Showing papers on "Typing published in 1989"

Ribosomal RNA Gene Restriction Patterns Provide Increased Sensitivity for Typing Salmonella typhi Strains

Abstract: To date, epidemiologic associations among strains of Salmonella typhi are based exclusively on phage typing, which may be of limited value if a common phage type is involved. Analysis of ribosomal RNA gene restriction patterns allows separation of most independently isolated strains of identical phage types. The sensitivity of the method is dependent on the restriction enzymes used to digest chromosomal DNA. It was highest for PstI, which separated 16 of 20 strains that belonged to 8 phage types including 3 untypable strains. Three strains differed in their phage types but had identical ribosomal RNA gene restriction patterns. Also, two pairs of strains indistinguishable by phage typing exhibited identical patterns; however, two of these strains were expected to be identical because they were isolated from two patients who were likely exposed to the same source. Ribosomal RNA gene restriction patterns appear to be stable. Thus, the method may complement phage typing and aid in further differentiation of strains.

Method for hla dp typing

Abstract: A process for determining the genotype of an individual with respect to the alleles at the HLA DP locus involves obtaining a sample of nucleic acid from the individual, and hybridizing the nucleic acids with a panel of probes specific for variant segments of DPalpha and DPbeta genes. Because the variation between DPbeta alleles is highly dispersed throughout the second exon of the DPbeta gene, the discovery of many different DPbeta alleles makes the process far more discriminating and informative than cellular, RFLP, or serological methods. The process can also be carried out on amplified nucleic acid produced by the polymerase chain reaction using primers specific for the second exon of the DPalpha and DPbeta genes. HLA DP DNA typing methods are useful in the prevention of graft rejection and host versus graft disease, in determining susceptibility to autoimmune diseases, in providing evidence concerning the derivation from an individual of forensic samples, and in paternity testing.

Subdivision of Salmonella enteritidis phage types by plasmid profile typing

Abstract: Differentiation of Salmonella enteritidis by plasmid profile typing has been compared to differentiation by phage typing. Examination of the type strains of the 27 S. enteritidis phage types showed that only 11 profile patterns could be identified. Moreover, two profile patterns were found in 15 of the type strains, including those of the two most common phage types in Britain, types 4 and 8. On this basis, plasmid profile typing is not as sensitive as phage typing for the primary subdivision of S. enteritidis. When differentiation of 534 strains of the 27 phage types was attempted using plasmid profiles, variation in pattern suitable for epidemiological subdivision was found in 13 phage types and there were 9 profile patterns in strains of phage type 4. Plasmid profile typing can, therefore, be regarded as an effective adjunct to phage typing for the subdivision of S. enteritidis.

Assessment of DNA fingerprinting for rapid identification of outbreaks of systemic candidiasis.

Abstract: DNA fingerprinting was assessed as an improved typing system for Candida albicans aimed at speeding the implementation of cross infection control measures in outbreaks of systemic candidiasis. The study was carried out with 45 previously characterised isolates from five different outbreaks and with 96 unrelated isolates from a mixed control population. Sixteen different genotypes were produced. Results were obtainable within days, reproducibility was high, and there was good discrimination among different outbreaks. Compared with existing typing systems DNA fingerprinting provides a robust system that may be used rapidly to identify outbreaks of nosocomial candidiasis in laboratories with no specialist skill in typing C albicans.

Pseudomonas cepacia Typing Systems: Collaborative Study to Assess Their Potential in Epidemiologic Investigations

Abstract: To determine the utility of available Pseudomonas cepacia typing systems for confirming the relatedness of isolates, we applied these methods to isolates associated with previously investigated nosocomial outbreaks. We compared chromosome analysis, serologic reactions, biochemical tests, bacteriocin production and susceptibility, and antimicrobial susceptibility in their ability to determine outbreak relatedness. Chromosome analysis, serologic reactions, and biochemical tests were each demonstrated to be epidemiologically useful methods for typing isolates. Determination of the sensitivity and specificity of these typing techniques will facilitate their application in the epidemiologic study of this increasingly important nosocomial pathogen.

Restriction enzyme analysis of plasmid DNA and bacteriophage typing of paired Staphylococcus aureus blood culture isolates.

Abstract: We compared restriction enzyme analysis of plasmid (REAP) DNA profiling with bacteriophage typing for determination of similarities and differences among 50 pairs of Staphylococcus aureus blood isolates from patients with multiple positive blood cultures Isolates from 17 pairs did not have detectable plasmids Isolates from 33 pairs had plasmids classified into 17 distinct REAP DNA profiles Paired isolates from 31 of these episodes were identical to one another By phage typing, 35 pairs had strong lytic reactions to a phage(s), 9 pairs lacked strong reactions, and 6 pairs consisted of a strongly reactive isolate and an isolate with no strong reaction to a phage When consolidated into 11 general phage groups, pairs from 44 of the 50 episodes were in the same general group REAP DNA profiles were highly reproducible (99%), whereas phage typing was not REAP DNA profiling is superior to phage typing as a technique for determining similarities and differences among S aureus blood isolates Images

Use of a pilin gene probe to study molecular epidemiology of Pseudomonas aeruginosa.

