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Biomedical subjects

Jean Swings

Publications and source records attributed to Jean Swings.

At least 73 records · Page 4Linked to original sources
PubMed2005

Detection and characterization of tet(M) in tetracycline-resistant Listeria strains from human and food-processing origins in Belgium and France.

In the present study, three Listeria monocytogenes strains and one Listeria innocua strain out of a collection of 241 Listeria isolates from human and food-processing sources were found to display resistance to tetracycline (TC) due to the presence of the tet(M) gene. Through sequence analysis, it was shown that tet(M) genes in two of the isolates belong to sequence homology group (SHG) II, a group comprising chromosomally encoded tet(M) genes previously found in Staphylococcus aureus and in lactobacilli. The tet(M) genes of the two other L. monocytogenes strains were associated with a member of the Tn916-Tn1545 family of conjugative transposons and were closely related to SHG III, which harbours enterococcal tet(M) genes associated with Tn916. One of these transposon-containing strains was able to transfer the tet(M) gene to Enterococcus faecalis recipient strain JH2-2. Collectively, these sequence and conjugation data indicate that the acquisition of tet(M) by Listeria strains may be triggered by successive transfers between other Gram-positive organisms.

Base Sequence↗
PubMed2005

Application of multilocus sequence analysis (MLSA) for rapid identification of Enterococcus species based on rpoA and pheS genes.

The aim of this study was to evaluate the use of RNA polymerase alpha subunit (rpoA) and phenylalanyl-tRNA synthase (pheS) gene sequences as species identification tools for enterococci. Ninety-six representative strains comprising all currently recognized Enterococcus species were examined. rpoA gene sequences generated a robust classification into species groups similar to the one based on 16S rRNA gene sequence analysis. On the other hand, the pheS gene is a fast-evolving clock even better suited for species delineation than the rpoA gene, but not for recognition of species groups within Enterococcus as determined by both rpoA and 16S rRNA genes. All enterococcal species were clearly differentiated on the basis of their rpoA and pheS sequences. Evaluation of intraspecies variation showed that both rpoA and pheS genes have a high degree of homogeneity among strains of the same species. Strains of the same enterococcal species have at least 99% rpoA and 97% pheS gene sequence similarity, whereas, different enterococcal species have at maximum 97% rpoA and 86% pheS gene sequence similarity. It was concluded that both genes can be used as reliable tools for identification of clinical and environmental species of Enterococcus and are efficient screening methods for the detection of novel species. The sequence data obtained in this study were compared to the available atpA and 16S rRNA gene sequences. The MLSA approach to Enterococcus taxonomy provides portable, highly reproducible data with lower costs for rapid identification of all enterococcal species.

Bacterial Typing Techniques↗
PubMed2005

Pathogenicity of vibrios to rainbow trout (Oncorhynchus mykiss, Walbaum) and Artemia nauplii.

The taxonomy of marine vibrios has changed rapidly over the last two decades, and a wealth of new species have been identified. Many Vibrio species are pathogenic to fish and crustaceans; however, little is known about the virulence of many of the novel species. The purpose of this study was to determine the ability of various recent isolates of vibrios to cause disease in rainbow trout (Oncorhynchus mykiss, Walbaum) and crustacea, i.e. Artemia nauplii. Of 56 isolates, representing 26 species of Enterovibrio, Photobacterium and Vibrio, obtained from a diversity of healthy and diseased aquatic animal hosts and water samples from many geographical locations, Vibrio brasiliensis, V. coralliilyticus, V. ezurae, V. fortis, V. kanaloaei, V. neptunius, V. rotiferianus and V. tubiashii were pathogenic to rainbow trout and Artemia nauplii with mortalities of up to 100%. The extracellular products of these pathogenic isolates were harmful to the animal models. In contrast, cultures of Enterovibrio norvegicus, E. coralii, Photobacterium rosenbergii, Vibrio campbellii, V. chagasii, V. cyclitrophicus, V. gallicus, V. gigasii, V. hepatarius, V. hispanicus, V. lentus, V. nereis, V. pacini, V. pomeroyi, V. shilonii, V. superstes, V. tasmaniensis and V. xuii demonstrated either non- or low virulence in the animal models.

