Harmonization of whole- genome sequencing for outbreak surveillance of Enterobacteriaceae and Enterococci
| Autor: | Paul H. M. Savelkoul, Lieke B. van Alphen, Klaas Mensaert, Dieter De Coninck, Herman Goossens, Christian J. P. A. Hoebe, Natascha Perales Selva, Christine Lammens, Sien De Koster, Casper Jamin, Stefanie van Koeveringe, Katrien De Bruyne |
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| Přispěvatelé: | Medische Microbiologie, MUMC+: DA MMI Toegelatenen (9), RS: CAPHRI - R4 - Health Inequities and Societal Participation, MUMC+: DA Medische Microbiologie en Infectieziekten (5), I-4-1-Hlth Study Group |
| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
Klebsiella pneumoniae
ring-trial nosocomial pathogens Correspondence Locus (genetics) Single-nucleotide polymorphism Pathogens and Epidemiology Polymorphism Single Nucleotide Genome beta-Lactamases Disease Outbreaks 03 medical and health sciences Antibiotic resistance Bacterial Proteins Enterobacteriaceae Drug Resistance Multiple Bacterial nl bacterial typing Escherichia coli Casper casper Humans PHYLOGENETIC ANALYSIS Typing antimicrobial resistance Genotyping Biology Research Articles Phylogeny 030304 developmental biology Whole genome sequencing Genetics 0303 health sciences whole genome sequencing biology jamin@mumc 030306 microbiology harmonisation Outbreak General Medicine bacterial typing biology.organism_classification ALIGNMENT Enterococcus Human medicine Genome Bacterial Multilocus Sequence Typing |
| Zdroj: | Microbial Genomics, 7(7):000567. Microbiology Society Microbial Genomics |
| ISSN: | 2057-5858 |
| Popis: | Whole-genome sequencing (WGS) is becoming the de facto standard for bacterial typing and outbreak surveillance of resistant bacterial pathogens. However, interoperability for WGS of bacterial outbreaks is poorly understood. We hypothesized that harmonization of WGS for outbreak surveillance is achievable through the use of identical protocols for both data generation and data analysis. A set of 30 bacterial isolates, comprising of various species belonging to the Enterobacteriaceae family and Enterococcus genera, were selected and sequenced using the same protocol on the Illumina MiSeq platform in each individual centre. All generated sequencing data were analysed by one centre using BioNumerics (6.7.3) for (i) genotyping origin of replications and antimicrobial resistance genes, (ii) core-genome multi-locus sequence typing (cgMLST) for Escherichia coli and Klebsiella pneumoniae and whole-genome multi-locus sequencing typing (wgMLST) for all species. Additionally, a split k-mer analysis was performed to determine the number of SNPs between samples. A precision of 99.0% and an accuracy of 99.2% was achieved for genotyping. Based on cgMLST, a discrepant allele was called only in 2/27 and 3/15 comparisons between two genomes, for E. coli and K. pneumoniae, respectively. Based on wgMLST, the number of discrepant alleles ranged from 0 to 7 (average 1.6). For SNPs, this ranged from 0 to 11 SNPs (average 3.4). Furthermore, we demonstrate that using different de novo assemblers to analyse the same dataset introduces up to 150 SNPs, which surpasses most thresholds for bacterial outbreaks. This shows the importance of harmonization of data-processing surveillance of bacterial outbreaks. In summary, multi-centre WGS for bacterial surveillance is achievable, but only if protocols are harmonized. |
| Databáze: | OpenAIRE |
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