and characterization of the alpha(1,3/4) fucosyltransferase of Helicobacter pylori

The gastric pathogen Helicobacter pylori can express the histo blood group antigens, which are on the surface of many human cells. Most H. pylori strains express the type II carbohydrates, Lewis X and Y, whereas a small population express the type I carbohydrates, Lewis A and B. The expression of Lewis A and Lewis X, as in the case of H. pylori strain UA948, requires the addition of fucose in alpha1,4 and alpha1,3 linkages to type I or type II carbohydrate backbones, respectively. This work describes the cloning and characterization of a single H. pylori fucosyltransferase (FucT) enzyme, which has the ability to transfer fucose to both of the aforementioned linkages in a manner similar to the human fucosyltransferase V (Fuc-TV). Two homologous copies of the fucT gene have been identified in each of the genomes sequenced. The characteristic adenosine and cytosine tracts in the amino terminus and repeated regions in the carboxyl terminus are present in the DNA encoding the two UA948fucT genes, but these genes also contain differences when compared with previously identified H. pylori fucTs. The UA948fucTa gene encodes an approximately 52-kDa protein containing 475 amino acids, whereas UA948fucTb does not encode a full-length FucT protein. In vitro, UA948FucTa appears to add fucose with a greater than 5-fold preference for type II chains but still retains significant activity using type I acceptors. The addition of the fucose to the type II carbohydrate acceptors, by UA948FucTa, does not appear to be affected by fucosylation at other sites on the carbohydrate acceptor, but the rate of fucose transfer is affected by terminal fucosylation of type I acceptors. Through mutational analysis we demonstrate that only FucTa is active in this H. pylori isolate and that inactivation of this enzyme eliminates expression of all Lewis antigens.

Lipopolysaccharide structures of Helicobacter pylori genomic strains 26695 and J99, mouse model H. pylori Sydney strain, H. pylori P466 carrying sialyl Lewis X, and H. pylori UA915 expressing Lewis B classification of H. pylori lipopolysaccharides into glycotype families

This study describes the molecular makeup of the cell-wall lipopolysaccharides (LPSs) (O-chain polysaccharide-->core oligosaccharide-->lipid A) from five Helicobacter pylori strains: H. pylori 26695 and J99, the complete genome sequences of which have been published, the established mouse model Sydney strain (SS1), and the symptomatic strains P466 and UA915. All chemical and serological experiments were performed on the intact LPSs. H. pylori 26695 and SS1 possessed either a low-Mr semi-rough-form LPS carrying mostly a single Ley type-2 blood-group determinant in the O-chain region covalently attached to the core oligosaccharide or a high-Mr smooth-form LPS, as did strain J99, with an elongated partially fucosylated type-2 N-acetyllactosamine (polyLacNAc) O-chain polymer, terminated mainly by a Lex blood-group determinant, connected to the core oligosaccharide. In the midst of semi-rough-form LPS glycoforms, H. pylori 26695 and SS1 also expressed in the O-chain region a difucosylated antigen, alpha-L-Fucp(1-3)-alpha-L-Fucp(1-4)-beta-D-GlcpNAc, and the cancer-cell-related type-1 or type-2 linear B-blood-group antigen, alpha-D-Galp(1-3)-beta-D-Galp(1-3 or 4)-beta-D-GlcpNAc. The LPS of H. pylori strain P466 carried the cancer-associated type-2 sialyl Lex blood-group antigen, and the LPS from strain UA915 expressed a type-1 Leb blood-group unit. These findings should aid investigations that focus on identifying and characterizing genes responsible for LPS biosynthesis in genomic strains 26695 and J99, and in understanding the role of H. pylori LPS in animal model studies. The LPSs from the H. pylori strains studied to date were grouped into specific glycotype families.

Mutation as an origin of genetic variability in Helicobacter pylori

The availability of two complete Helicobacter pylori genome sequences and recent studies of its population genetics have provided a detailed picture of genetic diversity in this important human gastric pathogen. It is believed that, in addition to genetic recombination, de novo mutation could have a role in generating the high level of genetic variation in H. pylori.

