Mechanism of metronidazole resistance in Helicobacter pylori: comparison of the rdxA gene sequences in 30 strains

The rdxA gene of 30 independently isolated Helicobacter pylori strains was sequenced. A comparison of the rdxA sequences revealed a higher percentage of amino acid substitutions in the corresponding protein than in other housekeeping genes. Out of 122 point mutations, 41 were missense and 4 were nonsense. A resistant strain with a nucleotide insertion in the rdxA sequence was also found. With the exception of the point mutations and the insertion generating a stop signal, no particular nucleotide mutation or amino acid substitution could be associated to metronidazole resistance. Moreover, phylogenetic analysis of the 30 nucleotide sequences did not demonstrate specific clusters associated with the resistance phenotype.

Phylogeny of the scathophagidae (Diptera, calyptratae) based on mitochondrial DNA sequences

The family Scathophagidae constitutes, together with members of the families Muscidae, Fannidae, and Anthomyiidae, the Muscoidea superfamily. The species Scathophaga stercoraria has been used extensively to investigate questions in animal ecology and evolution, particularly as a model system for studies of sperm competition and life history evolution. However, no phylogenetic studies have ever been performed on the Scathophagidae and the relationships within this family remain unclear. This study represents a molecular approach aimed at uncovering the phylogenetic relationships among 61 species representing 22 genera of Scathophagidae. A fragment of the terminal region of the mitochondrial gene COI (subunit I of the cytochrome oxidase gene) was sequenced in scathophagid species covering a wide geographic area, as well as a diverse spectrum of ecological habitats. Several clades grouping different genera and species have been identified, but the resolution power of the COI was insufficient to establish the exact relationships between these clades. The molecular data confirm the existence of a group consisting of the genera Delina, Chylizosoma, and Americina, which could represent the subfamily Delinae. Concerning the controversial position of the genus Phrosia, our data clearly suggest that it should be removed from the Delinae and placed within the genus Cordilura. Monophyly of most genera was confirmed, except for the genus Scathophaga, which should be divided into several different taxa.

Identification of two genetic groups in Bacteroides fragilis by multilocus enzyme electrophoresis: distribution of antibiotic resistance (cfiA, cepA) and enterotoxin (bft) encoding genes

Ninety-three Bacteroides fragilis strains of different origin were analysed by multilocus enzyme electrophoresis (MLEE). Fourteen of the 15 genetic loci analysed were polymorphic, whilst nucleoside phosphorylase was monomorphic. There was a mean of six alleles per locus and a mean genetic diversity of 0.393. Cluster analysis identified 90 electrophoretic types (ETs) separated into two major phylogenetic divisions at a genetic distance of 0.70. Division I consisted of 81 ETs carrying the endogenous class A beta-lactamase gene cepA, whereas division II comprised 9 ETs carrying the class B beta-lactamase gene cfiA, but not cepA. The presence of these two genes was assessed by PCR and the expression of the cfiA gene was investigated by determining the level of resistance to the antibiotic imipenem. MLEE showed a smaller genetic distance among the genotypes of the imipenem-resistant than among the imipenem-susceptible strains. No other particular cluster was observed. The enterotoxin gene (bft) was detected by PCR: DNA sequencing of the products obtained showed that the different bft alleles (bft-1, bft-2 and bft-3) were scattered randomly troughout the phylogenetic tree. No association between distinct clones and clinical manifestations (sepsis, abscesses, diarrhoea), geographical origin or host origin (human or animal) could be found.

