Does virulence assessment of Vibrio anguillarum using sea bass (Dicentrarchus labrax) larvae correspond with genotypic and phenotypic characterization?

Background: Vibriosis is one of the most ubiquitous fish diseases caused by bacteria belonging to the genus Vibrio such as Vibrio (Listonella) anguillarum. Despite a lot of research efforts, the virulence factors and mechanism of V. anguillarum are still insufficiently known, in part because of the lack of standardized virulence assays. Methodology/Principal Findings: We investigated and compared the virulence of 15 V. anguillarum strains obtained from different hosts or non-host niches using a standardized gnotobiotic bioassay with European sea bass (Dicentrarchus labrax L.) larvae as model hosts. In addition, to assess potential relationships between virulence and genotypic and phenotypic characteristics, the strains were characterized by random amplified polymorphic DNA (RAPD) and repetitive extragenic palindromic PCR (rep-PCR) analyses, as well as by phenotypic analyses using Biolog's Phenotype MicroArray (TM) technology and some virulence factor assays. Conclusions/Significance: Virulence testing revealed ten virulent and five avirulent strains. While some relation could be established between serotype, genotype and phenotype, no relation was found between virulence and genotypic or phenotypic characteristics, illustrating the complexity of V. anguillarum virulence. Moreover, the standardized gnotobiotic system used in this study has proven its strength as a model to assess and compare the virulence of different V. anguillarum strains in vivo. In this way, the bioassay contributes to the study of mechanisms underlying virulence in V. anguillarum

MALDI-TOF/MS identification of species from the Acinetobacter baumannii (Ab) group revisited: inclusion of the novel A. seifertii and A. dijkshoorniae species

OBJECTIVES: Rapid identification of Acinetobacter species is critical since members of the A. baumannii (Ab) group differ in antibiotic susceptibility and clinical outcomes. A. baumannii, A. pittii and A. nosocomialis can be identified by MALDI-TOF/MS, while the novel species A. seifertii and A. dijkshoorniae cannot. Low identification rates for A. nosocomialis have also been reported. We evaluated the use of MALDI-TOF/MS to identify isolates of A. seifertii and A. dijkshoorniae and revisited the identification of A. nosocomialis to update the Bruker taxonomy database. METHODS: Species characterisation was performed by rpoB-clustering and MLSA. MALDI-TOF/MS spectra were recovered from formic acid/acetonitrile bacterial extracts overlaid with alpha-cyano-4-hydroxy-cinnamic acid matrix on a MicroflexLT in linear positive mode and 2,000-20,000 m/z range mass. Spectra were examined with the ClinProTools v2.2 software. Mean spectra (MSP) were created with the BioTyper software. RESULTS: Seventy-eight Acinetobacter isolates representative of the Ab group were used to calculate the average spectra/species and generate pattern recognition models. Species-specific peaks were identified for all species, and MSPs derived from 3 A. seifertii, 2 A. dijkshoorniae and 2 A. nosocomialis strains were added to the Bruker taxonomy database, allowing successful identification of all isolates using spectra from either bacterial extracts or direct colonies, resulting in a positive predictive value (PPV) of 99.6% (777/780) and 96.8% (302/312), respectively. CONCLUSIONS: The use of post-processing data software identified statistically significant species-specific peaks to generate reference signatures for rapid accurate identification of species within the Ab group, providing relevant information for the clinical management of Acinetobacter infections

Acinetobacter dijkshoorniae sp. nov., a new member of the Acinetobacter calcoaceticus-Acinetobacter baumannii complex mainly recovered from clinical samples in different countries

The recent advances in bacterial species identification methods have led to the rapid taxonomic diversification of the genus Acinetobacter. In the present study, phenotypic and molecular methods have been used to determine the taxonomic position of a group of 12 genotypically distinct strains belonging to the Acinetobacter calcoaceticus-Acinetobacter baumannii (ACB) complex, initially described by Gerner-Smidt and Tjernberg in 1993, that are closely related to A. pittii. Strains characterized in this study originated mostly from human samples obtained in different countries over a period of 15 years. rpoB and MLST sequences were compared against those of 94 strains representing all species included in the ACB complex. Cluster analysis based on such sequences showed that all 12 strains grouped together in a distinct clade closest to A. pittii that was supported by bootstrap values of 99%. Values of average nucleotide identity based on BLAST between the genome sequence of strain JVAP01 (NCBI accession n masculine. LJPG00000000) and those of other species from the ACB were always < 91.2%, supporting the species status of the group. In addition, the metabolic characteristics of the group matched those of the ACB complex and the analysis of their protein signatures by matrix-assisted laser desorption ionization-time-of-flight mass spectrometry identified some specific peaks. Our results support the designation of these strains as a novel species and we propose the name A. dijkshoorniae sp. nov. The type strain is JVAP01T (CECT 9134T, LMG 29605T)

Synergy between UV and NaOCl for disinfection and biofilm treatment in closed water circuits

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Phenotypic characterization of Brettanomyces bruxellensis strains for the tolerance to stresses encountered during second generation bioethanol production

