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

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

doi:10.3389/fmicb.2020.01273

Abstract

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 (blaCTX–M groups 1, 2, and 9, blaCMY, blaSHV, and blaTEM) and carbapenemases (blaIMP, blaKPC, blaNDM, blaOXA, blaSFC1, blaVIM) 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 Escherichia coli, Klebsiella pneumoniae, Stenotrophomonas maltophilia, and a Paraburkholderia spp. Identified β-lactamases and ESBLs include blaCTX–M, blaTEM, blaCMY, blaSHV and a possible blaKPC-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.

Highlights

Antibiotic resistant bacteria (ARB) is a global public health threat that jeopardizes the successful treatment of infectious disease (World Health Organization [WHO], 2014)
The predominant ESBL detected in clinical settings is derived from blaCTX−M (Bora et al, 2014), which is most frequently identified in Enterobacteriaceae (Pitout et al, 2005)
We found that fecal samples from Norwegian patients with signs of intestinal infection were colonized with a surprisingly high frequency of intestinal pathogenic E. coli (IPEC)/extraintestinal pathogenic E. coli (ExPEC) heteropathogenic strains (Lindstedt et al, 2018)

Summary

Introduction

Antibiotic resistant bacteria (ARB) is a global public health threat that jeopardizes the successful treatment of infectious disease (World Health Organization [WHO], 2014). Due to persistent exposure of bacterial strains to these antibiotics, extendedspectrum β-lactamases (ESBLs) have evolved that hydrolyze the β-lactam ring, rendering these vital antibiotics ineffective (Reeba et al, 2019). ESBLs have emerged as one of the most clinically significant resistance mechanisms associated with limited therapeutic options (Pitout et al, 2005). The predominant ESBL detected in clinical settings is derived from blaCTX−M (Bora et al, 2014), which is most frequently identified in Enterobacteriaceae (Pitout et al, 2005). ESBL-producing bacteria commonly exhibit co-resistance to many other classes of antibiotics, further impeding the successful treatment of bacterial infections (Chaudhary and Aggarwal, 2004)

Methods

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Discussion

Conclusion