Research Article: Exploration of antibiotic resistance risks in a veterinary teaching hospital with Oxford Nanopore long read sequencing

Date Published: May 30, 2019

Publisher: Public Library of Science

Author(s): Kanishka Indiwari Kamathewatta, Rhys Nathan Bushell, Neil David Young, Mark Anthony Stevenson, Helen Billman-Jacobe, Glenn Francis Browning, Marc Serge Marenda, Yi Luo.


The Oxford Nanopore MinION DNA sequencing device can produce large amounts of long sequences, typically several kilobases, within a few hours. This long read capacity was exploited to detect antimicrobial resistance genes (ARGs) in a large veterinary teaching hospital environment, and to assess their taxonomic origin, genetic organisation and association with mobilisation markers concurrently. Samples were collected on eight occasions between November 2016 and May 2017 (inclusive) in a longitudinal study. Nanopore sequencing was performed on total DNA extracted from the samples after a minimal enrichment step in broth. Many ARGs present in the veterinary hospital environment could potentially confer resistance to antimicrobials widely used in treating infections of companion animals, including aminoglycosides, extended-spectrum beta-lactams, sulphonamides, macrolides, and tetracyclines. High-risk ARGs, defined here as single or multiple ARGs associated with pathogenic bacterial species or with mobile genetic elements, were shared between the intensive care unit (ICU) patient cages, a dedicated laundry trolley and a floor cleaning mop-bucket. By contrast, a floor surface from an office corridor without animal contact and located outside the veterinary hospital did not contain such high-risk ARGs. Relative abundances of high-risk ARGs and co-localisation of these genes on the same sequence read were higher in the laundry trolley and mop bucket samples, compared to the ICU cages, suggesting that amplification of ARGs is likely to occur in the collection points for hospital waste. These findings have prompted the implementation of targeted intervention measures in the veterinary hospital to mitigate the risks of transferring clinically important ARGs between sites and to improve biosecurity practices in the facility.

Partial Text

In bacterial populations, the resistome is defined as “the collection of all genes that could contribute to a phenotype of antibiotic resistance” [1]. In human hospitals, monitoring of patient and environmental microbiomes has revealed complex patterns of surface colonisation and pervasive exchanges of resistance genes [2, 3]. While animal-associated microbiomes and resistomes have been studied in livestock flora [4, 5] as well as in farm environments and effluents [6–9], relatively few investigations have been carried out in veterinary hospitals. Large veterinary teaching hospitals accommodate a transient population of animals with various resident flora, infectious status, and previous exposure histories to antibiotics. This unique environment could act as a mixing reservoir for antimicrobial resistance genes (ARGs) to and from various sources including humans and animals. Most veterinary teaching hospitals have active and passive surveillance programs to monitor infectious risks and antimicrobial resistance trends associated with their patients [10], but the presence and diversity of ARGs in the hospital environment is often not explored. Therefore, we sought to determine the presence of ARGs in such environmental systems and to map their associations with their bacterial hosts or mobile genetic elements (MGEs).

Nanopore sequencing is a convenient and portable method for routine monitoring of environmental risks associated with infectious agents and antimicrobial resistance in veterinary hospitals. Our findings identified possible transfers of ARGs between interconnected environmental sites and identified waste collection points as significant amplifying reservoirs for clinically important ARGs. This work has led to improving biosecurity practices in the investigated premises and demonstrated the usefulness of rapid DNA sequencing to implement evidence-based operational measures for infection control in veterinary facilities.