Novel macrolide-lincosamide-streptogramin B resistance gene <i>erm</i>(56) in <i>Trueperella pyogenes</i>

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ABSTRACT

Whole-genome sequence analysis of a macrolide, lincosamide, streptogramin B (MLS _B)-resistant Trueperella pyogenes from a dog revealed a new 23S ribosomal RNA methylase gene erm(56). Expression of the cloned erm(56) confers resistance to MLS _B in T. pyogenes and Escherichia coli. The erm(56) gene was flanked by two IS 6100 integrated on the chromosome next to a sul1-containing class 1 integron. GenBank query revealed additional erm(56)-containing elements in another T. pyogenes and in Rothia nasimurium from livestock.

IMPORTANCE

A novel 23S ribosomal RNA methylase gene erm(56) flanked by insertion sequence IS 6100 was identified in a Trueperella pyogenes isolated from the abscess of a dog and was also present in another T. pyogenes and in Rothia nasimurium from livestock. It was shown to confer resistance to macrolide, lincosamide, streptogramin B antibiotics in T. pyogenes and E. coli, indicating functionality in both Gram-positive and Gram-negative bacteria. The detection of erm(56) on different elements in unrelated bacteria from different animal sources and geographical origins suggests that it has been independently acquired and likely selected by the use of antibiotics in animals.

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Assembly of long, error-prone reads using repeat graphs

Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin … (2019)

Accurate genome assembly is hampered by repetitive regions. Although long single molecule sequencing reads are better able to resolve genomic repeats than short-read data, most long-read assembly algorithms do not provide the repeat characterization necessary for producing optimal assemblies. Here, we present Flye, a long-read assembly algorithm that generates arbitrary paths in an unknown repeat graph, called disjointigs, and constructs an accurate repeat graph from these error-riddled disjointigs. We benchmark Flye against five state-of-the-art assemblers and show that it generates better or comparable assemblies, while being an order of magnitude faster. Flye nearly doubled the contiguity of the human genome assembly (as measured by the NGA50 assembly quality metric) compared with existing assemblers.

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PHASTER: a better, faster version of the PHAST phage search tool

David L. Arndt, Jason Grant, Ana Marcu … (2016)

PHASTER (PHAge Search Tool – Enhanced Release) is a significant upgrade to the popular PHAST web server for the rapid identification and annotation of prophage sequences within bacterial genomes and plasmids. Although the steps in the phage identification pipeline in PHASTER remain largely the same as in the original PHAST, numerous software improvements and significant hardware enhancements have now made PHASTER faster, more efficient, more visually appealing and much more user friendly. In particular, PHASTER is now 4.3× faster than PHAST when analyzing a typical bacterial genome. More specifically, software optimizations have made the backend of PHASTER 2.7X faster than PHAST, while the addition of 80 CPUs to the PHASTER compute cluster are responsible for the remaining speed-up. PHASTER can now process a typical bacterial genome in 3 min from the raw sequence alone, or in 1.5 min when given a pre-annotated GenBank file. A number of other optimizations have also been implemented, including automated algorithms to reduce the size and redundancy of PHASTER's databases, improvements in handling multiple (metagenomic) queries and higher user traffic, along with the ability to perform automated look-ups against 14 000 previously PHAST/PHASTER annotated bacterial genomes (which can lead to complete phage annotations in seconds as opposed to minutes). PHASTER's web interface has also been entirely rewritten. A new graphical genome browser has been added, gene/genome visualization tools have been improved, and the graphical interface is now more modern, robust and user-friendly. PHASTER is available online at www.phaster.ca.

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clinker & clustermap.js: automatic generation of gene cluster comparison figures

Cameron Gilchrist, Yit-Heng Chooi, Peter Robinson (2021)

Genes involved in biological pathways are often collocalised in gene clusters, the comparison of which can give valuable insights into their function and evolutionary history. However, comparison and visualization of gene cluster similarity is a tedious process, particularly when many clusters are being compared. Here, we present clinker, a Python based tool and clustermap.js, a companion JavaScript visualization library, which used together can automatically generate accurate, interactive, publication-quality gene cluster comparison figures directly from sequence files. Source code and documentation for clinker and clustermap.js is available on GitHub (github.com/gamcil/clinker and github.com/gamcil/clustermap.js, respectively) under the MIT license. clinker can be installed directly from the Python Package Index via pip. Supplementary data are available at Bioinformatics online.

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Author and article information

Contributors

Emma Marchionatti:

ORCID: https://orcid.org/0000-0002-9113-5829

Role: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: SoftwareRole: ValidationRole: VisualizationRole: Writing – original draft

Vincent Perreten:

ORCID: https://orcid.org/0000-0001-5722-9445

Role: ConceptualizationRole: Data curationRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SoftwareRole: SupervisionRole: ValidationRole: VisualizationRole: Writing – review and editing

Paul D. Fey: Role: Editor

Journal

Journal ID (nlm-ta): mSphere

Journal ID (iso-abbrev): mSphere

Journal ID (publisher-id): mSphere

Title: mSphere

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

ISSN (Electronic): 2379-5042

Publication date (Electronic, pub): 07 July 2023

Publication date (Electronic, collection): Jul-Aug 2023

Publication date PMC-release: 07 July 2023

Volume: 8

Issue: 4

Electronic Location Identifier: e00239-23

Affiliations

[1 ] Division of Molecular Bacterial Epidemiology and Infectious Diseases, Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern; , Bern, Switzerland

[2 ] Clinic for Ruminants, Department of Clinical Veterinary Science, Vetsuisse Faculty, University of Bern; , Bern, Switzerland

University of Nebraska Medical Center; , Omaha, Nebraska, USA

Author notes

Address correspondence to Vincent Perreten, vincent.perreten@ 123456unibe.ch

The authors declare no conflict of interest.

Author information

Emma Marchionatti https://orcid.org/0000-0002-9113-5829

Vincent Perreten https://orcid.org/0000-0001-5722-9445

Article

Publisher ID: 00239-23 Publisher ID: msphere.00239-23

DOI: 10.1128/msphere.00239-23

PMC ID: 10470526

PubMed ID: 37417762

SO-VID: 896c1488-ea36-44fa-a3a8-4d7300049943

License:

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

History

Date received : 02 May 2023

Date accepted : 30 May 2023

Page count

supplementary-material: 1, authors: 2, Figures: 2, Tables: 1, References: 19, Pages: 7, Words: 3037

Funding

Funded by: UB | Institute of Veterinary Bacteriology, University of Bern (IVB);

Award ID: REF-660-50

Award Recipient : Vincent Perreten

Funded by: Clinical Research Platform, Vetsuisse Faculty, University of Bern;

Award ID: REF-600-19

Award Recipient : Emma Marchionatti

Custom metadata

cover-date July/August 2023

Keywords: macrolides-lincosamides-streptogramin b,mechanisms of resistance,dna sequencing,gene expression

Data availability:

Keywords: macrolides-lincosamides-streptogramin b, mechanisms of resistance, dna sequencing, gene expression

Novel macrolide-lincosamide-streptogramin B resistance gene erm(56) in Trueperella pyogenes

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ABSTRACT

IMPORTANCE

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Most cited references 19

Assembly of long, error-prone reads using repeat graphs

PHASTER: a better, faster version of the PHAST phage search tool

clinker & clustermap.js: automatic generation of gene cluster comparison figures

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