Shotgun sequencing of sonication fluid for the diagnosis of orthopaedic implant-associated infections with Cutibacterium acnes as suspected causative agent
Orthopaedic implant-associated infections (OIAIs) due to Cutibacterium acnes can be difficult to diagnose. The aim of this pilot study was to determine if metagenomic next-generation sequencing (mNGS) can provide additional information to improve the diagnosis of C. acnes OIAIs. mNGS was performed o...
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| Format: | Article |
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Frontiers Media S.A.
2023-05-01
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| Series: | Frontiers in Cellular and Infection Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fcimb.2023.1165017/full |
| _version_ | 1827946158107918336 |
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| author | Diana Salomi Ponraj Michael Lund Jeppe Lange Jeppe Lange Anja Poehlein Axel Himmelbach Thomas Falstie-Jensen Nis Pedersen Jørgensen Christen Ravn Holger Brüggemann |
| author_facet | Diana Salomi Ponraj Michael Lund Jeppe Lange Jeppe Lange Anja Poehlein Axel Himmelbach Thomas Falstie-Jensen Nis Pedersen Jørgensen Christen Ravn Holger Brüggemann |
| author_sort | Diana Salomi Ponraj |
| collection | DOAJ |
| description | Orthopaedic implant-associated infections (OIAIs) due to Cutibacterium acnes can be difficult to diagnose. The aim of this pilot study was to determine if metagenomic next-generation sequencing (mNGS) can provide additional information to improve the diagnosis of C. acnes OIAIs. mNGS was performed on sonication fluid (SF) specimens derived from 24 implants. These were divided into three groups, based on culture results: group I, culture-negative (n = 4); group II, culture-positive for C. acnes (n = 10); and group III, culture-positive for other bacteria (n = 10). In group I, sequence reads from C. acnes were detected in only one SF sample, originating from a suspected case of OIAIs, which was SF and tissue culture-negative. In group II, C. acnes sequences were detected in 7/10 samples. In group III, C. acnes sequence reads were found in 5/10 samples, in addition to sequence reads that matched the bacterial species identified by culture. These samples could represent polymicrobial infections that were missed by culture. Taken together, mNGS was able to detect C. acnes DNA in more samples compared to culture and could be used to identify cases of suspected C. acnes OIAIs, in particular regarding possible polymicrobial infections, where the growth of C. acnes might be compromised due to a fast-growing bacterial species. However, since SF specimens are usually low-biomass samples, mNGS is prone to DNA contamination, possibly introduced during DNA extraction or sequencing procedures. Thus, it is advisable to set a sequence read count threshold, taking into account project- and NGS-specific criteria. |
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| institution | Directory Open Access Journal |
| issn | 2235-2988 |
| language | English |
| last_indexed | 2024-03-13T10:54:43Z |
| publishDate | 2023-05-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Cellular and Infection Microbiology |
| spelling | doaj.art-d28c11ab8fef46eb8db9b4c67f5d82042023-05-17T05:31:21ZengFrontiers Media S.A.Frontiers in Cellular and Infection Microbiology2235-29882023-05-011310.3389/fcimb.2023.11650171165017Shotgun sequencing of sonication fluid for the diagnosis of orthopaedic implant-associated infections with Cutibacterium acnes as suspected causative agentDiana Salomi Ponraj0Michael Lund1Jeppe Lange2Jeppe Lange3Anja Poehlein4Axel Himmelbach5Thomas Falstie-Jensen6Nis Pedersen Jørgensen7Christen Ravn8Holger Brüggemann9Department of Clinical Medicine, Aarhus University, Aarhus, DenmarkDepartment of Biomedicine, Aarhus University, Aarhus, DenmarkDepartment of Clinical Medicine, Aarhus University, Aarhus, DenmarkDepartment of Orthopaedic Surgery, Regional Hospital, Horsens, DenmarkDepartment of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, GermanyLeibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, GermanyDepartment of Orthopaedic Surgery, Aarhus University Hospital, Aarhus, DenmarkDepartment of Infectious Diseases, Aarhus University Hospital, Aarhus, DenmarkDepartment of Orthopaedic Surgery, Aarhus University Hospital, Aarhus, DenmarkDepartment of Biomedicine, Aarhus University, Aarhus, DenmarkOrthopaedic implant-associated infections (OIAIs) due to Cutibacterium acnes can be difficult to diagnose. The aim of this pilot study was to determine if metagenomic next-generation sequencing (mNGS) can provide additional information to improve the diagnosis of C. acnes OIAIs. mNGS was performed on sonication fluid (SF) specimens derived from 24 implants. These were divided into three groups, based on culture results: group I, culture-negative (n = 4); group II, culture-positive for C. acnes (n = 10); and group III, culture-positive for other bacteria (n = 10). In group I, sequence reads from C. acnes were detected in only one SF sample, originating from a suspected case of OIAIs, which was SF and tissue culture-negative. In group II, C. acnes sequences were detected in 7/10 samples. In group III, C. acnes sequence reads were found in 5/10 samples, in addition to sequence reads that matched the bacterial species identified by culture. These samples could represent polymicrobial infections that were missed by culture. Taken together, mNGS was able to detect C. acnes DNA in more samples compared to culture and could be used to identify cases of suspected C. acnes OIAIs, in particular regarding possible polymicrobial infections, where the growth of C. acnes might be compromised due to a fast-growing bacterial species. However, since SF specimens are usually low-biomass samples, mNGS is prone to DNA contamination, possibly introduced during DNA extraction or sequencing procedures. Thus, it is advisable to set a sequence read count threshold, taking into account project- and NGS-specific criteria.https://www.frontiersin.org/articles/10.3389/fcimb.2023.1165017/fullCutibacterium acnesshotgun sequencingmetagenomicsorthopaedic implant-associated infectionsprosthetic infectionssonication fluid |
| spellingShingle | Diana Salomi Ponraj Michael Lund Jeppe Lange Jeppe Lange Anja Poehlein Axel Himmelbach Thomas Falstie-Jensen Nis Pedersen Jørgensen Christen Ravn Holger Brüggemann Shotgun sequencing of sonication fluid for the diagnosis of orthopaedic implant-associated infections with Cutibacterium acnes as suspected causative agent Frontiers in Cellular and Infection Microbiology Cutibacterium acnes shotgun sequencing metagenomics orthopaedic implant-associated infections prosthetic infections sonication fluid |
| title | Shotgun sequencing of sonication fluid for the diagnosis of orthopaedic implant-associated infections with Cutibacterium acnes as suspected causative agent |
| title_full | Shotgun sequencing of sonication fluid for the diagnosis of orthopaedic implant-associated infections with Cutibacterium acnes as suspected causative agent |
| title_fullStr | Shotgun sequencing of sonication fluid for the diagnosis of orthopaedic implant-associated infections with Cutibacterium acnes as suspected causative agent |
| title_full_unstemmed | Shotgun sequencing of sonication fluid for the diagnosis of orthopaedic implant-associated infections with Cutibacterium acnes as suspected causative agent |
| title_short | Shotgun sequencing of sonication fluid for the diagnosis of orthopaedic implant-associated infections with Cutibacterium acnes as suspected causative agent |
| title_sort | shotgun sequencing of sonication fluid for the diagnosis of orthopaedic implant associated infections with cutibacterium acnes as suspected causative agent |
| topic | Cutibacterium acnes shotgun sequencing metagenomics orthopaedic implant-associated infections prosthetic infections sonication fluid |
| url | https://www.frontiersin.org/articles/10.3389/fcimb.2023.1165017/full |
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