Misidentification of Klebsiella variicola isolated from neonates in two German hospitals

Background: As part of routine surveillance, we investigated the epidemiology of what was presumed to be Klebsiella pneumoniae isolates that were isolated from skin swabs from neonates in two separate German hospitals.Material/methods: Ten isolates from 10 neonates from hospital A, and 19 isolates from hospital B (17 neonates, one mother's milk and one environmental sample) were collected. Presumptive species identification of K. pneumoniae was determined by MALD-TOF at the local microbiology diagnostic laboratories. Total DNA was purified and whole genomes were sequenced using the MiSeq platform. We used our in-house ad-hoc core-genome MLST scheme (cgMLST) with a core-genome of 3079 alleles to investigate their molecular epidemiology. Traditional 7-loci MLST and the acquired resistome was investigated using ResFinder.Results: Our cgMLST scheme identified three identical isolates in Hospital A. The remaining seven isolates differed from one another by >2500 alleles. In contrast, in hospital B there were two distinct clusters of 14 and 5 isolates. Within a cluster, there were 0-4 alleles different, and 2965 allelic differences between the clusters. The ResFinder KmerFinder-2.1 species identifier revealed that two unrelated isolates from hospital A, and the cluster of five isolates from hospital B were Klebsiella variicola. The remaining isolates were confirmed as K. pneumoniae. The rpoB gene sequences when analysed at the curated phylogentic database leBIBI confirmed the K. variicola species identification. All K. variicola isolates carried the oqxA-like, oqxB-like, fosA-like resistance genes as well as LEN-beta-lactamases. Furthermore one isolate from hospital A was also in possession of tetD and SHV-1 resistance genes. In addition, the K. variicola isolates all possessed the nfi gene for nitrogen fixation, which illustrates their environmental background. Seven-loci MLST revealed that hospital A K. variicola were single or double locus variants of ST-619 or ST-1563, while in hospital B they were all ST-1423. Interestingly, isolates in the Pasteur MLST database with these STs were deposited as K. pneumoniae.Conclusions: These data illustrate that MALDI-TOF is unable to distinguish between the hospital pathogen K. pneumoniae and the closely related K. variicola. Furthermore, there appears to be misidentification of isolates in the MLST database. These data suggest that K. variicola may be involved in nosocomial cross transmission and that its clinical impact needs further investigation.