Abstract
Antimicrobial resistance (AMR) is an increasing and urgent issue for human health worldwide, as it leads to the reduction of available antibiotics to treat bacterial infections, in turn increasing hospital stays and lethality. Therefore, the study and genomic surveillance of bacterial carriers of resistance in and outside of clinical settings is of utter importance. A colony of multidrug resistant (MDR) bacteria identified as Klebsiella spp., by 16S rDNA amplicon sequencing, has been isolated from an urban lake in Brazil, during a drug-degrading bacterial prospection. Genomic analyses revealed the bacteria as Klebsiella pneumoniae species. Furthermore, the in silico Multilocus Sequence Typing (MLST) identified the genome as a new sequence type, ST5236. The search for antimicrobial resistance genes (ARGs) detected the presence of genes against beta-lactams, fosfomycin, acriflavine and efflux pumps, as well as genes for heavy metal resistance. Of particular note, an extended-spectrum beta-lactamase gene (blaCTX-M-15) has been detected in close proximity to siphoviridae genes, while a carbapenemase gene (KPC-2) has been found in an extrachromosomal contig, within a novel non-Tn4401 genetic element (NTEKPC). An extrachromosomal contig found in the V3 isolate is identical to a contig of a K. pneumoniae isolate from a nearby hospital, which indicates a putative gene flow from the hospital network into Paranoá lake. The discovery of a MDR isolate in this lake is worrisome, as the region has recently undergone periods of water scarcity causing the lake, which receives treated wastewater effluent, and is already used for recreational purposes, to be used as an environmental buffer for drinking water reuse. Altogether, our results indicate an underrepresentation of environmental K. pneumoniae among available genomes, which may hamper the understanding of the population dynamics of the species in the environment and its consequences in the spread of ARGs and virulence genes.
Highlights
The World Health Organization (WHO) recognizes antimicrobial resistance (AMR) as an urgent global issue with impending increases in mortality rates, hospitalization length and cross-contamination risks, as well as overall economic losses (World Health Organization [WHO], 2015)
In the present study we describe a multidrug resistant (MDR) NTCKPC-bearing K. pneumoniae strain belonging to a novel Sequence type (ST) that has been found during a prospection for xenobiotic-degrading bacteria in an artificial urban Sanger sequencing in the High-Performance sequencing center lake, next to a wastewater treatment plant (WWTP)
The genome was identified as K. pneumoniae by the Type Strain Genome Server (TYGS), and this result was further validated with average nucleotide identity (ANI) analyses against available Klebsiella genomes in NCBI Refseq, showing the K. pneumoniae strain 2504 (GCF_011044895.1), from a study in Russia on hypervirulent K. pneumoniae isolates (PRJNA606163), as the closest genome available with 99.71 ANI index
Summary
The World Health Organization (WHO) recognizes antimicrobial resistance (AMR) as an urgent global issue with impending increases in mortality rates, hospitalization length and cross-contamination risks, as well as overall economic losses (World Health Organization [WHO], 2015). In spite of this problem, global antibiotic gross consumption and consumption per capita increased 65 and 39%, respectively, from 2000 to 2015. NGS can be useful in order to track the ever-increasing dissemination of antimicrobial resistance genes (ARGs) (Mitchell and Simner, 2019; Ransom et al, 2020)
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