Evidence of horizontal gene transfer between human and animal commensal Escherichia coli strains identified by microarray

Bacteria exchange genetic material by horizontal gene transfer (HGT). To evaluate the impact of HGT on Escherichia coli genome plasticity, 19 commensal strains collected from the intestinal floras of humans and animals were analyzed by microarrays. Strains were hybridized against an oligoarray containing 2700 E. coli K12 chromosomal genes. A core (genes shared among compared genomes) and a flexible gene pool (genes unique for each genome) have been identified. Analysis of hybridization signals evidenced 1015 divergent genes among the 19 strains and each strain showed a specific genomic variability pattern. Four hundred and fifty-eight genes were characterized by higher rates of interstrain variation and were considered hyperdivergent. These genes are not randomly distributed onto the chromosome but are clustered in precise regions. Hyperdivergent genes belong to the flexible gene pool and show a specific GC content, differing from that of the chromosome, indicating acquisition by HGT. Among these genes, those involved in defense mechanisms and cell motility as well as intracellular trafficking and secretion were far more represented than others. The observed genome plasticity contributes to the maintenance of genetic diversity and may therefore be a source of evolutionary adaptation and survival.

Comparative genomic hybridization and physiological characterization of environmental isolates indicate that significant (eco-)physiological properties are highly conserved in the species Escherichia coli

Escherichia coli, the common inhabitant of the mammalian intestine, exhibits considerable intraspecies genomic variation, which has been suggested to reflect adaptation to different ecological niches. Also, regulatory trade-offs, e.g. between catabolic versatility and stress protection, are thought to result in significant physiological differences between strains. For these reasons, the relevance of experimental observations made for 'domesticated' E. coli strains with regard to the behaviour of this species in its natural environments is often questioned and doubts are frequently raised on the status of E. coli as a defined species. The variability of important (eco-)physiological functions, such as carbon substrate uptake and breakdown capabilities, as well as stress defence mechanisms, in the genomes of commensal and pathogenic E. coli strains were therefore investigated. Furthermore, (eco-)physiological properties of environmental strains were compared to standard laboratory strain K-12 MG1655. Catabolic, stress protection, and carbon- and energy source transport operons showed a very low intraspecies variability in 57 commensal and pathogenic E. coli. Environmental isolates adapted to glucose-limited growth in a similar way as E. coli MG1655, namely by increasing their catabolic flexibility and by inducing high-affinity substrate uptake systems. The results obtained indicate that significant (eco-)physiological properties are highly conserved in the natural population of E. coli. This questions the proposed dominant role of horizontal gene transfer for niche adaptation.

Distribution and characterization of integrons in Escherichia coli strains of animal and human origin

One hundred and twenty clinical and commensal Escherichia coli strains isolated in Switzerland from humans and from companion and farm animals were analysed for the prevalence of integrons of classes 1, 2, and 3 and for the characterization of their gene cassettes. The relationships between integron carriage and host category, and between integron carriage and phylogenetic E. coli lineage were also analysed. Integrons were detected in 48 (40%) of the isolates and were thus widely disseminated in the human and animal E. coli strains considered. Moreover, the association between integron carriage and certain animal categories (farm animals) suggests that animals that are raised for economic purposes might be exposed to a major antibiotic pressure. Finally, our data confirm that E. coli commensal strains represent a significant source of antibiotic-resistant determinants.

Human adaptive immune system Rag2-/-gamma(c)-/- mice

Although many biologic principles are conserved in mice and humans, species-specific differences exist, for example, in susceptibility and response to pathogens, that often do not allow direct implementation of findings in experimental mice to humans. Research in humans, however, for ethical and practical reasons, is largely restricted to in vitro assays that lack components and the complexity of a living organism. To nevertheless study the human hematopoietic and immune system in vivo, xenotransplantation assays have been developed that substitute human components to small animals. Here, we summarize our recent findings that transplantation of human cord blood CD34(+) cells to newborn Rag2(-/-)gamma(c)(-/-) mice leads to de novo development of major functional components of the human adaptive immune system. These human adaptive immune system Rag2(-/-)gamma(c)(-/-) (huAIS-RG) mice can now be used as a technically straightforward preclinical model to evaluate in vivo human adaptive immune system development as well as immune responses, for example, to vaccines or live infectious pathogens.

