Cargando…
ClermonTyping: an easy-to-use and accurate in silico method for Escherichia genus strain phylotyping
The genus Escherichia is composed of Escherichia albertii, E. fergusonii, five cryptic Escherichia clades and E. coli sensu stricto. Furthermore, the E. coli species can be divided into seven main phylogroups termed A, B1, B2, C, D, E and F. As specific lifestyles and/or hosts can be attributed to t...
Autores principales: | , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Microbiology Society
2018
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6113867/ https://www.ncbi.nlm.nih.gov/pubmed/29916797 http://dx.doi.org/10.1099/mgen.0.000192 |
_version_ | 1783351090816745472 |
---|---|
author | Beghain, Johann Bridier-Nahmias, Antoine Le Nagard, Hervé Denamur, Erick Clermont, Olivier |
author_facet | Beghain, Johann Bridier-Nahmias, Antoine Le Nagard, Hervé Denamur, Erick Clermont, Olivier |
author_sort | Beghain, Johann |
collection | PubMed |
description | The genus Escherichia is composed of Escherichia albertii, E. fergusonii, five cryptic Escherichia clades and E. coli sensu stricto. Furthermore, the E. coli species can be divided into seven main phylogroups termed A, B1, B2, C, D, E and F. As specific lifestyles and/or hosts can be attributed to these species/phylogroups, their identification is meaningful for epidemiological studies. Classical phenotypic tests fail to identify non-sensu stricto E. coli as well as phylogroups. Clermont and colleagues have developed PCR assays that allow the identification of most of these species/phylogroups, the triplex/quadruplex PCR for E. coli phylogroup determination being the most popular. With the growing availability of whole genome sequences, we have developed the ClermonTyping method and its associated web-interface, the ClermonTyper, that allows a given strain sequence to be assigned to E. albertii, E. fergusonii, Escherichia clades I–V, E. coli sensu stricto as well as to the seven main E. coli phylogroups. The ClermonTyping is based on the concept of in vitro PCR assays and maintains the principles of ease of use and speed that prevailed during the development of the in vitro assays. This in silico approach shows 99.4 % concordance with the in vitro PCR assays and 98.8 % with the Mash genome-clustering tool. The very few discrepancies result from various errors occurring mainly from horizontal gene transfers or SNPs in the primers. We propose the ClermonTyper as a freely available resource to the scientific community at: http://clermontyping.iame-research.center/. |
format | Online Article Text |
id | pubmed-6113867 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Microbiology Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-61138672018-08-30 ClermonTyping: an easy-to-use and accurate in silico method for Escherichia genus strain phylotyping Beghain, Johann Bridier-Nahmias, Antoine Le Nagard, Hervé Denamur, Erick Clermont, Olivier Microb Genom Methods Paper The genus Escherichia is composed of Escherichia albertii, E. fergusonii, five cryptic Escherichia clades and E. coli sensu stricto. Furthermore, the E. coli species can be divided into seven main phylogroups termed A, B1, B2, C, D, E and F. As specific lifestyles and/or hosts can be attributed to these species/phylogroups, their identification is meaningful for epidemiological studies. Classical phenotypic tests fail to identify non-sensu stricto E. coli as well as phylogroups. Clermont and colleagues have developed PCR assays that allow the identification of most of these species/phylogroups, the triplex/quadruplex PCR for E. coli phylogroup determination being the most popular. With the growing availability of whole genome sequences, we have developed the ClermonTyping method and its associated web-interface, the ClermonTyper, that allows a given strain sequence to be assigned to E. albertii, E. fergusonii, Escherichia clades I–V, E. coli sensu stricto as well as to the seven main E. coli phylogroups. The ClermonTyping is based on the concept of in vitro PCR assays and maintains the principles of ease of use and speed that prevailed during the development of the in vitro assays. This in silico approach shows 99.4 % concordance with the in vitro PCR assays and 98.8 % with the Mash genome-clustering tool. The very few discrepancies result from various errors occurring mainly from horizontal gene transfers or SNPs in the primers. We propose the ClermonTyper as a freely available resource to the scientific community at: http://clermontyping.iame-research.center/. Microbiology Society 2018-06-19 /pmc/articles/PMC6113867/ /pubmed/29916797 http://dx.doi.org/10.1099/mgen.0.000192 Text en © 2018 The Authors http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Methods Paper Beghain, Johann Bridier-Nahmias, Antoine Le Nagard, Hervé Denamur, Erick Clermont, Olivier ClermonTyping: an easy-to-use and accurate in silico method for Escherichia genus strain phylotyping |
title | ClermonTyping: an easy-to-use and accurate in silico method for Escherichia genus strain phylotyping |
title_full | ClermonTyping: an easy-to-use and accurate in silico method for Escherichia genus strain phylotyping |
title_fullStr | ClermonTyping: an easy-to-use and accurate in silico method for Escherichia genus strain phylotyping |
title_full_unstemmed | ClermonTyping: an easy-to-use and accurate in silico method for Escherichia genus strain phylotyping |
title_short | ClermonTyping: an easy-to-use and accurate in silico method for Escherichia genus strain phylotyping |
title_sort | clermontyping: an easy-to-use and accurate in silico method for escherichia genus strain phylotyping |
topic | Methods Paper |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6113867/ https://www.ncbi.nlm.nih.gov/pubmed/29916797 http://dx.doi.org/10.1099/mgen.0.000192 |
work_keys_str_mv | AT beghainjohann clermontypinganeasytouseandaccurateinsilicomethodforescherichiagenusstrainphylotyping AT bridiernahmiasantoine clermontypinganeasytouseandaccurateinsilicomethodforescherichiagenusstrainphylotyping AT lenagardherve clermontypinganeasytouseandaccurateinsilicomethodforescherichiagenusstrainphylotyping AT denamurerick clermontypinganeasytouseandaccurateinsilicomethodforescherichiagenusstrainphylotyping AT clermontolivier clermontypinganeasytouseandaccurateinsilicomethodforescherichiagenusstrainphylotyping |