Eradication of Borrelia burgdorferi infection in primary marginal zone B-cell lymphoma of the skin

Primary cutaneous B-cell lymphomas have been associated with Borrelia burgdorferi, the spirochete responsible for Lyme disease. Recently, cutaneous marginal zone B-cell lymphoma has been proposed as a distinct clinical-pathological entity. We report a case of primary cutaneous marginal zone lymphoma, associated with B burgdorferi infection. Polymerase chain reaction (PCR) amplification of the third complementarity determining region (CDR3) of the immunoglobulin heavy chain gene showed the presence of a monoclonal lymphoproliferation, therefore strengthening the histological diagnosis of a malignant process. B burgdorfer-specific hbb gene sequences were detected by PCR in the lymphoma tissue at diagnosis but not after antibiotic treatment. A nearly complete clinical and histological regression was observed after B burgdorferi eradication, with immunohistochemistry studies showing disappearance of plasma cell differentiation and a marked decline in the number of CD3+ T cells and Ki-67+ cells. Our case confirms the link between B burgdorferi and some cutaneous lymphomas. The disappearance of the microorganism accompanied by the unequivocal decrease of most indicators of active T- and B-cell immune response strongly supported a pathogenetic role for B burgdorferi in sustaining an antigen-driven development and growth of this cutaneous marginal zone lymphoma. Antibiotic therapy (analogous to Helicobacter pylori infection in gastric MALT lymphoma) might be helpful with the aim of averting or at least deferring the indication for more aggressive treatment.

Phylogenetic relationships among muscoidea (Diptera: calyptratae) based on mitochondrial DNA sequences

The utility of a mitochondrial DNA (mtDNA) fragment of about 1100 bp (including partial COI and COII sequences and tRNALeu) for evolutionary studies in Muscoidea is discussed. The species investigated are Scathophaga stercoraria, Microprosopa pallidicauda and Trichopalpus fraterna (family Scathophagidae), Musca domestica (Muscidae), Lasiomma seminitidum (Anthomyiidae) and Fannia armata (Fanniidae). Comparisons were made with published mtDNA sequences of Drosophila, Anopheles and three Calliphoridae species. The molecular phylogeny obtained here matches the classical morphological taxonomy reasonably well. This varies considerably, however, at different taxonomical levels. At a high taxonomic level, there is a clear separation between the Nematocera and the Brachycera, but the Calyptratae-Acalyptratae division is not always supported. At a lower taxonomic level, all species belonging to the same family are well grouped, but at an intermediate level, within the Calyptratae, it is impossible to clearly separate the Muscoidea and Calliphoridae, preventing a firm conclusion on the phylogenetic relationships among Muscoidea families. The entire COI sequence of S. stercoraria, as well as other mtDNA sequences (including the proximal portions of the COI gene, tRNATrp, tRNACys and tRNATyr genes) in Muscoidea species, are also presented and discussed.

Prevalence of Helicobacter pylori and hepatitis C virus infections among non-Hodgkin's lymphoma patients in Southern Switzerland

BACKGROUND AND OBJECTIVE

Several recent studies have reported a high rate of previous hepatitis C virus (HCV) infection in patients with non-Hodgkin's lymphoma (NHL). However, it appears that there are marked geographical differences in the prevalence of HCV among NHL patients. There is further controversy concerning a possible pathogenetic link between HCV and certain histologic lymphoma subtypes, in particular MALT lymphomas, and it has recently been speculated that HCV might be involved in the multistep process of gastric lymphoma genesis, in addition to the well established role of chronic Helicobacter pylori infection. The aim of this study was to investigate the prevalence of HCV and H. pylori infections in patients with B-cell NHL in Southern Switzerland.

DESIGN AND METHODS

One hundred and eighty newly diagnosed HIV-negative B-cell NHL patients, consecutively seen at a referral oncology center in Southern Switzerland between 1990 and 1995 were prospectively studied. A microparticle enzyme immunoassay was used to detect antibodies to HCV. Serologic determination of HCV genotype was done by the Murex method. The quantitative detection of IgG anti-H. pylori was performed by the Biorad GAP test.

RESULTS

Infection with HCV was detected in 17/180 patients (9.4%; 95% C.I., 6%-15%). This prevalence is significantly higher than that observed in a large survey of 5424 new blood donors from the same area tested in 1992-97 (0.9%; 95% C.I., 0.7-1.2). Neither histologic subtypes nor specific extranodal presentations of NHL were associated with a higher prevalence of HCV. HCV serotype 2 (corresponding to genotypes 2a-c) was the most common. HCV infection was significantly associated with a shorter progression-free survival at both univariate and multivariate analysis. Anti-Helicobacter antibodies were detected in 81/180 patients (45%; 95% C.I., 38%-53%) and H. pylori infection was significantly associated with the development of primary lymphomas of the stomach.

