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J Clin Microbiol. 2017 Mar;55(3):908-913. doi: 10.1128/JCM.02242-16. Epub 2017 Jan 4.

High Interlaboratory Reproducibility and Accuracy of Next-Generation-Sequencing-Based Bacterial Genotyping in a Ring Trial.

Author information

1
Institute of Hygiene, University Hospital Münster, Münster, Germany mellmann@uni-muenster.de.
2
Department of Microbiology and Infection Control, Statens Serum Institut (SSI), Copenhagen, Denmark.
3
Institute of Hygiene, University Hospital Münster, Münster, Germany.
4
Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
5
Molecular and Experimental Mycobacteriology, Forschungszentrum Borstel, Leibniz-Zentrum für Medizin und Biowissenschaften, Borstel, Germany.
6
German Center for Infection Research (DZIF), Borstel, Germany.
7
Department of Periodontology and Restorative Dentistry, University Hospital Münster, Münster, Germany.

Abstract

Today, next-generation whole-genome sequencing (WGS) is increasingly used to determine the genetic relationships of bacteria on a nearly whole-genome level for infection control purposes and molecular surveillance. Here, we conducted a multicenter ring trial comprising five laboratories to determine the reproducibility and accuracy of WGS-based typing. The participating laboratories sequenced 20 blind-coded Staphylococcus aureus DNA samples using 250-bp paired-end chemistry for library preparation in a single sequencing run on an Illumina MiSeq sequencer. The run acceptance criteria were sequencing outputs >5.6 Gb and Q30 read quality scores of >75%. Subsequently, spa typing, multilocus sequence typing (MLST), ribosomal MLST, and core genome MLST (cgMLST) were performed by the participants. Moreover, discrepancies in cgMLST target sequences in comparisons with the included and also published sequence of the quality control strain ATCC 25923 were resolved using Sanger sequencing. All five laboratories fulfilled the run acceptance criteria in a single sequencing run without any repetition. Of the 400 total possible typing results, 394 of the reported spa types, sequence types (STs), ribosomal STs (rSTs), and cgMLST cluster types were correct and identical among all laboratories; only six typing results were missing. An analysis of cgMLST allelic profiles corroborated this high reproducibility; only 3 of 183,927 (0.0016%) cgMLST allele calls were wrong. Sanger sequencing confirmed all 12 discrepancies of the ring trial results in comparison with the published sequence of ATCC 25923. In summary, this ring trial demonstrated the high reproducibility and accuracy of current next-generation sequencing-based bacterial typing for molecular surveillance when done with nearly completely locked-down methods.

KEYWORDS:

cgMLST; interlaboratory reproducibility; molecular subtyping; ring trial; whole-genome sequencing

PMID:
28053217
PMCID:
PMC5328459
DOI:
10.1128/JCM.02242-16
[Indexed for MEDLINE]
Free PMC Article

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