Characterization of the cryptic Escherichia lineages: rapid identification and prevalence
Identifieur interne : 002172 ( Istex/Curation ); précédent : 002171; suivant : 002173Characterization of the cryptic Escherichia lineages: rapid identification and prevalence
Auteurs : Olivier Clermont [France] ; David M. Gordon [Australie] ; Sylvain Brisse [France] ; Seth T. Walk [États-Unis] ; Erick Denamur [France]Source :
- Environmental Microbiology [ 1462-2912 ] ; 2011-09.
English descriptors
- KwdEn :
- Achtman mlst scheme, Albertii, Albertii strains, Appl environ microbiol, Blackwell publishing, Chua, Clade, Clermont, Coli, Coli strains, Contingency analysis, Cryptic, Cryptic clade strains, Cryptic clades, Cryptic escherichia clades, Cryptic escherichia lineages, Cryptic lineages, Environmental microbiology, Escherichia, Escherichia clade, Escherichia coli, Faecal, Fergusonii, Fergusonii strains, Genetic structure, Genotype, Institute pasteur scheme, Likelihood ratio, Lineage, Lysine, Mammal, Microbiol, Microbiology, Mlst, Mlst data, Mlst results, Nucleotide sequence data, Ornithine, Phylogenetic, Phylogenetic tree, Phylogeny, Picard, Population genetics, Primer, Relative abundance, Tenaillon, Triplex, Triplex method, Water samples, Yjaa.
- Teeft :
- Achtman mlst scheme, Albertii, Albertii strains, Appl environ microbiol, Blackwell publishing, Chua, Clade, Clermont, Coli, Coli strains, Contingency analysis, Cryptic, Cryptic clade strains, Cryptic clades, Cryptic escherichia clades, Cryptic escherichia lineages, Cryptic lineages, Environmental microbiology, Escherichia, Escherichia clade, Escherichia coli, Faecal, Fergusonii, Fergusonii strains, Genetic structure, Genotype, Institute pasteur scheme, Likelihood ratio, Lineage, Lysine, Mammal, Microbiol, Microbiology, Mlst, Mlst data, Mlst results, Nucleotide sequence data, Ornithine, Phylogenetic, Phylogenetic tree, Phylogeny, Picard, Population genetics, Primer, Relative abundance, Tenaillon, Triplex, Triplex method, Water samples, Yjaa.
Abstract
Strains phenotypically indistinguishable from Escherichia coli and belonging to at least five distinct cryptic lineages, named Escherichia clades I to V, that are genetically divergent from E. coli yet members of the genus have been recently found using multi‐locus sequence typing (MLST). Very few epidemiological data are available on these strains as their detection by MLST is not suitable for large‐scale studies. In this work, we developed a rapid PCR method based on aes and chuA allele‐specific amplifications that assigns a strain a cryptic lineage membership. By screening more than 3500 strains with this approach, we show that the cryptic lineages of Escherichia are unlikely to be detected in human faecal samples (2–3% frequency) and even less likely to be isolated from extra‐intestinal body sites (< 1% frequency). They are more abundant in animal faeces ranging from 3–8% in non‐human mammals to 8–28% in birds. Overall, the strains from the clade V are the most abundant and from the clade II very rare. These results suggest that members of the cryptic clades are unlikely to be of significance to human and health but may influence the use of ‘E. coli’ as an indicator of water quality.
Url:
DOI: 10.1111/j.1462-2920.2011.02519.x
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<front><div type="abstract" xml:lang="en">Strains phenotypically indistinguishable from Escherichia coli and belonging to at least five distinct cryptic lineages, named Escherichia clades I to V, that are genetically divergent from E. coli yet members of the genus have been recently found using multi‐locus sequence typing (MLST). Very few epidemiological data are available on these strains as their detection by MLST is not suitable for large‐scale studies. In this work, we developed a rapid PCR method based on aes and chuA allele‐specific amplifications that assigns a strain a cryptic lineage membership. By screening more than 3500 strains with this approach, we show that the cryptic lineages of Escherichia are unlikely to be detected in human faecal samples (2–3% frequency) and even less likely to be isolated from extra‐intestinal body sites (< 1% frequency). They are more abundant in animal faeces ranging from 3–8% in non‐human mammals to 8–28% in birds. Overall, the strains from the clade V are the most abundant and from the clade II very rare. These results suggest that members of the cryptic clades are unlikely to be of significance to human and health but may influence the use of ‘E. coli’ as an indicator of water quality.</div>
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