INTERPRETATION AND CONCLUSIONS

A high prevalence of HCV infection was detected in NHL lymphoma patients and was associated with a shorter time to lymphoma progression. HCV infection was not correlated with primary gastric presentation or with MALT-type histology. Our findings further support the key role of H.pylori infection in the pathogenesis of primary gastric lymphoma of MALT-type. The possible role of HCV in the pathogenesis of NHL should be further investigated.

High frequency of non-B subtypes in newly diagnosed HIV-1 infections in Switzerland

HIV-1 subtypes were determined in newly diagnosed residents of Switzerland. Blood was anonymously collected from patients with a first confirmed positive HIV-1 test result. Viral DNA from the env V3-V5 region was amplified by nested polymerase chain reaction (PCR) and screened for subtype B by heteroduplex mobility assay. All amplicons not identified as B were sequenced. From November 1996 to February 1998, 206 samples were analyzed. Main transmission risks were unprotected heterosexual (55.7%) or homosexual (27.1%) sexual contact or intravenous drug use (12.9%). Subtype B dominated in patients of Swiss, other European, American, or Asian citizenship; particularly high frequencies were found in homosexuals (97%) and drug users (94%). Non-B subtypes including A, C, D, E, F, G, H, a possible B/F recombinant, and a sequence related to J were present in 28.2% (95% confidence interval [CI], 22.9%-35.0%). Non-B were frequent in African citizens (95%), heterosexually infected individuals (44%), and women (43%). Heterosexually infected Swiss males harbored non-B strains in 18% and females in 33%. The results document a change in the epidemiology of newly diagnosed HIV-1 infections in Switzerland: predominance of heterosexual transmission and a high frequency of non-B subtypes.

Arguments against the involvement of Borrelia burgdorferi sensu lato in Alzheimer's disease

The involvement of spirochaetes, such as the aetiologic agent of Lyme borreliosis, Borrelia burgdorferi sensu lato, in Alzheimer's disease (AD), a common neuropathology, has been proposed by several groups in the past. In our laboratory, brains from 10 AD patients were analysed for the presence of B. burgdorferi sensu lato by both standard and nested PCR techniques based on various target regions, such as the hbb gene (encoding the histone-like protein HBb), the fla gene (flagellin), the rrl-rrf ribosomal intergenic spacer region and the rrs gene (encoding 16S rRNA). In addition, ELISA and Western blot tests for the detection of antibodies against spirochaetal antigens were performed on 27 sera from clinical AD patients. Using these methods, we did not obtain any evidence of the involvement of B. burgdorferi in Alzheimer's disease.

Tick zoonoses in the southern part of Switzerland (Canton Ticino): occurrence of Borrelia burgdorferi sensu lato and Rickettsia sp

The diversity and the distribution of tick species and their infection rates by the pathogenic micro-organism Borrelia burgdorferi sensu lato, the etiologic agent of Lyme borreliosis, and Rickettsia sp., were studied in Canton Ticino (the southern part of Switzerland). Ticks specimens collected from animals and humans were classified and analysed for the presence of both pathogens. In particular, PCR analysis was performed for the detection of Borrelia spirochetes in Ixodes ricinus and Ixodes hexagonus, and the hemolymph test was done on Rhipicephalus sanguineus for the detection of Rickettsia sp. PCR assays, performed on 424 of the 989 collected ticks, revealed a low rate of infection (around 2%) of both vectors I. ricinus and I. hexagonus by B. burgdorferi sensu lato. These results are in agreement with the modest number of Lyme borreliosis cases yearly recorded in Ticino. Further, through analysis of DNA sequences, the strains carried by the infected ticks were identified as belonging to the genomic group VS116. The widespread finding of the Mediterranean species Rhipicephalus sanguineus in different locations from July 1994 to October 1995 demonstrates its establishment in Ticino. Of the 210 specimens collected, 70 were analysed and one was infected by Rickettsia sp.

