News from the MedVetKlebs project: description of novel Klebsiella species, and development of a real-time PCR assay for K. pneumoniae detection in complex samples.
One of the main objectives of the MedVetKlebs project is the development of novel methods to detect Klebsiella pneumoniae in complex environments such as foods and soil. In order to achieve this goal, it is important to define the target species precisely, and delineate it from closely-related taxa. Two updates of the Klebsiella taxonomy were therefore published. First, two novel taxa closely related to K. pneumoniae were discovered and described: K. africana and K. variicola subsp. tropica (https://doi.org/10.1016/j.resmic.2019.02.003; https://doi.org/10.1016/j.resmic.2019.09.001).
Second, in collaboration with the JPIAMR-funded SpARK project (https://www.jpiamr.eu/supportedprojects/third-joint-callresult/ ), two novel species previously misidentified as K. oxytoca were described: Klebsiella pasteurii and Klebsiella spallanzanii (https://doi.org/10.3389/fmicb.2019.02360). The novel taxa can be identified using MALDI-TOF mass spectrometry, which discriminates them from K. pneumoniae, K. oxytoca and other Klebsiella members. Therefore, reference spectra of the novel taxa should be incorporated in the future into the reference MALDI-TOF databases. The novel species were isolated from clinical or fecal carriage samples.
As all members of the K. pneumoniae species complex can cause infections, we designed a novel qPCR method that detects at the same time K. pneumoniae and its related species K. variicola, K. quasipneumoniae, K. quasivariicola and K. africana. This novel assay is based on a molecular target, the ZKIR intergenic region, which is universally conserved in, and unique to, the K. pneumoniae complex. The ZKIR qPCR assay is specific for its target group of pathogens, as all strains from other species were negative. The assay was tested for detection in soil samples and proved very sensitive, allowing to detect 0.15 CFU per gram after overnight sample enrichment. This novel method was subsequently implemented in several institutions participating in the MedVetKlebs consortium, and successfully used to detect bacteria belonging to the K. pneumoniae species complex in salads and chicken meat. To accelerate the dissemination of this novel detection tool, a detailed protocol was made publicly available through the dedicated protocols.io platform (dx.doi.org/10.17504/protocols.io.7n6hmhe).