Metagenomics: a new frontier for routine pathology testing of gastrointestinal pathogens
Abstract Background Accurate and comprehensive identification of enteropathogens, causing infectious gastroenteritis, is essential for optimal patient treatment and effective isolation processes in health care systems. Traditional diagnostic techniques are well established and optimised in low-cost...
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BMC
2025-01-01
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| Series: | Gut Pathogens |
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| Online Access: | https://doi.org/10.1186/s13099-024-00673-1 |
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| author | Nicola Z. Angel Mitchell J. Sullivan Areej Alsheikh-Hussain Liang Fang Samantha MacDonald Alena Pribyl Blake Wills Gene W. Tyson Philip Hugenholtz Donovan H. Parks Paul Griffin David L. A. Wood |
| author_facet | Nicola Z. Angel Mitchell J. Sullivan Areej Alsheikh-Hussain Liang Fang Samantha MacDonald Alena Pribyl Blake Wills Gene W. Tyson Philip Hugenholtz Donovan H. Parks Paul Griffin David L. A. Wood |
| author_sort | Nicola Z. Angel |
| collection | DOAJ |
| description | Abstract Background Accurate and comprehensive identification of enteropathogens, causing infectious gastroenteritis, is essential for optimal patient treatment and effective isolation processes in health care systems. Traditional diagnostic techniques are well established and optimised in low-cost formats. However, thorough testing for a wider range of causal agents is time consuming and remains limited to a subset of pathogenic organisms. Metagenomic next-generation sequencing (mNGS) allows the identification of all pathogens in a sample in a single test, without a reliance on culture or introduction of target selection bias. This study aims to determine the ability to routinely apply mNGS testing, in comparison to traditional culture or polymerase chain reaction (PCR) based tests, for the identification of causal pathogens for gastrointestinal infections. Results The performance of mNGS, PCR and microscopy, culture and sensitivity (MCS) assays was established using 2,619 prospectively collected faecal samples from patients with symptomology indicative of infectious gastroenteritiss. Commonly experienced pathogens including Aeromonas spp, Campylobacter spp, Salmonella spp and Giardia spp, in single and co-infected patients, were used to establish test outcomes. When testing for these organisms, using the combined result from either or both PCR and MCS testing as the comparator, the mNGS assay had clinically acceptable sensitivity (89.2–100%). Further, the mNGS assay detected 14 additional enteropathogens, that were either not detected or not tested, by initial PCR/MCS testing. Conclusions The advantage of mNGS compared to other syndromic testing systems is the broad range of detectable targets and the ability to interrogate samples without clinician informed or assay specific bias. With the development of newer sequencing assays, it is now feasible to test for a wide range of target organisms in a sample using a single mNGS test. Overall, the mNGS based approach enabled pathogen detection that was comparable to conventional diagnostics and was shown to have the potential to be extended for the detection of many pathogens and genes of clinical interest. In conclusion, the mNGS assay offers an easy, sample to answer workflow with rapid detection of enteropathogens and has the potential to improve diagnosis, therapy and infection control precautions. |
| format | Article |
| id | doaj-art-b3174e7a38684c03acfdec30b79dbb1f |
| institution | Kabale University |
| issn | 1757-4749 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | BMC |
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| series | Gut Pathogens |
| spelling | doaj-art-b3174e7a38684c03acfdec30b79dbb1f2025-01-19T12:25:18ZengBMCGut Pathogens1757-47492025-01-0117111710.1186/s13099-024-00673-1Metagenomics: a new frontier for routine pathology testing of gastrointestinal pathogensNicola Z. Angel0Mitchell J. Sullivan1Areej Alsheikh-Hussain2Liang Fang3Samantha MacDonald4Alena Pribyl5Blake Wills6Gene W. Tyson7Philip Hugenholtz8Donovan H. Parks9Paul Griffin10David L. A. Wood11Microba Pty LtdMicroba Pty LtdMicroba Pty LtdMicroba Pty LtdMicroba Pty LtdMicroba Pty LtdMicroba Pty LtdMicroba Pty LtdMicroba Pty LtdMicroba Pty LtdMicroba Pty LtdMicroba Pty LtdAbstract Background Accurate and comprehensive identification of enteropathogens, causing infectious gastroenteritis, is essential for optimal patient treatment and effective isolation processes in health care systems. Traditional diagnostic techniques are well established and optimised in low-cost formats. However, thorough testing for a wider range of causal agents is time consuming and remains limited to a subset of pathogenic organisms. Metagenomic next-generation sequencing (mNGS) allows the identification of all pathogens in a sample in a single test, without a reliance on culture or introduction of target selection bias. This study aims to determine the ability to routinely apply mNGS testing, in comparison to traditional culture or polymerase chain reaction (PCR) based tests, for the identification of causal pathogens for gastrointestinal infections. Results The performance of mNGS, PCR and microscopy, culture and sensitivity (MCS) assays was established using 2,619 prospectively collected faecal samples from patients with symptomology indicative of infectious gastroenteritiss. Commonly experienced pathogens including Aeromonas spp, Campylobacter spp, Salmonella spp and Giardia spp, in single and co-infected patients, were used to establish test outcomes. When testing for these organisms, using the combined result from either or both PCR and MCS testing as the comparator, the mNGS assay had clinically acceptable sensitivity (89.2–100%). Further, the mNGS assay detected 14 additional enteropathogens, that were either not detected or not tested, by initial PCR/MCS testing. Conclusions The advantage of mNGS compared to other syndromic testing systems is the broad range of detectable targets and the ability to interrogate samples without clinician informed or assay specific bias. With the development of newer sequencing assays, it is now feasible to test for a wide range of target organisms in a sample using a single mNGS test. Overall, the mNGS based approach enabled pathogen detection that was comparable to conventional diagnostics and was shown to have the potential to be extended for the detection of many pathogens and genes of clinical interest. In conclusion, the mNGS assay offers an easy, sample to answer workflow with rapid detection of enteropathogens and has the potential to improve diagnosis, therapy and infection control precautions.https://doi.org/10.1186/s13099-024-00673-1InfectionPathogenGastrointestinalMetagenomicsFaecalEnteropathogens |
| spellingShingle | Nicola Z. Angel Mitchell J. Sullivan Areej Alsheikh-Hussain Liang Fang Samantha MacDonald Alena Pribyl Blake Wills Gene W. Tyson Philip Hugenholtz Donovan H. Parks Paul Griffin David L. A. Wood Metagenomics: a new frontier for routine pathology testing of gastrointestinal pathogens Gut Pathogens Infection Pathogen Gastrointestinal Metagenomics Faecal Enteropathogens |
| title | Metagenomics: a new frontier for routine pathology testing of gastrointestinal pathogens |
| title_full | Metagenomics: a new frontier for routine pathology testing of gastrointestinal pathogens |
| title_fullStr | Metagenomics: a new frontier for routine pathology testing of gastrointestinal pathogens |
| title_full_unstemmed | Metagenomics: a new frontier for routine pathology testing of gastrointestinal pathogens |
| title_short | Metagenomics: a new frontier for routine pathology testing of gastrointestinal pathogens |
| title_sort | metagenomics a new frontier for routine pathology testing of gastrointestinal pathogens |
| topic | Infection Pathogen Gastrointestinal Metagenomics Faecal Enteropathogens |
| url | https://doi.org/10.1186/s13099-024-00673-1 |
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