Diversity of the population of Tick-borne encephalitis virus infecting Ixodes ricinus ticks in an endemic area of central Switzerland (Canton Bern)

Tick-borne encephalitis virus (TBEV), a member of the genus Flavivirus, has a positive-strand RNA genome containing a single open reading frame flanked by non-coding regions (NCRs). Ixodes ricinus ticks (n=307) were collected from vegetation in a natural TBEV focus in Belp, Switzerland. The presence and identity of the virus were determined by nested RT-PCR followed by sequencing of the 5′-terminal region that comprises the 5′ NCR and the capsid-encoding region (C). The presence of the western European TBEV subtype (W-TBEV) genome was detected in 14.3 % of the ticks. Nucleotide sequence analysis revealed a high variability of 55.5 %. In particular, four DNA fragments (CS ‘A’, CS ‘B’, the folding-stem structure and the start codon) showed substantial heterogeneity, which has the potential of compromising replication, translation and packaging of the viral genome. This variability may reflect a viral strategy to select the fittest RNA molecule to produce a viral infection in the different vertebrate hosts that may be encountered by the ticks. It may also indicate a possible ancient introduction of TBEV to the Belp site. In addition, it may contribute to explaining the annual low incidence of tick-borne encephalitis in the natural focus of Belp, despite the high prevalence of TBEV genomes in ticks.

Gastroretentive dosage forms: Overview and special case of Helicobacter pylori

The challenge to develop efficient gastroretentive dosage forms began about 20 years ago, following the discovery of Helicobacter pylori by Warren and Marshall. In order to understand the real difficulty of increasing the gastric residence time of a dosage form, we have first summarized the important physiologic parameters, which act upon the gastric residence time. Afterwards, we have reviewed the different drug delivery systems designed until now, i.e. high-density, intragastric floating, expandable, superporous hydrogel, mucoadhesive and magnetic systems. Finally, we have focused on gastroretentive dosage forms especially designed against H. pylori, including specific targeting systems against this bacterium.

Presence of potentially pathogenic Babesia sp. for human in Ixodes ricinus in Switzerland

We have designed and performed a new PCR method based on the 18S rRNA in order to individuate the presence and the identity of Babesia parasites. Out of 1159 Ixodes ricinus (Acari: Ixodidae) ticks collected in four areas of Switzerland, nine were found to contain Babesia DNA. Sequencing of the short amplicon obtained (411-452 bp) allowed the identification of three human pathogenic species: Babesia microti, B. divergens, for the first time in Switzerland, Babesia sp. EU1. We also report coinfections with B. sp. EU1-Borrelia burgdorferi sensu stricto and Babesia sp. EU1-B. afzelii.

Diversity within Borrelia burgdorferi sensu lato genospecies in Switzerland by recA gene sequence

A total of 874 Ixodes ricinus ticks were collected in Switzerland to investigate the genetic diversity of the Borrelia population. We integrated to the RT-PCR method the DNA sequence analysis of a 162-bp fragment of the recA gene. Five genospecies were detected: Borrelia afzelii, Borrelia burgdorferi s.s., Borrelia garinii, Borrelia valaisiana, and Borrelia lusitaniae. A heterogeneous distribution was observed within the B. burgdorferi s.l. genospecies. The most prevalent and diverse genospecies found in Switzerland was Borrelia afzelii, which might suggest a rapid evolution of this genospecies.

Development of a human adaptive immune system in cord blood cell-transplanted mice

Because ethical restrictions limit in vivo studies of the human hemato-lymphoid system, substitute human to small animal xenotransplantation models have been employed. Existing models, however, sustain only limited development and maintenance of human lymphoid cells and rarely produce immune responses. Here we show that intrahepatic injection of CD34+ human cord blood cells into conditioned newborn Rag2-/-gammac-/- mice leads to de novo development of B, T, and dendritic cells; formation of structured primary and secondary lymphoid organs; and production of functional immune responses. This provides a valuable model to study development and function of the human adaptive immune system in vivo.

