References of "Taminiau, Bernard"
     in
Bookmark and Share    
Full Text
Peer Reviewed
See detailClostridium difficile infection in elderly nursing home residents.
Rodriguez Diaz, Cristina ULg; Korsak Koulagenko, Nicolas ULg; Taminiau, Bernard ULg et al

in Anaerobe (in press), 23

Age-related changes in intestinal flora and host defences, the receipt of antibiotic treatment, and the presence of underlying diseases are some of the most common risk factors associated with Clostridium ... [more ▼]

Age-related changes in intestinal flora and host defences, the receipt of antibiotic treatment, and the presence of underlying diseases are some of the most common risk factors associated with Clostridium difficile infection. Therefore, retirement care facilities for elderly people have been pinpointed as frequent sources of contamination. There is only limited data regarding the presence and epidemiology of C. difficile in nursing homes, and this gap in the current literature emphasises the need to gain a better understanding of the situation in order to prevent the emergence of new outbreaks among this population group. [less ▲]

Detailed reference viewed: 7 (2 ULg)
Full Text
Peer Reviewed
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 ▲]

Detailed reference viewed: 43 (1 ULg)
Full Text
Peer Reviewed
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 ▲]

Detailed reference viewed: 23 (11 ULg)
Peer Reviewed
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 ▲]

Detailed reference viewed: 17 (0 ULg)
Full Text
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 ▲]

Detailed reference viewed: 33 (3 ULg)
Full Text
Peer Reviewed
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)

Detailed reference viewed: 32 (3 ULg)
Peer Reviewed
See detailL'analyse par séquençage à haut débit révèle la variabilité génétique et la pression de sélection dans différentes régions génomiques du norovirus murin durant sa réplication in vitro
Mauroy, Axel ULg; Taminiau, Bernard ULg; Nezer, Carine et al

Conference (2014, March)

Le norovirus murin (MuNoV), un virus à ARN de polarité positive appartenant à la famille des Caliciviridae, est considéré comme un modèle adéquat pour les infections humaines à norovirus, une des causes ... [more ▼]

Le norovirus murin (MuNoV), un virus à ARN de polarité positive appartenant à la famille des Caliciviridae, est considéré comme un modèle adéquat pour les infections humaines à norovirus, une des causes étiologiques les plus importantes dans les cas de gastroentérite épidémique ou sporadique dans le monde entier. Quatre cadres de lecture ouverts (ORF) sont décrits au sein de son génome : l’ORF1 code les protéine non structurales (NS), dont l’ARN polymérase ARN dépendante virale (RdRp) ; l’ORF2 code l’unique protéine de capside (VP1), dans laquelle sont décrites deux régions : une relativement conservée (domaine « shell ») et une autre beaucoup plus variable (domaine « protruding ») ; l’ORF3 code une protéine structurale mineure ; et l’ORF4, actuellement uniquement décrit chez les virus génétiquement apparentés au MuNoV, code un facteur de virulence. Dans cette étude, nous démontrons par séquençage à haut débit que, durant des passages successifs du MuNoV en culture cellulaire, les taux de substitution, estimés par inférences Bayésiennes, n’ont pas significativement différé au travers des cinq régions génomiques ciblées à l’exception d’une région bien précise. Ces taux étaient similaires pour quatre régions englobant des séquences partielles codant les protéines non structurales NS1-2, NS5, NS6 et NS7 (RdRp) et VP1 dans sa région conservée (incluant également l’ORF4). Dans la région codant partiellement la protéine structurale mineure, ce taux de substitution, exprimé en substitution/site/jour, a été cependant estimé être plus élevée d’au moins une unité logarithmique. La localisation précise des mutations ponctuelles détectées (substitution, délétion et insertion) est rapportée ainsi que l’augmentation ou la diminution quantitative du nombre des séquences qui les présentaient au cours de dix passages successifs en culture cellulaire. Les localisations des mutations non silencieuses ont aussi été représentées dans une modélisation tridimensionnelle de quatre des cinq régions étudiées. Ces résultats ont d’importantes implications pour différents champs de recherche sur les norovirus, spécialement en termes de diagnostic, de méthodologie de classification et d’évolution génétique. [less ▲]

