Cantonal Institute of Microbiology

Bellinzona, Switzerland

Cantonal Institute of Microbiology

Bellinzona, Switzerland
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Gaia V.,Cantonal Institute of Microbiology | Gaia V.,National Reference Center for Legionella | Casati S.,Cantonal Institute of Microbiology | Casati S.,National Reference Center for Legionella | And 2 more authors.
Systematic and Applied Microbiology | Year: 2011

A set of reference strains representing 38 different Legionella species were submitted to Whole Cell Mass Spectrometry (WCMS) with MALDI-TOF.The dendrogram computed from strain mass spectral patterns obtained by WCMS was compared to the phylogenetic tree obtained from macrophage infectivity potentiator (mip) sequences. The trees inferred from these two methods revealed significant homologies.Using 453 Legionella isolates previously characterized by genotyping, it was possible to create species-specific SuperSpectra, using appropriate sets of spectral masses, allowing unambiguous differentiation and identification of the most frequently isolated Legionella species. These SuperSpectra were tested for their suitability to identify Legionella strains isolated from water samples, cooling towers, potting soils and patient specimens deposited at the Swiss National Reference Centre for Legionella and previously identified by molecular methods such as mip gene sequencing.99.1% of the tested strains isolated from the environment could be correctly identified by comparison with the new SuperSpectra. The identification of Legionella spp. by MALDI-TOF MS is rapid, easy to perform and has the advantage of being time- and cost-saving, in comparison to sequence-based identification. © 2010 Elsevier GmbH.

Casati S.,Cantonal Institute of Microbiology | Conza L.,Cantonal Institute of Microbiology | Bruin J.,Regional Public Health Laboratory Kennemerland | Gaia V.,Cantonal Institute of Microbiology
Clinical Microbiology and Infection | Year: 2010

Data on the presence of Legionellae outside the aquatic environment are scarce. Alternative ecosystems that could act as a reservoir for Legionella spp. have been investigated to identify unconventional contaminated substrates that are able to produce bioaerosols. We considered eight green waste collection sites including three composting facilities. Legionella pneumophila sg 1-15, Legionella bozemanii, Legionella cincinnatiensis, Legionella jamestowniensis, Legionella micdadei and L. oakridgensis were isolated from samples taken at six of the eight sites. The degree of contamination ranged from 103 to 108 CFU/g. Compost facilities appear to comprise an important reservoir for Legionellae. © 2009 The Authors. Journal Compilation © 2009 European Society of Clinical Microbiology and Infectious Diseases.

Conza L.,Cantonal Institute of Microbiology | Casati S.,Cantonal Institute of Microbiology | Gaia V.,Cantonal Institute of Microbiology
BMC Microbiology | Year: 2013

Background: The efficiency of recovery and the detection limit of Legionella after co-culture with Acanthamoeba polyphaga are not known and so far no investigations have been carried out to determine the efficiency of the recovery of Legionella spp. by co-culture and compare it with that of conventional culturing methods. This study aimed to assess the detection limits of co-culture compared to culture for Legionella pneumophila in compost and air samples. Compost and air samples were spiked with known concentrations of L. pneumophila. Direct culturing and co-culture with amoebae were used in parallel to isolate L. pneumophila and recovery standard curves for both methods were produced for each sample. Results: The co-culture proved to be more sensitive than the reference method, detecting 102-103 L. pneumophila cells in 1 g of spiked compost or 1 m3 of spiked air, as compared to 105-106 cells in 1 g of spiked compost and 1 m3 of spiked air. Conclusions: Co-culture with amoebae is a useful, sensitive and reliable technique to enrich L. pneumophila in environmental samples that contain only low amounts of bacterial cells. © 2013 Conza et al; licensee BioMed Central Ltd.

Benagli C.,Cantonal Institute of Microbiology | Rossi V.,Cantonal Institute of Microbiology | Dolina M.,Cantonal Institute of Microbiology | Tonolla M.,Cantonal Institute of Microbiology | And 2 more authors.
PLoS ONE | Year: 2011

Background: Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) allows rapid and reliable identification of microorganisms, particularly clinically important pathogens. Methodology/Principal Findings: We compared the identification efficiency of MALDI-TOF MS with that of Phoenix®, API® and 16S ribosomal DNA sequence analysis on 1,019 strains obtained from routine diagnostics. Further, we determined the agreement of MALDI-TOF MS identifications as compared to 16S gene sequencing for additional 545 strains belonging to species of Enterococcus, Gardnerella, Staphylococcus, and Streptococcus. For 94.7% of the isolates MALDI-TOF MS results were identical with those obtained with conventional systems. 16S sequencing confirmed MALDI-TOF MS identification in 63% of the discordant results. Agreement of identification of Gardnerella, Enterococcus, Streptococcus and Staphylococcus species between MALDI-TOF MS and traditional method was high (Crohn's kappa values: 0.9 to 0.93). Conclusions/Significance: MALDI-TOF MS represents a rapid, reliable and cost-effective identification technique for clinically relevant bacteria. © 2011 Benagli et al.

