Enterobacter cloacae complex taxonomic incongruence may lead to misidentification of outbreaks and hinder infection control in real time.

The Enterobacter cloacae complex (ECC) are important nosocomial pathogens involved in hospital outbreaks. They present a significant challenge for accurate species identification, hindering outbreak detection and investigation. Nevertheless, many clinical laboratories report identification of these organisms at the species level. Here we report on several outbreaks of which recognition was delayed due to ECC erroneous species identification by common laboratory methods. We evaluated different classification approaches, including Vitek-2, mass spectrometry, 16 S rRNA sequencing, Fourier-transform infrared (FT-IR) spectroscopy and genomic-based methods. We collected 63 ECC isolates reported in a single hospital over 18 months and chose 17 isolates that were temporary close but recognized as different species by MALDI-TOF MS, and thus not suspected of being related. Whole genome sequencing followed by Average Nucleotide Identity (ANI) analysis revealed that those isolates represented several outbreaks. Using ANI analysis as the gold standard for ECC species identification, core-genome MLST (cgMLST) was the most accurate method, followed by FT-IR typing. We therefore suggest that clinical laboratories should report ECC isolates as such, without specifying the species. Alternatively, infection control teams need to be informed that all ECC isolates should be regarded as potentially related, regardless of their specific species designation.