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Limitations in predicting reduced susceptibility to third generation cephalosporins in Escherichia coli based on whole genome sequence data
Prediction of antibiotic resistance from whole genome sequence (WGS) data has been proposed. However, the performance of WGS data analysis for this matter may be influenced by the resistance mechanism’s biology. This study compared traditional antimicrobial susceptibility testing with whole genome s...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10688838/ https://www.ncbi.nlm.nih.gov/pubmed/38033151 http://dx.doi.org/10.1371/journal.pone.0295233 |
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author | Heydecke, Anna Yin, Hong Tano, Eva Sütterlin, Susanne |
author_facet | Heydecke, Anna Yin, Hong Tano, Eva Sütterlin, Susanne |
author_sort | Heydecke, Anna |
collection | PubMed |
description | Prediction of antibiotic resistance from whole genome sequence (WGS) data has been proposed. However, the performance of WGS data analysis for this matter may be influenced by the resistance mechanism’s biology. This study compared traditional antimicrobial susceptibility testing with whole genome sequencing for identification of extended-spectrum beta-lactamases (ESBL) in a collection of 419 Escherichia coli isolates. BLASTn-based prediction and read mapping with srst2 gave matching results, and in 381/419 (91%) isolates WGS was congruent with phenotypic testing. Incongruent results were grouped by potential explanations into biological-related and sequence analysis-related results. Biological-related explanations included weak ESBL-enzyme activity (n = 4), inconclusive phenotypic ESBL-testing (n = 4), potential loss of plasmid during subculturing (n = 7), and other resistance mechanisms than ESBL-enzymes (n = 2). Sequence analysis-related explanations were cut-off dependency for read depth (n = 5), too stringent (n = 3) and too loose cut-off for nucleotide identity and coverage (n = 13), respectively. The results reveal limitations of both traditional antibiotic susceptibility testing and sequence-based resistance prediction and highlight the need for evidence-based standards in sequence analysis. |
format | Online Article Text |
id | pubmed-10688838 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-106888382023-12-01 Limitations in predicting reduced susceptibility to third generation cephalosporins in Escherichia coli based on whole genome sequence data Heydecke, Anna Yin, Hong Tano, Eva Sütterlin, Susanne PLoS One Research Article Prediction of antibiotic resistance from whole genome sequence (WGS) data has been proposed. However, the performance of WGS data analysis for this matter may be influenced by the resistance mechanism’s biology. This study compared traditional antimicrobial susceptibility testing with whole genome sequencing for identification of extended-spectrum beta-lactamases (ESBL) in a collection of 419 Escherichia coli isolates. BLASTn-based prediction and read mapping with srst2 gave matching results, and in 381/419 (91%) isolates WGS was congruent with phenotypic testing. Incongruent results were grouped by potential explanations into biological-related and sequence analysis-related results. Biological-related explanations included weak ESBL-enzyme activity (n = 4), inconclusive phenotypic ESBL-testing (n = 4), potential loss of plasmid during subculturing (n = 7), and other resistance mechanisms than ESBL-enzymes (n = 2). Sequence analysis-related explanations were cut-off dependency for read depth (n = 5), too stringent (n = 3) and too loose cut-off for nucleotide identity and coverage (n = 13), respectively. The results reveal limitations of both traditional antibiotic susceptibility testing and sequence-based resistance prediction and highlight the need for evidence-based standards in sequence analysis. Public Library of Science 2023-11-30 /pmc/articles/PMC10688838/ /pubmed/38033151 http://dx.doi.org/10.1371/journal.pone.0295233 Text en © 2023 Heydecke et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Heydecke, Anna Yin, Hong Tano, Eva Sütterlin, Susanne Limitations in predicting reduced susceptibility to third generation cephalosporins in Escherichia coli based on whole genome sequence data |
title | Limitations in predicting reduced susceptibility to third generation cephalosporins in Escherichia coli based on whole genome sequence data |
title_full | Limitations in predicting reduced susceptibility to third generation cephalosporins in Escherichia coli based on whole genome sequence data |
title_fullStr | Limitations in predicting reduced susceptibility to third generation cephalosporins in Escherichia coli based on whole genome sequence data |
title_full_unstemmed | Limitations in predicting reduced susceptibility to third generation cephalosporins in Escherichia coli based on whole genome sequence data |
title_short | Limitations in predicting reduced susceptibility to third generation cephalosporins in Escherichia coli based on whole genome sequence data |
title_sort | limitations in predicting reduced susceptibility to third generation cephalosporins in escherichia coli based on whole genome sequence data |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10688838/ https://www.ncbi.nlm.nih.gov/pubmed/38033151 http://dx.doi.org/10.1371/journal.pone.0295233 |
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