Hahn D.,Texas State University | Mirza B.,Texas State University | Benagli C.,Cantonal Institute of Microbiology | Vogel G.,Mabritec AG | And 2 more authors.
Systematic and Applied Microbiology | Year: 2011

Matrix-assisted laser desorption ionization-time-of-flight (MALDI-TOF) mass spectrometry (MS) was evaluated as a technique to characterize strains of the nitrogen-fixing actinomycete Frankia. MALDI-TOF MS reliably distinguished 37 isolates within the genus Frankia and assigned them to their respective host infection groups, i.e., the Alnus/. Casuarina and the Elaeagnus host infection groups. The assignment of individual strains to sub-groups within the respective host infection groups was consistent with classification based on comparative sequence analysis of nifH gene fragments, confirming the usefulness of MALDI-TOF MS as a rapid and reliable tool for the characterization of Frankia strains. © 2010 Elsevier GmbH.

Guidi V.,Microbial Ecology Group | Guidi V.,Cantonal Institute of Microbiology | Patocchi N.,Bolle Of Magadino Foundation | Luthy P.,ETH Zurich | And 2 more authors.
Applied and Environmental Microbiology | Year: 2011

Recurrent treatments with Bacillus thuringiensis subsp. israelensis are required to control the floodwater mosquito Aedes vexans that breeds in large numbers in the wetlands of the Bolle di Magadino Reserve in Canton Ticino, Switzerland. Interventions have been carried out since 1988. In the present study, the spatial distribution of resting B. thuringiensis subsp. israelensis spores in the soil was measured. The B. thuringiensis subsp. israelensis concentration was determined in soil samples collected along six transects covering different elevations within the periodically flooded zones. A total of 258 samples were processed and analyzed by quantitative PCR that targeted an identical fragment of 159 bp for the B. thuringiensis subsp. israelensis cry4Aa and cry4Ba genes. B. thuringiensis subsp. israelensis spores were found to persist in soils of the wetland reserve at concentrations of up to 6.8 log per gram of soil. Continuous accumulation due to regular treatments could be excluded, as the decrease in spores amounted to 95.8% (95% confidence interval, 93.9 to 97.7%). The distribution of spores was correlated to the number of B. thuringiensis subsp. israelensis treatments, the elevation of the sampling point, and the duration of the flooding periods. The number of B. thuringiensis subsp. israelensis treatments was the major factor influencing the distribution of spores in the different topographic zones (P < 0.0001). These findings indicated that B. thuringiensis subsp. israelensis spores are rather immobile after their introduction into the environment. © 2011, American Society for Microbiology.

Samuels G.J.,U.S. Department of Agriculture | Ismaiel A.,U.S. Department of Agriculture | Bon M.-C.,European Biological Control Laboratory EBCL | De Respinis S.,Cantonal Institute of Microbiology | Petrini O.,Cantonal Institute of Microbiology
Mycologia | Year: 2010

Analysis of a worldwide collection of strains of Trichoderma asperellum sensu lato using multilocus genealogies of four genomic regions (tef1, rpb2, act, ITS1, 2 and 5.8s rRNA), sequence polymorphism- derived (SPD) markers, matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) of the proteome and classical mycological techniques revealed two morphologically cryptic sister species within T. asperellum, T. asperellum, T. asperelloides sp. nov. and a third closely related but morphologically distinct species. T. yunnanense. Trichoderma asperellum and T. asperelloides have wide sympatric distribution on multiple continents; T. yunnanense is represented by a single strain from China. Several strains reported in the literature or represented in GenBank as T. asperellum are re-identified as T. asperelloides. Four molecular SPD typing patterns (I-IV) were found over a large geographic range. Patterns I-III were produced only by T. asperellum and pattern IV by T. asperelloides and T. yunnanense. Pattern I was found in North America, South America, Africa and Europe and Asia (Saudi Arabia). Pattern III was found in Africa, North America, South America and Asia, not in Europe. Pattern II was found only in Cameroon (central Africa) and Peru. Pattern IV was found in all continents. All SPD II pattern strains formed a strongly supported subclade within the T. asperellum clade in the phylogenetic tree based on rpb2 and MLS (combined multilocus sequence). The diversity of DNA sequences, SPD markers and polypeptides in T. asperellum suggests that further speciation is under way within T. asperellum. MALDI-TOF MS distinguished T. yunnanense from related taxa by UPGMA clustering, but separation between T. asperellum and T. asperelloides was less clear. © 2010 by The Mycological Society of America.

