Next-generation sequencing for hypothesis-free genomic detection of invasive tropical infections in poly-microbially contaminated, formalin-fixed, paraffin-embedded tissue samples – a proof-of-principle assessment
Abstract Background The potential of next-generation sequencing (NGS) for hypothesis-free pathogen diagnosis from (poly-)microbially contaminated, formalin-fixed, paraffin embedded tissue samples from patients with invasive fungal infections and amebiasis was investigated. Samples from patients with...
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doaj-f0ea672960eb4a3c838911c4fc56068e2020-11-25T01:47:55ZengBMCBMC Microbiology1471-21802019-04-0119111910.1186/s12866-019-1448-0Next-generation sequencing for hypothesis-free genomic detection of invasive tropical infections in poly-microbially contaminated, formalin-fixed, paraffin-embedded tissue samples – a proof-of-principle assessmentHagen Frickmann0Carsten Künne1Ralf Matthias Hagen2Andreas Podbielski3Jana Normann4Sven Poppert5Mario Looso6Bernd Kreikemeyer7Department of Microbiology and Hospital Hygiene, Bundeswehr Hospital HamburgDepartment of Bioinformatics, Max-Planck Institute for Heart and Lung Research Bad NauheimDepartment of Preventive Medicine, Bundeswehr Medical AcademyInstitute for Microbiology, Virology and Hygiene, University Medicine RostockInstitute for Microbiology, Virology and Hygiene, University Medicine RostockSwiss Tropical and Public Health InstituteDepartment of Bioinformatics, Max-Planck Institute for Heart and Lung Research Bad NauheimInstitute for Microbiology, Virology and Hygiene, University Medicine RostockAbstract Background The potential of next-generation sequencing (NGS) for hypothesis-free pathogen diagnosis from (poly-)microbially contaminated, formalin-fixed, paraffin embedded tissue samples from patients with invasive fungal infections and amebiasis was investigated. Samples from patients with chromoblastomycosis (n = 3), coccidioidomycosis (n = 2), histoplasmosis (n = 4), histoplasmosis or cryptococcosis with poor histological discriminability (n = 1), mucormycosis (n = 2), mycetoma (n = 3), rhinosporidiosis (n = 2), and invasive Entamoeba histolytica infections (n = 6) were analyzed by NGS (each one Illumina v3 run per sample). To discriminate contamination from putative infections in NGS analysis, mean and standard deviation of the number of specific sequence fragments (paired reads) were determined and compared in all samples examined for the pathogens in question. Results For matches between NGS results and histological diagnoses, a percentage of species-specific reads greater than the 4th standard deviation above the mean value of all 23 assessed sample materials was required. Potentially etiologically relevant pathogens could be identified by NGS in 5 out of 17 samples of patients with invasive mycoses and in 1 out of 6 samples of patients with amebiasis. Conclusions The use of NGS for hypothesis-free pathogen diagnosis from contamination-prone formalin-fixed, paraffin-embedded tissue requires further standardization.http://link.springer.com/article/10.1186/s12866-019-1448-0NGSNext-generation sequencingHypothesis-free diagnosis of infectionInvasive fungal infectionsInvasive amebiasisFFPE, formalin-fixed, paraffin-embedded samples |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Hagen Frickmann Carsten Künne Ralf Matthias Hagen Andreas Podbielski Jana Normann Sven Poppert Mario Looso Bernd Kreikemeyer |
spellingShingle |
Hagen Frickmann Carsten Künne Ralf Matthias Hagen Andreas Podbielski Jana Normann Sven Poppert Mario Looso Bernd Kreikemeyer Next-generation sequencing for hypothesis-free genomic detection of invasive tropical infections in poly-microbially contaminated, formalin-fixed, paraffin-embedded tissue samples – a proof-of-principle assessment BMC Microbiology NGS Next-generation sequencing Hypothesis-free diagnosis of infection Invasive fungal infections Invasive amebiasis FFPE, formalin-fixed, paraffin-embedded samples |
author_facet |
Hagen Frickmann Carsten Künne Ralf Matthias Hagen Andreas Podbielski Jana Normann Sven Poppert Mario Looso Bernd Kreikemeyer |
author_sort |
Hagen Frickmann |
title |
Next-generation sequencing for hypothesis-free genomic detection of invasive tropical infections in poly-microbially contaminated, formalin-fixed, paraffin-embedded tissue samples – a proof-of-principle assessment |
title_short |
Next-generation sequencing for hypothesis-free genomic detection of invasive tropical infections in poly-microbially contaminated, formalin-fixed, paraffin-embedded tissue samples – a proof-of-principle assessment |
title_full |
Next-generation sequencing for hypothesis-free genomic detection of invasive tropical infections in poly-microbially contaminated, formalin-fixed, paraffin-embedded tissue samples – a proof-of-principle assessment |
title_fullStr |
Next-generation sequencing for hypothesis-free genomic detection of invasive tropical infections in poly-microbially contaminated, formalin-fixed, paraffin-embedded tissue samples – a proof-of-principle assessment |
title_full_unstemmed |
Next-generation sequencing for hypothesis-free genomic detection of invasive tropical infections in poly-microbially contaminated, formalin-fixed, paraffin-embedded tissue samples – a proof-of-principle assessment |
title_sort |
next-generation sequencing for hypothesis-free genomic detection of invasive tropical infections in poly-microbially contaminated, formalin-fixed, paraffin-embedded tissue samples – a proof-of-principle assessment |
publisher |
BMC |
series |
BMC Microbiology |
issn |
1471-2180 |
publishDate |
2019-04-01 |
description |
Abstract Background The potential of next-generation sequencing (NGS) for hypothesis-free pathogen diagnosis from (poly-)microbially contaminated, formalin-fixed, paraffin embedded tissue samples from patients with invasive fungal infections and amebiasis was investigated. Samples from patients with chromoblastomycosis (n = 3), coccidioidomycosis (n = 2), histoplasmosis (n = 4), histoplasmosis or cryptococcosis with poor histological discriminability (n = 1), mucormycosis (n = 2), mycetoma (n = 3), rhinosporidiosis (n = 2), and invasive Entamoeba histolytica infections (n = 6) were analyzed by NGS (each one Illumina v3 run per sample). To discriminate contamination from putative infections in NGS analysis, mean and standard deviation of the number of specific sequence fragments (paired reads) were determined and compared in all samples examined for the pathogens in question. Results For matches between NGS results and histological diagnoses, a percentage of species-specific reads greater than the 4th standard deviation above the mean value of all 23 assessed sample materials was required. Potentially etiologically relevant pathogens could be identified by NGS in 5 out of 17 samples of patients with invasive mycoses and in 1 out of 6 samples of patients with amebiasis. Conclusions The use of NGS for hypothesis-free pathogen diagnosis from contamination-prone formalin-fixed, paraffin-embedded tissue requires further standardization. |
topic |
NGS Next-generation sequencing Hypothesis-free diagnosis of infection Invasive fungal infections Invasive amebiasis FFPE, formalin-fixed, paraffin-embedded samples |
url |
http://link.springer.com/article/10.1186/s12866-019-1448-0 |
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