Detailed reference viewed: 15 (0 ULg)
Full Text
Peer Reviewed
See detailPsychrotrophic lactic acid bacteria associated with production batch recalls and sporadic cases of early spoilage in Belgium between 2010 and 2014
Pothakos, Vasileios; Taminiau, Bernard ULg; Huys, Geert et al

in International Journal of Food Microbiology (2014), 191

Between 2010 and 2014 several spoilage cases in Belgium occurring in retail foodstuffs prior to the end of shelf-life have been reported to our laboratory. Overall, seven cases involved strictly ... [more ▼]

Between 2010 and 2014 several spoilage cases in Belgium occurring in retail foodstuffs prior to the end of shelf-life have been reported to our laboratory. Overall, seven cases involved strictly psychrotrophic lactic acid bacteria (LAB) contamination in packaged and chilled-stored food products. The products derived either fromrecalls of entire production batches or as specimens of sporadic spoilage manifestations. Some of these samples were returned to the manufacturing companies by consumers who observed the alterations after purchasing the products. The products covered a wide range of foodstuffs (i.e. meat, dairy, vegetable, egg products and composite food) and denoted different spoilage defects. However, the microbiota determined by means of 16S rRNA gene high throughput sequencing analysis underpin few LAB genera (i.e. Leuconostoc, Lactobacillus, Weissella and Lactococcus), which are frequently encountered nowadays as specific spoilage organisms (SSO) albeit overlooked by mesophilic enumeration methods due to their strictly psychrotrophic character. The present study confirms the spreading of psychrotrophic LAB in Belgian food processing environments leading to unexpected spoilage, corroborating their spoilage dynamics and prevalence in all kinds of packaged and refrigerated foodstuffs in Northern Europe. [less ▲]

Detailed reference viewed: 8 (0 ULg)
Full Text
Peer Reviewed
See detailValidation of real-time PCR for detection of six major pathogens in seafood products
Taminiau, Bernard ULg; Korsak Koulagenko, Nicolas ULg; Lemaire et al

in Food Control (2014), 44

Seafood can pose a public health concern to consumers. It is often consumed rawand may be contaminated with several foodborne pathogens. In order to guarantee the safety of seafood, real-time polymerase ... [more ▼]

Seafood can pose a public health concern to consumers. It is often consumed rawand may be contaminated with several foodborne pathogens. In order to guarantee the safety of seafood, real-time polymerase chain reaction (PCR) protocols may be used as these enable results to be provided within 24 h. The first goal of our work was to develop real-time PCR protocols enabling the detection of six foodborne pathogens that may be present in seafood products (Campylobacter jejuni, Campylobacter coli, enterohemorrhagic Escherichia coli, Salmonella spp., Vibrio parahaemolyticus, and Vibrio vulnificus). The corresponding gene targets were: 50S/VS1, rfbE, ttr, tlh, and vvp. A multiplex PCR was also developed to detect the virulence genes of V. parahaemolyticus: tdh and trh. A total of 420 bacterial strains belonging to four different genera/strains were used in this study. Sensitivity and specificity were always 100%, except in the case of Salmonella spp., where three strains were not detected by our PCR protocols. The second objective of our work was to assess the detection limit of our real-time PCR protocols on artificially contaminated seafood products (raw shrimps, cooked shrimps, and raw mussels), purchased in public stores. Six different levels of contamination were assayed in four replicates for each matrix. The real-time PCR protocols enabled a better level of detection than the ISO methods, except for Salmonella in raw shrimps and for V. vulnificus in shrimps (raw and cooked). The estimated level of detection was between 1 and 47 cfu/25 g sample for the ISO norms and between 1 and 315 cfu/25 g sample for the realtime PCR protocols tailored in our work. The real-time PCRs developed in our work allowed for good selectivity, sensitivity, and specificity. The sensitivity on seafood products was estimated at a level of 100%, except for Salmonella (97%). In the spiking assays, the levels of detection were lower with the real-time PCR protocol than those obtained with the ISO method. This was not the case for V. vulnificus in raw and cooked shrimps and for Salmonella in raw shrimps. These real-time PCR protocols appear to be good alternative methods for surveillance of seafood products to ensure the absence of foodborne pathogens. One additional conclusion is that laboratories have to use enrichment media that are compatible with those recommended by ISO standards. This may facilitate the isolation of the pathogen if the real-time PCR protocol gives a suspect positive signal during the first step of the seafood analysis. [less ▲]