Contributions of genome sequencing to understanding the biology of Helicobacter pylori

About half of the world's population carries Helicobacter pylori, a gram-negative, spiral bacterium that colonizes the human stomach. The link between H. pylori and, ulceration as well as its association with the development of both gastric cancer and mucosa-associated lymphoid tissue lymphoma in humans is a serious public health concern. The publication of the genome sequences of two stains of H. pylori gives rise to direct evidence on the genetic diversity reported previously with respect to gene organization and nucleotide variability from strain to strain. The genome size of H. pylori strain 26695 is 1,6697,867 bp and is 1,643,831 bp for strain J99. Approximately 89% of the predicted open reading frames are common to both of the strains, confirming H. pylori as a single species. A region containing approximately 45% of H. pylori strain-specific open reading frames, termed the plasticity zone, is present on the chromosomes, verifying that some strain variability exists. Frequent alteration of nucleotides in the third position of the triplet codons and various copies of insertion elements on the individual chromosomes appear to contribute to distinct polymorphic fingerprints among strains analyzed by restriction fragment length polymorphisms, random amplified polymorphic DNA method, and repetitive element-polymerase chain reaction. Disordered chromosomal locations of some genes seen by pulsed-field gel electrophoresis are likely caused by rearrangement or inversion of certain segments in the genomes. Cloning and functional characterization of the genes involved in acidic survival, vacuolating toxin, cag-pathogenicity island, motility, attachment to epithelial cells, natural transformation, and the biosynthesis of lipopolysaccharides have considerably increased our understanding of the molecular genetic basis for the pathogenesis of H. pylori. The homopolymeric nucleotide tracts and dinucleotide repeats, which potentially regulate the on- and off-status of the target genes by the strand-slipped mispairing mechanism, are often found in the genes encoding the outer-membrane proteins, in enzymes for lipopolysaccharide synthesis, and within DNA modification/restriction systems. Therefore, these genes may be involved in the H. pylori-host interaction.

Antigenic mimicry between Helicobacter pylori and gastric mucosa: failure to implicate heat-shock protein Hsp60 using immunoelectron microscopy

BACKGROUND

Helicobacter pylori infection induces autoantibodies that cross-react with human gastric mucosa from infected individuals. Candidates for the antigens responsible for molecular mimicry causing autoreactivity include the heat-shock protein HspB (Hsp60, sometimes called Hsp54) or Lewis x and Lewis y carbohydrate antigens.

OBJECTIVE

Our goal was to investigate the involvement of HspB (Hsp60) in autoreactivity between H. pylori and gastric biopsy tissue.

MATERIALS AND METHODS

Immunoelectron microscopy was used to study cross-reactivity among biopsy tissues from a patient with gastritis, gastric ulcer, and duodenal ulcer and his own serum as well as reactivity with serum raised against HspB from H. pylori and monoclonal antibodies against Lewis antigens.

RESULTS

The patient serum reacted with gastric mucosa, and the antibodies involved were predominantly IgG. Antibody raised to H. pylori HspB (Hsp60) reacted only with H. pylori cells but not with gastric mucosal tissue. In contrast, monoclonal antibodies specific for Lewis x and Lewis y antigens reacted with both H. pylori and human gastric epithelial tissue.

CONCLUSIONS

Hsp60 (Hsp54) is unlikely to be involved in autoreactivity seen in individuals infected with H. pylori. In contrast, we could not rule out the role of Lewis x and Lewis y carbohydrate antigens, expressed as a component of H. pylori lipopolysaccharides, in molecular mimicry and autoantibody production.

Open and arthroscopic techniques for the treatment of traumatic anterior shoulder instability in Australian rules football players

Australian Rules football (ARF) is a potentially violent, overhead, body-contact sport. We reviewed 56 shoulders in patients who sustained their initial traumatic anterior subluxation or dislocation during ARF and who underwent reconstructive surgery for traumatic anterior instability, whether by arthroscopic or by open techniques. Patients were followed up for a mean of 29.4 months after operation, and clinical evaluation was performed with the Rowe grading system. Three types of surgical procedures were performed: arthroscopic suture repair, arthroscopic Bankart repair with an absorbable polyglyconate tack, and open capsular shift with repair of the Bankart lesion. Shoulders treated with arthroscopic suture repair had a 70% rate of recurrent subluxation or dislocation on return to ARF Dislocations treated arthroscopically with the biodegradable tack had a 38% rate of recurrence of instability; three fourths of the recurrences were after minimal to moderate trauma. Shoulders treated with an open capsular shift and Bankart procedure had a 30% rate of recurrent instability, with half of the recurrences caused by violent trauma. In the open group there were no failures in patients who did not return to ARF. We suggest that arthroscopic repair in shoulders with anterior instability and recurrent dislocation does not adequately address the plastic deformation of the anterior capsule that may occur after repeated episodes of dislocation. We advocate open shoulder procedures in ARF athletes to address all areas of the capsulolabral pathologic condition and to provide the most secure repair possible with minimal chance of recurrence.