A phylogenetic analysis of Borrelia burgdorferi sensu lato based on sequence information from the hbb gene, coding for a histone-like protein

We describe a phylogenetic investigation of Borrelia burgdorferi sensu lato, the causative agent of Lyme disease, based on a DNA sequence analysis of the hbb gene, which encodes protein HBb, a member of the family of histone-like proteins. Because of their intimate contact with the DNA molecule, these proteins are believed to be fairly conserved through evolution. In this study we proved that the hbb gene is suitable for phylogenetic inference in the genus Borrelia. The hbb gene, which is 327 bp long and encodes 108 amino acids, was sequenced for 39 strains, including 37 strains of B. burgdorferi sensu lato, 1 strain of Borrelia turicatae, and 1 strain of Borrelia parkeri. Genetic variability was determined at the sequence level by computational analysis. Briefly, 81 substitutions were scored at the DNA level. Only 25 of these substitutions were responsible for amino acid substitutions at the translational level. The signature region for bacterial histone-like proteins was found in hbb. Although variable at the nucleotide level, it was highly conserved at the deduced amino acid level. A phylogenetic tree for the genus Borrelia that was generated from multiple sequence alignments was consistent with previously published data derived from DNA-DNA hybridization and multilocus enzyme electrophoresis analyses. The subdivision of B. burgdorferi sensu lato into five species (B. burgdorferi sensu stricto, Borrelia garinii, Borrelia afzelii, Borrelia japonica, and "Borrelia andersonii") and at least four genomic groups (groups PotiB2, VS116, CA2, and DN127) was confirmed.

A nested polymerase chain reaction for the detection of Borrelia burgdorferi sensu lato based on a multiple sequence analysis of the hbb gene

A highly sensitive nested polymerase chain reaction method was designed for the detection of a wide spectrum of strains from Borrelia burgdorferi sensu lato. This technique allows the detection of as little as 3 fg of total genomic DNA extracted and purified from pure cultures of the organism, this amount corresponds to less than 10 organisms. Two sets of primers homologous to conserved spots in the coding region of the hbb gene, encoding a conserved histone-like protein, were constructed. These were based on a multiple sequence alignment of 39 strains representing all the genomic groups described in B. burgdorferi sensu lato.

Analysis of the genetic polymorphism of Borrelia burgdorferi sensu lato by multilocus enzyme electrophoresis

In recent years, Borrelia burgdorferi sensu lato has been subdivided into three species, Borrelia burgdorferi sensu stricto, Borrelia garinii, and Borrelia afzelii, and a new species restricted to Japan, Borrelia japonica, has been isolated from Ixodes ovatus. In addition, members of several new genomic groups have been found in America and in Europe, suggesting that there are additional genospecies. In order to study the diversity of B. burgdorferi sensu lato, we analyzed 54 isolates, cultured from humans and from different tick species and obtained from diverse geographic areas, including Europe, the United States, Japan, and the People's Republic of China. In order to investigate the genetic relationship between microorganisms that are transmitted by soft ticks and microorganisms that cause Lyme disease, we also included three strains of relapsing fever spirochetes. The method which we used was multilocus enzyme electrophoresis; 12 genetic loci were characterized on the basis of the electrophoretic mobilities of their products, and 50 distinct allele profiles (electrophoretic types) were distinguished. The mean genetic diversity per locus was 0.747. a cluster analysis of a matrix of genetic distances for pairs of electrophoretic types revealed 11 divisions that were separated at genetic distances greater than 0.65. Five of these divisions corresponded to B. burgdorferi sensu stricto, B. garinii, B. afzelii, B. japonica, and the newly proposed species "Borrelia andersonii." Our results also confirmed that there are two additional genomic groups in Europe and at least one additional group in the United States. The relapsing fever spirochetes were were not clearly separated from the spirochetes associated with Lyme disease. In conclusion, we believe that the previously proposed subdivision of B. burgdorferi sensu lato into only four species should be reconsidered.

