Core genome MLST and resistome analysis of Klebsiella pneumoniae using a clinically amenable workflow.
Anti-Bacterial Agents
/ pharmacology
Bacterial Typing Techniques
Electrophoresis, Gel, Pulsed-Field
Genome, Bacterial
Genotype
Humans
Klebsiella Infections
/ diagnosis
Klebsiella pneumoniae
/ classification
Microbial Sensitivity Tests
Multilocus Sequence Typing
Phenotype
Whole Genome Sequencing
Workflow
beta-Lactamases
Core genome multilocus sequence typing
Klebsiella pneumoniae
Pulse field gel electrophoresis
Whole genome sequencing
Journal
Diagnostic microbiology and infectious disease
ISSN: 1879-0070
Titre abrégé: Diagn Microbiol Infect Dis
Pays: United States
ID NLM: 8305899
Informations de publication
Date de publication:
May 2020
May 2020
Historique:
received:
07
11
2019
revised:
13
01
2020
accepted:
16
01
2020
pubmed:
27
2
2020
medline:
11
11
2020
entrez:
27
2
2020
Statut:
ppublish
Résumé
Whole genome sequencing (WGS) is replacing traditional microbiological typing methods for investigation of outbreaks in clinical settings. Here, we used a clinical microbiology laboratory core genome multilocus sequence typing (cgMLST) workflow to analyze 40 isolates of K. pneumoniae which are part of the Antimicrobial Resistance Leadership Group (ARLG) isolate collection, alongside 10 Mayo Clinic K. pneumoniae isolates, comparing results to those of pulsed-field gel electrophoresis (PFGE). Additionally, we used the WGS data to predict phenotypic antimicrobial susceptibility (AST). Thirty-one of 40 ARLG K. pneumoniae isolates belonged to the same PFGE type, all of which, alongside 3 isolates of different PFGE types, formed a large cluster by cgMLST. PFGE and cgMLST were completely concordant for the 10 Mayo Clinic K. pneumoniae isolates. For AST prediction, the overall agreement between phenotypic AST and genotypic prediction was 95.6%.
Identifiants
pubmed: 32098688
pii: S0732-8893(19)31118-6
doi: 10.1016/j.diagmicrobio.2020.114996
pmc: PMC7422488
mid: NIHMS1569834
pii:
doi:
Substances chimiques
Anti-Bacterial Agents
0
beta-Lactamases
EC 3.5.2.6
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
114996Subventions
Organisme : NIAID NIH HHS
ID : R01 AI100560
Pays : United States
Organisme : NIAID NIH HHS
ID : UM1 AI104681
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI072219
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI063517
Pays : United States
Organisme : BLRD VA
ID : I01 BX001974
Pays : United States
Informations de copyright
Copyright © 2020 Elsevier Inc. All rights reserved.
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