Tracking the environmental dissemination of carbapenem-resistant Klebsiella pneumoniae using whole genome sequencing

The emergence and dissemination of infections caused by carbapenem-resistant Klebsiella pneumoniae (CRKP) are of great concern worldwide, as there are limited options for their treatment. Thus, in this study, whole-genome sequencing (WGS) was applied to assess CRKP distribution and dissemination from hospital settings to the aquatic environment in order to identify the extent of the problem. Samples were collected from hospital wastewaters and receiving water bodies. Susceptible K. pneumoniae and CRKP were enumerated and isolated using standard methods. Seventeen CRKP were DNA-sequenced using an Illumina HiSeq X™ platform. De novo assembly and annotation were performed using SPAdes and RAST, respectively. The study analysed antibiotic resistance traits (antibiotic resistant genes, mobile genetic elements, and virulence genes) in CRKP isolates. Although influent of wastewater harboured the highest CRKP, wastewater treatment plants were efficient in reducing the threat. In terms of resistance per matrix, benthic sediment proved to harbour more CRKP (22.88%) versus susceptible K. pneumoniae, as revealed by their resistant quotient analysis, while effluent of wastewaters (4.21%) and water bodies (4.64%) had the lowest CRKP loads. The disseminating CRKP consisted of six sequence types (ST) - ST307 (n = 7), a novel ST3559 (n = 5), ST15 (n = 2), and one isolate of each of ST39, 152 and 298. All CRKP isolates harboured β-lactams (blaCTX-M-15 and blaOXA-1), quinolone (oqxA and oqxB) and fosfomycin (fosA) resistance genes as well as virulence genes. This study highlights the dissemination of 'high' importance and novel ST CRKP from hospital wastewater to waterbodies. This is concerning, particularly in the African context where a sizable number of people still rely on direct water resources for household use, including drinking. Further research is needed to systematically track the occurrence and distribution of these bacteria so as to mitigate their threat.