Cargando…
Detection of extended-spectrum beta-lactamase (ESBL) genes and plasmid replicons in Enterobacteriaceae using PlasmidSPAdes assembly of short-read sequence data
Knowledge of the epidemiology of plasmids is essential for understanding the evolution and spread of antimicrobial resistance. PlasmidSPAdes attempts to reconstruct plasmids using short-read sequence data. Accurate detection of extended-spectrum beta-lactamase (ESBL) genes and plasmid replicon genes...
Autores principales: | , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Microbiology Society
2020
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7478632/ https://www.ncbi.nlm.nih.gov/pubmed/32589571 http://dx.doi.org/10.1099/mgen.0.000400 |
_version_ | 1783580095692144640 |
---|---|
author | Stohr, Joep J.J.M. Kluytmans-van den Bergh, Marjolein F.Q. Wedema, Ronald Friedrich, Alexander W. Kluytmans, Jan A.J.W. Rossen, John W.A. |
author_facet | Stohr, Joep J.J.M. Kluytmans-van den Bergh, Marjolein F.Q. Wedema, Ronald Friedrich, Alexander W. Kluytmans, Jan A.J.W. Rossen, John W.A. |
author_sort | Stohr, Joep J.J.M. |
collection | PubMed |
description | Knowledge of the epidemiology of plasmids is essential for understanding the evolution and spread of antimicrobial resistance. PlasmidSPAdes attempts to reconstruct plasmids using short-read sequence data. Accurate detection of extended-spectrum beta-lactamase (ESBL) genes and plasmid replicon genes is a prerequisite for the use of plasmid assembly tools to investigate the role of plasmids in the spread and evolution of ESBL production in Enterobacteriaceae . This study evaluated the performance of PlasmidSPAdes plasmid assembly for Enterobacteriaceae in terms of detection of ESBL-encoding genes, plasmid replicons and chromosomal wgMLST genes, and assessed the effect of k-mer size. Short-read sequence data for 59 ESBL-producing Enterobacteriaceae were assembled with PlasmidSPAdes using different k-mer sizes (21, 33, 55, 77, 99 and 127). For every k-mer size, the presence of ESBL genes, plasmid replicons and a selection of chromosomal wgMLST genes in the plasmid assembly was determined. Out of 241 plasmid replicons and 66 ESBL genes detected by whole-genome assembly, 213 plasmid replicons [88 %; 95 % confidence interval (CI): 83.9–91.9] and 43 ESBL genes (65 %; 95 % CI: 53.1–75.6) were detected in the plasmid assemblies obtained by PlasmidSPAdes. For most ESBL genes (83.3 %) and plasmid replicons (72.0 %), detection results did not differ between the k-mer sizes used in the plasmid assembly. No optimal k-mer size could be defined for the number of ESBL genes and plasmid replicons detected. For most isolates, the number of chromosomal wgMLST genes detected in the plasmid assemblies decreased with increasing k-mer size. Based on our findings, PlasmidSPAdes is not a suitable plasmid assembly tool for short-read sequence data for ESBL-encoding plasmids of Enterobacteriaceae . |
format | Online Article Text |
id | pubmed-7478632 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Microbiology Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-74786322020-09-09 Detection of extended-spectrum beta-lactamase (ESBL) genes and plasmid replicons in Enterobacteriaceae using PlasmidSPAdes assembly of short-read sequence data Stohr, Joep J.J.M. Kluytmans-van den Bergh, Marjolein F.Q. Wedema, Ronald Friedrich, Alexander W. Kluytmans, Jan A.J.W. Rossen, John W.A. Microb Genom Research Article Knowledge of the epidemiology of plasmids is essential for understanding the evolution and spread of antimicrobial resistance. PlasmidSPAdes attempts to reconstruct plasmids using short-read sequence data. Accurate detection of extended-spectrum beta-lactamase (ESBL) genes and plasmid replicon genes is a prerequisite for the use of plasmid assembly tools to investigate the role of plasmids in the spread and evolution of ESBL production in Enterobacteriaceae . This study evaluated the performance of PlasmidSPAdes plasmid assembly for Enterobacteriaceae in