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Proteotyping of Clostridioides difficile as Alternate Typing Method to Ribotyping Is Able to Distinguish the Ribotypes RT027 and RT176 From Other Ribotypes

Clostridioides difficile, a Gram-positive spore-forming bacterium, is the leading cause of nosocomial diarrhea worldwide and therefore a substantial burden to the healthcare system. During the past decade, hypervirulent PCR-ribotypes (RT) e.g., RT027 or RT176 emerged rapidly all over the world, asso...

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Autores principales: Emele, Matthias F., Joppe, Felix M., Riedel, Thomas, Overmann, Jörg, Rupnik, Maja, Cooper, Paul, Kusumawati, R. Lia, Berger, Fabian K., Laukien, Friederike, Zimmermann, Ortrud, Bohne, Wolfgang, Groß, Uwe, Bader, Oliver, Zautner, Andreas E.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6747054/
https://www.ncbi.nlm.nih.gov/pubmed/31552001
http://dx.doi.org/10.3389/fmicb.2019.02087
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author Emele, Matthias F.
Joppe, Felix M.
Riedel, Thomas
Overmann, Jörg
Rupnik, Maja
Cooper, Paul
Kusumawati, R. Lia
Berger, Fabian K.
Laukien, Friederike
Zimmermann, Ortrud
Bohne, Wolfgang
Groß, Uwe
Bader, Oliver
Zautner, Andreas E.
author_facet Emele, Matthias F.
Joppe, Felix M.
Riedel, Thomas
Overmann, Jörg
Rupnik, Maja
Cooper, Paul
Kusumawati, R. Lia
Berger, Fabian K.
Laukien, Friederike
Zimmermann, Ortrud
Bohne, Wolfgang
Groß, Uwe
Bader, Oliver
Zautner, Andreas E.
author_sort Emele, Matthias F.
collection PubMed
description Clostridioides difficile, a Gram-positive spore-forming bacterium, is the leading cause of nosocomial diarrhea worldwide and therefore a substantial burden to the healthcare system. During the past decade, hypervirulent PCR-ribotypes (RT) e.g., RT027 or RT176 emerged rapidly all over the world, associated with both, increased severity and mortality rates. It is thus of great importance to identify epidemic strains such as RT027 and RT176 as fast as possible. While commonly used diagnostic methods, e.g., multilocus sequence typing (MLST) or PCR-ribotyping, are time-consuming, proteotyping offers a fast, inexpensive, and reliable alternative solution. In this study, we established a MALDI-TOF-based typing scheme for C. difficile. A total of 109 ribotyped strains representative for five MLST clades were analyzed by MALDI-TOF. MLST, based on whole genome sequences, and PCR-ribotyping were used as reference methods. Isoforms of MS-detectable biomarkers, typically ribosomal proteins, were related with the deduced amino acid sequences and added to the C. difficile proteotyping scheme. In total, we were able to associate nine biomarkers with their encoding genes and include them in our proteotyping scheme. The discriminatory capacity of the C. difficile proteotyping scheme was mainly based on isoforms of L28-M (2 main isoforms), L35-M (4 main isoforms), and S20-M (2 main isoforms) giving rise to at least 16 proteotyping-derived types. In our test population, five of these 16 proteotyping-derived types were detected. These five proteotyping-derived types did not correspond exactly to the included five MLST-based C. difficile clades, nevertheless the subtyping depth of both methods was equivalent. Most importantly, proteotyping-derived clade B contained only isolates of the hypervirulent RT027 and RT176. Proteotyping is a stable and easy-to-perform intraspecies typing method and a promising alternative to currently used molecular techniques. It is possible to distinguish the group of RT027 and RT176 isolates from non-RT027/non-RT176 isolates using proteotyping, providing a valuable diagnostic tool.