Animals↗
PubMed2005

Molecular diversity and characterization of tetracycline-resistant Staphylococcus aureus isolates from a poultry processing plant.

DNA fingerprinting and molecular characterization showed that the tetracycline-resistant Staphylococcus aureus population of a South African poultry processing plant comprised one or possibly several tet(K)-containing endemic clones that contaminated chicken and machinery surfaces at all sampled processing stages. The tet(K) gene was transferable by filter mating to S. aureus recipient 80CR5 and was located on a pT181-like plasmid.

Animals↗
PubMed2005

Surface microflora of four smear-ripened cheeses.

The microbial composition of smear-ripened cheeses is not very clear. A total of 194 bacterial isolates and 187 yeast isolates from the surfaces of four Irish farmhouse smear-ripened cheeses were identified at the midpoint of ripening using pulsed-field gel electrophoresis (PFGE), repetitive sequence-based PCR, and 16S rRNA gene sequencing for identifying and typing the bacteria and Fourier transform infrared spectroscopy and mitochondrial DNA restriction fragment length polymorphism (mtDNA RFLP) analysis for identifying and typing the yeast. The yeast microflora was very uniform, and Debaryomyces hansenii was the dominant species in the four cheeses. Yarrowia lipolytica was also isolated in low numbers from one cheese. The bacteria were highly diverse, and 14 different species, Corynebacterium casei, Corynebacterium variabile, Arthrobacter arilaitensis, Arthrobacter sp., Microbacterium gubbeenense, Agrococcus sp. nov., Brevibacterium linens, Staphylococcus epidermidis, Staphylococcus equorum, Staphylococcus saprophyticus, Micrococcus luteus, Halomonas venusta, Vibrio sp., and Bacillus sp., were identified on the four cheeses. Each cheese had a more or less unique microflora with four to nine species on its surface. However, two bacteria, C. casei and A. arilaitensis, were found on each cheese. Diversity at the strain level was also observed, based on the different PFGE patterns and mtDNA RFLP profiles of the dominant bacterial and yeast species. None of the ripening cultures deliberately inoculated onto the surface were reisolated from the cheeses. This study confirms the importance of the adventitious, resident microflora in the ripening of smear cheeses.

Bacteria↗
PubMed2005

Evaluation of new broth media for microdilution antibiotic susceptibility testing of Lactobacilli, Pediococci, Lactococci, and Bifidobacteria.

Nine pure or mixed broth media were evaluated for their suitabilities to determine MICs in a microdilution test of 19 antibacterial agents for lactic acid bacteria (LAB) of the genera Lactobacillus, Pediococcus, Lactococcus, and Bifidobacterium. A mixed formulation of Iso-Sensitest broth (90%) and deMan-Rogosa-Sharpe broth (10%) with or without supplementation with L-cysteine, referred to as the LAB susceptibility test medium, provided the most optimal medium basis in terms of growth support of nonenterococcal LAB and correct indication of MICs of international control strains.

Anti-Bacterial Agents↗
PubMed2005

Effects of bacteria on Artemia franciscana cultured in different gnotobiotic environments.

The use of probiotics is receiving considerable attention as an alternative approach to control microbiota in aquaculture farms, especially in hatching facilities. However, application with consistent results is hampered by insufficient information on their modes of action. To investigate whether dead bacteria (allowing investigation of their nutritional effect) or live bacteria (allowing evaluation of their probiotic effect) have any beneficial effect towards Artemia franciscana and, subsequently, if live bacteria have probiotic effects beyond the effects observed with dead bacteria, a model system was employed using gnotobiotic Artemia as a test organism. Nauplii were cultured in the presence of 10 bacterial strains combined with four different major axenic live feeds (two strains of Saccharomyces cerevisiae and two strains of Dunaliella tertiolecta) differing in their nutritional values. In combination with poor- and medium-quality live feeds, dead bacteria exerted a strong effect on Artemia survival but a rather weak or no effect on individual length and constituted a maximum of only 5.9% of the total ash-free dry weight supplied. These effects were reduced or even disappeared when medium- to good-quality major feed sources were used, possibly due to improvements in the health status of Artemia. Some probiotic bacteria, such as GR 8 (Cytophaga spp.), improved (not always significantly) the performance of nauplii beyond the effect observed with dead bacteria, independently of the feed supplied. The present approach can be an excellent system to study the exact mode of action of bacteria, especially if combined with challenge tests or other types of analysis (e.g., transcriptome and proteonomic analysis).

