Development of a real-time PCR method for the detection of fossil 16S rDNA fragments of phototrophic sulfur bacteria in the sediments of Lake Cadagno.

Lake Cadagno is a crenogenic meromictic lake situated in the southern range of the Swiss Alps characterized by a compact chemocline that has been the object of many ecological studies. The population dynamics of phototrophic sulfur bacteria in the chemocline has been monitored since 1994 with molecular methods such as 16S rRNA gene clone library analysis. To reconstruct paleo-microbial community dynamics, we developed a quantitative real-time PCR methodology for specific detection of 16S rRNA gene sequences of purple and green sulfur bacteria populations from sediment samples.

Candidatus "Thiodictyon syntrophicum", sp. nov., a new purple sulfur bacterium isolated from the chemocline of Lake Cadagno forming aggregates and specific associations with Desulfocapsa sp.

Strain Cad16(T) is a small-celled purple sulfur bacterium (PSB) isolated from the chemocline of crenogenic meromictic Lake Cadagno, Switzerland. Long term in situ observations showed that Cad16(T) regularly grows in very compact clumps of cells in association with bacteria belonging to the genus Desulfocapsa in a cell-to-cell three dimensional structure. Previously assigned to the genus Lamprocystis, Cad16(T), was here reclassified and assigned to the genus Thiodictyon.

Composition of bacterial and archaeal communities in freshwater sediments with different contamination levels (Lake Geneva, Switzerland).

The aim of this study was to compare the composition of bacterial and archaeal communities in contaminated sediments (Vidy Bay) with uncontaminated sediments (Ouchy area) of Lake Geneva using 16S rRNA clone libraries. Sediments of both sites were analysed for physicochemical characteristics including porewater composition, organic carbon, and heavy metals. Results show high concentrations of contaminants in sediments from Vidy.

Thiocystis chemoclinalis sp. nov. and Thiocystis cadagnonensis sp. nov., motile purple sulfur bacteria isolated from the chemocline of a meromictic lake.

Two isolates, designated CadH11(T) and Cad448(T), representing uncultured purple sulfur bacterial populations H and 448, respectively, in the chemocline of Lake Cadagno, a crenogenic meromictic lake in Switzerland, were obtained using enrichment and isolation conditions that resembled those used for cultured members of the genus Thiocystis. Phenotypic, genotypic and phylogenetic analyses of these isolates confirmed their assignment to the genus Thiocystis. However, 16S rRNA gene sequence similarities of 98.

Inter- and intra-specific characterization of tapeworms of the genus Diphyllobothrium (Cestoda: Diphyllobothriidea) from Switzerland, using nuclear and mitochondrial DNA targets.

Human diphyllobothriosis is caused by at least 14 species of cestodes belonging to the genus Diphyllobothrium. Molecular analysis by sequencing of nuclear and mitochondrial targets identifies some species at inter- and intra-specific level, and helps to reconstruct their phylogenetic relationships. Nevertheless, the suitability of further molecular targets deserves to be widened, and the comparison of samples of different geographical origin could allow their intra-specific characterization, which could also be useful for epidemiological purposes.

Aeromonas tecta sp. nov., isolated from clinical and environmental sources.

Five Aeromonas strains, isolated from both clinical and environmental sources and characterized by a polyphasic approach, including phylogenetic analysis derived from gyrB, rpoD, and 16S rRNA gene sequencing, as well as DNA-DNA hybridization, extensive biochemical and antibiotic susceptibility tests, were recognized as members of an unknown, or undescribed, Aeromonas species. These "Aeromonas eucrenophila-like" strains were closely related to the species A. eucrenophila and Aeromonas encheleia, but they were negative for indole and acid from glycerol tests.

Evaluation of recA sequencing for the classification of Aeromonas strains at the genotype level.

Aims: To evaluate the usefulness of partial recA sequences for the identification of Aeromonas strains at the genotype level.

Methods And Results: A partial recA sequence was obtained from 21 type or reference strains and 33 Aeromonas isolates, collected in the South of Switzerland from human, animal and aquatic environments. The 272 bp long recA fragments showed a mean interspecies divergence of 7.

First record of human infection with the tapeworm Diphyllobothrium nihonkaiense in North America.

The tapeworm Diphyllobothrium nihonkaiense (Cestoda: Diphyllobothriidea), originally described from Japan, is reported from a man in North America for the first time. Species identification was based on sequences of ribosomal (partial 18S rRNA) and mitochondrial (partial Cytochrome c Oxidase subunit I) genes of proglottids expelled from a Czech tourist who ate raw Pacific sockeye salmon (Oncorhynchus nerka) from British Columbia, Canada.