terms of detection of ESBL-encoding genes, plasmid replicons and chromosomal wgMLST genes, and assessed the effect of k-mer size. Short-read sequence data for 59 ESBL-producing Enterobacteriaceae were assembled with PlasmidSPAdes using different k-mer sizes (21, 33, 55, 77, 99 and 127). For every k-mer size, the presence of ESBL genes, plasmid replicons and a selection of chromosomal wgMLST genes in the plasmid assembly was determined. Out of 241 plasmid replicons and 66 ESBL genes detected by whole-genome assembly, 213 plasmid replicons [88 %; 95 % confidence interval (CI): 83.9–91.9] and 43 ESBL genes (65 %; 95 % CI: 53.1–75.6) were detected in the plasmid assemblies obtained by PlasmidSPAdes. For most ESBL genes (83.3 %) and plasmid replicons (72.0 %), detection results did not differ between the k-mer sizes used in the plasmid assembly. No optimal k-mer size could be defined for the number of ESBL genes and plasmid replicons detected. For most isolates, the number of chromosomal wgMLST genes detected in the plasmid assemblies decreased with increasing k-mer size. Based on our findings, PlasmidSPAdes is not a suitable plasmid assembly tool for short-read sequence data for ESBL-encoding plasmids of Enterobacteriaceae . Microbiology Society 2020-06-26 /pmc/articles/PMC7478632/ /pubmed/32589571 http://dx.doi.org/10.1099/mgen.0.000400 Text en © 2020 The Authors http://creativecommons.org/licenses/by-nc/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution NonCommercial License. |
spellingShingle | Research Article Stohr, Joep J.J.M. Kluytmans-van den Bergh, Marjolein F.Q. Wedema, Ronald Friedrich, Alexander W. Kluytmans, Jan A.J.W. Rossen, John W.A. Detection of extended-spectrum beta-lactamase (ESBL) genes and plasmid replicons in Enterobacteriaceae using PlasmidSPAdes assembly of short-read sequence data |
title | Detection of extended-spectrum beta-lactamase (ESBL) genes and plasmid replicons in Enterobacteriaceae using PlasmidSPAdes assembly of short-read sequence data |
title_full | Detection of extended-spectrum beta-lactamase (ESBL) genes and plasmid replicons in Enterobacteriaceae using PlasmidSPAdes assembly of short-read sequence data |
title_fullStr | Detection of extended-spectrum beta-lactamase (ESBL) genes and plasmid replicons in Enterobacteriaceae using PlasmidSPAdes assembly of short-read sequence data |
title_full_unstemmed | Detection of extended-spectrum beta-lactamase (ESBL) genes and plasmid replicons in Enterobacteriaceae using PlasmidSPAdes assembly of short-read sequence data |
title_short | Detection of extended-spectrum beta-lactamase (ESBL) genes and plasmid replicons in Enterobacteriaceae using PlasmidSPAdes assembly of short-read sequence data |
title_sort | detection of extended-spectrum beta-lactamase (esbl) genes and plasmid replicons in enterobacteriaceae using plasmidspades assembly of short-read sequence data |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7478632/ https://www.ncbi.nlm.nih.gov/pubmed/32589571 http://dx.doi.org/10.1099/mgen.0.000400 |
work_keys_str_mv | AT stohrjoepjjm detectionofextendedspectrumbetalactamaseesblgenesandplasmidrepliconsinenterobacteriaceaeusingplasmidspadesassemblyofshortreadsequencedata AT kluytmansvandenberghmarjoleinfq detectionofextendedspectrumbetalactamaseesblgenesandplasmidrepliconsinenterobacteriaceaeusingplasmidspadesassemblyofshortreadsequencedata AT wedemaronald detectionofextendedspectrumbetalactamaseesblgenesandplasmidrepliconsinenterobacteriaceaeusingplasmidspadesassemblyofshortreadsequencedata AT friedrichalexanderw detectionofextendedspectrumbetalactamaseesblgenesandplasmidrepliconsinenterobacteriaceaeusingplasmidspadesassemblyofshortreadsequencedata AT kluytmansjanajw detectionofextendedspectrumbetalactamaseesblgenesandplasmidrepliconsinenterobacteriaceaeusingplasmidspadesassemblyofshortreadsequencedata AT rossenjohnwa detectionofextendedspectrumbetalactamaseesblgenesandplasmidrepliconsinenterobacteriaceaeusingplasmidspadesassemblyofshortreadsequencedata |