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Updated: Nov 6, 2025

Identification of Rare Bacterial Pathogens by 16S rRNA Gene Sequencing and MALDI-TOF MS
Published on: July 11, 2016
Cutibacterium modestum and "Propionibacterium humerusii" represent the same species that is commonly misidentified as
Daniel Goldenberger1, Kirstine K Søgaard2,3, Aline Cuénod3
1Division of Clinical Bacteriology and Mycology, University Hospital Basel, University of Basel, Petersgraben 4, 4031, Basel, Switzerland. daniel.goldenberger@usb.ch.
Abstract:
Cutibacterium spp. play an increasing role in soft tissue and implant-associated infections. We isolated a novel Cutibacterium spp. from an implant and investigated this isolate using multiple identification approaches. Correct identification was hampered by inconsistent reference data. The isolate was characterised using conventional methods such as Gram stain, MALDI-TOF MS, and antimicrobial susceptibility testing against multiple antimicrobials. Partial 16S rRNA gene sequencing and whole genome sequencing were also performed. In addition, we summarised the available published sequence data and compared prior data to our strain. Conventional phenotypic identification of our isolate resulted in Cutibacterium spp. After analysis of 16S rRNA gene and genome sequences, our isolate was identified as C. modestum, a very recently described species. The 16S rRNA gene analysis was hampered by three incorrect nucleotides within the 16S rRNA gene reference sequence of C. modestum M12T (accession no. LC466959). We also clearly demonstrate that this novel species is identical to tentatively named "Propionibacterium humerusii". Retrospective data analysis indicates that C. modestum is a clinically important Cutibacterium species often misidentified as C. acnes. The isolation and identification of Cutibacterium spp. is still a challenge. The correct description of very recently named C. modestum and the availability of a correct 16S rRNA sequence of the type strain may help to clarify the taxonomical uncertainty concerning "P. humerusii". The novel C. modestum is an additional, clinically important species within the genus Cutibacterium and may represent a new member of the human skin microbiome.
Insights
A novel Cutibacterium species, identified as Cutibacterium modestum, was isolated from an implant infection. This species is often misidentified as Cutibacterium acnes, highlighting challenges in bacterial identification.
Area of Science:
- Microbiology
- Infectious Diseases
- Bacterial Taxonomy
Background:
- Cutibacterium species are increasingly implicated in soft tissue and implant-associated infections.
- Accurate identification of Cutibacterium species is crucial for effective treatment and understanding infection dynamics.
- Challenges exist in differentiating closely related Cutibacterium species due to inconsistent reference data.
Purpose of the Study:
- To isolate and identify a novel Cutibacterium species from an implant-associated infection.
- To characterize the isolate using a combination of conventional and molecular methods.
- To clarify the taxonomic status of the novel species and its relationship to existing species, including "Propionibacterium humerusii".
Main Methods:
- Conventional identification: Gram stain, MALDI-TOF MS, antimicrobial susceptibility testing.
- Molecular identification: Partial 16S rRNA gene sequencing and whole genome sequencing.
- Comparative analysis of isolate sequences with publicly available reference data.
Main Results:
- The isolate was identified as Cutibacterium modestum, a recently described species.
- 16S rRNA gene sequencing was initially hampered by inaccuracies in the reference sequence for C. modestum M12T.
- The study confirmed that the novel species is identical to the tentatively named "Propionibacterium humerusii".
Conclusions:
- Cutibacterium modestum is a clinically significant species often misidentified as C. acnes.
- Accurate identification methods and reliable reference sequences are essential for resolving taxonomic uncertainties.
- C. modestum represents an important addition to the genus Cutibacterium and the human skin microbiome.
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