References of "Taminiau, Bernard"
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See detailMetagenomic analysis of samples
Daube, Georges ULg; Taminiau, Bernard ULg; Nezer, Carine et al

Patent (in press)

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See detailUse of 16S rDNA Metagenetics and classical Microbiology to Assess the bacterial superficial Contamination Patterns in Bovines Classically Slaughtered or following the Halal Ritual
Korsak Koulagenko, Nicolas ULg; Taminiau, Bernard ULg; Hupperts, Caroline et al

Poster (2015, June 17)

In Belgium and in several European countries, two cattle slaughtering protocols exist: the classical method, that encompasses a stunning step before the sticking procedure, and the halal method, combining ... [more ▼]

In Belgium and in several European countries, two cattle slaughtering protocols exist: the classical method, that encompasses a stunning step before the sticking procedure, and the halal method, combining the stunning and the sticking in one single step. The main difference lies in the fact that, in the halal protocol, a single cut with a sharp knife is practiced directly on live cattle, instead of two cutting steps with two different knives for the sticking in the classical slaughtering technique. The unique section in the halal technique results generally in the cross section of trachea and esophagus of cattle. The aim of this study was to seek if the two slaughtering techniques were similar regarding the superficial contamination of carcasses, swabbed between 2 and 4 hours after the killing step. For this purpose, classical microbiological tests (TVC and Enterobacteriaceae) and 16S rDNA metagenetic analysis were carried out from 20 cattle carcasses (swabbing of “legal” zone – 1.600 cm2 – and in the neck area – 200 cm2). The classical microbiological results revealed no significant differences between the two slaughtering practices. Statistical analysis of pyrosequencing data showed that differences in bacterial population abundance between slaughtering methods were mainly found in the “legal” swabbing zone compared to the neck area. Bacterial genera belonging to Actinobacteria (Brevibacterium, Corynebacterium) were more aundant in “Halal” samples whereas populations from the Proteobacteria (Caulobacteraceae, Comamonadaceae, Bradyrhizobiaceae) and Firmicutes (Lactobacillus) were more abundand in the “classical” group. The analysis of OTU abundance of bacteria from the digestive or respiratory tract revealed no differences beteween groups. In conclusion, the slaughtering method does not influence the superficial microbiological pattern in terms of specific microbiological markers of the digestive or respiratory tract. However, precise analysis to the genus level underlines differences between methods, the legal swabbing zone being still the best sampling zone compared to the neckline. The next step will be the identification of precise contamination origin of the differences found between slaughtering methods. [less ▲]

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See detailCARRIAGE OF CLOSTRIDIUM DIFFICILE IN HOSPITAL PATIENTS IN SPAIN, INCLUDING MOLECULAR CHARACTERIZATION AND ANTIMICROBIAL SUSCEPTIBILITY OF THE ISOLATES
Rodriguez Diaz, Cristina ULg; Taminiau, Bernard ULg; Van Broeck, Johan et al

Poster (2015, May 21)

Increasing age, several co-morbidities, environmental contamination, antibiotic exposure and other intestinal perturbations appear to be the greatest risk factors for C. difficile infection (CDI ... [more ▼]

Increasing age, several co-morbidities, environmental contamination, antibiotic exposure and other intestinal perturbations appear to be the greatest risk factors for C. difficile infection (CDI). Therefore, hospitalized patients are considered particularly vulnerable to CDI. The main objective of this study was to evaluate the prevalence of C. difficile in a Spanish hospital and to characterize the isolates with respect to the PCR-ribotype, antibiotic resistance and toxin activity. In addition, multilocus sequence typing (MLST) was performed in order to study clonal relationships between C. difficile isolates obtained from two different countries. Culture of samples was performed in a selective medium cycloserine cefoxitin fructose cholate. An identification of the isolated colonies was done by PCR detection of tpi, tcdA, tcdB and cdtA genes. Toxic activity was confirmed by a cytotoxic immunoassay. Further characterization was performed by PCR ribotyping. MLST was used in order to determine genetic relationships between Spanish and Belgian C. difficile isolates recovered from hospital patients in both countries. C. difficile was frequently detected in hospitalized patients. The isolates belonged to different PCR ribotypes, including type 027. Most of the strains obtained harboured tcdA and tcdB genes. The number of positive faecal samples considerably increased among elderly patients over 65 years old. The multi-locus sequence typing (MLST) analysis showed that some Spanish and Belgian isolates cluster in the same lineage. This study reveals the circulation of toxigenic C. difficile in a Spanish hospital. The relatedness between Belgian and Spanish isolates indicate a common source or a lack of diversity from some PCR-ribotypes. Moreover, data obtained suggest that the combination of ribotyping and MLST is a good tool for the inter-laboratory comparison of strains among different countries. Continuous inter-country surveillance is suitable to understand the spread of C. difficile isolates among hospitalized patients. [less ▲]