Brettanomyces (teleomorph Dekkera) bruxellensis has been generally considered a spoilage yeast in fuel ethanol production plants. However, due to its peculiar carbon- and nitrogen metabolism, the yeast is also believed to hold great potential for bioethanol production in continuous reactors. Nevertheless, before actually being useful in the production of second generation bioethanol there are still some challenges to overcome. For example, the use of lignocellulosic biomass results in the need for an extensive pretreatment process during which often several inhibiting compounds are released, leading to less efficient or stuck fermentations. The objective of this study was to phenotypically characterize B. bruxellensis strains for tolerance to stresses typically encountered during second generation bioethanol fermentation and to develop a screening plate for the evaluation of yeast strains against stresses relevant for the second generation bioethanol production. To this end, a plate was developed containing a dose range of different inhibitors (i.e. vanillin, catechol, levulinic acid, formic acid, furfural, ethanol, low pH, and high osmotic pressure). Further the plate included a negative and positive control well. Subsequently, several B. bruxellensis strains from different ecological niches were screened using the developed plate. Plates were incubated for eight days at 25 °C and analyzed by the OmniLog incubator/reader (Biolog, Hayward, CA, USA). All analysis were performed in duplicate. The different B. bruxellensis strains were ranked by calculating the average well colour development (AWCD). Additionally, each strain was scored for its tolerance to the tested inhibitory conditions. This resulted in a huge variation among strains, demonstrating the need for screening a large collection of strains to identify superior yeast strains. Highly ranked B. bruxellensis strains can then be further tested for tolerance against a mixture of inhibitors and real hydrolyzed biomass fermentation broths. Additionally, features such as ethanol yield and performance in pilot plants should be evaluated to truly see its potential for industrial second generation bioethanol production.status: publishe

Peracetic acid oxidation as an alternative pre-treatment for the anaerobic digestion of waste activated sludge

Anaerobic digestion is generally considered to be an economic and environmentally friendly technology for treating waste activated sludge, but has some limitations, such as the time it takes for the sludge to be digested and also the ineffectiveness of degrading the solids. Various pre-treatment technologies have been suggested to overcome these limitations and to improve the biogas production rate by enhancing the hydrolysis of organic matter. This paper studies the use of peracetic acid for disintegrating sludge as a pre-treatment of anaerobic digestion. It has been proved that this treatment effectively leads to a solubilisation of organic material. A maximum increase in biogas production by 21% is achieved. High dosages of PAA lead to a decrease in biogas production. This is due to the inhibition of the anaerobic micro-organisms by the high VFA-concentrations. The evolution of the various VFAs during digestion is studied and the observed trends support this hypothesis.status: publishe

Evaluation of disinfection techniques for the treatment of biofilms in reused process water

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Optimization and evaluation of a DNA array for simultaneous detection of multiple Legionella species in environmental samples

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Characterization of the bacterial community composition in water of drinking water production and distribution systems in Flanders, Belgium

The quality of drinking water is influenced by its chemical and microbial composition which in turn may be affected by the source water and the different processes applied in drinking water purification systems. In this study, we investigated the bacterial diversity in different water samples from the production and distribution chain of thirteen drinking water production and distribution systems from Flanders (Belgium) that use surface water or groundwater as source water. Water samples were collected over two seasons from the source water, the processed drinking water within the production facility and out of the tap in houses along its distribution network. 454-pyrosequencing of 16S ribosomal RNA gene sequences revealed a total of 1,570 species-level bacterial operational taxonomic units. Strong differences in community composition were found between processed drinking water samples originating from companies that use surface water and other that use groundwater as source water. Proteobacteria was the most abundant phylum in all samples. Yet, several phyla including Actinobacteria were significantly more abundant in surface water while Cyanobacteria were more abundant in surface water and processed water originating from surface water. Gallionella, Acinetobacter, and Pseudomonas were the three most abundant genera detected. Members of the Acinetobacter genus were even found at a relative read abundance of up to 47.5% in processed water samples, indicating a general occurrence of Acinetobacter in drinking water (systems).status: publishe

Cupriavidus metallidurans Strains with Different Mobilomes and from Distinct Environments Have Comparable Phenomes

Cupriavidus metallidurans has been mostly studied because of its resistance to numerous heavy metals and is increasingly being recovered from other environments not typified by metal contamination. They host a large and diverse mobile gene pool, next to their native megaplasmids. Here, we used comparative genomics and global metabolic comparison to assess the impact of the mobilome on growth capabilities, nutrient utilization, and sensitivity to chemicals of type strain CH34 and three isolates (NA1, NA4 and H1130). The latter were isolated from water sources aboard the International Space Station (NA1 and NA4) and from an invasive human infection (H1130). The mobilome was expanded as prophages were predicted in NA4 and H1130, and a genomic island putatively involved in abietane diterpenoids metabolism was identified in H1130. An active CRISPR-Cas system was identified in strain NA4, providing immunity to a plasmid that integrated in CH34 and NA1. No correlation between the mobilome and isolation environment was found. In addition, our comparison indicated that the metal resistance determinants and properties are conserved among these strains and thus maintained in these environments. Furthermore, all strains were highly resistant to a wide variety of chemicals, much broader than metals. Only minor differences were observed in the phenomes (measured by phenotype microarrays), despite the large difference in mobilomes and the variable (shared by two or three strains) and strain-specific genomes.status: publishe