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Typing

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


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Journal ArticleDOI
TL;DR: Polymorphisms identified in this work offer robust phylogenetic signals that index both short- and long-term evolution and can complement currently employed typing schemes for outbreak ex- and inclusion, diagnostics, surveillance, and forensic studies.
Abstract: Multi isolate whole genome sequencing and typing for outbreak investigations has become a reality in the post-genomics era. We applied this technology to strains from Escherichia coli O157:H7 outbreaks. These include isolates from seven North America outbreaks, as well as multiple isolates from the same patient and from different infected individuals in the same household. Customized high-resolution bioinformatics sequence typing strategies were developed to assess the core genome and mobilome plasticity. Sequence typing was performed using an in-house single nucleotide polymorphism (SNP) discovery and validation pipeline. Discriminatory power becomes of particular importance for the investigation of isolates from outbreaks in which macrogenomic techniques such as pulse-field gel electrophoresis or multiple locus variable number tandem repeat analysis do not differentiate closely related organisms. We also characterized differences in the phage inventory, allowing us to identify plasticity among outbreak strains that is not detectable at the core genome level. Our comprehensive analysis of the mobilome identified multiple plasmids that have not previously been associated with this lineage. Applied phylogenomics approaches provide strong molecular evidence for exceptionally little heterogeneity of strains within outbreaks and demonstrate the value of intra-cluster comparisons, rather than basing the analysis on archetypal reference strains. Next generation sequencing and whole genome typing strategies provide the technological foundation for genomic epidemiology outbreak investigation utilizing its significantly higher sample throughput, cost efficiency, and phylogenetic relatedness accuracy. These phylogenomics approaches have major public health relevance in translating information from the sequence-based survey to support timely and informed countermeasures. Polymorphisms identified in this work offer robust phylogenetic signals that index both short- and longterm evolution and can complement currently employed typing schemes for outbreak ex- and inclusion, diagnostics, surveillance, and forensic studies.

44 citations

Journal ArticleDOI
TL;DR: This project addressed the question whether molecular typing for HLA class I also increases the efficacy of HLA matching in kidney transplantation and found that 183 DNA class I compatible transplants had a 15% higher one-year graft survival rate than 32 transplants for which DNA typing revealed a class I incompatibility.
Abstract: DNA typing for HLA class II improves the typing quality and this was shown previously to be relevant for kidney graft survival. In this project we addressed the question whether molecular typing for HLA class I also increases the efficacy of HLA matching in kidney transplantation. 215 HLA-A,-B,-DR zero-mismatched donor/recipient pairs as defined by serological typing were selected. Retrospective HLA-A and HLA-B typing was performed both by the PCR-SSP and the PCR-SSOP method. DNA typing for HLA-A revealed discrepant results to serology in 5.7% of the donors and 2.8% of the recipients. HLA-B typing discrepancies were found in 6.6% of the donors and 5.6% of the recipients. 10.4% of the donors and 6.5% of the recipients showed either an HLA-A or an HLA-B discrepancy Nearly one-third of the HLA-A discrepancies affected A19 splits. The most common reason for HLA-A discrepancies was the erroneous assignment of serological blanks, whereas HLA-B errors were caused mainly by the assignment of incorrect specificities. DNA typing allowed the definition of HLA-A and -B split specificities in all 118 "splitable" cases for which only broad specificities were reported based on serological typing. A total of 183 DNA class I compatible transplants had a 15% higher one-year graft survival rate than 32 transplants for which DNA typing revealed a class I incompatibility

44 citations

Journal ArticleDOI
TL;DR: Frequency information, based on a population of 5,000 individuals, has been established using a combination of molecular and serological typing data and PCR-SSOP detected the presence of a second HLA-A allele in over 10% of individuals who had been previously homozygous.
Abstract: A medium resolution PCR-SSOP typing method, using 26 digoxigenin labelled probes, has been established for the identification of HLA-A alleles. The system is capable of discriminating all of the serologically defined specificities except for eight heterozygous combinations which are however rare in Caucasians. The method has been applied to 1,838 individuals on the local bone marrow registry who either had only one detectable HLA-A antigen, or a HLA-A antigen whose presence had been queried using the serological technique or a broad HLA-A specificity assigned by the serological technique. In all but one case the serologically assigned antigens were detected with the PCR-SSOP method. In addition, PCR-SSOP detected the presence of a second HLA-A allele in over 10% of individuals who had been previously homozygous. Frequency information, based on a population of 5,000 individuals, has been established using a combination of molecular and serological typing data.

44 citations

Journal ArticleDOI
TL;DR: AP-PCR analysis provides a simple and practical approach to typing P. aeruginosa that is more discriminatory than traditional serotyping scheme and it is suggested that maximum discrimination can be achieved by a combination of both methods.
Abstract: Arbitrary primed PCR (AP-PCR) analysis was compared with serotyping as a means of high-resolution typing of Pseudomonas aeruginosa Seventy-four isolates from 3 different hospitals and 18 reference strains were studied Serotyping provided good index of discrimination, although eleven isolates could not be serotyped Genomic DNA was amplified with a single 10 nucleotide primer (sequence 5′-AGG GGT CTT G-3′) The strains were genetically diverse and 61 different AP-PCR profiles of 2–7 bands between 03 and 24 kb were obtained AP-PCR profiles were not consistently associated with serotypes, but they clearly subtyped strains of the same serotype Numerical analysis of AP-PCR patterns defined 7 groups at the 55% similarity level, and identified predominant strains in each hospital The results show that AP-PCR analysis provides a simple and practical approach to typing P aeruginosa that is more discriminatory than traditional serotyping scheme We suggest that maximum discrimination can be achieved by a combination of both methods

44 citations

Journal ArticleDOI
02 Dec 2015-PLOS ONE
TL;DR: The completion of the multiplex PCR technology that is able to identify all the 47 Penner serotypes types known for C. jejuni is reported.
Abstract: Campylobacter jejuni produces a polysaccharide capsule that is the major determinant of the Penner serotyping scheme. This passive slide agglutination typing system was developed in the early 1980’s and was recognized for over two decades as the gold standard for C. jejuni typing. A preliminary multiplex PCR technique covering 17 serotypes was previously developed in order to replace this classic serotyping scheme. Here we report the completion of the multiplex PCR technology that is able to identify all the 47 Penner serotypes types known for C. jejuni. The number of capsule types represented within the 47 serotypes is 35. We have applied this method to a collection of 996 clinical isolates from Thailand, Cambodia and Nepal and were able to successfully determine capsule types of 98% of these.

44 citations


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Performance
Metrics
No. of papers in the topic in previous years
YearPapers
2023329
2022690
2021145
2020126
2019136
2018147