ArticleApplied and environmental microbiology2008
Rapid determination of Escherichia coli O157:H7 lineage types and molecular subtypes by using comparative genomic fingerprinting.
Article in Applied and environmental microbiology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
14 citing papers in PubMed.
- An Emerging Foodborne Pathogen Spotlight: A Bibliometric Analysis and Scholarly Review ofAntibiotics (Basel, Switzerland) · 2024Review
- Genotypic Features of Clinical and BovineMicroorganisms · 2018Review
- Article
- Review
- Multilocus genotypic characterization of Escherichia coli O157:H7 recovered from food sources.Epidemiology and infection · 2015Article
- Characteristics of clinical Shiga toxin-producing Escherichia coli isolated from British Columbia.BioMed research international · 2013Article
- Comparison of molecular typing methods useful for detecting clusters of Campylobacter jejuni and C. coli isolates through routine surveillance.Journal of clinical microbiology · 2012Article
- Development and validation of a comparative genomic fingerprinting method for high-resolution genotyping of Campylobacter jejuni.Journal of clinical microbiology · 2012Article
- Article
- Genome signatures of Escherichia coli O157:H7 isolates from the bovine host reservoir.Applied and environmental microbiology · 2011Article
- Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions.BMC bioinformatics · 2010Article
- rhs genes are potential markers for multilocus sequence typing of Escherichia coli O157:H7 strains.Applied and environmental microbiology · 2009Article
- In silico genomic analyses reveal three distinct lineages of Escherichia coli O157:H7, one of which is associated with hyper-virulence.BMC genomics · 2009Article
- Genomic regions conserved in lineage II Escherichia coli O157:H7 strains.Applied and environmental microbiology · 2009Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In this study, variably absent or present (VAP) regions discovered through comparative genomics experiments were targeted for the development of a rapid, PCR-based method to subtype and fingerprint Escherichia coli O157:H7. Forty-four VAP loci were analyzed for discriminatory power among 79 E. coli O157:H7 strains of 13 phage types (PT). Twenty-three loci were found to maximize resolution among strains, generating 54 separate fingerprints, each of which contained strains of unique PT. Strains from the three previously identified major E. coli O157:H7 lineages, LSPA6-LI, LSPA6-LI/II, and LSPA6-LII, formed distinct branches on a dendrogram obtained by hierarchical clustering of comparative genomic fingerprinting (CGF) data. By contrast, pulsed-field gel electrophoresis (PFGE) typing generated 52 XbaI digestion profiles that were not unique to PT and did not cluster according to O157:H7 lineage. Our analysis identified a subpopulation comprised of 25 strains from a closed herd of cattle, all of which were of PT87 and formed a cluster distinct from all other E. coli O157:H7 strains examined. CGF found five related but unique fingerprints among the highly clonal herd strains, with two dominant subtypes characterized by a shift from the presence of locus fprn33 to its absence. CGF had equal resolution to PFGE typing but with greater specificity, generating fingerprints that were unique among phenotypically related E. coli O157:H7 lineages and PT. As a comparative genomics typing method that is amenable for use in high-throughput platforms, CGF may be a valuable tool in outbreak investigations and strain characterization.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.