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Background:  The predominant species in clinical  Enterobacter  isolates is  E. hormaechei . Many articles, clinicians, and GenBank submissions misname these strains as  E. cloacae . The lack of sequenced type strains or named species/subspecies for some clades in the  E. cloacae  complex complicate the issue.    Methods:  The genomes of the type strains for  Enterobacter hormaechei  subsp.  oharae ,  E .  hormaechei  subsp.  steigerwaltii , and  E. xiangfangensis , and two strains from Hoffmann clusters III and IV of the  E. cloacae  complex were sequenced. These genomes, the  E .  hormaechei  subsp.  hormaechei  type strain, and other available  Enterobacter  type strains were analysed in conjunction with all extant  Enterobacter  genomes in NCBI’s RefSeq using Average Nucleotide Identity (ANI).    Results:  There were five recognizable subspecies of  E. hormaechei :  E. hormaechei  subsp.  hoffmannii  subsp. nov.,  E. hormaechei  subsp.  xiangfangensis  comb. nov., and the three previously known subspecies. One of the strains sequenced from the  E. cloacae  complex was not a novel  E. hormaechei  subspecies but rather a member of a clade of a novel species:  E. roggenkampii  sp. nov..  E. muelleri  was determined to be a later heterotypic synonym of  E. asburiae  which should take precedence.    Conclusion:  The phylogeny of the  Enterobacter  genus, particularly the  cloacae  complex, was re-evaluated based on the type strain genome sequences and all other available  Enterobacter  genomes in RefSeq.

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Enterobacter hormaechei subsp. hoffmannii subsp. nov., Enterobacter hormaechei subsp. xiangfangensis comb. nov., Enterobacter roggenkampii sp. nov., and Enterobacter muelleri is a later heterotypic synonym of Enterobacter asburiae based on computational analysis of sequenced Enterobacter genomes.