AUTHOR=Finton Misti D. , Meisal Roger , Porcellato Davide , Brandal Lin T. , Lindstedt Bjørn-Arne 

TITLE=Whole Genome Sequencing and Characterization of Multidrug-Resistant (MDR) Bacterial Strains Isolated From a Norwegian University Campus Pond

JOURNAL=Frontiers in Microbiology

VOLUME=11

YEAR=2020

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2020.01273

DOI=10.3389/fmicb.2020.01273

ISSN=1664-302X

ABSTRACT=<p>The presence of extended-spectrum β-lactamase (ESBL)-producing bacteria in environmental sources has been reported worldwide and constitutes a serious risk of community-acquired infections with limited treatment options. The current study aimed to explore the presence of these worrisome bacteria in a pond located at the Norwegian University of Life Sciences in Ås, Norway. A total of 98 bacterial isolates survived growth on selective chromogenic media and were identified by 16S rRNA Sanger sequencing. All strains were evaluated for the presence of the most commonly found β-lactamases and ESBLs in clinical settings (<italic>bla</italic><sub>CTX–M</sub> groups 1, 2, and 9, <italic>bla</italic><sub>CMY</sub>, <italic>bla</italic><sub>SHV</sub>, and <italic>bla</italic><sub>TEM</sub>) and carbapenemases (<italic>bla</italic><sub>IMP</sub>, <italic>bla</italic><sub>KPC</sub>, <italic>bla</italic><sub>NDM</sub>, <italic>bla</italic><sub>OXA</sub>, <italic>bla</italic><sub>SFC1</sub>, <italic>bla</italic><sub>VIM</sub>) through multiplex PCR. A total of eight strains were determined to contain one or more genes of interest. Phenotypic resistance to 18 antimicrobial agents was assessed and isolates were subjected to whole genome sequencing through a combination of Oxford Nanopore’s MinION and Illumina’s MiSeq. Results revealed the presence of β-lactamase and ESBL-producing <italic>Escherichia coli</italic>, <italic>Klebsiella pneumoniae</italic>, <italic>Stenotrophomonas maltophilia</italic>, and a <italic>Paraburkholderia</italic> spp. Identified β-lactamases and ESBLs include <italic>bla</italic><sub>CTX–M</sub>, <italic>bla</italic><sub>TEM</sub>, <italic>bla</italic><sub>CMY</sub>, <italic>bla</italic><sub>SHV</sub> and a possible <italic>bla</italic><sub>KPC</sub>-like gene, with both documented and novel sequences established. In addition, two inducible β-lactamases were found, a class A β-lactamase (L1) and a cephalosporinase (L2). All strains were determined to be multidrug resistant and numerous resistance genes to non-β-lactams were observed. In conclusion, this study demonstrates that environmental sources are a potential reservoir of clinically relevant ESBL-producing bacteria that may pose a health risk to humans upon exposure.</p>