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Abstract

Background

Both 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.

Aim

We 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.

Methods

The 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.

Results

Our 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.

Conclusion

MGT 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.

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This work is licensed under a Creative Commons Attribution 4.0 International License.
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2020-05-21
2024-12-22
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Multilevel genome typing: genomics-guided scalable resolution typing of microbial pathogens
<p class="citation"> <span>Citation style for this article:</span> <span class="meta-value authors"> <a href="/search?value1=Michael+Payne&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Payne Michael</a>, <a href="/search?value1=Sandeep+Kaur&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Kaur Sandeep</a>, <a href="/search?value1=Qinning+Wang&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Wang Qinning</a>, <a href="/search?value1=Daneeta+Hennessy&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Hennessy Daneeta</a>, <a href="/search?value1=Lijuan+Luo&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Luo Lijuan</a>, <a href="/search?value1=Sophie+Octavia&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Octavia Sophie</a>, <a href="/search?value1=Mark+M.+Tanaka&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Tanaka Mark M.</a>, <a href="/search?value1=Vitali+Sintchenko&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Sintchenko Vitali</a>, <a href="/search?value1=Ruiting+Lan&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Lan Ruiting</a></span>. Multilevel genome typing: genomics-guided scalable resolution typing of microbial pathogens. <a href="/content/ecdc">Euro Surveill.</a> 2020;25(20):pii=1900519. <a href="https://doi.org/10.2807/1560-7917.ES.2020.25.20.1900519" title="doi link" target="_blank">https://doi.org/10.2807/1560-7917.ES.2020.25.20.1900519</a> <span class="ES_Article_citation"> <span class="generated">Received</span>: 13 Aug 2019;&nbsp;&nbsp; <span class="generated">Accepted</span>: 12 Nov 2019 </span> </p>
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