Prevalence of human T-cell leukemia virus types I and II in Switzerland

The retroviruses human immunodeficiency virus (HIV)-1/2 and human T-cell leukemia virus (HTLV)-I/II share modes of transmission, suggesting that efforts to monitor the current HIV-1 epidemic in Switzerland should be complemented by assessment of HTLV-I/II prevalence. This study presents an updated evaluation of HTLV-I/II infection among groups within the Swiss population polarized towards either low or increased risk of infection. Archived serum and peripheral blood mononuclear cell (PBMC) samples were examined for evidence of HTLV-I/II infection by enzyme-linked immunosorbant assay (ELISA), type-specific Western blot, type-specific polymerase chain reaction (PCR), DNA sequence analysis, and virus culture. Among blood donations obtained from low-risk Swiss donors, we report a complete lack of HTLV-II infection and the occurrence of HTLV-I infection limited to a prevalence of 0.079 per 100,000 (1/1,266,466). Among high-risk HIV-positive persons and HIV-negative persons at increased risk of HIV-infection, we report a focus of HTLV-I and HTLV-II infection at prevalence rates of 62 per 100,000 (1/1,620) and 309 per 100,000 (5/1,620), respectively. The finding of low HTLV-I/II prevalence among Swiss blood donors and containment of HTLV-I/II infection within known risk-groups does not support initiation of HTLV-I/II screening for Swiss blood, tissue, and organ donations.

Population genetics of Vibrio vulnificus: identification of two divisions and a distinct eel-pathogenic clone

Genetic relationships among 62 Vibrio vulnificus strains of different geographical and host origins were analyzed by multilocus enzyme electrophoresis (MLEE), random amplification of polymorphic DNA (RAPD), and sequence analyses of the recA and glnA genes. Out of 15 genetic loci analyzed by MLEE, 11 were polymorphic. Cluster analysis identified 43 distinct electrophoretic types (ETs) separating the V. vulnificus population into two divisions (divisions I and II). One ET (ET 35) included all indole-negative isolates from diseased eels worldwide (biotype 2). A second ET (ET 2) marked all of the strains from Israel isolated from patients who handled St. Peter's fish (biotype 3). RAPD analysis of the 62 V. vulnificus isolates identified 26 different profiles separated into two divisions as well. In general, this subdivision was comparable (but not identical) to that observed by MLEE. Phylogenetic analysis of 543 bp of the recA gene and of 402 bp of the glnA gene also separated the V. vulnificus population into two major divisions in a manner similar to that by MLEE and RAPD. Sequence data again indicated the overall subdivision of the V. vulnificus population into different biotypes. In particular, indole-negative eel-pathogenic isolates (biotype 2) on one hand and the Israeli isolates (biotype 3) on the other tended to cluster together in both gene trees. None of the methods showed an association between distinct clones and human clinical manifestations. Furthermore, except for the Israeli strains, only minor clusters comprising geographically related isolates were observed. In conclusion, all three approaches (MLEE, RAPD, and DNA sequencing) generated comparable but not always equivalent results. The significance of the two divisions (divisions I and II) still remains to be clarified, and a reevaluation of the definition of the biotypes is also needed.

Clinical implications of Mycobacterium kansasii species heterogeneity: Swiss National Survey

Several subtypes of Mycobacterium kansasii have been described, but their respective pathogenic roles are not clear. This study investigated the distribution of subtypes and the pathogenicity of M. kansasii strains (n = 191) isolated in Switzerland between 1991 and 1997. Demographic, clinical, and microbiological information was recorded from clinical files. Patients were classified as having an infection according to the criteria of the American Thoracic Society. Subtypes were defined by PCR-restriction enzyme analysis of the hsp65 gene. Subtype 1 comprised 67% of the isolates (n = 128), while subtypes 2 and 3 comprised 21% (n = 40) and 8% (n = 15), respectively. Other subtypes (subtypes 4 and 6 and a new subtype, 7) were recovered from only 4% of patients (n = 8). M. kansasii subtype 1 was considered pathogenic in 81% of patients, while M. kansasii subtype 2 was considered pathogenic in 67% of patients and other subtypes were considered pathogenic in 6% of patients. The majority of patients with M. kansasii subtype 2 were immunocompromised due to the use of corticosteroids (21% of patients) or coinfection with HIV (62.5% of patients). Subtyping M. kansasii may improve clinical management by distinguishing pathogenic from nonpathogenic subtypes.