Abstract: Strains of Pseudomonas aeruginosa from patients with cystic fibrosis (CF) are unusual. The majority have a rough lipopolysaccharide (LPS) which renders them nontypeable by conventional typing systems based on a serological reaction with the O polysaccharide of smooth LPS. We developed a new typing scheme using a pilin gene probe as a marker for hybridization with endonuclease-digested genomic DNA from P. aeruginosa. Twenty-one different restriction fragment length polymorphism (RFLP) types were found among 249 isolates. RFLP type 7 was recovered only from patients with thermal burns (9 of 14 isolates) in both Vancouver, British Columbia, and Edmonton, Alberta, Canada. None of the other RFLP types showed a clear predilection for disease state or environmental niche. Multiple morphologically different isolates from individual patients with CF were studied; each isolate in 33 of 40 sputum samples had an identical RFLP type, despite considerable LPS serotype heterogeneity. Sequential isolates from 23 patients were studied; in 10 isolates there was a clear change in both the RFLP and the LPS serotype. We conclude that patients with CF usually harbor a single P. aeruginosa RFLP type in their sputa, but that one strain can replace another as the predominant colonizing type. Images

Fine-structure genetic mapping of human chromosomes using the polymerase chain reaction on single sperm: experimental design considerations.

Abstract: The polymerase chain reaction (PCR) makes it possible to rapidly generate a very large number of copies of a specific region of DNA. Application of PCR to individual human sperm cells permits the typing of a large number of independent male meiotic events. If the donor male is heterozygous at three loci, sperm typing using PCR will permit ordering of loci in a manner analogous to classical methods of experimental genetics. Sequential analysis of trios of loci by sperm typing will provide a very accurate means of ordering any number of tightly linked loci. Here, we describe experimental design and sample-size issues raised by the application of sperm typing by PCR for mapping human chromosomes, and we demonstrate that sperm typing will be an efficient method for generating fine-structure human genetic maps.

Typing of Aeromonas strains by DNA restriction endonuclease analysis and polyacrylamide gel electrophoresis of cell envelopes.

Abstract: The outer membrane protein (OMP) composition (OMP typing) of 46 fecal Aeromonas strains from hybridization groups (HGs) 1 (A hydrophila; n = 10), 4 (A caviae; n = 16), and 8 (A veronii; n = 20) were examined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis as a phenotypic typing method Almost every isolate of HG-1 and HG-8 had a unique OMP profile, in contrast to isolates of HG-4, which were separated into five different OMP types It was possible to recognize HGs 1, 4, and 8 by OMP profiles Twenty-three Aeromonas strains from HGs 1 (n = 5), 4 (n = 10), and 8 (n = 8) were tested by whole-cell DNA restriction endonuclease analysis (REA) as a genetic typing method All strains tested by REA (with SmaI) had different DNA digestion patterns Although additional DNA-rRNA hybridization analyses with SmaI and 16S and 23S rRNAs from Escherichia coli showed a reduction in the number of restriction bands to 8 to 13 hybridized fragments, the discriminative value was less when compared with that obtained by REA The individual differences found by REA were used to analyze whether patients remained colonized by the same Aeromonas strain Of 11 patients with diarrhea, 2 had a different isolate on repeat culture In addition, one of nine tested fecal samples contained two Aeromonas isolates with different REA patterns These results indicate that during diarrheal disease the intestinal tract may be colonized simultaneously with different Aeromonas isolates Images

Typing of human rhinoviruses based on sequence variations in the 5' non-coding region.

Abstract: Summary Unambiguous assignment of restriction enzyme patterns to six individual serotypes of human rhinovirus was accomplished after amplification of a 380 bp DNA fragment derived from the 5′ non-coding region. This was possible even though serotypes 1A and 1B and serotypes 2 and 49 differed only at 10 and 15 positions respectively. The method utilizes the conserved and variable components of this part of the genome and provides the basis for a simple and rapid method for typing of human rhinoviruses.

A method of HLA class II typing using non‐radioactive labelled oligonucleotides

Abstract: The typing of HLA class II genes using molecular biology techniques has brought undoubtedly new insights in the analysis of their polymorphism. Particularly interesting is the dot-blot analysis of enzymatically-amplified genomic DNA hybridized with sequence-specific oligonucleotides. In order to use this technique of typing on a routine basis, we established a non-radioactive detection method of enzymatically-amplified genomic DNA dot-blots. We could clearly demonstrate that, using biotin-labelled specific oligonucleotides, it was possible to specifically discriminate between DQB1 first domain DNA sequences displaying three, two or even only one base-pair difference at a given codon position. The very satisfactory sensitivity level reached by this non-radioactive detection method could safely allow its use for clinical applications of HLA typing at the DNA level.

