Complete Genome Sequence of Multi-Drug Resistant Klebsiella Quasipneumoniae Isolated for The First Time from A Wastewater Treatment Plant in Slovenia

Introduction

In recent years, the fate of antimicrobial resistance genes (ARGs) released to wastewaters has received increasing interest [1] and there is a worldwide consensus that raw municipal wastewater, treated effluent and wastewater sludge are reservoirs of ARGs and crucial hotspots for the evolution and spread of antibiot¬ic resistance [2]. Klebsiella quasipneumoniae is a common in¬testinal commensal bacterium that is widely distributed in the environment. It is an important human pathogen causing both nosocomial and community-acquired infections [3].

Infections caused by Carbapenemase-producing Enterobacteri¬aceae (CPE) are of greatest interest in clinical practice because carbapenems are often the last resort for antimicrobial action [4].

Klebsiella quasipneumoniae isolates KB-161219-C and KB- 161219-D were obtained from untreated and treated wastewater, respectively, in Ljubljana, Slovenia, in December 2019. DNA was extracted using the DNAeasy Blood & Tissue Kit (Qiagen, Netherlands) and quantified using the Qubit dsDNA HS assay Kit (Invitrogen, USA) in a Qubit 3.0 fluorometer (Invitrogen, USA), following the manufactures instructions. Sequencing li¬braries were prepared with the Nextera DNA Flex Library Prepa¬ration Kit (Illumina, USA) and barcoded with Nextera DNA CD indexes (Illumina, USA). The genomes were sequenced using the Miseq Reagent Kit V3 500 cycles (Illumina, USA) on a Mis¬eq sequencer (Illumina, USA).

High-quality contigs were obtained using Velvet 1.2.10 and both belong to the MSLT ST 138. KB-61219-C generated 196 contigs and an estimated genome length of 5.958.270 bp. KB- 161219-D generated 197 contigs and an estimated genome length of 5.955.847 bp. The complete genomes were annotated using RAST tool kit (RASTtk). KB-161219-C has 6.006 pro¬tein conding sequences (CDS), 76 transfer RNA (tRNA), and 4 ribossomal RNA (rRNA). The annotation included 1.063 hypo-thetical proteins and 4.943 protein with functional assignments. KB-161219-D contains 6.013 protein conding sequences (CDS), 76 transfer RNA (tRNA), and 4 ribossomal RNA (rRNA). The annotation included 1.067 hypothetical proteins and 4.946 pro¬tein with functional assignments. This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession numbers SAMN15818748 and SAMN15818747. As¬sembled contigs were submitted to ResFinder 4.0 in the web service of the Center for Genomic Epidemiology and results are summarized in [Table 1].

This study reports the isolation and genomic characterization of two novel multidrug-resistant isolates of Klebsiella quasipneu¬moniae, isolated from a municipal wastewater treatment plant in Slovenia. The detection and characterization of these isolates show the spread of pathogenic and multidrug-resistant strains into the environment, especially concerning due to fact that CPE harbour highly transferable and broad-spectrum resistance plas¬mids. This work highlights the need to monitor bacteria carrying beta-lactam resistance genes in the environment, food and clini¬cal settings, in order to better understand their impact and role in the transmission of ARGs [1-5].

Table 1: Antimicrobial resistance genes of Klebsiella quasipneumoniae using the tool ResFinder 4.0 in the web service of the Center for Genomic Epidemiology

Funding

This work was funded by the Department for Public Microbiolo-gy, National Institute of Health, Environment and Food, Ljublja¬na, Slovenia and with the financial support from the Regional Government of Castilla y León and the FEDER program (proj¬ects CLU 2017-09, CL-EI-2021-07, UIC315 and VA266P20).

Competing interests

None declared.

Ethical approval

Not required.

References