Harmonization of whole-genome sequencing for outbreak surveillance of Enterobacteriaceae and Enterococci

• Published in: Microbial genomics 2021-07, Vol.7 (7)
• Main Authors: Jamin, Casper, De Koster, Sien, van Koeveringe, Stefanie, De Coninck, Dieter, Mensaert, Klaas, De Bruyne, Katrien, Perales Selva, Natascha, Lammens, Christine, Goossens, Herman, Hoebe, Christian, Savelkoul, Paul, van Alphen, Lieke
• Format: Article
• Language: English
• Subjects: Bacterial Proteins - genetics; beta-Lactamases - genetics; Disease Outbreaks; Drug Resistance, Multiple, Bacterial - genetics; Enterobacteriaceae - classification; Enterobacteriaceae - genetics; Enterobacteriaceae - isolation & purification; Enterococcus - classification; Enterococcus - drug effects; Enterococcus - genetics; Escherichia coli - classification; Escherichia coli - drug effects; Escherichia coli - genetics; Genome, Bacterial - genetics; Humans; Klebsiella pneumoniae - classification; Klebsiella pneumoniae - drug effects; Klebsiella pneumoniae - genetics; Multilocus Sequence Typing; Phylogeny; Polymorphism, Single Nucleotide - genetics; Whole Genome Sequencing - methods
• ISSN: 2057-5858; 2057-5858
• DOI: 10.1099/mgen.0.000567

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 family and 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 and and whole-genome multi-locus sequencing typing (wgMLST) for all species. Additionally, a split -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 and 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 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.