Use of amplified fragment length polymorphism in molecular typing of Legionella pneumophila and application to epidemiological studies

A novel method for molecular typing of organisms, amplified fragment length polymorphism analysis, was tested for its suitability in epidemiological studies in medical microbiology. Amplified fragment length polymorphism analysis, originally developed for typing crop plants, consists of a simple restriction-ligation reaction and a subsequent PCR amplification. In a single-step reaction, the genomic DNA is digested and the restriction fragments are ligated to specially constructed adapters. PCR amplification of such tagged restriction fragments with primers complementary to the adapters allows the detection of restriction fragment length polymorphisms upon resolution on agarose gels. The method is fast, efficient, and reproducible for typing strains of Legionella pneumophila isolated from both humans and the environment. The accuracy of the method was tested by comparison with standard restriction fragment length polymorphism typing performed with both a ribosomal and a genomic probe.

Association between different clinical manifestations of Lyme disease and different species of Borrelia burgdorferi sensu lato

Borrelia burgdorferi sensu lato, the aetiological agent of Lyme disease, has been subdivided into three species: B. burgdorferi sensu stricto, B. garinii and B. afzelii. We and other authors have hypothesized an association between the three species of B. burgdorferi sensu lato and some of the different clinical manifestations of Lyme disease. In order to demonstrate this hypothesis, we analysed twenty-nine isolates cultured from patients with different symptoms. The method used was multilocus enzyme electrophoresis: twelve genetic loci were characterized on the basis of the electrophoretic mobility of their products, and twenty-eight distinctive allele profiles (electrophoretic types) were distinguished, among which mean genetic diversity per locus was 0.649. Cluster analysis of a matrix of genetic distances between paired electrophoretic types revealed three primary divisions separated at genetic distances greater than 0.7 and corresponding to the three species of B. burgdorferi sensu lato. Ten strains obtained from skin of patients with erythema chronicum migrans (the primary stage of the disease) were assigned to the three different species. All the six strains isolated from patients with acrodermatitis chronica atrophicans were of the species B. afzelii, which was not found to be associated with another chronic manifestation of Lyme disease. Arthritis was caused prevalently by B. burgdorferi sensu stricto, and neuroborreliosis by B. burgdorferi sensu stricto and B. garinii. In conclusion, our results confirm the association between some of the different chronic manifestations of the disease and the species of B. burgdorferi sensu lato.

[Diarrhea and peritonitis in infection caused by type A beta hemolytic streptococcus]

During the last years the cases of severe group A streptococcus infection have increased. The clinical manifestation of this streptococcal toxic shock syndrome is similar to the better known toxic shock syndrome (TSS) provocated by staphylococcus. Shock, bacteremia and acute respiratory distress syndrome are common features, and death has been associated with this infection in 30% of patients. We present the case of a 46-year-old man who fell gravely ill with sepsis, diarrhoe, scarlatina rash, desquamation of hands and feet and acute abdomen caused by group A streptococcus infection. Finally we discussed the possible port of entry of this infection, the different clinical manifestation and the concepts of treatment.

[Multicenter evaluation of oral antibiotics: resistance behavior in 5 Swiss centers]

The susceptibility of 2196 fresh clinical isolates to twelve different oral compounds was assessed in five Swiss microbiology institutions during summer 1992. A standardized microdilution system including all other material necessary was employed to assess the antibacterial activity of penicillin G, ampicillin, ampicillin + sulbactam, amoxycillin + clavulanic acid, cefadroxil, cephalexin, cefaclor, cefuroxime, cefetamet, doxycycline, erythromycin and clindamycin. The aminopenicillins (including the beta-lactamase inhibitor combinations) were highly active against the streptococci, in combination with a beta-lactamase inhibitor they covered the majority of the bla+ E. coli and Proteus mirabilis and between 60 to 80% of the Klebsiella spp. and Proteus vulgaris isolates. All the cephalosporins exhibited good activity against the streptococci, they were active against Gram-negative fermentative rods to a varying degree. Cefetamet was also active against many cefaclor and cefuroxime-resistant isolates. A considerable part of the species studied exhibited resistance to doxycycline; the observed resistance of S. agalactia, P. mirabilis, and Morganella morganii agreed with previous findings. Most of the Streptococcus spp. were inhibited by erythromycin and clindamycin. There were only single penicillin resistant S. pneumoniae isolates in the five Swiss centers. Taking account of the above particulars the epidemiology of antimicrobial resistance in Switzerland can be considered satisfactory.