Nomenclature for new tetracycline resistance determinants

Letters of the English alphabet have heretofore been used to name tetracycline resistance determinants. Since all 26 letters have now been used, a nomenclature employing numerals is recommended for future determinants, and one laboratory has offered to coordinate the assignment of numerals.

Characterization of gram-positive tellurite resistance encoded by the Streptococcus pneumoniae tehB gene

Streptococcus pneumoniae is a Gram-positive bacterium which is naturally resistant to tellurite. In this study, we cloned and sequenced a homologue of the Escherichia coli tellurite resistance gene tehB from S. pneumoniae. It encoded a protein of 284 amino acids which is 86 residues longer than E. coli TehB, but similar in size to Haemophilus influenzae TehB and Eikenella corrodens hemagglutinin (Hag1) as well as homologues from Actinobacillus actinomycetemcomitans, Neisseria gonorrhoeae and Neisseria meningitidis. The S. pneumoniae TehB displayed 46-58% identity (52-68% similarity) to these proteins. The results in this study showed that the S. pneumoniae tehB alone not only conferred on E. coli high level resistance to tellurite, but also caused filamentous morphology in E. coli.

Characterization of the Tra2 region of the IncHI1 plasmid R27

In this study, the DNA sequence of one of the transfer regions of the IncHI1 plasmid R27 was determined. This region, which corresponds to coordinates 0-40 on the R27 map has been called the Tra2 region, and is believed to be involved in mating pair formation. DNA sequence analysis of the transfer region identified 11 open reading frames which showed similarities to the transfer genes from other conjugative systems. The R27 transfer genes appear to most closely resemble the genes from the F plasmid and Sphingomonas aromaticivorans plasmid pNL1, both within the individual genes and in the overall gene order. The Tra2 region is also distinct in that replication, partitioning, and stability genes are found in the middle of the transfer region. The R27 Tra2 region also contains a gene, trhF, which appears to be related to the TraF genes of Agrobacterium and Rhizobium species. This, along with the temperature-sensitive transfer system found in both H plasmids and Agrobacterium, leads to the speculation that the R27 transfer region evolved from both ancestral F-like and P-like plasmids.

Sequencing and characterization of Salmonella typhi plasmid R27 (incompatibility group HI1) trhC, a transfer gene encoding a potential nucleoside triphosphate-binding domain

IncHI1 plasmids are one of the few plasmids known to mediate multiple antibiotic resistance in Salmonella typhi. These plasmids are temperature-sensitive for transfer and R27 is the prototype plasmid. DNA sequencing within the Tra2 region of R27, encoding genes involved in mating pair formation, identified trhC encoding the TrhC protein of 90,000 Da, which was visualized using an in vitro transcription/translation system. Expression of the TrhC protein also identified two smaller protein products of approximately 23 and 25 kDa which are predicted to be protease digestion products. The migration of these smaller products changed when the reactions were run at 28 vs 37 degrees C. The TrhC protein contained a putative nucleotide triphosphate-binding protein and exhibited sequence similarities with several other proteins implicated in bacterial conjugation, including TraC (F), TraB (pKM101), VirB4 (Ti), TrbE (RP4). Phylogenetic analysis showed TrhC was most closely related to TraC. Mini-Tn10 insertions in trhC generated transfer defective mutants, and no pili were specified by the trhC mutants. The trhC gene appeared to be a hot spot for transposon insertion as 37.5% mapped into this open reading frame. One trhC mutant, pDT2990, was able to be complemented by a cloned trhC gene giving a transfer frequency of 1 x 10(-3) transconjugants per recipient in an 18-h mating, whereas the wild-type transfer frequency of R27 was 1 x 10(-2) transconjugants per recipient.

