Emergence of Cutibacterium avidum with <i>erm</i>(X) on a Mobile Genetic Element Identical to That of Cutibacterium acnes

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ABSTRACT

We determined that the Cutibacterium avidum isolate TP-CV302, from a patient with acne vulgaris in Japan, had the macrolide-clindamycin resistance factor erm(X) located on Tn 5432. Although this mobile genetic element (MGE) is well recognized in Cutibacterium acnes, it has not been found in Cutibacterium avidum.

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BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons

Nabil-Fareed Alikhan, Nicola Petty, Nouri L. Ben Zakour … (2011)

Background Visualisation of genome comparisons is invaluable for helping to determine genotypic differences between closely related prokaryotes. New visualisation and abstraction methods are required in order to improve the validation, interpretation and communication of genome sequence information; especially with the increasing amount of data arising from next-generation sequencing projects. Visualising a prokaryote genome as a circular image has become a powerful means of displaying informative comparisons of one genome to a number of others. Several programs, imaging libraries and internet resources already exist for this purpose, however, most are either limited in the number of comparisons they can show, are unable to adequately utilise draft genome sequence data, or require a knowledge of command-line scripting for implementation. Currently, there is no freely available desktop application that enables users to rapidly visualise comparisons between hundreds of draft or complete genomes in a single image. Results BLAST Ring Image Generator (BRIG) can generate images that show multiple prokaryote genome comparisons, without an arbitrary limit on the number of genomes compared. The output image shows similarity between a central reference sequence and other sequences as a set of concentric rings, where BLAST matches are coloured on a sliding scale indicating a defined percentage identity. Images can also include draft genome assembly information to show read coverage, assembly breakpoints and collapsed repeats. In addition, BRIG supports the mapping of unassembled sequencing reads against one or more central reference sequences. Many types of custom data and annotations can be shown using BRIG, making it a versatile approach for visualising a range of genomic comparison data. BRIG is readily accessible to any user, as it assumes no specialist computational knowledge and will perform all required file parsing and BLAST comparisons automatically. Conclusions There is a clear need for a user-friendly program that can produce genome comparisons for a large number of prokaryote genomes with an emphasis on rapidly utilising unfinished or unassembled genome data. Here we present BRIG, a cross-platform application that enables the interactive generation of comparative genomic images via a simple graphical-user interface. BRIG is freely available for all operating systems at http://sourceforge.net/projects/brig/.

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Antimicrobial susceptibility and phylogenetic analysis of Propionibacterium acnes isolated from acne patients in Japan between 2013 and 2015

Keisuke Nakase, Nobukazu Hayashi, Yui Akiyama … (2017)

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Antibiotic resistance to Propionobacterium acnes: worldwide scenario, diagnosis and management.

Kabir Sardana, Tanvi Gupta, Vijay Garg … (2015)

Antibiotic resistance in cutaneous Propionobacterium is a global problem. As a general rule, resistance levels are high to macrolides, trimethoprim/sulfamethoxazole and clindamycin, while tetracyclines and levofloxacin have low resistance potential. Newer preparations like doxycycline MR and doxycycline 20 mg are subantimicrobial and may not lead to resistance. Sampling techniques are crucial to determine resistance. Genomic evaluation using 16S ribosomal RNA gene sequencing can be useful in diagnosing mutations and mapping phylotypes of Propionobacterium acnes. Resistance may lead to slow response and relapses. Apart from benzoyl peroxide, azelaic acid, topical dapsone, oral zinc and retinoids, novel molecules with little resistance potential include octadecenedioic acid, phytosphingosine, lauric acid, retapamulin, resveratrol, T-3912 and NB-003. The use of oral retinoids and non-antibiotics like zinc can prevent resistance and help reduce the dependence on antibiotics.

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Author and article information

Contributors

Hidemasa Nakaminami:

ORCID: https://orcid.org/0000-0003-2889-8257

Frank J. Stewart: Role: Editor

Journal

Journal ID (nlm-ta): Microbiol Resour Announc

Journal ID (iso-abbrev): Microbiol Resour Announc

Journal ID (publisher-id): mra

Title: Microbiology Resource Announcements

Publisher: American Society for Microbiology (1752 N St., N.W., Washington, DC )

ISSN (Electronic): 2576-098X

Publication date (Electronic, pub): 5 June 2023

Publication date (Electronic, collection): July 2023

Publication date PMC-release: 5 June 2023

Volume: 12

Issue: 7

Electronic Location Identifier: e00178-23

Affiliations

[a ] Department of Clinical Microbiology, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan

Montana State University

Author notes

The authors declare no conflict of interest.

Author information

Juri Koizumi https://orcid.org/0000-0001-6874-2236

Keisuke Nakase https://orcid.org/0000-0002-9205-3008

Hidemasa Nakaminami https://orcid.org/0000-0003-2889-8257

Article

Publisher ID: 00178-23 Publisher ID: mra.00178-23

DOI: 10.1128/mra.00178-23

PMC ID: 10353459

PubMed ID: 37272804

SO-VID: f51a2b3a-11f6-4518-86a9-85478caa1560

License:

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

History

Date received : 12 March 2023

Date accepted : 24 May 2023

Page count

Figures: 1, Tables: 0, Equations: 0, References: 9, Pages: 2, Words: 1140

Funding

Funded by: MEXT | Japan Society for the Promotion of Science (JSPS), FundRef https://doi.org/10.13039/501100001691;

Award ID: 21K15303

Award Recipient : Keisuke Nakase

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cover-date July 2023

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Emergence of Cutibacterium avidum with erm(X) on a Mobile Genetic Element Identical to That of Cutibacterium acnes

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Most cited references 9

BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons

Antimicrobial susceptibility and phylogenetic analysis of Propionibacterium acnes isolated from acne patients in Japan between 2013 and 2015

Antibiotic resistance to Propionobacterium acnes: worldwide scenario, diagnosis and management.

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