PubMed Health⌕ Search

Biomedical subjects

Lea Valinsky

Publications and source records attributed to Lea Valinsky.

9 recordsLinked to original sources
PubMed2006

Vibrio cholerae strain typing and phylogeny study based on simple sequence repeats.

Vibrio cholerae is the etiological agent of cholera. Its natural reservoir is the aquatic environment. To date, practical typing of V. cholerae is mainly serological and requires about 200 antisera. Simple sequence repeats (SSR), also termed VNTR (for variable number of tandem repeats), provide a source of high genomic polymorphism used in bacterial typing. Here we describe an SSR-based typing method that combines the variation in highly mutable SSR loci, with that of shorter, relatively more stable mononucleotide repeat (MNR) loci, for accurate and rapid typing of V. cholerae. In silico screening of the V. cholerae genome revealed thousands of perfect SSR tracts with an average frequency of one SSR every 152 bp. A panel of 32 V. cholerae strains, representing both clinical and environmental isolates, was tested for polymorphism in SSR loci. Two strategies were applied to identify SSR variation: polymorphism of SSR tracts longer than 12 bp (L-SSR) assessed by capillary fragment-size analysis and MNR polymorphism assessed by sequencing. The nine L-SSR loci tested were all polymorphic, displaying 2 to 13 alleles per locus. Sequence analysis of eight MNR-containing loci (MNR-multilocus sequence typing [MLST]) provided information on both variations in the MNR tract itself, and single nucleotide polymorphism (SNP) in their flanking sequences. Phylogenetic analysis of the combined SSR data showed a clear discrimination between the clinical strains belonging to O1 and O139 serogroups, and the environmental isolates. Furthermore, discrimination between 27 strains of the 32 strains was achieved. SSR-based typing methods combining L-SSR and MNR-MLST were found to be efficient for V. cholerae typing.

Bacterial Typing Techniques↗
PubMed2006

A large food-borne outbreak of group A streptococcal pharyngitis in an industrial plant: potential for deliberate contamination.

Contamination of food with streptococci could present with unusual outbreaks that may be difficult to recognize in the early stages. This is demonstrated in a large food-borne outbreak of streptococcal pharyngitis that occurred in 2003 in a factory in Israel. The outbreak was reported to the public health services on July 2 and an epidemiologic investigation was initiated. Cases and controls were interviewed and throat swabs were taken. An estimated 212 cases occurred within the first 4 days, the peak occurring on the second day. There was a wave of secondary cases during an additional 11 days. The early signs were of a respiratory illness including sore throat, weakness and fever, with high absenteeism rates suggesting a respiratory illness. As part of a case-control study, cases and controls were interviewed and throat swabs taken. Illness was significantly associated with consumption of egg-mayonnaise salad (odds ratio 4.2, 95% confidence interval 1.4-12.6), suggesting an incubation period of 12-96 hours. The initial respiratory signs of food-borne streptococcal pharyngitis outbreaks could delay the identification of the vehicle of transmission. This could be particularly problematic in the event of deliberate contamination.

Bioterrorism↗
PubMed2005

Classification of oligonucleotide fingerprints: application for microbial community and gene expression analyses.

MOTIVATION: Oligonucleotide fingerprinting of ribosomal RNA genes (OFRG) is a procedure that sorts rRNA gene (rDNA) clones into taxonomic groups through a series of hybridization experiments. The hybridization signals are classified into three discrete values 0, 1 and N, where 0 and 1, respectively, specify negative and positive hybridization events and N designates an uncertain assignment. This study examined various approaches for classifying the values including Bayesian classification with normally distributed signal data, Bayesian classification with the exponentially distributed data, and with gamma distributed data, along with tree-based classification. All classification data were clustered using the unweighted pair group method with arithmetic mean. RESULTS: The performance of each classification/clustering procedure was compared with results from known reference data. Comparisons indicated that the approach using the Bayesian classification with normal densities followed by tree clustering out-performed all others. The paper includes a discussion of how this Bayesian approach may be useful for the analysis of gene expression data.

Algorithms↗
PubMed2004

Endemic occurrence of infections by multidrug-resistant Escherichia coli of four unique serotypes in the elderly population of Israel.

During a period of four years, multidrug-resistant Escherichia coli of particular serotypes have been isolated from 255 elderly (>65 years) patients from four hospitals in central Israel. 83% of the isolates belonged to one of four predominant serotypes (O153:H31, O101:H-, O2:H42, and O102:H6). All isolates were producers of extended spectrum beta-lactamases and resistant to ciprofloxacin. To our knowledge, the involved serotypes have hitherto not been reported as etiological agents of extraintestinal human infections (MEDLINE). Pulsed-field gel electrophoresis of isolates from one of the most frequent serotypes indicated a clonal relationship between them. Further investigation of these strains and analysis of their virulence factors may help to confine their spread.

Aged↗
PubMed2004

Group G streptococcal bacteremia in Jerusalem.