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See detailAssociation of classical microbiology and 16S rDNA metagenetic Aanalysis to evaluate the presence of Clostridium difficile ina a belgian nursing home
Rodriguez Diaz, Cristina ULg; Taminiau, Bernard ULg; Avesani, Véronique et al

Poster (2015, April 01)

Increasing age, several co-morbidities, environmental contamination, antibiotic exposure and other intestinal perturbations appear to be the greatest risk factors for C. difficile infection (CDI ... [more ▼]

Increasing age, several co-morbidities, environmental contamination, antibiotic exposure and other intestinal perturbations appear to be the greatest risk factors for C. difficile infection (CDI). Therefore, elderly care home residents are considered particularly vulnerable to CDI. The main objective of this study was to evaluate and follow the prevalence of C. difficile in a Belgian nursing home. During a 4-month period, stool samples from a group of 23 elderly care home residents were collected weekly. A C. difficile microbiological detection scheme was performed along with an overall microbial biodiversity study of the faeces content by Targeted Metagenomic analysis. Culture of samples was performed in a selective medium cycloserine cefoxitin fructose cholate. An identification of the isolated colonies was done by PCR detection of tpi, tcdA, tcdB and cdtA genes. Toxic activity was confirmed by a cytotoxic immunoassay. Further characterization was performed by PCR ribotyping. The Metagenomic analysis was targeted on the v1-v3 hyper-variable region of 16S rDNA. The taxonomical assignment of the populations was performed with MOTHUR and Blast algorithms. Seven out of 23 (30.4%) residents were (at least one week) positive for C. difficile. The most common PCR-ribotype identified was 027. Targeted Metagenomic analyses reveals that each resident has his own bacterial imprint, which is stable during the entire study. Residents’ positives for C. difficile by classical microbiology showed an important proportion of C. difficile sequences. However, Metagenomics analysis can’t substitute targeted protocols. It was not used as a diagnostic tool to detect C. difficile but rather to determine the identification and correlations of the major bacterial populations that are present in the gut microbiota. In conclusion, this unique association of classical microbiology protocol with pyrosequencing allowed to follow C. difficile in patients and to identify several other bacterial populations whose abundance is correlated with C. difficile. [less ▲]

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See detailSoil microbial community composition changes according to the tillage practice and plant development stage
Degrune, Florine ULg; Dufrêne, Marc ULg; Taminiau, Bernard ULg et al

Poster (2015, April)

Agricultural practices have a strong impact on soil bacterial and fungal community composition. Furthermore, microbial community composition can change with the stage of plant development. We are ... [more ▼]

Agricultural practices have a strong impact on soil bacterial and fungal community composition. Furthermore, microbial community composition can change with the stage of plant development. We are interested in exploring these effects in relation to changes induced by agriculture (conventional and reduced tillage) and plant stage (germination and flowering) in soil conditions. Here, instead of examining this impact at a high taxonomic level such as phylum and/or class, thus missing potentially relevant information from lower levels, we propose an original method: exploiting the available sequence information at the lowest taxonomic level attainable for each operational taxonomic unit. Results show that some microbial communities were impacted only by the tillage practice , while others were impacted only by the stage of plant. Changes in microbial community composition could be due to the soil conditions induced by the soil practice and the stage of plant. [less ▲]

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See detailA novel sub-phylum method discriminates better the impact of crop management on soil microbial community
Degrune, Florine ULg; Dufrêne, Marc ULg; Colinet, Gilles ULg et al

in Agronomy for Sustainable Development (2015)

Soil microorganisms such as mycorrhizae and plant-growth-promoting rhizobacteria have beneficial effects on crop productivity. Agricultural practices are known to impact soil microbial communities, but ... [more ▼]