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spelling pubmed-67470542019-09-24 Proteotyping of Clostridioides difficile as Alternate Typing Method to Ribotyping Is Able to Distinguish the Ribotypes RT027 and RT176 From Other Ribotypes Emele, Matthias F. Joppe, Felix M. Riedel, Thomas Overmann, Jörg Rupnik, Maja Cooper, Paul Kusumawati, R. Lia Berger, Fabian K. Laukien, Friederike Zimmermann, Ortrud Bohne, Wolfgang Groß, Uwe Bader, Oliver Zautner, Andreas E. Front Microbiol Microbiology Clostridioides difficile, a Gram-positive spore-forming bacterium, is the leading cause of nosocomial diarrhea worldwide and therefore a substantial burden to the healthcare system. During the past decade, hypervirulent PCR-ribotypes (RT) e.g., RT027 or RT176 emerged rapidly all over the world, associated with both, increased severity and mortality rates. It is thus of great importance to identify epidemic strains such as RT027 and RT176 as fast as possible. While commonly used diagnostic methods, e.g., multilocus sequence typing (MLST) or PCR-ribotyping, are time-consuming, proteotyping offers a fast, inexpensive, and reliable alternative solution. In this study, we established a MALDI-TOF-based typing scheme for C. difficile. A total of 109 ribotyped strains representative for five MLST clades were analyzed by MALDI-TOF. MLST, based on whole genome sequences, and PCR-ribotyping were used as reference methods. Isoforms of MS-detectable biomarkers, typically ribosomal proteins, were related with the deduced amino acid sequences and added to the C. difficile proteotyping scheme. In total, we were able to associate nine biomarkers with their encoding genes and include them in our proteotyping scheme. The discriminatory capacity of the C. difficile proteotyping scheme was mainly based on isoforms of L28-M (2 main isoforms), L35-M (4 main isoforms), and S20-M (2 main isoforms) giving rise to at least 16 proteotyping-derived types. In our test population, five of these 16 proteotyping-derived types were detected. These five proteotyping-derived types did not correspond exactly to the included five MLST-based C. difficile clades, nevertheless the subtyping depth of both methods was equivalent. Most importantly, proteotyping-derived clade B contained only isolates of the hypervirulent RT027 and RT176. Proteotyping is a stable and easy-to-perform intraspecies typing method and a promising alternative to currently used molecular techniques. It is possible to distinguish the group of RT027 and RT176 isolates from non-RT027/non-RT176 isolates using proteotyping, providing a valuable diagnostic tool. Frontiers Media S.A. 2019-09-10 /pmc/articles/PMC6747054/ /pubmed/31552001 http://dx.doi.org/10.3389/fmicb.2019.02087 Text en Copyright © 2019 Emele, Joppe, Riedel, Overmann, Rupnik, Cooper, Kusumawati, Berger, Laukien, Zimmermann, Bohne, Groß, Bader and Zautner. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Emele, Matthias F.
Joppe, Felix M.
Riedel, Thomas
Overmann, Jörg
Rupnik, Maja
Cooper, Paul
Kusumawati, R. Lia
Berger, Fabian K.
Laukien, Friederike
Zimmermann, Ortrud
Bohne, Wolfgang
Groß, Uwe
Bader, Oliver
Zautner, Andreas E.
Proteotyping of Clostridioides difficile as Alternate Typing Method to Ribotyping Is Able to Distinguish the Ribotypes RT027 and RT176 From Other Ribotypes
title Proteotyping of Clostridioides difficile as Alternate Typing Method to Ribotyping Is Able to Distinguish the Ribotypes RT027 and RT176 From Other Ribotypes
title_full Proteotyping of Clostridioides difficile as Alternate Typing Method to Ribotyping Is Able to Distinguish the Ribotypes RT027 and RT176 From Other Ribotypes
title_fullStr Proteotyping of Clostridioides difficile as Alternate Typing Method to Ribotyping Is Able to Distinguish the Ribotypes RT027 and RT176 From Other Ribotypes
title_full_unstemmed Proteotyping of Clostridioides difficile as Alternate Typing Method to Ribotyping Is Able to Distinguish the Ribotypes RT027 and RT176 From Other Ribotypes
title_short Proteotyping of Clostridioides difficile as Alternate Typing Method to Ribotyping Is Able to Distinguish the Ribotypes RT027 and RT176 From Other Ribotypes
title_sort proteotyping of clostridioides difficile as alternate typing method to ribotyping is able to distinguish the ribotypes rt027 and rt176 from other ribotypes
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6747054/
https://www.ncbi.nlm.nih.gov/pubmed/31552001
http://dx.doi.org/10.3389/fmicb.2019.02087
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