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Genomic diversity within the enterobacter cloacae complex

Author: Paauw, A. · Caspers, M.P.M. · Schuren, F.H.J. · Leverstein-van Hall, M.A. · Delétoile, A. · Montijn, R.C. · Verhoef, J. · Fluit, A.C.
Type:article
Date:2008
Institution: TNO Kwaliteit van Leven · KvL
Source:PLoS ONE, 8, 3
Identifier: 240960
doi: doi:10.1371/journal.pone.0003018
Article number: No.: e3018
Keywords: Biology · Cladistics · comparative genomic hybridization · Enterobacter hormaechei · microarray analysis · molecular evolution · multilocus sequence typing · species comparison · species identification · bacterial genome · DNA sequence · nucleic acid hybridization · phylogeny · Enterobacter · Enterobacter cloacae · Genetic Variation · Genome, Bacterial · Genotype · Nucleic Acid Hybridization · Phylogeny · Sequence Analysis, DNA · Food and Nutrition · Healthy Living

Abstract

Background: Isolates of the Enterobacter cloacae complex have been increasingly isolated as nosocomial pathogens, but phenotypic identification of the E. cloacae complex is unreliable and irreproducible. Identification of species based on currently available genotyping tools is already superior to phenotypic identification, but the taxonomy of isolates belonging to this complex is cumbersome. Methodolgy/Principal Findings: This study shows that multilocus sequence analysis and comparative genomic hybridization based on a mixed genome array is a powerful method for studying species assignment within the E. cloacae complex. The E. cloacae complex is shown to be evolutionarily divided into two clades that are genetically distinct from each other. The younger first clade is genetically more homogenous, contains the Enterobacter hormaechei species and is the most frequently cultured Enterobacter species in hospitals. The second and older clade consists of several (sub)species that are genetically more heterogonous. Genetic markers were identified that could discriminate between the two clades and cluster 1. Conclusions/Significance: Based on genomic differences it is concluded that some previously defined (clonal and heterogenic) (sub)species of the E. cloacae complex have to be redefined because of disagreements with known or proposed nomenclature. However, further improved identification of the redefined species will be possible based on novel markers presented here. © 2008 Paauw et al. Chemicals / CAS: Bacterial Proteins; DNA, Bacterial