Towards personalised anti-microbial and immune approaches to infections in acute care. Can real-time genomic-informed diagnosis of pathogens, and immune-focused therapies improve outcomes for patients? An observational, experimental study protocol.
<h4>Introduction</h4>Infection causes a vast burden of disease, with significant mortality, morbidity and costs to health-care systems. However, identifying the pathogen causative infection can be challenging, resulting in high use of broad-spectrum antibiotics, much of which may be inap...
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2024-01-01
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| Series: | PLoS ONE |
| Online Access: | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0298425&type=printable |
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| author | Samuel Quarton Kirsty McGee Nicola Cumley Mahboobeh Behruznia Charlotte Jeff Kylie Belchamber Michael Cox David Thickett Aaron Scott Dhruv Parekh Alan McNally Elizabeth Sapey |
| author_facet | Samuel Quarton Kirsty McGee Nicola Cumley Mahboobeh Behruznia Charlotte Jeff Kylie Belchamber Michael Cox David Thickett Aaron Scott Dhruv Parekh Alan McNally Elizabeth Sapey |
| author_sort | Samuel Quarton |
| collection | DOAJ |
| description | <h4>Introduction</h4>Infection causes a vast burden of disease, with significant mortality, morbidity and costs to health-care systems. However, identifying the pathogen causative infection can be challenging, resulting in high use of broad-spectrum antibiotics, much of which may be inappropriate. Novel metagenomic methods have potential to rapidly identify pathogens, however their clinical utility for many infections is currently unclear. Outcome from infection is also impacted by the effectiveness of immune responses, which can be impaired by age, co-morbidity and the infection itself. The aims of this study are twofold: To compare diversity of organisms identified and time-to-result using metagenomic methods versus traditional culture -based techniques, to explore the potential clinical role of metagenomic approaches to pathogen identification in a range of infections.To characterise the ex vivo function of immune cells from patients with acute infection, exploring host and pathogen-specific factors which may affect immune function and overall outcomes.<h4>Methods</h4>This is a prospective observational study of patients with acute infection. Patients with symptoms suggestive of an acute infection will be recruited, and blood and bodily fluid relevant to the site of infection collected (for example, sputum and naso-oropharyngeal swabs for respiratory tract infections, or urine for a suspected urinary tract infection). Metagenomic analysis of samples will be compared to traditional microbiology, alongside the antimicrobials received. Blood and respiratory samples such as bronchoalveolar lavage will be used to isolate immune cells and interrogate immune cell function. Where possible, similar samples will be collected from matched participants without a suspected infection to determine the impact of infection on both microbiome and immune cell function. |
| first_indexed | 2024-04-24T13:47:36Z |
| format | Article |
| id | doaj.art-d70d2820fc574cd6899b4d6a08500860 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-04-24T13:47:36Z |
| publishDate | 2024-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-d70d2820fc574cd6899b4d6a085008602024-04-04T05:34:33ZengPublic Library of Science (PLoS)PLoS ONE1932-62032024-01-01193e029842510.1371/journal.pone.0298425Towards personalised anti-microbial and immune approaches to infections in acute care. Can real-time genomic-informed diagnosis of pathogens, and immune-focused therapies improve outcomes for patients? An observational, experimental study protocol.Samuel QuartonKirsty McGeeNicola CumleyMahboobeh BehruzniaCharlotte JeffKylie BelchamberMichael CoxDavid ThickettAaron ScottDhruv ParekhAlan McNallyElizabeth Sapey<h4>Introduction</h4>Infection causes a vast burden of disease, with significant mortality, morbidity and costs to health-care systems. However, identifying the pathogen causative infection can be challenging, resulting in high use of broad-spectrum antibiotics, much of which may be inappropriate. Novel metagenomic methods have potential to rapidly identify pathogens, however their clinical utility for many infections is currently unclear. Outcome from infection is also impacted by the effectiveness of immune responses, which can be impaired by age, co-morbidity and the infection itself. The aims of this study are twofold: To compare diversity of organisms identified and time-to-result using metagenomic methods versus traditional culture -based techniques, to explore the potential clinical role of metagenomic approaches to pathogen identification in a range of infections.To characterise the ex vivo function of immune cells from patients with acute infection, exploring host and pathogen-specific factors which may affect immune function and overall outcomes.<h4>Methods</h4>This is a prospective observational study of patients with acute infection. Patients with symptoms suggestive of an acute infection will be recruited, and blood and bodily fluid relevant to the site of infection collected (for example, sputum and naso-oropharyngeal swabs for respiratory tract infections, or urine for a suspected urinary tract infection). Metagenomic analysis of samples will be compared to traditional microbiology, alongside the antimicrobials received. Blood and respiratory samples such as bronchoalveolar lavage will be used to isolate immune cells and interrogate immune cell function. Where possible, similar samples will be collected from matched participants without a suspected infection to determine the impact of infection on both microbiome and immune cell function.https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0298425&type=printable |
| spellingShingle | Samuel Quarton Kirsty McGee Nicola Cumley Mahboobeh Behruznia Charlotte Jeff Kylie Belchamber Michael Cox David Thickett Aaron Scott Dhruv Parekh Alan McNally Elizabeth Sapey Towards personalised anti-microbial and immune approaches to infections in acute care. Can real-time genomic-informed diagnosis of pathogens, and immune-focused therapies improve outcomes for patients? An observational, experimental study protocol. PLoS ONE |
| title | Towards personalised anti-microbial and immune approaches to infections in acute care. Can real-time genomic-informed diagnosis of pathogens, and immune-focused therapies improve outcomes for patients? An observational, experimental study protocol. |
| title_full | Towards personalised anti-microbial and immune approaches to infections in acute care. Can real-time genomic-informed diagnosis of pathogens, and immune-focused therapies improve outcomes for patients? An observational, experimental study protocol. |
| title_fullStr | Towards personalised anti-microbial and immune approaches to infections in acute care. Can real-time genomic-informed diagnosis of pathogens, and immune-focused therapies improve outcomes for patients? An observational, experimental study protocol. |
| title_full_unstemmed | Towards personalised anti-microbial and immune approaches to infections in acute care. Can real-time genomic-informed diagnosis of pathogens, and immune-focused therapies improve outcomes for patients? An observational, experimental study protocol. |
| title_short | Towards personalised anti-microbial and immune approaches to infections in acute care. Can real-time genomic-informed diagnosis of pathogens, and immune-focused therapies improve outcomes for patients? An observational, experimental study protocol. |
| title_sort | towards personalised anti microbial and immune approaches to infections in acute care can real time genomic informed diagnosis of pathogens and immune focused therapies improve outcomes for patients an observational experimental study protocol |
| url | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0298425&type=printable |
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