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Genotypic Characterization (genotypic + characterization)
Selected AbstractsGenotypic characterization of Porphyromonas gingivalis isolated from subgingival plaque and blood sample in positive bacteremia subjects with periodontitisJOURNAL OF CLINICAL PERIODONTOLOGY, Issue 9 2008P. Juliana Pérez-Chaparro Abstract Aim: The objective of this study was to investigate clonal relationship among Porphyromonas gingivalis isolated from subgingival plaque and blood samples in positive transient bacteremia subjects with periodontitis. Material and Methods: Unrelated patients with general chronic periodontitis or general aggressive periodontitis requiring scaling and root planing (SRP) were included in the study. Genotyping of each isolate was performed using pulsed field gel electrophoresis technique. Genetic relatedness of strains isolated within an individual or between different patients was determined by dendogram analysis. Results: Following SRP, from 16 patients, seven patients showed positive P. gingivalis bacteremia and nine were negative. Thirty-two strains were isolated from subgingival plaque and blood samples before and during induced transient bacteremia. The majority of the patients harboured one clonal type. Two patients showed different clones in plaque and blood samples suggesting that more than one clone can be found in subgingival plaque. P. gingivalis isolates from periodontitis patients after transient bacteremia following SRP, revealed a high heterogeneity among isolates. Conclusion: In 6/16 subjects the same P. gingivalis isolate was found in the blood and in oral cavity. P. gingivalis heterogeneity suggests no association of a unique clonal type with transient bacteremia. [source] Investigation of measles and rubella outbreaks in Tamil Nadu, India,2003JOURNAL OF MEDICAL VIROLOGY, Issue 4 2006Nalini Ramamurty Abstract The aims of the present study were to confirm measles outbreaks by detection of measles-specific IgM antibodies, isolation of measles virus, and genetic characterization to document the circulating genotypes in Tamil Nadu. Eight outbreaks were reported from six districts of Tamil Nadu, India during the period Jan,Dec 2003. Blood samples were collected for serology, urine, and throat swabs for virus isolation. Genotypic characterization of measles isolates was based on the sequence of the N gene. All the clinically suspected outbreaks (n,=,8) were confirmed by serology; six out of the eight as measles and two as combination of measles and rubella highlighting the need to carry out rubella serology on measles-negative samples. Genetic characterization of three isolates obtained revealed one as genotype D4 and two as D8. Measles genotypes D4 and D8 were found to circulate in three districts of Tamil Nadu. It is necessary to be aware of the circulating genotypes within the geographical area. The information would be valuable to evaluate control measures and identify viral transmission and importation. J. Med. Virol. 78:508,513, 2006. © 2006 Wiley-Liss, Inc. [source] Genotypic characterization of hospital Enterococcus faecalis strains using multiple-locus variable-number tandem-repeat analysisLETTERS IN APPLIED MICROBIOLOGY, Issue 1 2009E. Wa, ecka Abstract Aims:, The level of genetic diversity and relationships between the specific genotypes and the distribution of virulence determinants among Enterococcus faecalis strains isolated from patients hospitalized in different wards of two hospitals were investigated. Methods and Results:, Fifty-six clinical strains of E. faecalis, isolated from patients hospitalized in the period of 1999,2004 in several wards in Wroc,aw (Poland), were analysed by multiple-locus variable-number tandem-repeat analysis (MLVA). Analysis of seven genomic loci identified 40 novel genotypes among the analysed E. faecalis strains, with two major genomic groups, designated I and II, distinguished at a cut-off of 35%. With a similarity cut-off of 85·7%, the genotypes could be combined into 12 clusters (C1,C12), containing at least two isolates. The remaining 18 MLVA types were represented by a single isolate. Conclusions:, Based on the data obtained by MLVA, it was found that (i) many E. faecalis isolates recovered from patients from the wards whose location allowed the potential transmission of micro-organisms, belonged to closely related MLVA types and (ii) possible relationships between specific E. faecalis genotype and the virulence factors lipase, haemolysin and esp gene can exist. Significance and Impact of the Study:, Our study confirms that MLVA is a suitable method for the epidemiological study of E. faecalis and for the first time shows possible relationships between specific genotypes and such virulence determinants, i.e. lipase, haemolysin and esp gene. [source] Genotypic characterization of Pseudomonas aeruginosa strains recovered from patients with cystic fibrosis after initial and subsequent colonizationPEDIATRIC PULMONOLOGY, Issue 4 2001Anne Munck MD Abstract Chronic infection by Pseudomonas aeruginosa (PA) in patients with