Population Genetics of the Nomenspecies Enterobacter cloacae

Abstract

The genetic heterogeneity of the nomenspecies Enterobacter cloacae is well known. Enterobacter asburiae, Enterobacter cancerogenus, Enterobacter dissolvens, Enterobacter hormaechei, Enterobacter kobei, and Enterobacter nimipressuralis are closely related to it and are subsumed in the so-called E. cloacae complex. DNA-DNA hybridization studies performed previously identified at least five DNA-relatedness groups of this complex. In order to analyze the genetic structure and the phylogenetic relationships between the clusters of the nomenspecies E. cloacae, 206 strains collected from 22 hospitals, a veterinarian, and an agricultural center in 11 countries plus all 13 type strains of the genus and reference strain CDC 1347-71 R were examined with a combination of sequence and PCR-restriction fragment length polymorphism (PCR-RFLP) analyses of the three housekeeping genes hsp60, rpoB, and hemB as well as ampC, the gene of a class C ␤-lactamase. Based on the neighbor-joining tree of the hsp60 sequences, 12 genetic clusters (I to XII) and an unstable sequence crowd (xiii) were identified. The robustness of the genetic clusters was confirmed by analyses of rpoB and hemB sequences and ampC PCR-RFLPs. Sequence crowd xiii split into two groups after rpoB analysis. Only three strains formed a cluster with the type strain of E. cloacae, indicating that the minority of isolates identified as E. cloacae truly belong to the species; 13% of strains grouped with other type strains of the genus, suggesting that the phenotypes of these species seem to be more heterogeneous than so far believed. Three clusters represented 70% of strains, but none of them included a type or reference strain. The genetic clustering presented in this study might serve as a framework for future studies dealing with taxonomic, evolutionary, epidemiological, or pathogenetic characteristics of bacteria belonging to the E. cloacae complex.Enterobacter cloacae has become increasingly important as a nosocomial pathogen, accounting for up to 5% of hospitalacquired septicemias, 5% of nosocomial pneumonias, 4% of nosocomial urinary tract infections, and 10% of postsurgical peritonitis cases (18,35,39). Besides its clinical significance, E. cloacae plays an important role as a pathogen in plants (2, 34) and insects (15) and is ubiquitous in the terrestrial and aquatic environments (22). This diversity of habitats is mirrored by the genetic variety of the nomenspecies E. cloacae, which has been demonstrated in several studies by biotyping and serotyping (16, 47), ribotyping and phage typing (46), pulsed-field gel electrophoresis and enterobacterial repetitive intergenic consensus PCR (ERIC-PCR) (18), and internal transcribed spacer-PCR and random amplification of polymorphic DNA (RAPD)-PCR (6). The 16S ribosomal DNA (rDNA) sequences of E. cloacae did not form a coherent cluster but built a patchy tree, in which the clusters of E. cloacae strains interfused with those of Enterobacter aerogenes, Escherichia coli, Citrobacter species, and Leclercia species. This refl...

Specific Distribution within the Enterobacter cloacae Complex of Strains Isolated from Infected Orthopedic Implants

“…Other targets for use for the molecular identification of isolates within the Enterobacter genus have been described, such as the oriC locus (23), gyrB (6), rpoB (8,21), and hsp60 (8). Sequence analysis of a fragment of the hsp60 gene showed that the E. cloacae nomenspecies could be divided into 12 genetic clusters (clusters I to XII) and one sequence crowd (sequence crowd xiii).…”

“…steigerwallti (cluster VIII) (10). Species names were not attributed to clusters III, IV, and IX and to sequence crowd xiii, although at least cluster III is of significant clinical importance (8,26).…”

“…These microorganisms are saprophytic in the environment and commensal in the enteric flora since they are found in soil and sewage, as well as in the human gastrointestinal tract (17,22). The taxonomy of the Enterobacter genus has been iteratively updated (8)(9)(10)(11)(12)19). Several species are described in this taxon (Enterobacter aerogenes, E. amnigenus, E. cancerogenus, E. cowanii, E. gergoviae, E. intermedius, E. pyrinus), as is a genetic complex, referred to as the "E. cloacae complex," in which other species have been identified (E. asburiae, E. kobei, E. ludwigii, E. hormaechei, E. nimipressuralis, and E. cloacae).…”

“…Sequence analysis of a fragment of the hsp60 gene showed that the E. cloacae nomenspecies could be divided into 12 genetic clusters (clusters I to XII) and one sequence crowd (sequence crowd xiii). Specific names could be attributed to some of the genetic clusters: E. asburiae (cluster I) (9), E. kobei (cluster II) (9), E. ludwigii (cluster V) (11), E. nimipressuralis (cluster X) (8), E. cloacae subsp. cloacae (cluster XI) (9), and E. cloacae subsp.…”

Chromosomal cephalosporinase in Enterobacter hormaechei as an ancestor of ACT-1 plasmid-mediated AmpC β-lactamase

“…16S rRNA gene sequencing was performed using primers 8F and 1541R (Table 1) (Zhou et al, 1995) and the results were analysed using the EzTaxon server (Chun et al, 2007) and MEGA software (http://www.megasoftware.net). The primers for PCR and sequencing of the hsp60 gene were Hsp60 For and Hsp60 Rev (Table 1; Hoffmann & Roggenkamp, 2003). The DNA-DNA relatedness between strain YMC/KN/03/21 and the type strains of E. hormaechei CCUG 27126 T and E. asburiae CCUG 25714 T were evaluated using DNA-DNA hybridization.…”