Helicobacter pylori and its genome: lessons from the treasure map

The availability of the complete genome sequence of Helicobacter pylori 26695 has opened new avenues for research in the molecular biology of this gastric pathogen. The present review gives a general overview of H pylori obtained from the complete genome sequence and compares this with data previously obtained from cloning and functional studies of H pylori. The cagA pathogenicity island of 40 kilobases, which encodes a type IV secretion system, is discussed. The diversity of H pylori genomes is well known, yet new data indicate that some aspects of the genome, particularly outer membrane protein genes, are conserved. Genes encoding proteins involved in molecular mimicry between bacterium and gastric epithelial tissue, specifically those encoding Lewis X and Lewis Y antigens, are discussed. The large number of DNA restriction and modification genes and their role in H pylori infection are considered. Finally, gene transfer is discussed. The availability of the complete genome sequence of H pylori 26695 and the soon to be available sequence of J99 will speed up and assist in the analysis of H pylori genes and their encoded proteins. The genomes of both strains will be useful as references with which other H pylori genomes can be compared.

Multiplex sequence analysis demonstrates the competitive growth advantage of the A-to-G mutants of clarithromycin-resistant Helicobacter pylori

Clarithromycin resistance in Helicobacter pylori is due to point mutation within the 23S rRNA. We examined the growth rates of different types of site-directed mutants and demonstrated quantitatively the competitive growth advantage of A-to-G mutants over other types of mutants by a multiplex sequencing assay. The results provide a rational explanation of why A-to-G mutants are predominantly observed among clarithromycin-resistant clinical isolates.

Bacterial tellurite resistance

Tellurium compounds are used in several industrial processes, although they are relatively rare in the environment. Genes associated with tellurite resistance (TeR) are found in many pathogenic bacteria. Tellurite can be detoxified through interactions with cellular thiols, such as glutathione, or a methyltransferase-catalyzed reaction, although neither process appears involved in plasmid-mediated TeR.

Molecular genetic basis for the variable expression of Lewis Y antigen in Helicobacter pylori: analysis of the alpha (1,2) fucosyltransferase gene

Helicobacter pylori lipopolysaccharides (LPS) express human oncofetal antigens Lewis X and Lewis Y. The synthesis of Lewis Y involves the actions of alpha (1,3) and alpha (1,2) fucosyltransferases (FucTs). Here, we report the molecular cloning and characterization of genes encoding H. pylori alpha (1,2) FucT (Hp fucT2) from various H. pylori strains. We constructed Hp fucT2 knock-out mutants and demonstrated the loss of Lewis Y production in these mutants by enzyme-linked immunosorbent assay (ELISA) and immunoelectron microscopy. The Hp fucT2 gene contains a hypermutable sequence [poly (C) and TAA repeats], which provides a possibility of frequent shifting into and out of coding frame by a polymerase slippage mechanism. Thus, the Hp fucT2 gene displays two major genotypes, consisting of either a single full-length open reading frame (ORF; as in the strain UA802) or truncated ORFs (as in the strain 26695). In vitro expression of Hp fucT2 genes demonstrated that both types of the gene have the potential to produce the full-length protein. The production of the full-length protein by the 26695 fucT2 gene could be attributed to translational-1 frameshifting, as a perfect translation frameshift cassette resembling that of the Escherichia coli dnaX gene is present. Examination of the strain UA1174 revealed that its fucT2 gene has a frameshifted ORF at the DNA level, which cannot be compensated by translation frameshifting, accounting for its Lewis Y off phenotype. In another strain, UA1218, the fucT2 gene is apparently turned off because of the loss of its promoter. Based on these data, we proposed a model for the variable expression of Lewis Y by H. pylori, in which regulation at the level of replication slippage (mutation), transcription and translation of the fucT2 gene may all be involved.

Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori

Helicobacter pylori, one of the most common bacterial pathogens of humans, colonizes the gastric mucosa, where it appears to persist throughout the host's life unless the patient is treated. Colonization induces chronic gastric inflammation which can progress to a variety of diseases, ranging in severity from superficial gastritis and peptic ulcer to gastric cancer and mucosal-associated lymphoma. Strain-specific genetic diversity has been proposed to be involved in the organism's ability to cause different diseases or even be beneficial to the infected host and to participate in the lifelong chronicity of infection. Here we compare the complete genomic sequences of two unrelated H. pylori isolates. This is, to our knowledge, the first such genomic comparison. H. pylori was believed to exhibit a large degree of genomic and allelic diversity, but we find that the overall genomic organization, gene order and predicted proteomes (sets of proteins encoded by the genomes) of the two strains are quite similar. Between 6 to 7% of the genes are specific to each strain, with almost half of these genes being clustered in a single hypervariable region.