Conza L.,Cantonal Institute of Microbiology | Pagani S.C.,Cantonal Institute of Microbiology | Gaia V.,Cantonal Institute of Microbiology
PLoS ONE | Year: 2013

Several species of Legionella cause Legionnaires' disease (LD). Infection may occur through inhalation of Legionella or amoebal vesicles. The reservoirs of Legionella are water, soil, potting soil and compost. Some species of free-living amoebae (FLA) that are naturally present in water and soil were described as hosts for Legionella. This study aimed to understand whether or not the composting facilities could be sources of community-acquired Legionella infections after development of bioaerosols containing Legionella or FLA. We looked for the presence of Legionella (by co-culture) and FLA (by culture) in composts and bioaerosols collected at four composting facilities located in southern Switzerland. We investigated the association between the presence of Legionella and compost and air parameters and presence of FLA. Legionella spp. (including L. pneumophila) were detected in 69.3% (61/88) of the composts and FLA (mainly Acanthamoeba, Vermamoeba, Naegleria and Stenamoeba) in 92.0% (81/88). L. pneumophila and L. bozemanii were most frequently isolated. FLA as potential host for Legionella spp. were isolated from 40.9% (36/88) of the composts in all facilities. In Legionella-positive samples the temperature of compost was significantly lower (P = 0.012) than in Legionella-negative samples. Of 47 bioaerosol samples, 19.1% (9/47) were positive for FLA and 10.6% (5/47) for L. pneumophila. Composts (62.8%) were positive for Legionella and FLA contemporaneously, but both microorganisms were never detected simultaneously in bioaerosols. Compost can release bioaerosol containing FLA or Legionella and could represent a source of infection of community-acquired Legionella infections for workers and nearby residents. © 2013 Conza et al.

Conza L.,Cantonal Institute of Microbiology | Casati S.,Cantonal Institute of Microbiology | Limoni C.,Data Management | Gaia V.,Cantonal Institute of Microbiology
BMJ Open | Year: 2013

Objectives: The aim of this study was to identify meteorological factors that could be associated with an increased risk of community-acquired Legionnaires' disease (LD) in two Swiss regions. Design: Retrospective epidemiological study using discriminant analysis and multivariable Poisson regression. Setting: We analysed legionellosis cases notified between January 2003 and December 2007 and we looked for a possible relationship between incidence rate and meteorological factors. Participants: Community-acquired LD cases in two Swiss regions, the Canton Ticino and the Basle region, with climatically different conditions were investigated. Primary outcome measures: Vapour pressure, temperature, relative humidity, wind, precipitation and radiation recorded in weather stations of the two Swiss regions during the period January 2003 and December 2007. Results: Discriminant analysis showed that the two regions are characterised by different meteorological conditions. A multiple Poisson regression analysis identified region, temperature and vapour pressure during the month of infection as significant risk factors for legionellosis. The risk of developing LD was 129.5% (or 136.4% when considering vapour pressure instead of temperature in the model) higher in the Canton Ticino as compared to the Basle region. There was an increased relative risk of LD by 11.4% (95% CI 7.70% to 15.30%) for each 1 hPa rise of vapour pressure or by 6.7% (95% CI 4.22% to 9.22%) for 1°C increase of temperature. Conclusions: In this study, higher water vapour pressure and heat were associated with a higher risk of community-acquired LD in two regions of Switzerland.

Haller L.,University of Geneva | Tonolla M.,University of Geneva | Tonolla M.,Cantonal Institute of Microbiology | Zopfi J.,University of Lausanne | And 3 more authors.
Water Research | Year: 2011

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. Particularly, high contents of fresh organic matter and nutrients led to intense mineralisation, which was dominated by sulphate-reduction and methanogenesis. The bacterial diversity in Vidy sediments was significantly different from the communities in the uncontaminated sediments. Phylogenetic analysis revealed a large proportion of Betaproteobacteria clones in Vidy sediments related to Dechloromonas sp., a group of dechlorinating and contaminant degrading bacteria. Deltaproteobacteria, including clones related to sulphate-reducing bacteria and Fe(III)-reducing bacteria (Geobacter sp.) were also more abundant in the contaminated sediments. The archaeal communities consisted essentially of methanogenic Euryarchaeota, mainly found in the contaminated sediments rich in organic matter. Multiple factor analysis revealed that the microbial community composition and the environmental variables were correlated at the two sites, which suggests that in addition to environmental parameters, pollution may be one of the factors affecting microbial community structure. © 2010 Elsevier Ltd.

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