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
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 objectiv...
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doaj-833b267cf2fc45c7b679bae86f2417e02020-11-24T23:26:38ZengSciendoIrish Journal of Agricultural and Food Research2009-90292016-12-01552819010.1515/ijafr-2016-0008ijafr-2016-0008Comparison of methods for the identification and sub-typing of O157 and non-O157 Escherichia coli serotypes and their integration into a polyphasic taxonomy approachPrieto-Calvo M.A.0Omer M.K.1Alvseike O.2López M.3Alvarez-Ordóñez A.4Prieto M.5Department of Food Hygiene and Food Technology, Faculty of Veterinary Medicine, University of León, León, SpainAnimalia – Norwegian Meat and Poultry Research Center, Oslo, NorwayAnimalia – Norwegian Meat and Poultry Research Center, Oslo, NorwayDepartment of Food Hygiene and Food Technology, Faculty of Veterinary Medicine, University of León, León, SpainDepartment of Food Hygiene and Food Technology, Faculty of Veterinary Medicine, University of León, León, SpainDepartment of Food Hygiene and Food Technology, Faculty of Veterinary Medicine, University of León, León, SpainPhenotypic, 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.http://www.degruyter.com/view/j/ijafr.2016.55.issue-2/ijafr-2016-0008/ijafr-2016-0008.xml?format=INTFT-IR spectroscopygenotypingITS sequencingpolyphasic taxonomyVTEC |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Prieto-Calvo M.A. Omer M.K. Alvseike O. López M. Alvarez-Ordóñez A. Prieto M. |
spellingShingle |
Prieto-Calvo M.A. Omer M.K. Alvseike O. López M. Alvarez-Ordóñez A. Prieto M. 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 FT-IR spectroscopy genotyping ITS sequencing polyphasic taxonomy VTEC |
author_facet |
Prieto-Calvo M.A. Omer M.K. Alvseike O. López M. Alvarez-Ordóñez A. Prieto M. |
author_sort |
Prieto-Calvo M.A. |
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 |
title_short |
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 |
title_full |
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 |
title_fullStr |
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 |
title_full_unstemmed |
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 |
title_sort |
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 |
publisher |
Sciendo |
series |
Irish Journal of Agricultural and Food Research |
issn |
2009-9029 |
publishDate |
2016-12-01 |
description |
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. |
topic |
FT-IR spectroscopy genotyping ITS sequencing polyphasic taxonomy VTEC |
url |
http://www.degruyter.com/view/j/ijafr.2016.55.issue-2/ijafr-2016-0008/ijafr-2016-0008.xml?format=INT |
work_keys_str_mv |
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