Backward compatibility of whole genome sequencing data with MLVA typing using a new MLVAtype shiny application for Vibrio cholerae


Autoři: Jérôme Ambroise aff001;  Léonid M. Irenge aff001;  Jean-François Durant aff001;  Bertrand Bearzatto aff001;  Godfrey Bwire aff002;  O. Colin Stine aff003;  Jean-Luc Gala aff001
Působiště autorů: Center for Applied Molecular Technologies, Institute of Clinical and Experimental Research, Université catholique de Louvain, Brussels, Belgium aff001;  Ministry of Health Uganda, Department of Community Health, Kampala, Uganda aff002;  University of Maryland School of Medicine, Department of Epidemiology and Public Health, Baltimore, Maryland, United States of America aff003
Vyšlo v časopise: PLoS ONE 14(12)
Kategorie: Research Article
doi: 10.1371/journal.pone.0225848

Souhrn

Background

Multiple-Locus Variable Number of Tandem Repeats (VNTR) Analysis (MLVA) is widely used by laboratory-based surveillance networks for subtyping pathogens causing foodborne and water-borne disease outbreaks. However, Whole Genome Sequencing (WGS) has recently emerged as the new more powerful reference for pathogen subtyping, making a data conversion method necessary which enables the users to compare the MLVA identified by either method. The MLVAType shiny application was designed to extract MLVA profiles of Vibrio cholerae isolates from WGS data while ensuring backward compatibility with traditional MLVA typing methods.

Methods

To test and validate the MLVAType algorithm, WGS-derived MLVA profiles of nineteen Vibrio cholerae isolates from Democratic Republic of the Congo (n = 9) and Uganda (n = 10) were compared to MLVA profiles generated by an in silico PCR approach and Sanger sequencing, the latter being used as the reference method.

Results

Results obtained by Sanger sequencing and MLVAType were totally concordant. However, the latter were affected by censored estimations whose percentage was inversely proportional to the k-mer parameter used during genome assembly. With a k-mer of 127, less than 15% estimation of V. cholerae VNTR was censored. Preventing censored estimation was only achievable when using a longer k-mer size (i.e. 175), which is not proposed in the SPAdes v.3.13.0 software.

Conclusion

As NGS read lengths and qualities tend to increase with time, one may expect the increase of k-mer size in a near future. Using MLVAType application with a longer k-mer size will then efficiently retrieve MLVA profiles from WGS data while avoiding censored estimation.

Klíčová slova:

Dideoxy DNA sequencing – Genomic libraries – Polymerase chain reaction – Sequence assembly tools – Sequence motif analysis – Tandem repeats – Uganda – Vibrio cholerae


Zdroje

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Článek vyšel v časopise

PLOS One


2019 Číslo 12