Comparison of methods for the identification and sub-typing of O157 and non-O157 Escherichia coli serotypes and their integration into a polyphasic taxonomy approach
dc.contributor.author | Prieto-Calvo, M.A. | * |
dc.contributor.author | Omer, M.K. | * |
dc.contributor.author | Alveseike, O. | * |
dc.contributor.author | Lopez, M. | * |
dc.contributor.author | Alvarez-Ordonez, Avelino | * |
dc.contributor.author | Prieto, Maria Luz | * |
dc.date.accessioned | 2017-06-16T14:14:33Z | |
dc.date.available | 2017-06-16T14:14:33Z | |
dc.date.issued | 30/12/2016 | |
dc.identifier.citation | Prieto-Calvo, M., Omer, M., Alvseike, O., et al. (2016). Comparison of methods for the identification and sub-typing of O157 and non-O157 Escherichia coli serotypes and their integration into a polyphasic taxonomy approach. Irish Journal of Agricultural and Food Research, 55(2), pp. 81-90, doi:10.1515/ijafr-2016-0008 | en_GB |
dc.identifier.issn | 2009-9029 | |
dc.identifier.issn | 0791-6833 (print) | |
dc.identifier.uri | http://hdl.handle.net/11019/1146 | |
dc.description | peer-reviewed | en_GB |
dc.description.abstract | Phenotypic, chemotaxonomic and genotypic data from 12 strains of Escherichia coli were collected, including carbon source utilisation profiles, ribotypes, sequencing data of the 16S–23S rRNA internal transcribed region (ITS) and Fourier transform-infrared (FT-IR) spectroscopic profiles. The objectives were to compare several identification systems for E. coli and to develop and test a polyphasic taxonomic approach using the four methodologies combined for the sub-typing of O157 and non-O157 E. coli. The nucleotide sequences of the 16S–23S rRNA ITS regions were amplified by polymerase chain reaction (PCR), sequenced and compared with reference data available at the GenBank database using the Basic Local Alignment Search Tool (BLAST) . Additional information comprising the utilisation of carbon sources, riboprint profiles and FT-IR spectra was also collected. The capacity of the methods for the identification and typing of E. coli to species and subspecies levels was evaluated. Data were transformed and integrated to present polyphasic hierarchical clusters and relationships. The study reports the use of an integrated scheme comprising phenotypic, chemotaxonomic and genotypic information (carbon source profile, sequencing of the 16S–23S rRNA ITS, ribotyping and FT-IR spectroscopy) for a more precise characterisation and identification of E. coli. The results showed that identification of E. coli strains by each individual method was limited mainly by the extension and quality of reference databases. On the contrary, the polyphasic approach, whereby heterogeneous taxonomic data were combined and weighted, improved the identification results, gave more consistency to the final clustering and provided additional information on the taxonomic structure and phenotypic behaviour of strains, as shown by the close clustering of strains with similar stress resistance patterns. | en_GB |
dc.description.sponsorship | The authors acknowledge the financial contribution of the Spanish INIA, the Research Council of Norway (project 178230/I10), Foundation for Levy on Foods, the Norwegian Research Fees Fund for Agricultural Goods, the Norwegian Independent Meat and Poultry Association, Nortura SA and NHO Matog Landbruk. | en_GB |
dc.language.iso | en | en_GB |
dc.publisher | Teagasc (Agriculture and Food Development Authority), Ireland | en_GB |
dc.relation.ispartofseries | Irish Journal of Agricultural and Food Research;vol 55 | |
dc.subject | FT-IR spectroscopy | en_GB |
dc.subject | genotyping; | en_GB |
dc.subject | ITS sequencing; | en_GB |
dc.subject | polyphasic taxonomy; | en_GB |
dc.subject | VTEC | en_GB |
dc.title | Comparison of methods for the identification and sub-typing of O157 and non-O157 Escherichia coli serotypes and their integration into a polyphasic taxonomy approach | en_GB |
dc.type | Article | en_GB |
dc.identifier.doi | https://doi.org/10.1515/ijafr-2016-0008 | |
dc.contributor.sponsor | Research Council of Norway | |
dc.contributor.sponsor | INIA, Spain | |
dc.contributor.sponsor | Foundation for Levy on Foods | |
dc.contributor.sponsor | Norwegian Research Fees Fund for Agricultural Goods | |
dc.contributor.sponsor | Norwegian Independent Meat and Poultry Association | |
dc.contributor.sponsorGrantNumber | 178230/I10 | |
refterms.dateFOA | 2018-01-12T08:49:15Z |
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IJAFR, volume 55, no. 2, 2016 [12]
Irish Journal of Agricultural & Food Research, Volume 55, Number 2, 2016 -
IJAFR, volume 55, no. 2, 2016 [12]
Irish Journal of Agricultural & Food Research, Volume 55, Number 2, 2016 -
Food Quality & Sensory Science [174]