Soil microorganisms such as mycorrhizae and plant-growth-promoting rhizobacteria have beneficial effects on crop productivity. Agricultural practices are known to impact soil microbial communities, but past studies examining this impact have focused mostly on one or two taxonomic levels, such as phylum and class, thus missing potentially relevant information from lower levels. Therefore we propose here an original, sub-phylum method for studying how agricultural practices modify microbial communities. This method involves exploiting the available sequence information at the lowest taxonomic level attainable for each operational taxonomic unit. In order to validate this novel method we assessed microbial community composition using 454 pyrosequencing of 16S and 28S rRNA genes, then we compared the results with results of a phylum-level analysis. Agricultural practices included conventional tillage, reduced tillage, residue removal and residue retention. Results show that, at the lowest taxonomic level attainable, tillage is the main factor influencing both bacterial community composition, accounting for 13% of the variation, and fungal community composition, accounting for 18% of the variation. Whereas phylum-level analysis failed to reveal any effect of soil practice on bacterial community composition, and missed the fact that different members of the same phylum responded differently to tillage practice. For instance, the fungal phylum Chytridiomycota showed no impact of soil treatment, while sub-phylum-level analysis revealed an impact of tillage practice on the Chytridiomycota sub-groups Gibberella, which includes a notorious wheat pathogen, and Trichocomaceae. This clearly demonstrates the necessity of exploiting the information obtainable at sub-phylum level when assessing the effects of agricultural practice on microbial communities. [less ▲]

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See detailClostridium difficile from food and surface samples in a Belgian nursing home: An unlikely source of contamination
Rodriguez Diaz, Cristina ULg; Korsak Koulagenko, Nicolas ULg; Taminiau, Bernard ULg et al

in Anaerobe (2015), 32

This study investigates the contamination of foods and surfaces with Clostridium difficile in a single nursing home. C. difficile PCR-ribotype 078 was found in one food sample and in none of the tested ... [more ▼]

This study investigates the contamination of foods and surfaces with Clostridium difficile in a single nursing home. C. difficile PCR-ribotype 078 was found in one food sample and in none of the tested surfaces. These results indicate that food and surfaces are an unlikely source of C. difficile infection in this setting. [less ▲]

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See detailCecal drop reflects the chickens' cecal microbiome, fecal drop does not.
Pauwels, J.; Taminiau, Bernard ULg; Janssens, Guy ULg et al

in Journal of microbiological methods (2015)

Microbiota in the gastro-intestinal tract are closely related to both the intestinal and overall health of the host. Experimental chickens have always been euthanized in order to identify and quantify the ... [more ▼]

Microbiota in the gastro-intestinal tract are closely related to both the intestinal and overall health of the host. Experimental chickens have always been euthanized in order to identify and quantify the bacteria in cecal content. In this study, quantification and identification of the microbial populations in cecal drop, cecal content and fecal drop samples from chickens showed that cecal drop contains a bacterial community that is very similar (concerning bacterial diversity, richness and species composition) to cecal content, as opposed to the bacterial community found in fecal drop. Cecal drop analysis thus allows for longitudinal experiments on chickens' cecal bacteria. The varying results in the analysis of fecal samples questions the method's reliability in reflecting the true cecal microbiota in chickens. [less ▲]

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See detailNon Digestible Oligosaccharides Modulate the Gut Microbiota to Control the Development of Leukemia and Associated Cachexia in Mice.
Bindels, Laure B.; Neyrinck, Audrey M.; Salazar, Nuria et al

in PloS one (2015), 10(6), 0131009

We tested the hypothesis that changing the gut microbiota using pectic oligosaccharides (POS) or inulin (INU) differently modulates the progression of leukemia and related metabolic disorders. Mice were ... [more ▼]

