Sharing of carbapenemase-encoding plasmids between Enterobacteriaceae in UK sewage uncovered by MinION sequencing.

Catherine Ludden,Theodore Gouliouris,Nicholas M Brown,Beth Blane,Martin Hunt,Katie L Hopkins,Julian Parkhill,Francesc Coll,Alan Tracey,Sandra Reuter,Sharon J Peacock,Neil Woodford,Kim Judge,Plamena Naydenova

doi:10.1099/mgen.0.000114

Abstract

Dissemination of carbapenem resistance among pathogenic Gram-negative bacteria is a looming medical emergency. Efficient spread of resistance within and between bacterial species is facilitated by mobile genetic elements. We hypothesized that wastewater contributes to the dissemination of carbapenemase-producing Enterobacteriaceae (CPE), and studied this through a cross-sectional observational study of wastewater in the East of England. We isolated clinically relevant species of CPE in untreated and treated wastewater, confirming that waste treatment does not prevent release of CPE into the environment. We observed that CPE-positive plants were restricted to those in direct receipt of hospital waste, suggesting that hospital effluent may play a role in disseminating carbapenem resistance. We postulated that plasmids carrying carbapenemase genes were exchanged between bacterial hosts in sewage, and used short-read (Illumina) and long-read (MinION) technologies to characterize plasmids encoding resistance to antimicrobials and heavy metals. We demonstrated that different CPE species (Enterobacter kobei and Raoultella ornithinolytica) isolated from wastewater from the same treatment plant shared two plasmids of 63 and 280 kb. The former plasmid conferred resistance to carbapenems (blaOXA-48), and the latter to numerous drug classes and heavy metals. We also report the complete genome sequence for Enterobacter kobei. Small, portable sequencing instruments such as the MinION have the potential to improve the quality of information gathered on antimicrobial resistance in the environment.

Highlights

The global rise of carbapenemase-producing Enterobacteriaceae (CPE) over the last decade represents a major threat to public health [1,2,3]
Plant location was selected with reference to hospital waste, with ten plants situated immediately downstream of acute NHS Hospital Trust facilities and ten plants not connected to acute hospital effluent (Fig. 1)
Half (50 %) of the assembly is contained in contigs greater than or equal to a contig of this size. †There is no MinION only assembly for VRES0259 as the data for this isolate was only sufficient to make a hybrid assembly. This is the first report of CPE being recovered from wastewater at UK sewage treatment plants

Summary

Introduction

The global rise of carbapenemase-producing Enterobacteriaceae (CPE) over the last decade represents a major threat to public health [1,2,3]. CPE are often resistant to several additional classes of antibiotics, which may limit therapeutic options to drugs with a higher toxicity profile. Invasive infections caused by CPE are associated. The development of interventions that prevent further CPE dissemination requires delineation of their reservoirs and routes of spread, combined with accurate characterization of the mobile elements that transfer carbapenemase genes within and between bacterial species

Methods

Results

Conclusion