Typing of Clostridium difficile causing diarrhoea in an orthopaedic ward.

Abstract: In an outbreak of diarrhoeal disease in an orthopaedic ward Clostridium difficile was isolated from all six patients with diarrhoea. Attempts were made to type these isolates by means of antibiogram, detection of pre-formed enzymes, analysis of surface proteins by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) and immunoblotting, and plasmid profile analysis. This showed that a single strain (type E) indistinguishable by the four distinct methods of typing, was isolated from all six patients at some time during their episodes of diarrhoea. Relapse was caused by the acquisition of a new strain in two patients, and by re-emergence or reacquisition of the original strain in two patients. The immunochemical method was the most sensitive and discriminatory of the typing strategies adopted.

HLA Class II Typing by the Workshop Defined RFLP Specificities in Unrelated Individuals

Abstract: The Southern blot component of the Tenth International Workshop (WS) was based on the study of 70 cell lines, most of which were homozygous for the HLA complex. Thirty-four different, DR, DQ, Dw haplotypes emerged from serologic and Dw typings. The Tenth Workshop analysis demonstrates conclusively that almost all of these 34 haplotypes can be detected using RFLP techniques. This method, therefore, provides a convenient tool for accurate typing, which can now be based on a standard method. The aim of this chapter is to discuss the practical aspects of DR-DQ RFLP typing.

Evaluation of numerical analysis of SDS-PAGE of protein patterns for typing Enterobacter cloacae.

Abstract: Twenty cultures comprising 13 clinical isolates of Enterobacter cloacae from two hospitals, the type and another reference stain of E. cloacae and the type strains of four other Enterobacter sp. and of Escherichia coli, were characterized by one-dimensional sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) of whole-cell proteins. The protein patterns were highly reproducible and were used as the basis of a numerical analysis which divided the clinical isolates into nine clearly defined protein types. Comparison with established typing methods indicated that the discrimination of SDS-PAGE was similar to that achieved with conventional typing methods and all strain groups recognized by combined sero/phage typing were also found by SDS-PAGE. In addition, protein typing sub-divided a group of four serotype O3 isolates that were difficult to distinguish by phage typing. We conclude that high-resolution SDS-PAGE of proteins provides an effective method of typing isolates of E. cloacae.

HLA-Dw and HLA-DP Typing of the Reference Panel of B-Lymphoblastoid Cell Lines

Abstract: Cellular typing for HLA-Dw and HLA-DPw within the Tenth International Histocompatibility Workshop was incorporated into the Workshop component on T-cell Recognition of HLA Class II Molecules. Separate Workshop components on Dw and DPw typing for identification of new specificities using homozygous typing cells (HTC) or primed lymphocyte typing (PLT) were not designed as part of the Tenth Workshop. It was, however, essential that accurate information was obtained for HLA-Dw and HLA-DPw specificities for the Reference Panel of B- Lymphoblastoid Cell Lines. A working group consisting of the authors of this paper was established for this purpose. Whenever possible, any residual PBL from the cell line donors was collected and distributed to several interested laboratories for cellular typing studies. In the case of DP, typing was also performed using the B-cell lines themselves. DP typing was performed by four groups: Sell and Eckels, Hartzman and Robbins, Odum and Svejgaard, and Farrell and Honeyman. The results of the DP typing studies are shown in Table 1. Consensus assignments of HLA-Dw and HLA-DPw specificities are incorporated into Table 4B in the paper entitled “Description of the Reference Panel of B-Lymphoblastoid Cell Lines for Factors of the HLA System” by Yang et al. (this volume).

Genetic typing in a cluster of Legionella pneumophila infections.

Abstract: Legionella pneumophila strains isolated from six patients, three air-conditioning- and cooling tower-derived strains, and three hot water supply-derived strains were analyzed by three genetic typing methods. The results of the whole-cell DNA restriction endonuclease analysis and the restriction patterns based on genes coding for rRNA correlated with each other and demonstrated that the patient isolates were indistinguishable from the air-conditioning- and cooling tower-derived isolates but differed markedly from the hot water supply-derived isolates. The patient and air-conditioning- and cooling tower-derived strains contained plasmids of the same molecular weight; the hot water supply-derived strains were plasmidless. These results indicated that the cooling tower or the air-conditioning system was the environmental source for the examined cluster of Legionnaires disease strains.

Preliminary studies on monocine typing of Listeria monocytogenes strains.

