Rapid detection and capture of clinical Escherichia coli strains mediated by OmpA-targeting nanobodies
Abstract Escherichia coli is a major cause of blood stream and urinary tract infections. Owing to the spread of antimicrobial resistance, it is often treated with an inadequate antibiotic. With the aim to accelerate the diagnostics of this key pathogen, we used the flycode technology to generate nan...
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Nature Portfolio
2025-07-01
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| Series: | Communications Biology |
| Online Access: | https://doi.org/10.1038/s42003-025-08345-9 |
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| author | Michèle Sorgenfrei Lea M. Hürlimann Andrea Printz Fanny Wegner Damien Morger Fabian Ackle Mélissa M. Remy Grzegorz Montowski Hans-Anton Keserue Aline Cuénod Frank Imkamp Adrian Egli Peter M. Keller Markus A. Seeger |
| author_facet | Michèle Sorgenfrei Lea M. Hürlimann Andrea Printz Fanny Wegner Damien Morger Fabian Ackle Mélissa M. Remy Grzegorz Montowski Hans-Anton Keserue Aline Cuénod Frank Imkamp Adrian Egli Peter M. Keller Markus A. Seeger |
| author_sort | Michèle Sorgenfrei |
| collection | DOAJ |
| description | Abstract Escherichia coli is a major cause of blood stream and urinary tract infections. Owing to the spread of antimicrobial resistance, it is often treated with an inadequate antibiotic. With the aim to accelerate the diagnostics of this key pathogen, we used the flycode technology to generate nanobodies against the conserved and highly abundant outer membrane protein OmpA. Two nanobodies each recognizing a different isoform of OmpA were shown by flow cytometry to recognize > 91% of 85,680 E. coli OmpA sequences deposited in a large bacterial genome database. Crystal structures of these nanobodies in complex with the respective OmpA isoform revealed interactions with all four surface accessible loops of OmpA. Steric hindrance caused by dense O-antigen layers initially impeded reliable capture of clinical E. coli strains. By generating nanobody constructs with long linkers and by thinning the O-antigen layer through alterations to growth medium and buffers, we achieved to capture < 50 CFU/mL. Our work provides a framework to generate nanobodies for the specific and sensitive detection and capture of clinically relevant pathogenic bacteria. |
| format | Article |
| id | doaj-art-bd8f232528af43a488388001f5cc58c3 |
| institution | Kabale University |
| issn | 2399-3642 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Communications Biology |
| spelling | doaj-art-bd8f232528af43a488388001f5cc58c32025-08-20T04:03:06ZengNature PortfolioCommunications Biology2399-36422025-07-018111710.1038/s42003-025-08345-9Rapid detection and capture of clinical Escherichia coli strains mediated by OmpA-targeting nanobodiesMichèle Sorgenfrei0Lea M. Hürlimann1Andrea Printz2Fanny Wegner3Damien Morger4Fabian Ackle5Mélissa M. Remy6Grzegorz Montowski7Hans-Anton Keserue8Aline Cuénod9Frank Imkamp10Adrian Egli11Peter M. Keller12Markus A. Seeger13Institute of Medical Microbiology, University of ZurichInstitute of Medical Microbiology, University of ZurichInstitute of Medical Microbiology, University of ZurichInstitute of Medical Microbiology, University of Zurichrqmicro AGInstitute of Medical Microbiology, University of ZurichInstitute for Infectious Diseases, University of Bernrqmicro AGrqmicro AGInstitute of Medical Microbiology, University of ZurichInstitute of Medical Microbiology, University of ZurichInstitute of Medical Microbiology, University of ZurichInstitute for Infectious Diseases, University of BernInstitute of Medical Microbiology, University of ZurichAbstract Escherichia coli is a major cause of blood stream and urinary tract infections. Owing to the spread of antimicrobial resistance, it is often treated with an inadequate antibiotic. With the aim to accelerate the diagnostics of this key pathogen, we used the flycode technology to generate nanobodies against the conserved and highly abundant outer membrane protein OmpA. Two nanobodies each recognizing a different isoform of OmpA were shown by flow cytometry to recognize > 91% of 85,680 E. coli OmpA sequences deposited in a large bacterial genome database. Crystal structures of these nanobodies in complex with the respective OmpA isoform revealed interactions with all four surface accessible loops of OmpA. Steric hindrance caused by dense O-antigen layers initially impeded reliable capture of clinical E. coli strains. By generating nanobody constructs with long linkers and by thinning the O-antigen layer through alterations to growth medium and buffers, we achieved to capture < 50 CFU/mL. Our work provides a framework to generate nanobodies for the specific and sensitive detection and capture of clinically relevant pathogenic bacteria.https://doi.org/10.1038/s42003-025-08345-9 |
| spellingShingle | Michèle Sorgenfrei Lea M. Hürlimann Andrea Printz Fanny Wegner Damien Morger Fabian Ackle Mélissa M. Remy Grzegorz Montowski Hans-Anton Keserue Aline Cuénod Frank Imkamp Adrian Egli Peter M. Keller Markus A. Seeger Rapid detection and capture of clinical Escherichia coli strains mediated by OmpA-targeting nanobodies Communications Biology |
| title | Rapid detection and capture of clinical Escherichia coli strains mediated by OmpA-targeting nanobodies |
| title_full | Rapid detection and capture of clinical Escherichia coli strains mediated by OmpA-targeting nanobodies |
| title_fullStr | Rapid detection and capture of clinical Escherichia coli strains mediated by OmpA-targeting nanobodies |
| title_full_unstemmed | Rapid detection and capture of clinical Escherichia coli strains mediated by OmpA-targeting nanobodies |
| title_short | Rapid detection and capture of clinical Escherichia coli strains mediated by OmpA-targeting nanobodies |
| title_sort | rapid detection and capture of clinical escherichia coli strains mediated by ompa targeting nanobodies |
| url | https://doi.org/10.1038/s42003-025-08345-9 |
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