cystic fibrosis (CF) is preceded by a period of colonization and acute infection. Early aggressive antibiotic treatment of initial colonisation may prevent or at least delay chronic pulmonary infection. We initiated treatment with a combination of IV ,-lactam tobramycin, followed by nebulized colistin when PA was first isolated from patients with CF. Subsequent serial PA isolates obtained from these colonized CF patients were characterized by means of molecular methods to determine whether they were genetically related to the initial strain. Initial colonization was eradicated in all 19 patients. All patients reacquired PA within 3,25 months during the 3 years of follow-up. Fourteen patients acquired a new PA strain with a distinct genotypic profile, suggesting a new source of contamination. Five patients had two PA isolates with identical genotypes, suggesting either previous undetected respiratory tract colonization or a persistent environmental source of contamination. Pediatr Pulmonol. 2001; 32:288,292. © 2001 Wiley-Liss, Inc. [source] Contrasting microcystin production and cyanobacterial population dynamics in two Planktothrix -dominated freshwater lakesENVIRONMENTAL MICROBIOLOGY, Issue 10 2005Ingmar Janse Summary Microcystin concentrations in two Dutch lakes with an important Planktothrix component were related to the dynamics of cyanobacterial genotypes and biovolumes. Genotype composition was analysed by using denaturing gradient gel electrophoresis (DGGE) profiling of the intergenic transcribed spacer region of the rrn operon (rRNA-ITS), and biovolumes were measured by using microscopy. In Lake Tjeukemeer, microcystins were present throughout summer (maximum concentration 30 µg l,1) while cyanobacterial diversity was low and very constant. The dominant phototroph was Planktothrix agardhii. In contrast, Lake Klinckenberg showed a high microcystin peak (up to 140 µg l,1) of short duration. In this lake, cyanobacterial diversity was higher and very dynamic with apparent genotype successions. Several genotypes derived from DGGE field profiles matched with genotypes from cultures isolated from field samples. The microcystin peak measured in Lake Klinckenberg could be confidently linked to a bloom of Planktothrix rubescens, as microscopic and genotypic analysis showed identity of bloom samples and a toxin-producing P. rubescens culture. Toxin-producing genotypes were detected in the microbial community before they reached densities at which they were detected by using microscopy. Cyanobacterial biovolumes provided additional insights in bloom dynamics. In both lakes, the microcystin content per cell was highest at the onset of the blooms. Our results suggest that while genotypic characterization of a lake can be valuable for detection of toxic organisms, for some lakes a monitoring of algal biomass has sufficient predictive value for an assessment of toxin production. [source] Phenotypic and genotypic characterization of encapsulated Escherichia coli isolated from blooms in two Australian lakesENVIRONMENTAL MICROBIOLOGY, Issue 5 2005Michelle L. Power Summary Escherichia coli has long been used as an indicator organism for water quality assessment. Recently there has been an accumulation of evidence that suggests some strains of this organism are able to proliferate in the environment, a characteristic that would detract from its utility as an indicator of faecal pollution. Phenotypic and genotypic characterization of E. coli isolated from blooms in two Australian lakes, separated by a distance of approximately 200 km, identified that the blooms were dominated by three E. coli strains. A major phenotypic similarity among the three bloom strains was the presence of a group 1 capsule. Genetic characterization of a conserved region of the cps gene cluster, which encodes group 1 capsules, identified a high degree of genetic variation within the bloom isolates. This differs from previously described encapsulated E. coli strains which are highly conserved at the cps locus. The phenotypic or genotypic profiles of the bloom strains were not identified in 435 E. coli strains isolated from vertebrates. The occurrence of these encapsulated strains suggests that some E. coli have evolved a free-living lifestyle and do not require a host in order to proliferate. The presence of the same three strains in bloom events in different geographical regions of a temperate climate, and at different times, indicates that free-living E. coli strains are able to persist in these water reservoirs. This study provides further evidence of circumstances where caution is required in using E. coli as an indicator organism for water quality. [source] Characterization of bacterial pectinolytic strains involved in the water retting processENVIRONMENTAL MICROBIOLOGY, Issue 9 2003Elena Tamburini Summary Pectinolytic microorganisms involved in the water retting process were characterized. Cultivable mesophilic anaerobic and aerobic bacteria were isolated from unretted and water-retted material. A total of 104 anaerobic and 23 aerobic pectinolytic strains were identified. Polygalacturonase activity was measured in the supernatant of cell cultures; 24 anaerobic and nine aerobic isolates showed an enzymatic activity higher than the reference strains Clostridium felsineum and Bacillus subtilis respectively. We performed the first genotypic characterization of the retting microflora by a 16S amplified ribosomal DNA restriction analysis (ARDRA). Anaerobic isolates were divided into five different groups, and the aerobic isolates were clustered into three groups. 