Multilevel genome typing: genomics-guided scalable resolution typing of microbial pathogens

BackgroundBoth long- and short-term epidemiology are fundamental to disease control and require accurate bacterial typing. Genomic data resulting from implementation of whole genome sequencing in many public health laboratories can potentially provide highly sensitive and accurate descriptions of st...

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Bibliographic Details
Published in:Euro surveillance : bulletin européen sur les maladies transmissibles 2020-05, Vol.25 (20), p.1
Main Authors: Payne, Michael, Kaur, Sandeep, Wang, Qinning, Hennessy, Daneeta, Luo, Lijuan, Octavia, Sophie, Tanaka, Mark M, Sintchenko, Vitali, Lan, Ruiting
Format: Article
Language:English
Subjects:
Bacterial infections
Bacterial Typing Techniques
Disease Outbreaks
Disease prevention
Epidemiology
Genomes
Genomics
Humans
Multilocus Sequence Typing - methods
Public health
Salmonella Infections - diagnosis
Salmonella typhimurium - genetics
Salmonella typhimurium - isolation & purification
Serogroup
Whole Genome Sequencing - methods
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Summary:BackgroundBoth long- and short-term epidemiology are fundamental to disease control and require accurate bacterial typing. Genomic data resulting from implementation of whole genome sequencing in many public health laboratories can potentially provide highly sensitive and accurate descriptions of strain relatedness. Previous typing efforts using these data have mainly focussed on outbreak detection.AimWe aimed to develop multilevel genome typing (MGT), using consecutive multilocus sequence typing (MLST) schemes of increasing sizes, stepping up from seven-gene MLST to core genome MLST, to allow examination of genetic relatedness at multiple resolution levels.MethodsThe system was applied to serovar Typhimurium. The MLST scheme used at each step (MGT level), defined a given MGT-level specific sequence type (ST). The list of STs generated from all of these increasing MGT levels, was named a genome type (GT). Using MGT, we typed 9,096 previously characterised isolates with publicly available data.ResultsOur approach could identify previously described Typhimurium populations, such as the DT104 multidrug resistance lineage (GT 19-2-11) and two invasive lineages of African isolates (GT 313-2-3 and 313-2-752). Further, we showed that MGT-derived clusters can accurately distinguish five outbreaks from each other and five background isolates.ConclusionMGT provides a universal and stable nomenclature at multiple resolutions for . Typhimurium strains and could be implemented as an internationally standardised strain identification system. While established so far only for Typhimurium, the results here suggest that MGT could form the basis for typing systems in other similar microorganisms.
ISSN:1560-7917
1025-496X
1560-7917
DOI:10.2807/1560-7917.ES.2020.25.20.1900519