Rhipicephalus ticks infected with Rickettsia and Coxiella in Southern Switzerland (Canton Ticino)

Ticks of the Rhipicephalus sanguineus species complex may be vector of various pathogens including Rickettsia conorii (the etiological agent of the Mediterranean spotted fever) and Coxiella burnetii (cause of the Query (Q) fever). R. sanguineus ticks have been imported in several parts of central and northern Europe, especially in environments such as kennels and houses providing the appropriate microclimatic conditions and the blood source necessary for their survival. Since 1940 these ticks have occasionally been recorded in Switzerland. In Ticino (the southern part of Switzerland), they have been reported since 1980 and their probable establishment in this area has been suggested in the '90s. By means of PCR and direct sequencing, we tested the identity of these ticks (using 12S rDNA gene) and the occurrence of Rickettsia spp. (using 16S rDNA, gltA and OmpA genes) as well as Coxiella sp. (using 16S rDNA). The results indicated that in Ticino, two different tick species coexist, i.e. R. sanguineus sensu stricto and Rhipicephalus turanicus. A few individuals of R. sanguineus sensu stricto are infected with Rickettsia massiliae/Bar29, which are strains of unknown pathogenicity. Coxiella sp., an endosymbiont of Rhipicephalus ticks, has also been identified in both tick species. Due to climatic changes towards global warming, imported tick species may therefore adapt to new area and might be considered as epidemiological markers for a number of infectious agents transmitted by them.

RecA and glnA sequences separate the bacteroides fragilis population into two genetic divisions associated with the antibiotic resistance genotypes cepA and cfiA

The sequences of part of the glutamine synthetase-encoding gene (glnA) and of the RecA-encoding gene (recA) were determined and aligned for 45 Bacteroides fragilis isolates from different clinical and geographical origin. The patterns of sequence divergence of glnA and recA were very similar. The sequences of a 303-bp fraction of recA showed 45 nucleotide substitutions, 40 of which allowed the separation of B. fragilis into two major divisions, which were not found when the deduced amino acid sequences were considered. The 687-bp sequences analysed for the glnA gene showed 112 nucleotide substitutions, 96 of which separated the population into the same two divisions as those described for recA. In this case, the deduced amino acid sequences showed this subdivision as well: three of the six observed amino acid substitutions were division-specific. Within the two divisions, both genes presented a high degree of sequence conservation. Each B. fragilis division was associated with the presence of a different antibiotic resistance gene: cepA encoding a serine-beta-lactamase (division I) and cfiA encoding a metallo-beta-lactamase (division II). No particular clusters associated with geographical or clinical origin, or with the production of an enterotoxin were observed. Sequencing of the cfiA gene allowed identification of two different alleles in division II. However, no association of these different cfiA alleles with the expression of imipenem resistance was observed. In conclusion, the phylogenetic patterns observed by sequencing recA and glnA are in agreement with those obtained previously by MLEE (multilocus enzyme electrophoresis). Thus, it appears that the evolution of recA and glnA genes is similar to that of the whole chromosome of B. fragilis. Horizontal gene transfer between divisions I and II seems to be low, at best. However, the results of the present study could not clarify definitively whether divisions I and II should be considered as two different B. fragilis genospecies.

Molecular population genetic analysis of Campylobacter jejuni HS:19 associated with Guillain-Barré syndrome and gastroenteritis

Infection with Campylobacter jejuni serotype HS:19 is associated with the development of Guillain-Barré syndrome (GBS). To determine whether a particular HS:19 clone is associated with GBS, multilocus enzyme electrophoresis (MLEE) was used to analyze a worldwide collection of isolates. There were 34 electropherotypes (ETs) in 3 phylogenetic clusters among 83 C. jejuni isolates. Cluster I contained all HS:19 strains, and a single ET (ET4) accounted for most HS:19 strains. HS:19 strains did not occur in any of the other clusters. ET4 contained isolates from different geographic locations, indicating global spread of this clone. Furthermore, ET4 contained isolates from patients with uncomplicated enteritis and GBS, as well as isolates from animal sources. The results of this study show that HS:19 strains comprise a clonal, although not monomorphic, population, which is distinct from non-HS:19 strains within C. jejuni. A unique clone associated with GBS was not identified by use of MLEE.