84.6% of the anaerobic and 82.6% of the aerobic isolates consisted of two main haplotypes. Partial 16S rRNA gene sequences were determined for 12 strains, representative of each haplotype. All anaerobic strains were assigned to the Clostridium genus, whereas the aerobic isolates were assigned to either the Bacillus or the Paenibacillus genus. Anaerobic isolates with high polygalacturonase (PG) activity belong to two clearly distinct phylogenetic clusters related to C. acetobutylicum,C. felsineum and C. saccharobutylicum species. Aerobic isolates with high PG activity belong to two clearly distinct phylogenetic clusters related to B. subtilisT and B. pumilusT. [source] Phenotypic and genotypic characterization of urease-positive thermophilic Campylobacters (UPTC) isolated from shellfishINTERNATIONAL JOURNAL OF FOOD SCIENCE & TECHNOLOGY, Issue 6 2003John E. Moore First page of article [source] Identification of Bacillus spp. from Bikalga, fermented seeds of Hibiscus sabdariffa: phenotypic and genotypic characterizationJOURNAL OF APPLIED MICROBIOLOGY, Issue 1 2008L.I.I. Ouoba Abstract Aims:, To identify Bacillus spp. responsible of the fermentation of Hibiscus sabdariffa for production of Bikalga, an alkaline fermented food used as a condiment in Burkina Faso. Methods and Results:, Seventy bacteria were isolated from Bikalga produced in different regions of Burkina Faso and identified by phenotyping and genotyping using PCR amplification of the 16S-23S rDNA intergenic transcribed spacer (ITS-PCR), repetitive sequence-based PCR (rep-PCR) and DNA sequencing. The isolates were characterized as motile, rod-shaped, endospore forming, catalase positive, Gram-positive bacteria. ITS-PCR allowed typing mainly at species level. Rep-PCR was more discriminative and allowed a typing at ssp. level. The DNA sequencing combined with the Blast search program and fermentation profiles using API 50CHB system allowed an identification of the bacteria as Bacillus subtilis, B. licheniformis, B. cereus, B. pumilus, B. badius, Brevibacillus bortelensis, B. sphaericus and B. fusiformis. B. subtilis were the predominant bacterium (42) followed by B. licheniformis (16). Conclusions:, Various species and ssp. of Bacillus are involved in fermentation of H. sabdariffa for production of Bikalga. Significance and Impact of the study:, Selection of starter cultures of Bacillus for controlled production of Bikalga, selection of probiotic bacteria. [source] Phenotypic and genotypic characterization of competitive exclusion products for use in poultryJOURNAL OF APPLIED MICROBIOLOGY, Issue 6 2003R.D. Wagner Abstract Aims: Phenotypic and genotypic bacteria identification methods were compared for their efficacy in determining the composition of competitive exclusion (CE) products. Methods and Results: Phenotypic methods used for bacterial identification were fatty acid methyl ester profiles, biochemical assays and carbohydrate utilization profiles. Genotypic methods were MicroSeq16S rRNA sequence analysis and BLAST searches of the GenBank sequence database. Agreement between phenotypic and genotypic methods for identification of bacteria isolated from the Preempt CE product was 20%. A defined test mixture of bacteria was identified to the species level 100% by BLAST analysis, 64% by MicroSeq and 36% by phenotypic techniques. Conclusions: The wide range of facultative and obligate anaerobic bacteria present in a CE product are more accurately identified with 16S rRNA sequence analyses than with phenotypic identification techniques. Significance and Impact of the Study: These results will provide guidelines for manufacturers of CE products to submit more reliable product information for market approval by regulatory agencies. [source] Discrepancies between the phenotypic and genotypic characterization of Lactococcus lactis cheese isolatesLETTERS IN APPLIED MICROBIOLOGY, Issue 6 2006M. De La Plaza Abstract Aims:, The use of randomly amplified polymorphic DNA (RAPD)-PCR fingerprinting and plasmid profiles to determine at the strain level, the similarity of Lactococcus lactis isolates obtained during sampling of traditional cheeses and to verify its correspondence to the selected phenotypic characteristics. Methods and Results:, A total of 45 L. lactis isolates were genotypically analysed by RAPD-PCR fingerprinting and plasmid patterns. Phenotypic traits used to compare strains were proteolytic, acidifying, aminotransferase (aromatic and branched chain aminotransferase) and , -ketoisovalerate decarboxylase (Kivd) activities. The results show that 23 isolates could be grouped in clusters that exhibited 