Enterobacter cloacae Complex: Clinical Impact and Emerging Antibiotic Resistance

Maria Lina Mezzatesta; Floriana Gona; Stefania Stefani


Future Microbiol. 2012;7(7):887-902. 

In This Article

Taxonomy & Identification

The genus Enterobacter was first described by Hormaeche and Edwards in 1960[7] and has undergone significant taxonomic modification over the last 50 years: Enterobacter agglomerans has been transferred to the genus Pantoea, and Enterobacter sakazakii was recently reassigned to the newly proposed genus Cronobacter.[8]

Currently, there are 22 species in the genus Enterobacter:[201]Enterobacter aerogenes, amnigenus, arachidis, asburiae, cancerogenus, cloacae, cowanii, dissolvens, gergoviae, helveticus, hormaechei, kobei, ludwigii, mori, nimipressuralis, oryzae, pulveris, pyrinus, radicincitans, soli, taylorae and turicensis.[9] Six of these species – E. cloacae, asburiae, hormaechei, kobei, ludwigii and nimipressuralis – are combined in the so-called E. cloacae complex, because most of them share a DNA relatedness with E. cloacae ranging from 61 to 67%.[6] The taxonomy of the E. cloacae complex is mainly based on whole-genome DNA–DNA hybridizations and phenotypic characteristics.

Briefly, the E. cloacae complex exhibits the general characteristics of the genus Enterobacter: they are catalase-positive, oxidase- and DNAase-negative, fermentative and nonpigmented. Their identification is routinely performed by using phenotypic methods: commercial systems for Enterobacteriaceae, API® 20E or Vitek® 2 (BioMerieux, France), are able to discriminate only E. cloacae and E. asburiae, while for the discrimination of the other species, Biotype 100™ (BioMérieux) system and other conventional tests are necessary.[10,11]

Table 1 summarizes some of the key tests for the phenotypic differentiation of the E. cloacae complex species; for example, the Voges–Proskauer test is the only one able to differentiate E. kobei from E. cloacae, while E. ludwigii identification is mainly possible by its ability to grow on 3-0-methyl-D-gluco-pyranose, while E. nimipressuralis is the only nonmotile species.[12,13]

Enterobacter spp. are unambiguously identified by molecular methods[14] by using the 16S rRNA gene, the oriC locus and gyrB.[8] Recently, hsp60- and rpoB-genotyping appeared to be promising novel methods. In particular, the first method uses genotypic identification, via sequencing, of a fragment of hsp60, which is able to discriminate 12 genetic clusters (clusters I–XII) as reported by Hoffmann and Roggenkamp.[6]

Specific names have been attributed to some of the genetic clusters; nine of the clusters correspond to species: E. asburiae (cluster I), E. kobei (cluster II), E. ludwigii (cluster V), E. hormaechei subsp. oharae (cluster VI), E. hormaechei subsp. hormaechei (cluster VII), E. hormaechei subsp. steigerwallti (cluster VIII), E. nimipressuralis (cluster X), E. cloacae subsp. cloacae (cluster XI) and E. cloacae subsp. dissolvens (cluster XII); while three clusters do not have specific names and are referred to as E. cloacae cluster III, E. cloacae cluster IV and E. cloacae cluster IX.[8] The second method consists of the sequencing of rpoB, and could be a valid alternative for strain identification because of the high resolution for differentiating between closely related species.

The degree of genomic diversity within the E. cloacae complex was recently reassessed by other genotypic methods. Two of these deserve some attention and are the multilocus sequence analysis and the comparative genomic hybridization. Multilocus sequence analysis identifies seven clusters within the E. cloacae complex, and each of these corresponds to one or more hsp60 gene sequencing-based genetic cluster. The microarray-based comparative genomic hybridization analysis is a powerful method for performing genome-wide studies on different bacteria.[5]

Recently, in 2012, the results on the use the matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) method for fast identification within the E. cloacae complex have demonstrated that it can be used for distinguishing E. cloacae and E. nimipressuralis; however, it is inadequate for distinguishing E. asburiae, E. hormaechei, E. kobei and E. ludwigii from E. cloacae. Instead, the combination of MALDI-TOF MS with the E. cloacae-specific duplex real-time PCR is an appropriate method for identification of the six species of the E. cloacae complex.[15]

The identification of the species within the E. cloacae complex, with respect to E. cloacae, in clinical specimens is important because it gives more information on their clinical relevance that otherwise could remain underestimated. An example is a case report of nosocomial urosepsis caused by E. kobei that was previously identified as E. cloacae.[16] From the antibiotic therapy point of view, the identification is less important because these species possess similar susceptibility patterns.

Finally, the identification by only phenotypic methods may lead to the misidentification of E. hormaechei as Cronobacter sakazakii, which prevents the full disclosure of sources, infections and of its virulence.[17]