Detailed reference viewed: 41 (19 ULg)
Full Text
Peer Reviewed
See detailComparative genomics to investigate the evolutionary development of the genus Bifidobacterium
Lugli, Gabriele; Milani, Christian; Turroni, Francesca et al

in Applied and Environmental Microbiology (2014)

Detailed reference viewed: 3 (0 ULg)
Full Text
Peer Reviewed
See detailGenome encyclopaedia of type strains of the genus Bifidobacterium
Milani, Christian; Lugli, Gabriele; Duranti, Sabrina et al

in Applied and Environmental Microbiology (2014)

Detailed reference viewed: 8 (1 ULg)
Full Text
Peer Reviewed
See detailMicrobiota characterization of a protected designation of origin Belgian cheese: Herve cheese, using metagenomic analysis.
Delcenserie, Véronique ULg; Taminiau, Bernard ULg; Delhalle, Laurent ULg et al

in Journal of Dairy Science (2014), 97

Herve cheese is a Belgian soft cheese with a washed rind, and is made from raw or pasteurized milk. The specific microbiota of this cheese has never previously been fully explored and the use of raw or ... [more ▼]

Herve cheese is a Belgian soft cheese with a washed rind, and is made from raw or pasteurized milk. The specific microbiota of this cheese has never previously been fully explored and the use of raw or pasteurized milk in addition to starters is assumed to affect the microbiota of the rind and the heart. The aim of the study was to analyze the bacterial microbiota of Herve cheese using classical microbiology and a metagenomic approach based on 16S ribosomal DNA pyrosequencing. Using classical microbiology, the total counts of bacteria were comparable for the 11 samples of tested raw and pasteurized milk cheeses, reaching almost 8 log cfu/g. Using the metagenomic approach, 207 different phylotypes were identified. The rind of both the raw and pasteurized milk cheeses was found to be highly diversified. However, 96.3 and 97.9% of the total microbiota of the raw milk and pasteurized cheese rind, respectively, were composed of species present in both types of cheese, such as Corynebacterium casei, Psychrobacter spp., Lactococcus lactis ssp. cremoris, Staphylococcus equorum, Vagococcus salmoninarum, and other species present at levels below 5%. Brevibacterium linens were present at low levels (0.5 and 1.6%, respectively) on the rind of both the raw and the pasteurized milk cheeses, even though this bacterium had been inoculated during the manufacturing process. Interestingly, Psychroflexus casei, also described as giving a red smear to Raclettetype cheese, was identified in small proportions in the composition of the rind of both the raw and pasteurized milk cheeses (0.17 and 0.5%, respectively). In the heart of the cheeses, the common species of bacteria reached more than 99%. The main species identified were Lactococcus lactis ssp. cremoris, Psychrobacter spp., and Staphylococcus equorum ssp. equorum. Interestingly, 93 phylotypes were present only in the raw milk cheeses and 29 only in the pasteurized milk cheeses, showing the high diversity of the microbiota. Corynebacterium casei and Enterococcus faecalis were more prevalent in the raw milk cheeses, whereas Psychrobacter celer was present in the pasteurized milk cheeses. However, this specific microbiota represented a low proportion of the cheese microbiota. This study demonstrated that Herve cheese microbiota is rich and that pasteurized milk cheeses are microbiologically very close to raw milk cheeses, probably due to the similar manufacturing process. The characterization of the microbiota of this particular protected designation of origin cheese was useful in enabling us to gain a better knowledge of the bacteria responsible for the character of this cheese. [less ▲]

