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Rapid metagenomics analysis of EMS vehicles for monitoring pathogen load using nanopore DNA sequencing

Pathogen monitoring, detection and removal are essential to public health and outbreak management. Systems are in place for monitoring the microbial load of hospitals and public health facilities with strategies to mitigate pathogen spread. However, no such strategies are in place for ambulances, wh...

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Autores principales: Sheahan, Taylor, Hakstol, Rhys, Kailasam, Senthilkumar, Glaister, Graeme D., Hudson, Andrew J., Wieden, Hans-Joachim
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6655686/
https://www.ncbi.nlm.nih.gov/pubmed/31339905
http://dx.doi.org/10.1371/journal.pone.0219961
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author Sheahan, Taylor
Hakstol, Rhys
Kailasam, Senthilkumar
Glaister, Graeme D.
Hudson, Andrew J.
Wieden, Hans-Joachim
author_facet Sheahan, Taylor
Hakstol, Rhys
Kailasam, Senthilkumar
Glaister, Graeme D.
Hudson, Andrew J.
Wieden, Hans-Joachim
author_sort Sheahan, Taylor
collection PubMed
description Pathogen monitoring, detection and removal are essential to public health and outbreak management. Systems are in place for monitoring the microbial load of hospitals and public health facilities with strategies to mitigate pathogen spread. However, no such strategies are in place for ambulances, which are tasked with transporting at-risk individuals in immunocompromised states. As standard culturing techniques require a laboratory setting, and are time consuming and labour intensive, our approach was designed to be portable, inexpensive and easy to use based on the MinION third-generation sequencing platform from Oxford Nanopore Technologies. We developed a transferable sampling-to-analysis pipeline to characterize the microbial community in emergency medical service vehicles. Our approach identified over sixty-eight organisms in ambulances to the genera level, with a proportion of these being connected with health-care associated infections, such as Clostridium spp. and Staphylococcus spp. We also monitored the microbiome of different locations across three ambulances over time, and examined the dynamic community of microorganisms found in emergency medical service vehicles. Observed differences identified hot spots, which may require heightened monitoring and extensive cleaning. Through metagenomics analysis it is also possible to identify how microorganisms spread between patients and colonize an ambulance over time. The sequencing results aid in the development of practices to mitigate disease spread, while also providing a useful tool for outbreak prediction through ongoing analysis of the ambulance microbiome to identify new and emerging pathogens. Overall, this pipeline allows for the tracking and monitoring of pathogenic microorganisms of epidemiological interest, including those related to health-care associated infections.
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spelling pubmed-66556862019-08-07 Rapid metagenomics analysis of EMS vehicles for monitoring pathogen load using nanopore DNA sequencing Sheahan, Taylor Hakstol, Rhys Kailasam, Senthilkumar Glaister, Graeme D. Hudson, Andrew J. Wieden, Hans-Joachim PLoS One Research Article Pathogen monitoring, detection and removal are essential to public health and outbreak management. Systems are in place for monitoring the microbial load of hospitals and public health facilities with strategies to mitigate pathogen spread. However, no such strategies are in place for ambulances, which are tasked with transporting at-risk individuals in immunocompromised states. As standard culturing techniques require a laboratory setting, and are time consuming and labour intensive, our approach was designed to be portable, inexpensive and easy to use based on the MinION third-generation sequencing platform from Oxford Nanopore Technologies. We developed a transferable sampling-to-analysis pipeline to characterize the microbial community in emergency medical service vehicles. Our approach identified over sixty-eight organisms in ambulances to the genera level, with a proportion of these being connected with health-care associated infections, such as Clostridium spp. and Staphylococcus spp. We also monitored the microbiome of different locations across three ambulances over time, and examined the dynamic community of microorganisms found in emergency medical service vehicles. Observed differences identified hot spots, which may require heightened monitoring and extensive cleaning. Through metagenomics analysis it is also possible to identify how microorganisms spread between patients and colonize an ambulance over time. The sequencing results aid in the development of practices to mitigate disease spread, while also providing a useful tool for outbreak prediction through ongoing analysis of the ambulance microbiome to identify new and emerging pathogens. Overall, this pipeline allows for the tracking and monitoring of pathogenic microorganisms of epidemiological interest, including those related to health-care associated infections. Public Library of Science 2019-07-24 /pmc/articles/PMC6655686/ /pubmed/31339905 http://dx.doi.org/10.1371/journal.pone.0219961 Text en © 2019 Sheahan et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Sheahan, Taylor
Hakstol, Rhys
Kailasam, Senthilkumar
Glaister, Graeme D.
Hudson, Andrew J.
Wieden, Hans-Joachim
Rapid metagenomics analysis of EMS vehicles for monitoring pathogen load using nanopore DNA sequencing
title Rapid metagenomics analysis of EMS vehicles for monitoring pathogen load using nanopore DNA sequencing
title_full Rapid metagenomics analysis of EMS vehicles for monitoring pathogen load using nanopore DNA sequencing
title_fullStr Rapid metagenomics analysis of EMS vehicles for monitoring pathogen load using nanopore DNA sequencing
title_full_unstemmed Rapid metagenomics analysis of EMS vehicles for monitoring pathogen load using nanopore DNA sequencing
title_short Rapid metagenomics analysis of EMS vehicles for monitoring pathogen load using nanopore DNA sequencing
title_sort rapid metagenomics analysis of ems vehicles for monitoring pathogen load using nanopore dna sequencing
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6655686/
https://www.ncbi.nlm.nih.gov/pubmed/31339905
http://dx.doi.org/10.1371/journal.pone.0219961
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