Tracheobronchitis caused by Aeromonas veronii biovar sobria after near-drowning.

A 19-year-old man developed an acute tracheobronchitis shortly after having been rescued from a near-drowning in a river where previous investigations had demonstrated the presence of 500 c.f.u.

Imported diphyllobothriasis in Switzerland: molecular evidence of Diphyllobothrium dendriticum (Nitsch, 1824).

We report for the first time in Switzerland a clinical case because of Diphyllobothrium dendriticum, identified by molecular methods. We discuss the potential for this imported species to infect local intermediate hosts and thus to achieve autochthonous cyclic transmission.

Diphyllobothrium nihonkaiense (Yamane et al., 1986) in Switzerland: first molecular evidence and case reports.

We report the first cases of locally-acquired Diphyllobothrium nihonkaiense (Yamane, Kamo, Bylund and Wikgren, 1986) in Switzerland, confirmed by genetic analysis (18S rRNA, COI and ITS1-5.8S rRNA-ITS2 genes). Diphyllobothriasis in this country is attributed to the tapeworm D.

Genetic relationships of Aeromonas strains inferred from 16S rRNA, gyrB and rpoB gene sequences.

Genetic relationships among bacterial strains belonging to the genus Aeromonas were inferred from 16S rRNA, gyrB and rpoB gene sequences. Twenty-eight type or collection strains of the recognized species or subspecies and 33 Aeromonas strains isolated from human and animal specimens as well as from environmental samples were included in the study. As reported previously, the 16S rRNA gene sequence is highly conserved within the genus Aeromonas, having only limited resolution for this very tight group of species.

Molecular identification of Bacillus thuringiensis var. israelensis to trace its fate after application as a biological insecticide in wetland ecosystems.

Aims: To determine the fate of viable Bacillus thuringiensis var. israelensis (Bti) spores dispersed in the environment, using a universally applicable molecular detection methodology.

Methods And Results: Soil samples were spread on growth medium, after a temperature selection of the spores.

Molecular identification of an uncultured bacterium ("morphotype R") in meromictic Lake Cadagno, Switzerland.

Comparative sequence analysis of almost complete 16S rRNA genes of members of the Desulfobacteriaceae retrieved from two gene clone libraries of uncultured bacteria of the chemocline of Lake Cadagno, Switzerland, resulted in the molecular identification of nine sequences, with a tight cluster of five sequences that represented at least three different populations of bacteria with homology values of 95% and 93% to their closest cultured relatives Desulfomonile tiedjei and Desulfomonile limimaris, respectively. In situ hybridization with probes DsmA455 targeting two subpopulations and DsmB455 targeting one subpopulation, detected bacteria with a peculiar morphology previously described as "morphotype R". The individual probes detected about the same number of cells in all samples and together added up to represent all cells of "morphotype R" suggesting that the basic ecophysiological requirements of the subpopulations might be similar.

Long-term population dynamics of phototrophic sulfur bacteria in the chemocline of Lake Cadagno, Switzerland.

Population analyses in water samples obtained from the chemocline of crenogenic, meromictic Lake Cadagno, Switzerland, in October for the years 1994 to 2003 were studied using in situ hybridization with specific probes. During this 10-year period, large shifts in abundance between purple and green sulfur bacteria and among different populations were obtained. Purple sulfur bacteria were the numerically most prominent phototrophic sulfur bacteria in samples obtained from 1994 to 2001, when they represented between 70 and 95% of the phototrophic sulfur bacteria.

Consensus sequence-based scheme for epidemiological typing of clinical and environmental isolates of Legionella pneumophila.

A previously described sequence-based epidemiological typing method for clinical and environmental isolates of Legionella pneumophila serogroup 1 was extended by the investigation of three additional gene targets and modification of one of the previous targets. Excellent typeability, reproducibility, and epidemiological concordance were determined for isolates belonging to both serogroup 1 and the other serogroups investigated. Gene fragments were amplified from genomic DNA, and PCR amplicons were sequenced by using forward and reverse primers.

Molecular typing of Yersinia frederiksenii strains by means of 16s rDNA and gyrB genes sequence analyses.

