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Sidorczuk, Katarzyna, Burdukiewicz, Michał, Cerk, Klara, Fritscher, Joachim, Kingsley, Robert A. 
ORCID: https://orcid.org/0000-0002-0194-6485, Schierack, Peter, Hildebrand, Falk and Kolenda, Rafał
(2024)
adhesiomeR: A tool for Escherichia coli adhesin classification and analysis.
BMC Genomics, 25.
ISSN 1471-2164
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Abstract
Adhesins are crucial factors in the virulence of bacterial pathogens such as Escherichia coli. However, to date no resources have been dedicated to the detailed analysis of E. coli adhesins. Here, we provide adhesiomeR software that enables characterization of the complete adhesin repertoire, termed the adhesiome. AdhesiomeR incorporates the most comprehensive database of E. coli adhesins and facilitates an extensive analysis of adhesiome. We demonstrate that adhesiomeR achieves 98% accuracy when compared with experimental analyses. Based on analysis of 15,000 E. coli genomes, we define novel adhesiome profiles and clusters, providing a nomenclature for a unified comparison of E. coli adhesiomes.
| Item Type: | Article |
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| Additional Information: | Availability of data and materials: E. coli genomes used in the study, including APEC and human-isolated ETEC, are available from NCBI Assembly (https://www.ncbi.nlm.nih.gov/assembly) database using accession numbers listed in Additional File 7. E. coli genomes used to create pangenomes are available from ECOR [32]. Metagenomic dataset was obtained from Hildebrand et al. [35]. All code used for data analysis is available at https://github.com/ksidorczuk/adhesiomeR-paper. AdhesiomeR is available as a web server at https://adhesiomer.quadram.ac.uk/ and as an R package from GitHub https://github.com/ksidorczuk/adhesiomeR. Funding Information: The authors gratefully acknowledge the support of the Biotechnology and Biological Sciences Research Council (BBSRC), part of UK Research and Innovation, Core Capability Grant BB/CCG2220/1 at the Earlham Institute this research was funded by the BBSRC Institute Strategic Programme Food Microbiome and Health BB/X011054/1 and its constituent project BBS/E/F/000PR13631 and Microbes and Food Safety BB/X011011/1 and its constituent projects BBS/E/F/000PR13634 and BBS/E/F/000PR13636, and BBSRC Core Capability Grant BB/CCG2260/1 at the Quadram Institute. This research was also supported by Earlham Institute ISP Decoding Biodiversity BBX011089/1, projects BBS/E/ER/230002A and BBS/E/ER/230002B, and Cellular Genomics BBX011070/1, project BBS/E/ER/230001A. FH and KS were supported by European Research Council H2020 StG (erc-stg-948219, EPYC). JF was supported by the UKRI Biotechnology and Biological Sciences Research Council Norwich Research Park Biosciences Doctoral Training Partnership, BB/T008717/1. RAK and RK were supported by BBSRC grant BB/W003155/1. |
| Uncontrolled Keywords: | adhesins,adhesiome,adhesion,escherichia coli,fimbriae,pathotype,virulence factor,biotechnology,genetics ,/dk/atira/pure/subjectarea/asjc/1300/1305 |
| Faculty \ School: | Faculty of Medicine and Health Sciences > Norwich Medical School Faculty of Science > School of Biological Sciences |
| Related URLs: | |
| Depositing User: | LivePure Connector |
| Date Deposited: | 23 Oct 2024 09:30 |
| Last Modified: | 01 Nov 2024 13:30 |
| URI: | https://ueaeprints.uea.ac.uk/id/eprint/97122 |
| DOI: | 10.1186/s12864-024-10525-6 |
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