Absence of clonality of Campylobacter jejuni in serotypes other than HS:19 associated with Guillain-Barré syndrome and gastroenteritis

Guillain-Barré syndrome (GBS) is recognized as a complication that occurs after Campylobacter infection. Certain Penner serotypes, such as HS:19, are linked particularly to GBS in some parts of the world, and there is good evidence for restricted genetic diversity in these isolates. However, GBS also occurs after Campylobacter infection due to other serotypes. Therefore, we asked whether Campylobacter jejuni non-HS:19 serotypes associated with GBS have a clonal structure and differ from strains isolated from patients with Campylobacter gastroenteritis. A worldwide selected population of C. jejuni non-HS:19 strains associated with GBS and gastroenteritis was analyzed by use of multilocus enzyme electrophoresis, automated ribotyping, pulsed-field gel electrophoresis, and flagellin gene typing. The results show that these isolates represent a heterogenic population and do not constitute a unique population across serotypes. No epidemiologic marker for GBS-associated strains was identified.

Population genetics of Helicobacter pylori in the southern part of Switzerland analysed by sequencing of four housekeeping genes (atpD, glnA, scoB and recA), and by vacA, cagA, iceA and IS605 genotyping

The population biology of 78 Helicobacter pylori strains (71 from Swiss Italian, 4 from East Asian and 3 from South African patients) was investigated by sequence analysis of four housekeeping genes: atpD, scoB, glnA and recA. The vacA genotype, the presence of cagA and IS605, the iceA allelic type, and the resistance to metronidazole, clarithromycin and amoxycillin were determined. A high percentage of DNA polymorphic sites (19.8% for atpD, 21.3% for scoB, 23.7% for glnA and 20.3% for recA) was found. The phylogenetic trees based on the nucleotide sequences of the four gene fragments showed different topologies and were incongruent. The virulence-associated markers were distributed over the dendrograms and no association was found with phylogenetic clusters or clinical manifestations (chronic gastritis, gastric or duodenal ulcer, MALT lymphoma). Moreover, the H ratios (calculated with the homoplasy test) ranged from 0.742 to 0.799, depending on the gene fragment examined. All these observations suggest that H. pylori exists as a recombinant population. The clustering of the strains according to their geographical origin (USA/Europe, East Asia, South Africa) that has recently been demonstrated elsewhere could only be confirmed for the East Asian vacA s1c strains. In contrast, the South African strains clustered together only in the atpD tree. Presumably, recombination at the different loci has masked the evolutionary relationship among the strains.

Clinical progression, survival, and immune recovery during antiretroviral therapy in patients with HIV-1 and hepatitis C virus coinfection: the Swiss HIV Cohort Study

BACKGROUND

Hepatitis C virus (HCV) infection is highly prevalent among HIV-1-infected individuals, but its contribution to the morbidity and mortality of coinfected patients who receive potent antiretroviral therapy is controversial. We used data from the ongoing Swiss HIV Cohort Study to analyse clinical progression of HIV-1, and the virological and immunological response to potent antiretroviral therapy in HIV-1-infected patients with or without concurrent HCV infection.

METHODS

We analysed prospective data on survival, clinical disease progression, suppression of HIV-1 replication, CD4-cell recovery, and frequency of changes in antiretroviral therapy according to HCV status in 3111 patients starting potent antiretroviral therapy.

RESULTS

1157 patients (37.2%) were coinfected with HCV, 1015 of whom (87.7%) had a history of intravenous drug use. In multivariate Cox's regression, the probability of progression to a new AIDS-defining clinical event or to death was independently associated with HCV seropositivity (hazard ratio 1.7 [95% CI 1.26-2.30]), and with active intravenous drug use (1.38 [1.02-1.88]). Virological response to antiretroviral therapy and the probability of treatment change were not associated with HCV serostatus. In contrast, HCV seropositivity was associated with a smaller CD4-cell recovery (hazard ratio for a CD4-cell count increase of at least 50 cells/microL=0.79 [0.72-0.87]).

INTERPRETATION

HCV and active intravenous drug use could be important factors in the morbidity and mortality among HIV-1-infected patients, possibly through impaired CD4-cell recovery in HCV seropositive patients receiving potent antiretroviral therapy. These findings are relevant for decisions about optimum timing for HCV treatment in the setting of HIV infection.

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.