Whole genome sequencing reveals resemblance between ESBL-producing and carbapenem resistant Klebsiella pneumoniae isolates from Austrian rivers and clinical isolates from hospitals

Sarah Lepuschitz,Simone Schill,Anna Stoeger,Shiva Pekard-Amenitsch,Steliana Huhulescu,Norbert Inreiter,Rainer Hartl,Heidrun Kerschner,Sieglinde Sorschag,Burkhard Springer,Sylvain Brisse,Franz Allerberger,Robert L Mach,Werner Ruppitsch

doi:10.1016/j.scitotenv.2019.01.179

Abstract

In 2016, the Austrian Agency for Health and Food Safety started a pilot project to investigate antimicrobial resistance in surface water. Here we report on the characterisation of carbapenem resistant and ESBL-producing K. pneumoniae isolates from Austrian river water samples compared to 95 clinical isolates recently obtained in Austrian hospitals.Ten water samples were taken from four main rivers, collected upstream and downstream of major cities in 2016. For subtyping and comparison, public core genome multi locus sequence typing (cgMLST) schemes were used. The presence of AMR genes, virulence genes and plasmids was extracted from whole genome sequence (WGS) data.In total three ESBL-producing strains and two carbapenem resistant strains were isolated. WGS based comparison of these five water isolates to 95 clinical isolates identified three clusters. Cluster 1 (ST11) and cluster 2 (ST985) consisted of doublets of carbapenem resistant strains (one water and one clinical isolate each). Cluster 3 (ST405) consisted of three ESBL-producing strains isolated from one water sample and two clinical specimens. The cities, in which patient isolates of cluster 2 and 3 were collected, were in concordance with the water sampling locations downstream from these cities. The genetic concordance between isolates from river water samples and patient isolates raises concerns regarding the release of wastewater treatment plant effluents into surface water. From a public health perspective these findings demand attention and strategies are required to minimize the spread of multiresistant strains to the environment.

Highlights

The Gram negative bacterium Klebsiella pneumoniae (K. pneumoniae) is a leading cause of human nosocomial infections, but can be acquired in the community (Podschun and Ullmann, 1998; Shon and Russo, 2012)
The aim of this study was to evaluate the diversity of extended spectrum beta-lactamases (ESBL) and carbapenemase-harboring K. pneumoniae in water samples collected in four main Austrian rivers and to compare them with clinical isolates to identify possible sources of anthropogenic pollution
A common outcome of our study was that all water samples from rivers taken before a city were negative for ESBL and carbapenemase-producing K. pneumoniae whereas all samples taken one to three kilometers downstream of main Austrian cities wastewater plant release points were positive, which shows the impact of wastewater effluents and anthropogenic pollution on the aquatic environment (Amos et al, 2014)

Summary

Introduction

The Gram negative bacterium Klebsiella pneumoniae (K. pneumoniae) is a leading cause of human nosocomial infections, but can be acquired in the community (Podschun and Ullmann, 1998; Shon and Russo, 2012). It can either be carried asymptomatically or can cause a wide spectrum of infections, for instance pneumonia; wound, soft tissue, urinary tract and bloodstream infections (Holt et al, 2015; Maatallah et al, 2014; Podschun and Ullmann, 1998). The global dissemination of carbapenemase-producing strains has been shown in rivers in different regions of the world (Khan et al, 2018; Mahon et al, 2017; Zarfel et al, 2017; Zurfluh et al, 2013)

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