Detailed reference viewed: 44 (27 ULg)
Full Text
Peer Reviewed
See detailCarriage and acquisition rates of Clostridium difficile in hospitalized horses, including molecular characterization, multilocus sequence typing and antimicrobial susceptibility of bacterial isolates
Rodriguez Diaz, Cristina ULg; Taminiau, Bernard ULg; Brévers, Bastien et al

in Veterinary Microbiology (2014)

lostridium difficile has been identified as a significant agent of diarrhoea and enterocolitis in both foals and adult horses. Hospitalization, antibiotic therapy or changes in diet may contribute to the ... [more ▼]

lostridium difficile has been identified as a significant agent of diarrhoea and enterocolitis in both foals and adult horses. Hospitalization, antibiotic therapy or changes in diet may contribute to the development of C. difficile infection. Horses admitted to a care unit are therefore at greater risk of being colonized. The aim of this study was to investigate the carriage of C. difficile in hospitalized horses and the possible influence of some risk factors in colonization. During a seven-month period, faecal samples and data relating the clinical history of horses admitted to a veterinary teaching hospital were collected. C. difficile isolates were characterized through toxin profiles, cytotoxicity activity, PCR-ribotyping, antimicrobial resistance and multilocus sequence typing (MLST). Ten isolates were obtained with a total of seven different PCR-ribotypes, including PCR-ribotype 014. Five of them were identified as toxinogenic. A high resistance to gentamicin, clindamycin and ceftiofur was found. MLST revealed four different sequencing types (ST), which included ST11, ST26, ST2 and ST15, and phylogenetic analysis showed that most of the isolates clustered in the same lineage. Clinical history suggests that horses frequently harbour toxigenic and non-toxigenic C. difficile and that in most cases they are colonized regardless of the reason for hospitalization; the development of diarrhoea is more unusual. [less ▲]

Detailed reference viewed: 12 (3 ULg)
Full Text
Peer Reviewed
See detailImpact of agricultural practices on soil microbial communities in Belgium
Degrune, Florine ULg; Taminiau, Bernard ULg; Dufrêne, Marc ULg et al

Poster (2013, December 11)

The use of fertilizers in agricultural soils is becoming a real environmental issue (an obvious example is eutrophication caused by leaching of phosphorus and nitrates). Much research has focused on ... [more ▼]

The use of fertilizers in agricultural soils is becoming a real environmental issue (an obvious example is eutrophication caused by leaching of phosphorus and nitrates). Much research has focused on finding ways to reduce the use of chemicals, and investigating microbial life may lead to solutions. We know that bacteria and fungi are deeply involved in nutrient cycles. Recently the emergence of massive parallel sequencing has enabled us to realize that microbial diversity is huger than we expected. With such a tool it should be possible to study how soil management practices affect the microbial diversity of agricultural soils. A few such studies have been conducted, most of them focusing on bacteria. For Belgium in particular, there is a lack of data on this topic. Here the aim was to see how residue management and tillage practices affect communities of both bacteria and fungi in Belgian agricultural soils. For this we used 454 pyrosequencing of 16S bacterial and 28S fungal rRNA genes. Soil samples came from an experiment in which faba beans were grown with four soil management practices (tillage and no tillage, with and without crop residues), each repeated four times in a Latin square. Several chemical and physical characteristics were measured on each sample. The results show that fungi and bacteria are both impacted by Tillage practices. The main soil drivers are Magnesium and Phosphorus for Fungi communities, and Phosphorus and Potassium for bacteria communities. Finally, the fungi variance observed between plots is explained at 38% by Tillage, Magnesium and phosphorus. And the bacteria variance is explained at 28% by Tillage, Phosphorus and Potassium. [less ▲]

