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

Mutshiene Deogratias Ekwanzala; John Barr Dewar; Ilunga Kamika; Maggy Ndombo Benteke Momba

doi:10.1016/j.scitotenv.2019.06.533

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

Sci Total Environ. 2019 Nov 15:691:80-92. doi: 10.1016/j.scitotenv.2019.06.533. Epub 2019 Jul 2.

Authors

Mutshiene Deogratias Ekwanzala¹, John Barr Dewar², Ilunga Kamika³, Maggy Ndombo Benteke Momba⁴

Affiliations

¹ Department of Environmental, Water and Earth Sciences, Tshwane University of Technology, Arcadia Campus, Private BagX680, Pretoria 0001, South Africa.
² Department of Life and Consumer Sciences, University of South Africa, Florida Campus, Johannesburg, South Africa.
³ Department of Environmental Sciences, University of South Africa, Science Campus, Johannesburg, South Africa.
⁴ Department of Environmental, Water and Earth Sciences, Tshwane University of Technology, Arcadia Campus, Private BagX680, Pretoria 0001, South Africa. Electronic address: mombamnb@tut.ac.za.

PMID: 31319261
DOI: 10.1016/j.scitotenv.2019.06.533

Abstract

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 (bla_CTX-M-15 and bla_OXA-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.

Keywords: Aquatic environment; Carbapenem-resistant; Klebsiella pneumoniae; Tracking; WGS; Wastewater.

MeSH terms

Anti-Bacterial Agents / metabolism*
Biodegradation, Environmental
Carbapenems / metabolism*
Drug Resistance, Bacterial / genetics*
Environmental Monitoring
Klebsiella pneumoniae / physiology*
Whole Genome Sequencing

Substances

Anti-Bacterial Agents
Carbapenems