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Ahle CM, Stødkilde-Jørgensen K, Poehlein A, et al. Comparison of three amplicon sequencing approaches to determine staphylococcal populations on human skin. BMC Microbiol. 2021;21(1):221doi: 10.1186/s12866-021-02284-1.
Ahle, C. M., Stødkilde-Jørgensen, K., Poehlein, A., Streit, W. R., Hüpeden, J., & Brüggemann, H. (2021). Comparison of three amplicon sequencing approaches to determine staphylococcal populations on human skin. BMC microbiology, 21(1), 221. https://doi.org/10.1186/s12866-021-02284-1
Ahle, Charlotte Marie, et al. "Comparison of three amplicon sequencing approaches to determine staphylococcal populations on human skin." BMC microbiology vol. 21,1 (2021): 221. doi: https://doi.org/10.1186/s12866-021-02284-1
Ahle CM, Stødkilde-Jørgensen K, Poehlein A, Streit WR, Hüpeden J, Brüggemann H. Comparison of three amplicon sequencing approaches to determine staphylococcal populations on human skin. BMC Microbiol. 2021 Jul 28;21(1):221. doi: 10.1186/s12866-021-02284-1. PMID: 34320945; PMCID: PMC8320028.
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BMC Microbiol. 2021 Jul 28;21(1):221. doi: 10.1186/s12866-021-02284-1.

Comparison of three amplicon sequencing approaches to determine staphylococcal populations on human skin.

BMC microbiology

Charlotte Marie Ahle, Kristian Stødkilde-Jørgensen, Anja Poehlein, Wolfgang R Streit, Jennifer Hüpeden, Holger Brüggemann

Affiliations

  1. Beiersdorf AG, Research & Development, Front End Innovation, 20245, Hamburg, Germany.
  2. Department of Microbiology and Biotechnology, University of Hamburg, 22609, Hamburg, Germany.
  3. Department of Biomedicine, Aarhus University, 8000, Aarhus, Denmark.
  4. Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, University of Göttingen, 37073, Göttingen, Germany.
  5. Department of Biomedicine, Aarhus University, 8000, Aarhus, Denmark. [email protected].

PMID: 34320945 PMCID: PMC8320028 DOI: 10.1186/s12866-021-02284-1

Abstract

BACKGROUND: Staphylococci are important members of the human skin microbiome. Many staphylococcal species and strains are commensals of the healthy skin microbiota, while few play essential roles in skin diseases such as atopic dermatitis. To study the involvement of staphylococci in health and disease, it is essential to determine staphylococcal populations in skin samples beyond the genus and species level. Culture-independent approaches such as amplicon next-generation sequencing (NGS) are time- and cost-effective options. However, their suitability depends on the power of resolution.

RESULTS: Here we compare three amplicon NGS schemes that rely on different targets within the genes tuf and rpsK, designated tuf1, tuf2 and rpsK schemes. The schemes were tested on mock communities and on human skin samples. To obtain skin samples and build mock communities, skin swab samples of healthy volunteers were taken. In total, 254 staphylococcal strains were isolated and identified to the species level by MALDI-TOF mass spectrometry. A subset of ten strains belonging to different staphylococcal species were genome-sequenced. Two mock communities with nine and eighteen strains, respectively, as well as eight randomly selected skin samples were analysed with the three amplicon NGS methods. Our results imply that all three methods are suitable for species-level determination of staphylococcal populations. However, the novel tuf2-NGS scheme was superior in resolution power. It unambiguously allowed identification of Staphylococcus saccharolyticus and distinguish phylogenetically distinct clusters of Staphylococcus epidermidis.

CONCLUSIONS: Powerful amplicon NGS approaches for the detection and relative quantification of staphylococci in human samples exist that can resolve populations to the species and, to some extent, to the subspecies level. Our study highlights strengths, weaknesses and pitfalls of three currently available amplicon NGS approaches to determine staphylococcal populations. Applied to the analysis of healthy and diseased skin, these approaches can be useful to attribute host-beneficial and -detrimental roles to skin-resident staphylococcal species and subspecies.

© 2021. The Author(s).

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