2026-07-21T08:13:16Zhttps://repisalud.isciii.es/rest/oai/requestoai:repisalud.isciii.es:20.500.12105/160152024-09-27T23:48:37Zcom_20.500.12105_2052com_20.500.12105_2051col_20.500.12105_19609
Repisalud
author
Fuesslin, Valeria
author
Krautwurst, Sebastian
author
Srivastava, Akash
author
Winter, Doris
author
Liedigk, Britta
author
Thye, Thorsten
author
Herrera-León, Silvia
author
Wohl, Shirlee
author
May, Jürgen
author
Fobil, Julius N
author
Eibach, Daniel
author
Marz, Manja
author
Schuldt, Kathrin
funder
Carl Zeiss Foundation
funder
Deutsche Forschungsgemeinschaft (Alemania)
2023-05-08T13:12:39Z
2023-05-08T13:12:39Z
2022-06
Front Microbiol. 2022 Jun 22;13:909692.
10.3389/fmicb.2022.909692
1664-302X
1664-302X
Frontiers in microbiology
35814690
http://hdl.handle.net/20.500.12105/16015
During the last decades, antimicrobial resistance (AMR) has become a global public health concern. Nowadays multi-drug resistance is commonly observed in strains of Vibrio cholerae, the etiological agent of cholera. In order to limit the spread of pathogenic drug-resistant bacteria and to maintain treatment options the analysis of clinical samples and their AMR profiles are essential. Particularly, in low-resource settings a timely analysis of AMR profiles is often impaired due to lengthy culturing procedures for antibiotic susceptibility testing or lack of laboratory capacity. In this study, we explore the applicability of whole genome sequencing for the prediction of AMR profiles of V. cholerae. We developed the pipeline CholerAegon for the in silico prediction of AMR profiles of 82 V. cholerae genomes assembled from long and short sequencing reads. By correlating the predicted profiles with results from phenotypic antibiotic susceptibility testing we show that the prediction can replace in vitro susceptibility testing for five of seven antibiotics. Because of the relatively low costs, possibility for real-time data analyses, and portability, the Oxford Nanopore Technologies MinION sequencing platform-especially in light of an upcoming less error-prone technology for the platform-appears to be well suited for pathogen genomic analyses such as the one described here. Together with CholerAegon, it can leverage pathogen genomics to improve disease surveillance and to control further spread of antimicrobial resistance.
eng
Antimicrobial resistance
AMR
Vibrio cholerae
Nanopore
MinION
Illumina
Prediction of Antibiotic Susceptibility Profiles of Vibrio cholerae Isolates From Whole Genome Illumina and Nanopore Sequencing Data: CholerAegon
journal article
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
URL
https://repisalud.isciii.es/bitstreams/77c1b3a0-c7aa-471d-836e-1f75c5cf0f86/download
File
MD5
a38161e7cdf1a601e543cc9e1c3e4202
967027
application/pdf
PredictionAntibioticSusceptibilityProfiles_2022.pdf
URL
https://repisalud.isciii.es/bitstreams/00cd94a0-e37e-462f-afe5-e794380241b6/download
File
MD5
cc14e52801dcd90e8213733d52880e36
76527
application/pdf
Table1_PredictionAntibioticSusceptibilityProfiles_2022.pdf
URL
https://repisalud.isciii.es/bitstreams/7a2e3b57-8950-4346-84ca-b27ca5d4aa63/download
File
MD5
9158568b62cc8f945029236b8282a344
80573
application/pdf
Table2_PredictionAntibioticSusceptibilityProfiles_2022.pdf
URL
https://repisalud.isciii.es/bitstreams/b1408305-7a55-4c2f-b765-0bc3ba623d5e/download
File
MD5
39f380a7b3f500b1cf8155576b62aae1
54829
application/pdf
Table3_PredictionAntibioticSusceptibilityProfiles_2022.pdf
URL
https://repisalud.isciii.es/bitstreams/e92343d3-0187-4338-88ba-aaa3ba43a4fb/download
File
MD5
8ab64090d78149a90917876d5317430e
40404
application/pdf
Table4_PredictionAntibioticSusceptibilityProfiles_2022.pdf
URL
https://repisalud.isciii.es/bitstreams/1135cc19-9848-4230-bba4-14145148bba9/download
File
MD5
6596241c0214d1ed5450e42d6ef9a1cf
29785
application/pdf
Table5_PredictionAntibioticSusceptibilityProfiles_2022.pdf
URL
https://repisalud.isciii.es/bitstreams/01f00b13-b966-45cc-9001-74101ee97326/download
File
MD5
32ecf2061aa96dd323e8dcace89b59ef
125189
application/pdf
Image1_PredictionAntibioticSusceptibilityProfiles_2022.pdf
URL
https://repisalud.isciii.es/bitstreams/3d542eca-ee3e-424c-be9c-9e7fd8d28d70/download
File
MD5
359fc6160dc6760c9c46d881f923b800
154909
application/pdf
Image2_PredictionAntibioticSusceptibilityProfiles_2022.pdf
URL
https://repisalud.isciii.es/bitstreams/d58b03e8-ff49-40da-8d37-53d72b6a73d9/download
File
MD5
3bc72edafea11a24f404813628903c17
56898
text/plain
PredictionAntibioticSusceptibilityProfiles_2022.pdf.txt
URL
https://repisalud.isciii.es/bitstreams/716912bb-8a97-436c-8cc1-92ce7427114d/download
File
MD5
537d34c199e6387c1d1b73434b561c2a
15979
text/plain
Table1_PredictionAntibioticSusceptibilityProfiles_2022.pdf.txt
URL
https://repisalud.isciii.es/bitstreams/b2f41c60-faa6-4951-aa9a-842293bdcebb/download
File
MD5
47204fda2dcd7ea0bf7513f102f44bd0
23835
text/plain
Table2_PredictionAntibioticSusceptibilityProfiles_2022.pdf.txt
URL
https://repisalud.isciii.es/bitstreams/01c9dc69-f377-4ed3-9819-07b3e94ac237/download
File
MD5
6c5acb7f609c052f08c2ed805a1ca477
9800
text/plain
Table3_PredictionAntibioticSusceptibilityProfiles_2022.pdf.txt
URL
https://repisalud.isciii.es/bitstreams/79cb249d-8d64-4aa6-a03e-948bbb199f43/download
File
MD5
e923660d6b594ada13be06d859216eff
5650
text/plain
Table4_PredictionAntibioticSusceptibilityProfiles_2022.pdf.txt
URL
https://repisalud.isciii.es/bitstreams/f2b00eb8-9606-4610-bd0b-c6d77ce606b3/download
File
MD5
9df85634950cee24e16f7503d776ed09
1338
text/plain
Table5_PredictionAntibioticSusceptibilityProfiles_2022.pdf.txt
URL
https://repisalud.isciii.es/bitstreams/e801f67a-97c8-44b7-ac4a-2ec3a842ca49/download
File
MD5
be7b16d7d827a22d17354364bcde77ba
565
text/plain
Image1_PredictionAntibioticSusceptibilityProfiles_2022.pdf.txt
URL
https://repisalud.isciii.es/bitstreams/c143569d-0422-4bc6-9d19-2a9a68f364ac/download
File
MD5
7b23aaab71e2e48e806b1bb184e35962
1034
text/plain
Image2_PredictionAntibioticSusceptibilityProfiles_2022.pdf.txt