We tested the hypothesis that changing the gut microbiota using pectic oligosaccharides (POS) or inulin (INU) differently modulates the progression of leukemia and related metabolic disorders. Mice were transplanted with Bcr-Abl-transfected proB lymphocytes mimicking leukemia and received either POS or INU in their diet (5%) for 2 weeks. Combination of pyrosequencing, PCR-DGGE and qPCR analyses of the 16S rRNA gene revealed that POS decreased microbial diversity and richness of caecal microbiota whereas it increased Bifidobacterium spp., Roseburia spp. and Bacteroides spp. (affecting specifically B. dorei) to a higher extent than INU. INU supplementation increased the portal SCFA propionate and butyrate, and decreased cancer cell invasion in the liver. POS treatment did not affect hepatic cancer cell invasion, but was more efficient than INU to decrease the metabolic alterations. Indeed, POS better than INU delayed anorexia linked to cancer progression. In addition, POS treatment increased acetate in the caecal content, changed the fatty acid profile inside adipose tissue and counteracted the induction of markers controlling beta-oxidation, thereby hampering fat mass loss. Non digestible carbohydrates with prebiotic properties may constitute a new nutritional strategy to modulate gut microbiota with positive consequences on cancer progression and associated cachexia. [less ▲]

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See detailShort communication: Evaluation of the microbiota of kefir samples using metagenetic analysis targeting the 16S and 26S ribosomal DNA fragments
Korsak Koulagenko, Nicolas ULg; Taminiau, Bernard ULg; Leclercq, Mathilde et al

in Journal of Dairy Science (2015), 98

Milk kefir is produced by fermenting milk in the presence of kefir grains. This beverage has several benefits for human health. The aim of this experiment was to analyze 5 kefir grains (and their products ... [more ▼]

Milk kefir is produced by fermenting milk in the presence of kefir grains. This beverage has several benefits for human health. The aim of this experiment was to analyze 5 kefir grains (and their products) using a targeted metagenetic approach. Of the 5 kefir grains analyzed, 1 was purchased in a supermarket, 2 were provided by the Ministry of Agriculture (Namur, Belgium), and 2 were provided by individuals. The metagenetic approach targeted the V1-V3 fragment of the 16S ribosomal (r)DNA for the grains and the resulting beverages at 2 levels of grain incorporation (5 and 10%) to identify the bacterial species population. In contrast, the 26S rDNA pyrosequencing was performed only on kefir grains with the aim of assessing the yeast populations. In parallel, pH measurements were performed on the kefir obtained from the kefir grains using 2 incorporation rates. Regarding the bacterial population, 16S pyrosequencing revealed the presence of 20 main bacterial species, with a dominance of the following: Lactobacillus kefiranofaciens, Lactococcus lactis ssp. cremoris, Gluconobacter frateurii, Lactobacillus kefiri, Acetobacter orientalis, and Acetobacter lovaniensis. An important difference was noticed between the kefir samples: kefir grain purchased from a supermarket (sample E) harbored a much higher proportion of several operational taxonomic units of Lactococcus lactis and Leuconostoc mesenteroides. This sample of grain was macroscopically different from the others in terms of size, apparent cohesion of the grains, structure, and texture, probably associated with a lower level of Lactobacillus kefiranofaciens. The kefir (at an incorporation rate of 5%) produced from this sample of grain was characterized by a lower pH value (4.5) than the others. The other 4 samples of kefir (5%) had pH values above 5. Comparing the kefir grain and the kefir, an increase in the population of Gluconobacter in grain sample B was observed. This was also the case for Acetobacter orientalis in sample D. In relation to 26S pyrosequencing, our study revealed the presence of 3 main yeast species: Naumovozymaspp., Kluyveromyces marxianus, and Kazachastania khefir. For Naumovozyma, further studies are needed to assess the isolation of new species. In conclusion, this study has proved that it is possible to establish the patterns of bacterial and yeast composition of kefir and kefir grain. This was only achieved with the use of high-throughput sequencing techniques. [less ▲]

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See detailThe effects of xylo-oligosaccharides on performance and microbiota in broiler chickens.
De Maesschalck, C.; Eeckhaut, V.; Maertens, L. et al

in Applied and environmental microbiology (2015)

In broiler chickens, feed additives, including prebiotics, are widely used to improve gut health and to stimulate performance. Xylo-oligosaccharides (XOS) are hydrolytic degradation products of ... [more ▼]