Animals↗
PubMed2005

Comparative nucleotide sequence analysis of polymorphic variable-number tandem-repeat Loci in Mycobacterium ulcerans.

We analyzed a set of variable-number tandem-repeat (VNTR) loci to assess their nucleotide sequence diversity in isolates of three Mycobacterium ulcerans genotypes. Sequence variants in two loci resulted in intraspecies resolution of Southeast Asian and Asian genotypes in contrast to a homogenous sequence composition among African isolates. Nucleotide sequence polymorphism in repeat units can enhance discrimination of VNTR loci.

Bacterial Typing Techniques↗
PubMed2005

Sequence-based typing of ade B as a potential tool to identify intraspecific groups among clinical strains of multidrug-resistant Acinetobacter baumannii.

Sequence analysis of an 850-bp fragment internal to the aspecific drug efflux gene ade B revealed 11 sequence types (STs) among a collection of 50 multidrug-resistant Acinetobacter baumannii (MDRAB) strains, including members of pan-European clones I, II, and III. The delineation of STs conformed with the intraspecific grouping of these strains previously determined by different DNA fingerprinting methods. Larger strain collections need to be screened to further explore the potential of sequence-based ade B typing as a universal tool for the monitoring of MDRAB clones.

Acinetobacter Infections↗
PubMed2005

Multilocus variable-number tandem repeat typing of Mycobacterium ulcerans.

The apparent genetic homogeneity of Mycobacterium ulcerans contributes to the poorly understood epidemiology of M. ulcerans infection. Here, we report the identification of variable number tandem repeat (VNTR) sequences as novel polymorphic elements in the genome of this species. A total of 19 potential VNTR loci identified in the closely related M. marinum genome sequence were screened in a collection of 23 M. ulcerans isolates, one Mycobacterium species referred to here as an intermediate species, and five M. marinum strains. Nine of the 19 loci were polymorphic in the three species (including the intermediate species) and revealed eight M. ulcerans and five M. marinum genotypes. The results from the VNTR analysis corroborated the genetic relationships of M. ulcerans isolates from various geographical origins, as defined by independent molecular markers. Although these results further highlight the extremely high clonal homogeneity within certain geographic regions, we report for the first time the discrimination of the two South American strains from Surinam and French Guyana. These findings support the potential of a VNTR-based genotyping method for strain discrimination within M. ulcerans and M. marinum.

Animals↗
PubMed2004

Distribution of tetracycline resistance genes in genotypically related and unrelated multiresistant Acinetobacter baumannii strains from different European hospitals.

The presence of tetracycline (TET) resistance genes was investigated in 49 genotypically related and unrelated multidrug-resistant Acinetobacter baumannii (MDRAB) strains from European hospitals including representatives of pan-European clones I and II. Except for one strain, all MDRAB strains displayed resistance to tetracycline (MIC range of 16 to > 512 microg/ml) but were susceptible (MIC < 4 microg/ml) or exhibited intermediate resistance (MIC of 4-8 microg/ml) to minocycline (MIN). In 37 strains, either tet(A) or tet(B) was detected and one of these strains possessed both tet(A) and tet(M). In addition, all MDRAB strains contained the aspecific efflux gene adeB irrespectively of whether they harbored tet genes or not. Repetitive DNA element (rep)-PCR fingerprinting using the (GTG)5 primer [(GTG)5-PCR] revealed that strains previously assigned to pan-European clones I and II were grouped into two separate clusters. In addition, these clusters also contained strains that had not been typed previously, indicating that (GTG)5-PCR is a valuable method for recognizing putative new members of MDRAB clones. Most, but not all, members of clones I and II were linked to the presence of either tet(A) or tet(B) and displayed different levels of TET resistance with MIC values of 32 to > 512 microg/ml and > 512 microg/ml, respectively. Of these two genes only tet(B) encodes an efflux of both TET and MIN, which was reflected by the relatively high MIC values for MIN (4 microg/ml) shown by the majority of the tet(B)-carrying clone II strains as opposed to the low MIC values for MIN (< 1 microg/ml) displayed by most tet(A)-containing clone I strains. Collectively, our phenotypic and genotypic resistance data support the therapeutic evaluation of second-generation tetracyclines like MIN as promising agents for treating MDRAB infections.