Detailed reference viewed: 64 (12 ULg)
Full Text
Peer Reviewed
See detailEvaluation of the bacterial diversity and its evolution during storage of fresh beef from British and Belgian origins under different atmosphere and temperature conditions
Didimo Imazaki, Pedro Henrique ULg; Tahiri, Assia ULg; Taminiau, Bernard ULg et al

Conference (2013, December 10)

The purpose of this study was to evaluate the bacterial diversity and its evolution during storage of fresh beef, depending on its origin, packaging and storage temperature, by using a metagenomic ... [more ▼]

The purpose of this study was to evaluate the bacterial diversity and its evolution during storage of fresh beef, depending on its origin, packaging and storage temperature, by using a metagenomic approach. Metagenomic analyzes revealed that the origin, atmosphere and temperature conditions influenced the selection of the predominant flora. Vacuum-packaged British samples presented higher concentrations of Lactobacillus algidus at the begging of the experiment than Belgian samples. Furthermore, the development of Lactobacillus algidus was favored in British and Belgian samples preserved under vacuum at −1 °C, while a predominance of Lactococcus piscium was observed for samples stored at +4 °C. These microorganisms have already been isolated from beef, but taking into account that the knowledge about these two species is currently limited, it is still not possible to state if the conservability of the tested samples was influenced by the presence of these bacteria. Moreover, storage under modified atmosphere favored the development of Leuconostoc gasicomitatum in both British and Belgian samples. This specie is often associated with spoilage of cold-stored modified-atmosphere-packaged (MAP) nutrient-rich foods. This result can partially explain the short shelf-life of the samples once they are stored under this condition. Metagenomics showed to be a useful tool to study the microbial population of a complex matrix since some of the identified genera could not have grown or have grown slowly in culture media commonly used. In addition, it helped to clarify the evolution of the bacterial ecosystem associated to meat during its storage. [less ▲]

Detailed reference viewed: 50 (12 ULg)
Full Text
See detailClostridium difficile: an emerging zoonotic pathogen ?
Rodriguez Diaz, Cristina ULg; Taminiau, Bernard ULg; Avesani, Véronique et al

Conference (2013, November 21)

Clostridium difficile is an anaerobic, spore-forming bacterium that remains the main cause of nosocomial diarrhoea in humans after use of antibiotics. C. difficile has also been described in other ... [more ▼]

Clostridium difficile is an anaerobic, spore-forming bacterium that remains the main cause of nosocomial diarrhoea in humans after use of antibiotics. C. difficile has also been described in other environments outside of hospitals, such as soil, river and seawater samples (Pasquale et al., 2011) and in animals, in which it can also cause enteric disease (Songer and Anderson, 2006). The possibility of transmission of C. difficile pathogenic isolates between animals, environments and humans has been suggested (Janezic et al., 2012). In recent years, the interest in C. difficile in food and in food animals has increased, leading to studying animals as a possible reservoir and a potential risk for food borne infections linked to C. difficile. Studies in various countries have determined differences in the prevalence of C. difficile in animals just before slaughter (Houser et al., 2012; Rodriguez et al., 2012) as well as in retail meat (Houser et al., 2012). In addition, many types, including PCR-ribotype 078, are present in humans, animals and meat (Janezic et al.; Weese et al., 2009). The objective of this study was to evaluate the presence of C. difficile at the slaughterhouse and in retail meat. Intestinal and carcass samples were collected from pigs and cattle at a single slaughterhouse. Raw meat (beef and pork) was obtained from the retail trade. C. difficile was isolated in 1% and 9.9% of the pig and cattle intestinal contents and in 7.9% and 7% of cattle and pig carcass samples respectively. From retail meat, C. difficile was recovered from 2.3% of the beef samples and from 4.7% of the pork samples. A total of 21 different PCR-ribotypes were identified with a large percentage of types 078 and 014. This study confirms that animals are carriers of C. difficile at slaughter, and that carcass contamination occurs inside the slaughterhouse. Furthermore the results obtained also reveal the presence of toxigenic C. difficile in retail meat in Belgium with a predominance of isolates correlated with the PCR-ribotypes involved in human C. difficile infections. [less ▲]

