CUTIS-SEQ, a flexible bilocus sequence typing scheme that provides high resolution of Cutibacterium acnes strains across all subspecies

Joseph McLaughlin, István Nagy, Georgios Miliotis, Andrew McDowell

Research output: Contribution to journalArticlepeer-review

2 Citations (Scopus)
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Abstract

Objectives: A ‘high resolution’ Single Locus Sequence Typing (SLST) scheme has been described for the anaerobic skin bacterium Cutibacterium acnes that seemingly discriminates sequence types (STs) to a level commensurate with previously described Multilocus Sequence Typing (MLST) methods (MLST 4; MLST 8; MLST 9). However, no quantifiable evaluation of SLST versus MLST for differentiation of C. acnes strains, especially in relation to the subspecies of the bacterium, known as C. acnes subsp. acnes (type I), C. acnes subsp. defendens (type II) and C. acnes subsp. elongatum (type III), has been performed which is vital given its increasing use. To address this, we examined the discriminatory power of SLST versus MLST with a large group of isolates representative of all subspecies. 

Methods: Simpson's index of diversity (D) was used for quantitative comparison of the resolving power of the SLST and MLST schemes for 186 isolates of C. acnes covering all three subspecies. 

Results: When strains were considered collectively, SLST and all three MLST approaches had similar D values > 90%. However, at the subspecies level there were significant differences between the methods, most strikingly a reduced discrimination of type II and type III strains (D <80%) by SLST versus MLST 8, and to a lesser extent MLST 4. The MLST 9 method also performed poorly for type II strains (D <70%), but did display the best results for type I (D = 90%). By combining the SLST locus with the camp2 gene sequence to create a novel and flexible high-resolution Bilocus Sequence Typing (BLST) scheme, known as CUTIS-SEQ typing (CUTIbacterium acneS BilocuS sEQuence Typing), we achieved improved resolution at both species and, critically, subspp. levels. 

Conclusions: CUTIS-SEQ provides an opportunity to improve differentiation of C. acnes isolates by SLST without significantly impacting laboratory workload, or compromising application to complex biological communities. A CUTIS-SEQ isolate database is now available as part of the C. acnes PubMLST database at https://pubmlst.org.

Original languageEnglish
Article number102671
Pages (from-to)1-8
Number of pages8
JournalAnaerobe
Volume79
Early online date29 Nov 2022
DOIs
Publication statusPublished (in print/issue) - 28 Feb 2023

Bibliographical note

Funding Information:
J.M. is currently funded by a British Skin Foundation studentship to A.M.D (Grant Project No. 025/s/16 ). The study also made use of the C. acnes PubMLST database and we also thank Keith Jolley for assistance in setting up the CUTIS-SEQ isolate database within this site.

Publisher Copyright:
© 2022 The Authors

Keywords

  • SLST
  • MLST
  • discrimination
  • Cutibacterium acnes
  • Recombination
  • CUTIS-SEQ typing
  • Discrimination

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