Cargando…
Rapid metagenomic sequencing for diagnosis and antimicrobial sensitivity prediction of canine bacterial infections
Antimicrobial resistance is a major threat to human and animal health. There is an urgent need to ensure that antimicrobials are used appropriately to limit the emergence and impact of resistance. In the human and veterinary healthcare setting, traditional culture and antimicrobial sensitivity testi...
Autores principales: | , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Microbiology Society
2023
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10438823/ https://www.ncbi.nlm.nih.gov/pubmed/37471128 http://dx.doi.org/10.1099/mgen.0.001066 |
_version_ | 1785092810652778496 |
---|---|
author | Ring, Natalie Low, Alison S. Wee, Bryan Paterson, Gavin K. Nuttall, Tim Gally, David Mellanby, Richard Fitzgerald, J. Ross |
author_facet | Ring, Natalie Low, Alison S. Wee, Bryan Paterson, Gavin K. Nuttall, Tim Gally, David Mellanby, Richard Fitzgerald, J. Ross |
author_sort | Ring, Natalie |
collection | PubMed |
description | Antimicrobial resistance is a major threat to human and animal health. There is an urgent need to ensure that antimicrobials are used appropriately to limit the emergence and impact of resistance. In the human and veterinary healthcare setting, traditional culture and antimicrobial sensitivity testing typically requires 48–72 h to identify appropriate antibiotics for treatment. In the meantime, broad-spectrum antimicrobials are often used, which may be ineffective or impact non-target commensal bacteria. Here, we present a rapid, culture-free, diagnostics pipeline, involving metagenomic nanopore sequencing directly from clinical urine and skin samples of dogs. We have planned this pipeline to be versatile and easily implementable in a clinical setting, with the potential for future adaptation to different sample types and animals. Using our approach, we can identify the bacterial pathogen present within 5 h, in some cases detecting species which are difficult to culture. For urine samples, we can predict antibiotic sensitivity with up to 95 % accuracy. Skin swabs usually have lower bacterial abundance and higher host DNA, confounding antibiotic sensitivity prediction; an additional host depletion step will likely be required during the processing of these, and other types of samples with high levels of host cell contamination. In summary, our pipeline represents an important step towards the design of individually tailored veterinary treatment plans on the same day as presentation, facilitating the effective use of antibiotics and promoting better antimicrobial stewardship. |
format | Online Article Text |
id | pubmed-10438823 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Microbiology Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-104388232023-08-19 Rapid metagenomic sequencing for diagnosis and antimicrobial sensitivity prediction of canine bacterial infections Ring, Natalie Low, Alison S. Wee, Bryan Paterson, Gavin K. Nuttall, Tim Gally, David Mellanby, Richard Fitzgerald, J. Ross Microb Genom Research Articles Antimicrobial resistance is a major threat to human and animal health. There is an urgent need to ensure that antimicrobials are used appropriately to limit the emergence and impact of resistance. In the human and veterinary healthcare setting, traditional culture and antimicrobial sensitivity testing typically requires 48–72 h to identify appropriate antibiotics for treatment. In the meantime, broad-spectrum antimicrobials are often used, which may be ineffective or impact non-target commensal bacteria. Here, we present a rapid, culture-free, diagnostics pipeline, involving metagenomic nanopore sequencing directly from clinical urine and skin samples of dogs. We have planned this pipeline to be versatile and easily implementable in a clinical setting, with the potential for future adaptation to different sample types and animals. Using our approach, we can identify the bacterial pathogen present within 5 h, in some cases detecting species which are difficult to culture. For urine samples, we can predict antibiotic sensitivity with up to 95 % accuracy. Skin swabs usually have lower bacterial abundance and higher host DNA, confounding antibiotic sensitivity prediction; an additional host depletion step will likely be required during the processing of these, and other types of samples with high levels of host cell contamination. In summary, our pipeline represents an important step towards the design of individually tailored veterinary treatment plans on the same day as presentation, facilitating the effective use of antibiotics and promoting better antimicrobial stewardship. Microbiology Society 2023-07-20 /pmc/articles/PMC10438823/ /pubmed/37471128 http://dx.doi.org/10.1099/mgen.0.001066 Text en © 2023 The Authors https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution. |
spellingShingle | Research Articles Ring, Natalie Low, Alison S. Wee, Bryan Paterson, Gavin K. Nuttall, Tim Gally, David Mellanby, Richard Fitzgerald, J. Ross Rapid metagenomic sequencing for diagnosis and antimicrobial sensitivity prediction of canine bacterial infections |
title | Rapid metagenomic sequencing for diagnosis and antimicrobial sensitivity prediction of canine bacterial infections |
title_full | Rapid metagenomic sequencing for diagnosis and antimicrobial sensitivity prediction of canine bacterial infections |
title_fullStr | Rapid metagenomic sequencing for diagnosis and antimicrobial sensitivity prediction of canine bacterial infections |
title_full_unstemmed | Rapid metagenomic sequencing for diagnosis and antimicrobial sensitivity prediction of canine bacterial infections |
title_short | Rapid metagenomic sequencing for diagnosis and antimicrobial sensitivity prediction of canine bacterial infections |
title_sort | rapid metagenomic sequencing for diagnosis and antimicrobial sensitivity prediction of canine bacterial infections |
topic | Research Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10438823/ https://www.ncbi.nlm.nih.gov/pubmed/37471128 http://dx.doi.org/10.1099/mgen.0.001066 |
work_keys_str_mv | AT ringnatalie rapidmetagenomicsequencingfordiagnosisandantimicrobialsensitivitypredictionofcaninebacterialinfections AT lowalisons rapidmetagenomicsequencingfordiagnosisandantimicrobialsensitivitypredictionofcaninebacterialinfections AT weebryan rapidmetagenomicsequencingfordiagnosisandantimicrobialsensitivitypredictionofcaninebacterialinfections AT patersongavink rapidmetagenomicsequencingfordiagnosisandantimicrobialsensitivitypredictionofcaninebacterialinfections AT nuttalltim rapidmetagenomicsequencingfordiagnosisandantimicrobialsensitivitypredictionofcaninebacterialinfections AT gallydavid rapidmetagenomicsequencingfordiagnosisandantimicrobialsensitivitypredictionofcaninebacterialinfections AT mellanbyrichard rapidmetagenomicsequencingfordiagnosisandantimicrobialsensitivitypredictionofcaninebacterialinfections AT fitzgeraldjross rapidmetagenomicsequencingfordiagnosisandantimicrobialsensitivitypredictionofcaninebacterialinfections |