Typing

About: Typing is a research topic. Over the lifetime, 5010 publications have been published within this topic receiving 146539 citations.

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

Comparison of four molecular typing methods to assess genetic relatedness of Candida albicans clinical isolates in Taiwan.

Abstract: This report describes the investigation of the genetic profiles of 53 Candida albicans isolates collected from 18 hospitals in Taiwan using three PFGE-based typing methods (PFGE karyotyping, and PFGE of SfiI and BssHII restriction fragments) and one repetitive-sequence-PCR (rep-PCR) method. All four methods were able to identify clonal related isolates from the same patients. PFGE-BssHII exhibited the highest discriminatory power by discriminating 40 genotypes, followed by PFGE-SfiI (35 genotypes) and then by rep-PCR (31 genotypes), while PFGE karyotyping exhibited the lowest discriminatory power (19 genotypes). High discriminatory power can also be achieved by combining typing methods with different typing mechanisms, such as rep-PCR and PFGE-based typing methods. The results also showed that the genotype of each isolate was patient-specific and not associated with the source of the isolation, geographic origin or antifungal resistance.

Random amplification of polymorphic DNA (RAPD) of Salmonella: strain differentiation and characterization of amplified sequences.

Abstract: Random amplification of polymorphic DNA (RAPD) was evaluated for its ability to differentiate Salmonella strains from various sources. Under defined conditions RAPD using a 10-mer primer (1254) produced a series of amplification products able to reproducibly distinguish strains representing 20 different serotypes of Salmonella. Primer 1254 also proved capable of discrimination between some but not all isolates of Salm. ser. Enteritidis and Salm. ser. Typhimurium, phage typing proving to be most discriminatory for the latter serotype. Cloning of fragments into a vector allowed sequencing and database searching for identification of fragments and an indication of criteria for primer template interaction in RAPD. Southern blotting using a digoxigenin-labelled probe allowed identification of related bands between RAPD profiles. These observations demonstrate the potential of rapid molecular typing by RAPD for the genomic typing of Salmonella strains.

Comparison of HLA‐DRB1 typing by DNA‐RFLP, PCR‐SSO and PCR‐SSP methods and their application in providing matched unrelated donors for bone marrow transplantation

Abstract: The aim of the study was to devise a strategy for large batch analysis to determine HLA Class II alleles exhibited by candidate bone marrow transplant donors and prospective recipients using previously published DNA-based typing techniques. Special attention was directed towards the technical aspects of procedures, the level of typing resolution and the speed of data analysis. 200 blood samples from volunteer bone marrow transplant donors typed serologically for HLA-DR and DQ were further investigated using three DNA-based typing methods: (i) restriction fragment length polymorphism (RFLP) analysis, (ii) polymerase chain reaction (PCR) amplification and subsequent hybridisation with sequence specific oligonucleotide probes (PCR-SSO), and (iii) PCR amplification with sequence specific primers (PCR-SSP) to resolve the DRB1* specificity of each individual. In general, the HLA-DR results obtained using PCR-SSO and PCR-SSP correlated well with each other. However, discordant results were obtained between PCR and RFLP based typing in 21 cases, especially in relation to DRB3* alleles associated with the DRB1 gene. These differences were due to three problems pertaining to RFLP analysis: i) alleles with identical DRB, DQA and DQB fragment sizes, ii) reliance on DQA and DQB results to assign the DRB genotype, and iii) a “new polymorphism” of DR7, in a DR7 homozygous, exhibiting a fragment similar in size to DR8. Our findings suggested a strategy requiring PCR-SSO analysis for initial low resolution class II typing involving large numbers of samples, while the use of PCR-SSP is reserved for small numbers of samples, for urgent samples or for situations where higher resolution is required. As the PCR-based methods are relatively quick, precise, simple and inexpensive, they have replaced RFLP analysis and become the routine approach for DR‘ typing in our laboratory.