Detailed reference viewed: 38 (0 ULg)
Full Text
See detailASSOCIATION OF CLASSICAL MICROBIOLOGY AND TARGETED METAGENOMIC ANALYSIS TO EVALUATE THE PRESENCE OF CLOSTRIDIUM DIFFICILE IN A BELGIAN NURSING HOME
Rodriguez Diaz, Cristina ULg; Taminiau, Bernard ULg; Korsak Koulagenko, Nicolas ULg et al

Conference (2013, October 22)

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. Surfaces and diary meals were also sampled in order to determinate the possible role of environmental and food contamination in the acquisition of CDI. 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. C. difficile was not detected in any of the tested meals or surfaces samples. For the stools samples, 6 of the 23 controlled residents were identified as C. difficile carriers. The isolates belonged to 4 different PCR ribotypes, including types 020 and 027. 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 ▲]

Detailed reference viewed: 36 (13 ULg)
Full Text
Peer Reviewed
See detailBacterial diversity and its evolution during storage of fresh beef from different origins under different atmosphere and temperature conditions
Didimo Imazaki, Pedro Henrique ULg; Tahiri, Assia ULg; Taminiau, Bernard ULg et al

Poster (2013, October 11)

The purpose of this study was to evaluate the bacterial diversity and its evolution during storage of fresh beef, depending on its origin, packaging and storage temperature. Two batches of three vacuum ... [more ▼]

The purpose of this study was to evaluate the bacterial diversity and its evolution during storage of fresh beef, depending on its origin, packaging and storage temperature. Two batches of three vacuum packed striploins from United Kingdom and Belgium were obtained from a food wholesaler located in the Walloon Region. Fifteen days after slaughter, the striploins were sliced and individually kept under vacuum for 30 days: i) at −1 °C; ii) at +4 °C and iii) at −1 °C for 15 days and then at +4 °C for 15 days. The bacterial diversity was evaluated by metagenomic approach 15, 30 and 45 days after slaughter. Furthermore, each 15 days part of the vacuum packed striploin slices were repacked under modified atmosphere (70 % O2/30 % CO2), stored at +4 °C for 2 days and at +8 °C for 5 days, and then analyzed. Metagenomic analysis revealed a selection of the initial flora depending on atmosphere and temperature conditions. The development of Lactobacillus algidus was favored in samples preserved under vacuum at −1 °C, while a predominance of Lactococcus piscium was observed for samples stored at +4 °C. Moreover, storage under modified atmosphere favored the development of Leuconostoc gasicomitatum. These microorganisms have already been isolated from beef, but no study has evaluated their role in food conservation. The next step of this study will be to isolate and characterize strains of Lactobacillus algidus from meat and to assess their bioprotective potential. [less ▲]

Detailed reference viewed: 32 (9 ULg)
Full Text
Peer Reviewed
See detailPredictive microbiology combined with metagenomic analysis targeted on the 16S rDNA : A new approach for food quality
Delhalle, Laurent ULg; Taminiau, Bernard ULg; Ellouze, Mariem et al

in Ellouze, Mariem; Tenenhaus-Aziza, Fanny (Eds.) Proceedings of thge 8th International Conference on predictive microbiology in foods (ICPMF8) (2013, September 18)