Abstract: About 58% of Listeria monocytogenes strains produced monocines. The titres of 1/2a monocines were higher than those of 4b strains.

Typing for HLA-DPB1*03 and HLA-DPB1*06 using allele-specific DNA in vitro amplification and allele-specific oligonucleotide probes. Detection of "new" DPB1*06 variants.

Abstract: DP gene typing using in vitro DNA amplification combined with sequence-specific oligonucleotide probes has recently been reported. The resulting DNA amplification was specific for theHLA-DPB locus. Typing for the individualDPB alleles was exclusively dependent on the hybridizations of the probes but hampered by close sequence homology between differentDP alleles yielding complex patterns of reactivity with a panel of probes. We report the combined use of allele-specific DNA in vitro amplification and allele-specific oligonucleotides in typing forDPB1*03 andDPB1*06. Complete concordance with PLT typing was observed for theDPB1*03 alleles, while in the DPB1*06 group, at least three variantDPB1*06 alleles were identified which have not been described previously.

HLA typing from human donor eyes.

Abstract: A method for HLA-ABC and HLA-DR typing of human donor eyes using pigmented retinal epithelial and uveal cells cultured in the presence of human recombinant γ-interferon is described.

Workshop Report for the HLA-DP Region

Abstract: Determination of the different DP alleles has become increasingly desirable during the last few years in studies of both graft rejection of transplants (1,2) and of new disease associations (3,4). DP typing has until now been done by the very laborious primed lymphocyte typing (PLT) technique, but lately good correlations between DP types defined by PLT typing and restriction fragment length polymorphism (RFLP) of the DP region has been established (5–7).

Frequencies of HLA-DP alleles in the four major types of leukaemia

Abstract: The frequencies of HLA-DP alleles in 50 acute lymphocytic, 43 acute non-lymphocytic, 50 chronic myelogenous and 51 chronic lymphocytic leukaemia patients were compared with 254 controls using primed lymphocyte typing In CLL and ANLL there were significantly decreased frequencies of DPw1 Decreased DPw1 and DPw3 was observed in ALL, but after correction for the number of comparisons made this was no longer significant However, in ALL, even after correction, there were significantly increased frequencies of DPw2 and DPw5, whereas in ANLL and CLL the only significant increases were of DP-blank, and in CML there were no positive or negative associations at all These results suggest an influence of DP alleles in disease susceptibility and resistance in three of the four major types of leukaemia

Monoclonal antibodies to protein I for serotyping of Neisseria gonorrhoeae: Correlation of serotype with bactericidal activity

Abstract: Seven monoclonal antibodies have been used for the serotyping of one hundred Neisseria gonorrhoeae wild strains, randomly selected from nine U.S. cities, and seven serotype reference strains by the co-agglutination method. As determined by gel-immunoradioassay, the monoclonal antibodies recognized the protein I trimer of a single or a limited subset of serotype reference strains. All but three strains were typable by one or two of the antibodies. The most common serotypes were 1.3 (26%), 1 (20%), 5 (17%), 5.7 (11%) and 9 (10%). To correlate typing results with ability for killing of these antibodies, susceptibility of typed and non-typed strains to killing was studied. Susceptibility was significantly associated with typing by the serotype 7 (p = 0.011) and serotype 9 (p = 0.033) specific monoclonal antibodies. Reaction of antibodies recognizing epitopes on the protein IB molecule with a given strain predicted in an average of 43% of strains (49% of strains of serotype 5, 62% of serotype 7, 29% of serotype 8, and 33% of serotype 9) its susceptibility to killing by the typing antibodies. In contrast, only 15% of the strains (15% of strains of serotype 1 and 15% of serotype 3) were killed by their typing antibodies, recognizing epitopes on the protein IA molecule. These monoclonal antibodies might prove to be important for the isolation and structural characterization of epitopes responsible for susceptibility of the gonococcus to killing and thus for the development of a vaccine against invasive gonococcal disease.

Electrophoretic typing of Enterobacter cloacae with a limited set of enzyme stains.

Abstract: Hospital isolates of Enterobacter cloacae were analysed by polyacrylamide gel electrophoresis for enzyme polymorphism and the results were compared with established serotyping, phage typing and biotyping techniques. Initially, the diversity of electromorphs of 13 enzymes was determined on a representative set of 62 distinct strains. Two broad clusters of strains were found in the species, and analysis by serotype suggested a limited diversity within the most frequent O serotypes. A subset of three enzymes, lactate dehydrogenase, 6-phosphogluconate dehydrogenase, glutamate dehydrogenase and an unidentified marker, were selected and used to type groups of hospital isolates. There was good general agreement between the two systems, although the enzyme method failed to distinguish between some strains with the same serotype. This method provided useful epidemiological information and, in the absence of established typing systems, it is a practical approach to subdividing the species.