Identification of Shiga-Toxigenic Escherichia coli outbreak isolates by a novel data analysis tool after matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.
The fast and reliable characterization of bacterial and fungal pathogens plays an important role in infectious disease control and tracking of outbreak agents. DNA based methods are the gold standard for epidemiological investigations, but they are still comparatively expensive and time-consuming. M...
Saved in:
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2017-01-01
|
| Series: | PLoS ONE |
| Online Access: | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0182962&type=printable |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1850230153046654976 |
|---|---|
| author | Martin Christner Dirk Dressler Mark Andrian Claudia Reule Orlando Petrini |
| author_facet | Martin Christner Dirk Dressler Mark Andrian Claudia Reule Orlando Petrini |
| author_sort | Martin Christner |
| collection | DOAJ |
| description | The fast and reliable characterization of bacterial and fungal pathogens plays an important role in infectious disease control and tracking of outbreak agents. DNA based methods are the gold standard for epidemiological investigations, but they are still comparatively expensive and time-consuming. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a fast, reliable and cost-effective technique now routinely used to identify clinically relevant human pathogens. It has been used for subspecies differentiation and typing, but its use for epidemiological tasks, e. g. for outbreak investigations, is often hampered by the complexity of data analysis. We have analysed publicly available MALDI-TOF mass spectra from a large outbreak of Shiga-Toxigenic Escherichia coli in northern Germany using a general purpose software tool for the analysis of complex biological data. The software was challenged with depauperate spectra and reduced learning group sizes to mimic poor spectrum quality and scarcity of reference spectra at the onset of an outbreak. With high quality formic acid extraction spectra, the software's built in classifier accurately identified outbreak related strains using as few as 10 reference spectra (99.8% sensitivity, 98.0% specificity). Selective variation of processing parameters showed impaired marker peak detection and reduced classification accuracy in samples with high background noise or artificially reduced peak counts. However, the software consistently identified mass signals suitable for a highly reliable marker peak based classification approach (100% sensitivity, 99.5% specificity) even from low quality direct deposition spectra. The study demonstrates that general purpose data analysis tools can effectively be used for the analysis of bacterial mass spectra. |
| format | Article |
| id | doaj-art-a688688dddab4fdc950906d8e3bd37c8 |
| institution | OA Journals |
| issn | 1932-6203 |
| language | English |
| publishDate | 2017-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj-art-a688688dddab4fdc950906d8e3bd37c82025-08-20T02:03:58ZengPublic Library of Science (PLoS)PLoS ONE1932-62032017-01-01129e018296210.1371/journal.pone.0182962Identification of Shiga-Toxigenic Escherichia coli outbreak isolates by a novel data analysis tool after matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.Martin ChristnerDirk DresslerMark AndrianClaudia ReuleOrlando PetriniThe fast and reliable characterization of bacterial and fungal pathogens plays an important role in infectious disease control and tracking of outbreak agents. DNA based methods are the gold standard for epidemiological investigations, but they are still comparatively expensive and time-consuming. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a fast, reliable and cost-effective technique now routinely used to identify clinically relevant human pathogens. It has been used for subspecies differentiation and typing, but its use for epidemiological tasks, e. g. for outbreak investigations, is often hampered by the complexity of data analysis. We have analysed publicly available MALDI-TOF mass spectra from a large outbreak of Shiga-Toxigenic Escherichia coli in northern Germany using a general purpose software tool for the analysis of complex biological data. The software was challenged with depauperate spectra and reduced learning group sizes to mimic poor spectrum quality and scarcity of reference spectra at the onset of an outbreak. With high quality formic acid extraction spectra, the software's built in classifier accurately identified outbreak related strains using as few as 10 reference spectra (99.8% sensitivity, 98.0% specificity). Selective variation of processing parameters showed impaired marker peak detection and reduced classification accuracy in samples with high background noise or artificially reduced peak counts. However, the software consistently identified mass signals suitable for a highly reliable marker peak based classification approach (100% sensitivity, 99.5% specificity) even from low quality direct deposition spectra. The study demonstrates that general purpose data analysis tools can effectively be used for the analysis of bacterial mass spectra.https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0182962&type=printable |
| spellingShingle | Martin Christner Dirk Dressler Mark Andrian Claudia Reule Orlando Petrini Identification of Shiga-Toxigenic Escherichia coli outbreak isolates by a novel data analysis tool after matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. PLoS ONE |
| title | Identification of Shiga-Toxigenic Escherichia coli outbreak isolates by a novel data analysis tool after matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. |
| title_full | Identification of Shiga-Toxigenic Escherichia coli outbreak isolates by a novel data analysis tool after matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. |
| title_fullStr | Identification of Shiga-Toxigenic Escherichia coli outbreak isolates by a novel data analysis tool after matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. |
| title_full_unstemmed | Identification of Shiga-Toxigenic Escherichia coli outbreak isolates by a novel data analysis tool after matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. |
| title_short | Identification of Shiga-Toxigenic Escherichia coli outbreak isolates by a novel data analysis tool after matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. |
| title_sort | identification of shiga toxigenic escherichia coli outbreak isolates by a novel data analysis tool after matrix assisted laser desorption ionization time of flight mass spectrometry |
| url | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0182962&type=printable |
| work_keys_str_mv | AT martinchristner identificationofshigatoxigenicescherichiacolioutbreakisolatesbyanoveldataanalysistoolaftermatrixassistedlaserdesorptionionizationtimeofflightmassspectrometry AT dirkdressler identificationofshigatoxigenicescherichiacolioutbreakisolatesbyanoveldataanalysistoolaftermatrixassistedlaserdesorptionionizationtimeofflightmassspectrometry AT markandrian identificationofshigatoxigenicescherichiacolioutbreakisolatesbyanoveldataanalysistoolaftermatrixassistedlaserdesorptionionizationtimeofflightmassspectrometry AT claudiareule identificationofshigatoxigenicescherichiacolioutbreakisolatesbyanoveldataanalysistoolaftermatrixassistedlaserdesorptionionizationtimeofflightmassspectrometry AT orlandopetrini identificationofshigatoxigenicescherichiacolioutbreakisolatesbyanoveldataanalysistoolaftermatrixassistedlaserdesorptionionizationtimeofflightmassspectrometry |