In broiler chickens, feed additives, including prebiotics, are widely used to improve gut health and to stimulate performance. Xylo-oligosaccharides (XOS) are hydrolytic degradation products of arabinoxylans that can be fermented by the gut microbiota. In the current study it was aimed to analyze the prebiotic properties of XOS when added to the broiler diet. Administration of XOS to chickens, on top of a wheat/rye-based diet, significantly improved the feed conversion ratio. XOS significantly increased villus length in the ileum. It also significantly increased numbers of lactobacilli in the colon and Clostridium cluster XIVa in the caeca. Moreover, the number of gene copies encoding the key bacterial enzyme for butyrate production, butyryl-CoA:acetate CoA-transferase, was significantly increased in the caeca of chickens administered XOS. In this group of chickens, at species level, Lactobacillus crispatus and Anaerostipes butyraticus were significantly increased in abundance in the colon and caecum, respectively. In vitro fermentation of XOS revealed cross-feeding between L. crispatus and A. butyraticus. Lactate, produced by L. crispatus during XOS fermentation, was utilized by the butyrate-producing Anaerostipes species. These data show the beneficial effects of XOS on broiler performance when added to the feed, which potentially can be explained by stimulation of butyrate-producing bacteria through cross-feeding of lactate and subsequent effects of butyrate on gastrointestinal function. [less ▲]

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See detailMetagenomic analysis of the bacterial microbiota linked to the traditional Algerian date product "Btana"
Abekhti, Abdelkader; Taminiau, Bernard ULg; Kihal, Mabrouk et al

in Annals of Microbiology (2015)

In this study, using high throughput pyrosequencing, we highlighted the bacterial diversity of the traditional Algerian date product "Btana" that is produced in southern Algeria using both direct (DBM ... [more ▼]

In this study, using high throughput pyrosequencing, we highlighted the bacterial diversity of the traditional Algerian date product "Btana" that is produced in southern Algeria using both direct (DBM) and indirect (UBM) methods. Metagenomic analysis yielded a total of 103,379 reads, with a 606 total operational taxonomic units (OTUs) detected. Firmicutes represented 84.79 % of the total pyrosequencing reads. Phylogenetic analysis revealed that the Bacillales represented 90.20 % ± 15.12 % of the total reads. Among the phylotypes detected, Bacillus was the dominant genus (39.53 %). While Bacillus megaterium was shared among all of the samples, its distribution varied widely. Non-metric multidimensional scaling (nMDS) analysis showed that UBM samples clustered together, and three main OTUs were found in these UBM samples: Paenibacillus polymyxa, Paenibacillus xylanexedens, and Planomicrobium JN082684. Correlation analysis showed no association between parametersof the samples (age, pH, water activity) and the specific microbiota. [less ▲]

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See detailThermophilic and cellulolytic consortium isolated from composting plants improves anaerobic digestion of cellulosic biomass: toward a microbial resource management approach
Kinet, Romain ULg; Destain, Jacqueline ULg; Hiligsmann, Serge ULg et al

in Bioresource Technology (2015)

A cellulolytic consortium was isolated from a composting plant in order to boost the initial hydrolysis step encountered in anaerobic digestion. Improvement of the cellulose degradation, as well as biogas ... [more ▼]

A cellulolytic consortium was isolated from a composting plant in order to boost the initial hydrolysis step encountered in anaerobic digestion. Improvement of the cellulose degradation, as well as biogas production, was observed for the cultures inoculated with the exogenous consortium. Metagenomics analyses pointed out a weak richness (related to the number of OTUs) of the exogenous consortium induced by the selective pressure (cellulose as sole carbon source) met during the initial isolation steps. Main microbial strains determined were strictly anaerobic and belong to the Clostridia class. During cellulose anaerobic degradation, pH drop induced a strong modification of the microbial population. Despite the fact that richness and evenness were very weak, the exogenous consortium was able to adapt and to maintain the cellulolytic degradation potential. This important result point out the fact that simplified microbial communities could be used in order to increase the robustness of mixed cultures involved in environmental biotechnology. [less ▲]

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See detailDetecting microbial patterns in relation to soil agricultural practices and the plant development stage
Degrune, Florine ULg; Dufrêne, Marc ULg; Taminiau, Bernard ULg et al

Poster (2014, December 02)

Agricultural practices have a strong impact on soil bacteria and fungi. Furthermore, microbial community composition can change with the stage of plant development. We are interested in exploring these ... [more ▼]

Agricultural practices have a strong impact on soil bacteria and fungi. Furthermore, microbial community composition can change with the stage of plant development. We are interested in exploring these effects in relation to changes induced by agriculture and plant stage in soil conditions. Some bacteria are influenced only by the plant stage, which induces changes in soil humidity, pH, nitrates, and carbon. We would thus expect these bacteria to be highly sensitive to these parameters. Other bacteria are affected only by the tillage practice applied. Further study is needed to identify the soil parameters responsible for this effect. The plant stage also has a great impact on fungal community composition. [less ▲]