OBJECTIVES The food spoilage process is mainly caused by alteration micro-organisms and classical culture-based methods have therefore been used to assess the microbiological quality of food. These ... [more ▼]

OBJECTIVES The food spoilage process is mainly caused by alteration micro-organisms and classical culture-based methods have therefore been used to assess the microbiological quality of food. These techniques are simple to implement but may not be relevant to understand the modifications of the microbial ecology which occur in the food product in response to different changes in the environmental conditions. Metagenomic analysis targeted on 16S ribosomal DNA can bring about a solution to this new need and elucidate microbial community structures, including the identification and quantification of culturable and non-culturable organisms, at a much higher resolution than was previously possible with culture-based methods to provide a picture of the microbial community. Combined with predictive microbiological models, a new approach was investigated to take into account the dynamics of the evolutions of the microbial community in food products. This work describes the application of a metagenomic analysis and predictive microbiology in order to study bacterial populations dynamics in perishable foods under different environmental conditions. METHODS 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 / diacetic acid mix (1.8% w/w) treatment. At each day of the trials, classical microbiological (total flora, lactic acid bacteria) 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. Libraries were sequenced on a GS junior sequencer using Titanium technology. The Bio- informatic pipeline using Mothur, Blast and Stamp was used to assign a taxonomical identity to the sequences and to obtain the bacterial population proportions of the samples (Schloss, Westcott et al. 2009). The major bacterial populations were thus identified and predictive microbiology models (Baranyi and Roberts 1994; Augustin, Zuliani et al. 2005) were used to assess the growth parameters. The model was validated using the data obtained at a dynamic temperature profile. RESULTS The metagenomic analysis of the samples shows that the bacterial populations from the day 0 sample to the post-shelf life sample have important modifications. Brochothrix and Psychrobacter were identified as the dominant flora. As expected, the storage temperature had a strong impact on the  bacterial evolutions. Moreover, the use of lactic acid/diacetic acid reveals the sensitivity of the different populations to the treatment. For the storage at 4°C, the initial dominance of Pseudomonas and Shewanella is slightly reduced during storage until shelf life, after which it drops to be replaced by Brochothrix and Psychrobacter. The addition of the preservation treatment has a statistical negative impact on the Psychrobacter and Acinetobacter populations. During the ageing assay (2 days at 4°C followed by 10 days at 8°C), the analysis underlines the influence of the temperature change on the onset of the Brochothrix and Psychrobacter dominance compared to the entire 4°C storage. Again, the preservation treatment delays this onset. Finally, at an abusive 12°C temperature, samples are quickly dominated by the Psychrobacter/Brochothrix pair after 2 days of storage. In this case, the lactic acid mix does not appear to be of any effective use. Adjustment of primary model was made on the major bacterial populations and simulation was made based on estimated growth rate. The simulations of the three major populations seem to be sufficient for this food product to predict 80 -90 % of the bacterial population at the end of the shelf life in function of the environmental conditions. CONCLUSIONS AND IMPACT OF THE STUDY Compared to culture based methods on selective media and previous independent culture techniques, metagenomic analysis combined with predictive microbiology gives more valuable information, and its use could be considered as a technique for quality control or for accurately determining shelf life. REFERENCES Augustin, J. C., V. Zuliani, et al. (2005). "Growth rate and growth probability of Listeria monocytogenes in dairy, meat and seafood products in suboptimal conditions." J Appl Microbiol 99(5): 1019-­‐1042. Baranyi, J. and T. A. Roberts (1994). "A dynamic approach to predicting bacterial growth in food." International Journal of Food Microbiology 23(3-­‐4): 277-­‐294. Schloss, P. D., S. L. Westcott, et al. (2009). "Introducing mothur: open-­‐source, platform-­‐independent, community-­‐supported software for describing and comparing microbial communities." Appl. Environ. Microbiol. 75(23): 7537-­‐7541. [less ▲]

Detailed reference viewed: 10 (0 ULg)