Acinetobacter Infections↗
PubMed2004

The usefulness of molecular techniques to assess the presence of Aeromonas spp. harboring virulence markers in foods.

A total of 78 raw and 123 processed and ready-to-eat retail food samples were used to assess the presence of motile Aeromonas spp. harboring virulence genes (cytotoxic enterotoxin and hemolysin genes) using a recently described PCR method in comparison with the conventional cultivation method based on the use of Ampicillin-Dextrin Agar (ADA) medium. With the ADA-based method, 65/201 (32.3%) samples showed presumptive Aeromonas spp. colonies whereas the PCR method revealed the presence of Aeromonas spp. harboring the targeted virulence genes in 51/201 (25.4%) of the tested samples. The rate of contaminated samples and the presence of pathogenic Aeromonas were significantly lower with both methods for processed than in case of raw samples. A polyphasic identification approach including biochemical and molecular techniques was applied to a selection of 34 PCR-positive presumptive Aeromonas isolates. Following fatty acid methyl ester (FAME) analysis and amplified fragment length polymorphism (AFLP) fingerprinting, a total of 33 isolates (97%) could be identified to the DNA hybridization group (HG) level. The majority of these isolates belonged to the species Aeromonas hydrophila HG3 (50%) and Aeromonas veronii biovar sobria (HG8/10) (38%). Molecular characterization of PCR amplicons obtained from these strains by PCR-Restriction Fragment Length Polymorphism (PCR-RFLP) fingerprinting and PCR-Amplicon Sequence Analysis (PCR-ASA) allowed classification of all strains in a known PCR-RFLP and PCR-ASA type. In conclusion, the current findings demonstrate that the combined use of PCR-based virulence marker detection, PCR-RFLP and PCR-ASA offers a rapid, sensitive, and specific system to assess the presence and prevalence of Aeromonas spp. harboring virulence markers in food samples.

Aeromonas↗
PubMed2004

Sliding window discretization: a new method for multiple band matching of bacterial genotyping fingerprints.

Microbiologists have traditionally applied hierarchical clustering algorithms as their mathematical tool of choice to unravel the taxonomic relationships between micro-organisms. However, the interpretation of such hierarchical classifications suffers from being subjective, in that a variety of ad hoc choices must be made during their construction. On the other hand, the application of more profound and objective mathematical methods--such as the minimization of stochastic complexity--for the classification of bacterial genotyping fingerprints data is hampered by the prerequisite that such methods only act upon vectorized data. In this paper we introduce a new method, coined sliding window discretization, for the transformation of genotypic fingerprint patterns into binary vector format. In the context of an extensive amplified fragment length polymorphism (AFLP) data set of 507 strains from the Vibrionaceae family that has previously been analysed, we demonstrate by comparison with a number of other discretization methods that this new discretization method results in minimal loss of the original information content captured in the banding patterns. Finally, we investigate the implications of the different discretization methods on the classification of bacterial genotyping fingerprints by minimization of stochastic complexity, as it is implemented in the BinClass software package for probabilistic clustering of binary vectors. The new taxonomic insights learned from the resulting classification of the AFLP patterns will prove the value of combining sliding window discretization with minimization of stochastic complexity, as an alternative classification algorithm for bacterial genotyping fingerprints.