Group G Streptococcus (GGS) can cause severe infections, including bacteremia. These organisms often express a surface protein homologous to the Streptococcus pyogenes M protein. We retrospectively studied the characteristics of patients from the Hadassah Medical Center with GGS bacteremia from 1989 to 2000. Ninety-four cases of GGS bacteremia were identified in 84 patients. The median age was 62 years, 54% were males, and 92% had underlying diseases (35% had a malignancy, and 35% had diabetes mellitus). The most frequent source for bacteremia was cellulitis (61%). emm typing of 56 available isolates disclosed 13 different types, including 2 novel types. Six patients had recurrent bacteremia with two to four bacteremic episodes, five had chronic lymphatic disorders, and two had emm type stG840.0 in every episode. Recurrent bacteremia has not been described for invasive group A Streptococcus. We describe an entity of recurrent GGS bacteremia, which is associated with lymphatic disorders and possibly with emm stG840.0.

Adolescent↗
PubMed2003

Bacterial rRNA genes associated with soil suppressiveness against the plant-parasitic nematode Heterodera schachtii.

The goal of this study was to identify bacteria involved in soil suppressiveness against the plant-parasitic nematode Heterodera schachtii. Since H. schachtii cysts isolated from the suppressive soil can transfer this beneficial property to nonsuppressive soils, analysis of the cyst-associated microorganisms should lead to the identification of the causal organisms. Our experimental approach was to identify bacterial rRNA genes (rDNA) associated with H. schachtii cysts obtained from soil mixtures with various levels of suppressiveness. We hypothesized that we would be able to identify bacteria involved in the suppressiveness by correlating population shifts with differing levels of suppressiveness. Soil treatments containing different amounts of suppressive and fumigation-induced nonsuppressive soils exhibited various levels of suppressiveness after two nematode generations. The 10%-suppressive-soil treatment contained numbers of eggs per gram of soil similar to those of the 100%-suppressive-soil treatment, indicating that the suppressive factor(s) had been transferred. Bacterial rDNA associated with H. schachtii cysts were identified using a culture-independent method termed oligonucleotide fingerprinting of rRNA genes. Bacteria from five major taxonomic groups (Actinobacteria, Cytophaga-Flexibacter-Bacteroides, alpha-Proteobacteria, beta-Proteobacteria, and gamma-Proteobacteria) were identified. Three bacterial rDNA groups contained clones that were more prevalent in the highly suppressive soil treatments than in the less suppressive treatments, indicating a potential involvement in the H. schachtii suppressiveness. When these three groups were examined with specific PCR analyses performed on H. schachtii cysts that developed in soils treated with three biocidal compounds, only one bacterial rDNA group with moderate to high sequence identity to rDNA from several Rhizobium species and uncultured alpha-proteobacterial clones was consistently associated with the highly suppressive treatments. A quantitative PCR analysis confirmed the association of this Rhizobium-like rDNA group with the H. schachtii suppressiveness.

Animals↗
PubMed2002

Oligonucleotide fingerprinting of rRNA genes for analysis of fungal community composition.

Thorough assessments of fungal diversity are currently hindered by technological limitations. Here we describe a new method for identifying fungi, oligonucleotide fingerprinting of rRNA genes (OFRG). ORFG sorts arrayed rRNA gene (ribosomal DNA [rDNA]) clones into taxonomic clusters through a series of hybridization experiments, each using a single oligonucleotide probe. A simulated annealing algorithm was used to design an OFRG probe set for fungal rDNA. Analysis of 1,536 fungal rDNA clones derived from soil generated 455 clusters. A pairwise sequence analysis showed that clones with average sequence identities of 99.2% were grouped into the same cluster. To examine the accuracy of the taxonomic identities produced by this OFRG experiment, we determined the nucleotide sequences for 117 clones distributed throughout the tree. For all but two of these clones, the taxonomic identities generated by this OFRG experiment were consistent with those generated by a nucleotide sequence analysis. Eighty-eight percent of the clones were affiliated with Ascomycota, while 12% belonged to BASIDIOMYCOTA: A large fraction of the clones were affiliated with the genera Fusarium (404 clones) and Raciborskiomyces (176 clones). Smaller assemblages of clones had high sequence identities to the Alternaria, Ascobolus, Chaetomium, Cryptococcus, and Rhizoctonia clades.

DNA Fingerprinting↗
PubMed2002

Analysis of bacterial community composition by oligonucleotide fingerprinting of rRNA genes.

One of the first steps in characterizing an ecosystem is to describe the organisms inhabiting it. For microbial studies, experimental limitations have hindered the ability to depict diverse communities. Here we describe oligonucleotide fingerprinting of rRNA genes (OFRG), a method that permits identification of arrayed rRNA genes (rDNA) through a series of hybridization experiments using small DNA probes. To demonstrate this strategy, we examined the bacteria inhabiting two different soils. Analysis of 1,536 rDNA clones revealed 766 clusters grouped into five major taxa: Bacillus, Actinobacteria, Proteobacteria, and two undefined assemblages. Soil-specific taxa were identified and then independently confirmed through cluster-specific PCR of the original soil DNA. Near-species-level resolution was obtained by this analysis as clones with average sequence identities of 97% were grouped in the same cluster. A comparison of these OFRG results with the results obtained in a denaturing gradient gel electrophoresis analysis of the same two soils demonstrated the significance of this methodological advance. OFRG provides a cost-effective means to extensively analyze microbial communities and should have applications in medicine, biotechnology, and ecosystem studies.

Bacteria↗