Whole genome sequencing of ESBL-producing bacterial isolates from Norwegian aquatic environmental samples

Beta-lactams are among the most used antibiotics in Norway and have several associated resistance mechanisms. Among the most concerning is the production of extended-spectrum beta-lactamases (ESBLs) and carbapenemases. Antibiotic resistance is intricate, complexed by evolution and dissemination of resistance genes and mechanisms. Research prospects include studying antibiotics and how they work (modes of actions) and studying bacteria´s ability to fight back (resistance mechanisms). Surveillance gives insight into resistance mechanisms, bacteria that harbour them and their dissemination. While Norwegian surveillance provides insight into ESBL prevalence in clinical settings and agriculture, environmental studies are not as vast. The aim here was to investigate ESBL-containing and carbapenem-resistant strains from Norwegian aquatic environmental samples, applying micro- and molecular biological methods including selective screening, 16S rRNA Sanger sequencing, MIC tests and multiplex PCR. ESBL, carbapenem and other resistance genes were characterized utilizing Illumina and Nanopore whole genome sequencing. Complete hybrid assemblies were obtained for isolates KA0, KA5 and KB3 which were characterized as non-identical but very similar Rahnella variigena strains (100%) and Herbasprillium huttiense (82%), respectively. Nanopore assemblies were obtained for isolates KA4, KA7 and KB8 which were characterized as R. variigena (100%), Pseudomonas laurentiana (100%) and Herbsapirillum aquaticum (70%), respectively. Class A beta-lactamase genes were found in all isolates except Pseudomonas isolate KA7. blaRAHN was plasmid harboured in all Rahnella isolates, which may be further environmentally disseminated. This study indicated that ESBL-encoding genes are prevalent in the Norwegian aquatic environment and pose the risk of spreading