100% identity in both their RAPD and plasmid patterns, indicating the probable isolation of dominant strains during the cheese sampling process. However, there were phenotypic differences between isolates within the same cluster that included the loss of relevant technological properties such as proteinase activity and acidifying capacity or high variation in their amino acid converting enzyme activities. Likewise, the analysis of a specific attribute, Kivd activity, indicated that 7 of 15 isolates showed no detectable activity despite the presence of the encoding (kivd) gene. Conclusion:, Phenotypic differences found between genotypically similar strains of L. lactis strains could be linked to differences in enzymatic expression. Significance and Impact of the Study:, Phenotypic analysis of L. lactis isolates should be considered when selecting strains with new cheese flavour forming capabilities. [source] Phenotypic and genotypic characterization of reference strains of the genus AspergillusMYCOSES, Issue 3-4 2001P.-M. Rath Aspergillus; Genotypisierung; Biotypisierung; SDS-PAGE; RAPD Summary. Twenty-five culture collection strains from four Aspergillus species (A. fumigatus n = 8, A. flavus n = 8, A. niger n= 4, A. nidulans n = 5) were characterized by four methods: (i) determination of patterns in an assimilation assay; (ii) protein pattern of whole mycelial cell lysates in the sodium dodecyl sulphate (SDS)-polyacrylamide gel electrophoresis (PAGE); (iii) reactivity of a pool serum obtained from cystic fibrosis patients with mycelial lysates in the immunoblot; and (iv) random amplification of polymorphic DNA (RAPD) with eight primers having arbitrary or repetitive sequences. In the assimilation assay the A. fumigatus strains showed identical patterns in contrast to the strains of the species A. flavus, A. niger, and A. nidulans, which each showed four patterns. In the SDS-PAGE no differences in the band patterns in the A. fumigatus strains were found, in contrast to the A. flavus (three patterns), A. nidulans (five patterns) and A. niger strains (two patterns). The immunoblot patterns were characteristic for each species with bands at 62 and 17/18 kDa in the A. fumigatus strains, at 51 and 18 kDa in the A. flavus strains, at 51 kDa in the A. niger strains, and at 51, 40 and 17/18 kDa in the A. nidulans strains allowing, however, no intraspecies typing. In the RAPD assay four out of eight primers gave interpretable patterns with 3,20 bands. None of the primers showed sufficient discriminatory power when used alone. However, when combining the results of two of the primers (5,-GTA TTG CCC T-3, and 5,-GAT AGA TAG ATA GAT A-3,) all strains except two A. fumigatus strains could be clearly separated from each other. It is concluded that the the RAPD assay showed the most discriminatory power in all Aspergillus species investigated. In contrast to the phenotypically similar A. fumigatus strains, the strains of the species A. flavus, A. nidulans and A. niger differed in their phenotypic characteristics. The presented data of strains from international culture collections may serve as basis for interlaboratory standardization of typing methods. Zusammenfassung. Fünfundzwanzig Aspergillus -Stämme aus internationalen Stammsammlungen (A. fumigatus n = 8, A. flavus n = 8, A. niger n = 4, A. nidulans n = 5) wurden mit vier Methoden charakterisiert: (1) Reaktionsmuster in einem Assimilationstest (2) Proteinmuster von Ganzzell-Lysaten in der SDS-PAGE (3) Reaktionsmuster eines Poolserums von Patienten mit Mukoviszidose mit Zellextrakten im Immunoblot und (4) random amplification of polymorphic DNA (RAPD) mit acht Primern zufälliger oder repetitiver Sequenz. Im Assimilationstest zeigten die A. fumigatus -Stämme identische Muster, während die Stämme der Spezies A.flavus, A. niger und A. nidulans je vier Reaktionsmuster aufwiesen. In der SDS-PAGE wiesen die A. fumigatus -Stämme identische Muster auf, während die A. flavus -Stämme drei, die A. niger -Stämme zwei, und die A. nidulans -Stämme fünf verschiedene Muster zeigten. Im Immunoblot waren die Muster für jede Spezies charakteristisch mit Banden bei 62 kDa und 17/18 kDa bei A. fumigatus, bei 51 kDa und 18 kDa bei A. flavus, bei 51 kDa bei A. niger und bei 51, 40 und 17/18 kDa bei A. nidulans. Eine Intraspezies-Typisierung gelang jedoch nicht. In der RAPD ergaben vier der acht Primer interpretierbare Muster mit 3 bis 20 Banden. Keiner der Primer alleine zeigte eine ausreichende Diskriminationskapazität. Wurden die Resultate von zwei Primern (5,-GTA TTG CCC T-3, and 5,-GAT AGA TAG ATA GAT A-3,) kombiniert, konnten mit Ausnahme von zwei A. fumigatus -Stämmen alle Isolate voneinander abgegrenzt werden. Die Ergebnisse zeigen, daß die RAPD die größte Diskriminationskapazität aufweist. Im Gegensatz zu den phänotypisch ähnlichen A. fumigatus -Stämmen unterschieden sich die Stämme der Spezies A. flavus, A. nidulans und A. niger voneinander. Die gezeigten Daten von Stämmen internationaler Stammsammlungen können als Grundlage für die Standardisierung von Typisierungsmethoden dienen. [source] | |||||||||||||