The phenospecies Yersinia frederiksenii is known to comprise three genospecies, indistinguishable on the basis of phenotypic characteristics. In previous works, 13 strains, identified biochemically as Y. frederiksenii, were characterized using Multilocus enzyme electrophoresis and Ribotyping.

Polyphasic taxonomic study of "Aeromonas eucrenophila-like" isolates from clinical and environmental sources.

In the current study, a group of 17 "Aeromonas eucrenophila-like" isolates from clinical and environmental origins was subjected to a polyphasic taxonomic characterization including ribotyping, 16S rDNA sequencing, FAFLP fingerprinting, and biochemical testing. Genotypic, phylogenetic, and phenotypic results were consistent with the conclusion that this group of 17 isolates may represent a currently undescribed Aeromonas taxon most closely related to A. eucrenophila HG6.

Current situation of human diphyllobothriasis in Europe.

Diphyllobothriasis, a parasitosis caused by the flatworm Diphyllobothrium latum, is contracted by consuming raw or undercooked freshwater fish. The aim of this study was to evaluate the situation of this parasitosis during the past 20 years in Europe through the analysis of databases and search engines (Medline, Cabi Helminthological abstracts,Yahoo, Google), and through a questionnaire sent to a network of European parasitologists and to microbiological laboratories located on the shores of the large Alpine lakes. This study has shown that several dozen cases have been reported each year in Finland and Sweden, that there have been numerous cases in the French or Italian speaking areas of subalpine lakes, and that sporadic cases only have been observed in Austria, Spain, Greece, Romania, Poland and Norway.

Current situation of human diphyllobothriasis in Europe.

Diphyllobothriasis, a parasitosis caused by the flatworm Diphyllobothrium latum, is contracted by consuming raw or undercooked freshwater fish. The aim of this study was to evaluate the situation of this parasitosis during the past 20 years in Europe through the analysis of databases and search engines (Medline, Cabi Helminthological abstracts,Yahoo, Google), and through a questionnaire sent to a network of European parasitologists and to microbiological laboratories located on the shores of the large Alpine lakes. This study has shown that several dozen cases have been reported each year in Finland and Sweden, that there have been numerous cases in the French or Italian speaking areas of subalpine lakes, and that sporadic cases only have been observed in Austria, Spain, Greece, Romania, Poland and Norway.

Arthrobacter woluwensis subacute infective endocarditis: case report and review of the literature.

We report a case of endocarditis due to Arthrobacter woluwensis and review the published reports of Arthrobacter species isolated from human clinical samples. A 39-year-old injection drug user presented with fever and a new heart murmur. A.

Sequence-based typing of Legionella pneumophila serogroup 1 offers the potential for true portability in legionellosis outbreak investigation.

Seven gene loci of Legionella pneumophila serogroup 1 were analyzed as potential epidemiological typing markers to aid in the investigation of legionella outbreaks. The genes chosen included four likely to be selectively neutral (acn, groES, groEL, and recA) and three likely to be under selective pressure (flaA, mompS, and proA). Oligonucleotide primers were designed to amplify 279- to 763-bp fragments from each gene.

Spatio-temporal distribution of phototrophic sulfur bacteria in the chemocline of meromictic Lake Cadagno (Switzerland).

Abstract In situ hybridization was used to study the spatio-temporal distribution of phototrophic sulfur bacteria in the permanent chemocline of meromictic Lake Cadagno, Switzerland. At all four sampling times during the year the numerically most important phototrophic sulfur bacteria in the chemocline were small-celled purple sulfur bacteria of two yet uncultured populations designated D and F. Other small-celled purple sulfur bacteria (Amoebobacter purpureus and Lamprocystis roseopersicina) were found in numbers about one order of magnitude lower.

Epidemiology of methicillin-resistant Staphylococcus aureus: results of a nation-wide survey in Switzerland.

Objective: To assess the epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) in Switzerland.

Material And Methods: One-year national survey of all MRSA cases detected in a large sample of Swiss healthcare institutions (HCI). Analysis of epidemiological and molecular typing data (PFGE) of MRSA strains.

Persistence of viral pathogens and bacteriophages during sewage treatment: lack of correlation with indicator bacteria.

The effects of different sewage treatments on the viral contamination in rivers which receive water from treatment plants without a final sand filtration step were investigated. They were all heavily contaminated with bacteriophages and human enteric viruses (detected by single step reverse transcription amplification followed by a nested polymerase chain reaction). Bacteriophages, but not faecal indicator organisms, were correlated with viral contamination.