Delineation of Borrelia burgdorferi sensu stricto, Borrelia garinii sp. nov., and group VS461 associated with Lyme borreliosis

We studied 48 Borrelia isolates that were associated with Lyme borreliosis or were isolated from ticks and identified three DNA relatedness groups by using the S1 nuclease method. The three DNA groups (genospecies) were associated with specific rRNA gene restriction patterns, protein electrophoresis patterns, and patterns of reactivity with murine monoclonal antibodies. Genospecies I corresponded to Borrelia burgdorferi sensu stricto since it contained the type strain of this species (strain ATCC 35210); this genospecies included 28 isolates from Europe and the United States. Genospecies II was named Borrelia garinii sp. nov. and included 13 isolates from Europe and Japan. Genospecies III (group VS461) included seven isolates from Europe and Japan.

Population genetic analysis of Borrelia burgdorferi isolates by multilocus enzyme electrophoresis

Fifty Borellia burgdorferi strains isolated from humans and ticks in Europe and the United States were analyzed by multilocus enzyme electrophoresis. Eleven genetic loci were characterized on the basis of the electrophoretic mobilities of their products. Ten loci were polymorphic. The average number of alleles per locus was 5.9, with a mean genetic diversity of 0.673 among electrophoretic types (ETs). The strains were grouped into 35 ETs constituting three main divisions (I, II, and III) separated at a genetic distance greater than 0.75. Divisions I, II, and III contained 13, 6, and 16 ETs, respectively. These findings, together with previous data from DNA hybridization and restriction enzyme analysis of rRNA genes, suggest that divisions I, II, and III may represent three distinct genomic species. All three divisions contained human clinical ETs. However, in division I, which includes the ET of the type strain of B. burgdorferi, the human pathogenic ETs constituted a single clone. The ETs of division I were from west-central Europe and the United States, whereas divisions II and III contained ETs from west-central and northern Europe but not from the United States. Finally, our data show that the genetic structure of B. burgdorferi populations is clonal.

Assignment of Listeria grayi and Listeria murrayi to a single species, Listeria grayi, with a revised description of Listeria grayi

The genomic relatedness between Listeria grayi and Listeria murrayi was reevaluated by using DNA-DNA hybridization, multilocus enzyme electrophoresis, and rRNA restriction fragment length polymorphism techniques. The high levels of similarity observed between the strains of these two species confirmed the data published since 1973 and indicated that they should be considered members of a single species. On grounds of priority, the species should be named L. grayi.

Typing of human, animal, food, and environmental isolates of Listeria monocytogenes by multilocus enzyme electrophoresis

In order to elucidate some aspects of the epidemiology of listeriosis in Switzerland, 181 strains of Listeria monocytogenes isolated from humans, animals, food, and the environment have been analyzed by multilocus enzyme electrophoresis at 21 enzyme loci. The clone responsible for several recent food-borne outbreaks in Switzerland and in North America (marked by electrophoretic type 1 and serovar 4b) has been found frequently among strains isolated from animals. Thus, animals may represent a major source of diffusion of this clone in the environment and in food, in which it has been found only sporadically, however. Two other unrelated clones (including strains belonging to serovars 1/2b and 1/2c) have often been isolated from meat but not from animals. These findings indicate that contamination of meat with L. monocytogenes might originate mainly from the environment in which it is processed rather than from animals themselves. This could explain the differences in the distribution of L. monocytogenes serovars isolated from meat and from animals.