Bacteria↗
PubMed2004

BOX-pCR fingerprinting as a powerful tool to reveal synonymous names in the genus Streptomyces. Emended descriptions are proposed for the species Streptomyces cinereorectus, S. fradiae, S. tricolor, S. colombiensis, S. filamentosus, S. vinaceus and S. phaeopurpureus.

The type strains of 451 validly described Streptomyces species were screened using the BOX-PCR fingerprint technique. Of the different primers tested, the BOX primer yielded the most robust and reproducible band patterns. The majority of the species (350) had an unique pattern each. A total number of 30 clusters were delineated comprising species with nearly identical patterns. Four of these clusters grouped synonymous Streptomyces species known from previous studies. A high correlation exists between BOX-PCR fingerprinting and DNA-DNA homology data. In the present study, the latter was confirmed for 7 additional BOX clusters and led to the following emended descriptions: S. cochleatus is a subjective synonym of S. cinereorectus, S. roseoflavus of S. fradiae, S. roseodiastaticus of S. tricolor, S. roseosporus of S. filamentosus, S. distallicus of S. colombiensis, S. arabicus of S. vinaceus and S. phaeoviridis of S. phaeopurpureus. Although not yet confirmed by DNA-DNA pairing studies, rep-PCR data suggested the presence of at least 33 additional junior synonyms.

DNA Fingerprinting↗
PubMed2004

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

In the current study, a group of 17 "Aeromonas eucrenophila-like" isolates from clinical and environmental origins was subjected to a polyphasic taxonomic characterization including ribotyping, 16S rDNA sequencing, FAFLP fingerprinting, and biochemical testing. Genotypic, phylogenetic, and phenotypic results were consistent with the conclusion that this group of 17 isolates may represent a currently undescribed Aeromonas taxon most closely related to A. eucrenophila HG6. In addition, comparison of newly obtained 16S rDNA sequencing data with published sequences demonstrated a high phylogenetic heterogeneity among isolates currently classified in the species A. encheleia.

Aeromonas↗
PubMed2004

Vibrio neonatus sp. nov. and Vibrio ezurae sp. nov. isolated from the gut of Japanese abalones.

Five alginolytic, facultative anaerobic, non-motile bacteria were isolated from the gut of Japanese abalones (Haliotis discus discus, H. diversicolor diversicolor and H. diversicolor aquatilis). Phylogenetic analyses based on 16S rRNA gene and gap gene sequences indicated that these strains are closely related to V. halioticoli. DNA-DNA hybridizations, FAFLP fingerprintings, and phylogenies of gap and 16S rRNA gene sequences showed that the five strains represent two species different from all currently described vibrios. The names Vibrio neonatus sp. nov. (IAM 15060T = LMG 19973T = HDD3-1T; mol% G+C of DNA is 42.1-43.9), and Vibrio ezurae sp. nov. (IAM 15061T = LMG 19970T = HDS1-1T; mol% G+C of DNA is 43.6-44.8) are proposed to encompass these new taxa. The two new species can be differentiated from V. halioticoli on the basis of several features, including beta-galactosidase activity, assimilation of glycerol, D-mannose and D-gluconate.

Aerobiosis↗
PubMed2004

Cellulophaga pacifica sp. nov.

Three marine, heterotrophic, aerobic, agarolytic, pigmented and gliding bacteria were isolated in June 2000 from a sea water sample that was collected in the Gulf of Peter the Great, Sea of Japan, and analysed in a polyphasic taxonomic study. 16S rDNA sequence analysis indicated that strains KMM 3664(T), KMM 3669 and KMM 3915 were members of the family Flavobacteriaceae. Based on phenotypic, chemotaxonomic, genotypic and phylogenetic data, the isolates were classified in the genus Cellulophaga as members of a novel species, Cellulophaga pacifica sp. nov. The type strain is KMM 3664(T) (=JCM 11735(T)=LMG 21938(T)).

Bacteria, Aerobic↗