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See detailPredictive microbiology combined with metagenomic analysis targeted on the 16S rDNA : A new approach for food quality
Delhalle, Laurent ULg; Ellouze, Mariem; Taminiau, Bernard ULg et al

Poster (2014, September 01)

The food spoilage process is mainly caused by alteration micro-organisms and classical culture-based methods may not be relevant to understand the modifications of the microbial ecology in food products ... [more ▼]

The food spoilage process is mainly caused by alteration micro-organisms and classical culture-based methods may not be relevant to understand the modifications of the microbial ecology in food products. Metagenomic analysis targeted on 16S ribosomal DNA can elucidate microbial community structures at a muche higher resolution than was previously possible. Combined with predictive microbiological models, a new approach was investigated to take into account bacterial populations dynamics in perishable foods under different environmental conditions. White pudding samples, a typical Belgian pork meat product, were packed under food wrap (atmospheric air condition). Durability studies were conducted at 4°C, 12°C and a dynamic temperature profile according to the NF V01-003 standards (4°C (1/3 of the shelf life) - 8°C (2/3 of the shelf life)) during 15 days. The effect of organic acids was also investigated using a lactic acid (1.8% w/w) treatment. At each day of the trials, classical microbiological (total flora) and 16S rDNA metagenomic analysis were carried out on all these samples. For the metagenomic analysis, a sequencing library was generated, targeting the V1-V3 region of the 16S rDNA. The two major bacterial populations were thus identified (Psychrobacter sp and Brochotrix thermosphacta) and predictive microbiology models used to assess the growth parameters. Cardinal parameters for temperature were collected on the two main bacterial species. The model was validated using the data obtained at a dynamic temperature profile. The results of the simulations for Psychrobacter sp and Brochotrix thermosphacta show a good compliance between predicted and observed data. Compared to culture based methods on selective media and previous independent culture techniques, metagenomic analysis combined with predictive microbiology gives more valuable information, and could be considered as a technological breakthrough to control the quality or for accurately determining shelf life. [less ▲]

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See detailMultilocus sequence typing analysis and antibiotic resistance of Clostridium difficile strains isolated from retail meat and humans in Belgium
Rodriguez Diaz, Cristina ULg; Taminiau, Bernard ULg; Avesani, Véronique et al

in Food Microbiology (2014), 42

Clostridium difficile has been isolated from food animals and meat, specially ground pork and ground beef. The recovered isolates were closely related to C. difficile human strains, indicating that ... [more ▼]

Clostridium difficile has been isolated from food animals and meat, specially ground pork and ground beef. The recovered isolates were closely related to C. difficile human strains, indicating that animals and food are possible transmission routes of human C. difficile infection. The main objective of this study was to characterize C. difficile isolates from retail meat and to compare with human isolates recovered from hospital patients in Belgium. Raw meat (beef and pork) was obtained from the retail trade. C. difficile was recovered from 2.3% of the beef samples and from 4.7% of the pork samples. A total of 4 different PCR-ribotypes were identified with a large percentage of types 078 and 014. Resistance to moxifloxacin and erythromycin was detected. The multi-locus sequence typing (MLST) analysis showed that meat and human isolates cluster in the same lineage. This study reveals the presence of toxigenic C. difficile in retail meat in Belgium with predominance PCR-ribotypes 078 and 014, which are among the four most prevalent ribotypes of C. difficile isolated from humans in Europe. [less ▲]

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See detailAntimicrobial and molecular analysis of Salmonella serovar Livingstone strains isolated from humans in Tunisia and Belgium
Guedda, Intissar; Taminiau, Bernard ULg; Ferjani, Asma et al

in Journal of Infection in Developing Countries [=JIDC] (2014), 8

Introduction: Salmonella Livingstone is one of the most common serotypes responsible for nosocomial outbreaks in Tunisia. In this study, 42 isolates of Salmonella Livingstone were analyzed. Most of these ... [more ▼]

Introduction: Salmonella Livingstone is one of the most common serotypes responsible for nosocomial outbreaks in Tunisia. In this study, 42 isolates of Salmonella Livingstone were analyzed. Most of these were isolated from humans (31 strains from Tunisia and 9 strains from Belgium) and 2 isolates came from food products (beef and pork). Methodology: All strains were characterized by antibiogram, multilocus sequence typing (MLST), and virulotyping. This last technique was carried out by simple PCR of five chromosomal genes (agfA, hin/H2, iroB, phoP/Q, and slyA) and two plasmid genes (spvA and spvC). Results: All Tunisian strains were resistant to amoxicillin, amoxicillin-clavulanic acid, ticarcillin, cefalotin, gentamicin, and kanamycin. They were also resistant to third-generation cephalosporin antibiotics (cefotaxim and ceftazidim). Belgian isolates were susceptible to all antibiotics tested. Further to MLST analyses, Tunisian strains belonged to the same sequence type, ST543. For Belgian isolates, eight strains had a ST543 profile, two strains had a ST638 profile, and one strain had a ST457 profile. Analyses of the virulence gene contents showed that strains isolated in different years and from different origins had the same virulence profile. These carried all five chromosomal genes and lacked plasmid-located virulence genes spvA and spvC. Conclusions: A combination of different typing methods showed that the majority of Belgian strains and all Tunisian strains were closely related; they belonged to the same sequence type (ST543) and had the same virulence profile, but different antibiotic resistance profiles depended on the country of origin. [less ▲]

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See detailHigh throughput sequencing analysis reveals genetic variability and selection pressure in different murine norovirus genomic regions during in vitro replication
Mauroy, Axel ULg; Taminiau, Bernard ULg; Nezer, Carine et al

Poster (2014, July)

Murine norovirus (MuNoV), a single stranded positive sense RNA virus belonging to the Caliciviridae family, is considered as a representative model for human norovirus infections, one of the most ... [more ▼]

Murine norovirus (MuNoV), a single stranded positive sense RNA virus belonging to the Caliciviridae family, is considered as a representative model for human norovirus infections, one of the most important etiological cause of both epidemic and sporadic gastroenteritis cases worldwide. Four open reading frames are described into its genome: ORF1 codes the non-structural (NS) proteins, including the viral RNA dependent RNA polymerase (RdRp); ORF2 codes the single capsid protein (VP1), wherein two domains are present: a relatively conserved domain (“shell”) and a more variable domain (“protruding”); ORF3 codes a minor structural protein; and ORF4, currently only found in viruses genetically related to MuNoV codes a virulence factor. In this study, we demonstrated by high throughput sequencing that, during serial passages of MuNoV in cell culture, the substitution rates, estimated by Bayesian inferences, did not significantly differ across the five targeted genomic regions except one. These rates were similar in four genomic regions encompassing partial non-structural 1-2 protein (NS1-2)-, NS5-, NS6-, NS7 (RdRp)- and VP1-coding sequences (coding the conserved part of the protein also including the ORF4 region). In the partial minor structural protein-coding region, this substitution rate was however estimated to be at least one log higher when expressed as substitution/site/day. The precise localisation of the detected nucleotide point mutations (substitution, deletion and insertion) were reported as well as the quantitative increase or decrease of the sequences harbouring them along ten cell culture passages. The non-silent amino acid mutations were also depicted in 3D models for four out of the five studied regions. These results have important implications for different norovirus research fields, especially in terms of diagnosis, classification methodology and genetic evolution. [less ▲]

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See detailComparison and molecular characterization of animal and human Clostridium difficile strains
Rodriguez Diaz, Cristina ULg; Taminiau, Bernard ULg; Korsak Koulagenko, Nicolas ULg et al

Poster (2014, May 07)

The main objective of this study was to characterize and compare animal and human C. difficile strains with respect to the PCR-ribotype and the antibiotic resistance. Multilocus sequence typing analysis ... [more ▼]

The main objective of this study was to characterize and compare animal and human C. difficile strains with respect to the PCR-ribotype and the antibiotic resistance. Multilocus sequence typing analysis (MLST) was performed in order to study clonal relationships of the isolates. [less ▲]

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See detailStudy of the microbial flora of steak tartare by metagenomic approach
Korsak Koulagenko, Nicolas ULg; Delhalle, Laurent ULg; Nezer, Carine et al

Poster (2014, May 06)

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