Multilocus Sequence Typing as a Replacement for Serotyping in Salmonella enterica
By Mark Achtman, J. Wain, F. Weill, S. Nair, Zhemin Zhou, V. Sangal, M. Krauland, James Hale, Heather Harbottle, A. Uesbeck and 3 more. PLoS Pathogens, 2012
647 citations recorded by the source corpus.
Salmonella enterica subspecies enterica is traditionally subdivided into serovars by serological and nutritional characteristics. We used Multilocus Sequence Typing (MLST) to assign 4,257 isolates from 554 serovars to 1092 sequence types (STs). The majority of the isolates and many STs were grouped into 138 genetically closely related clusters called eBurstGroups (eBGs). Many eBGs correspond to a serovar, for example most Typhimurium are in eBG1 and most Enteritidis are in eBG4, but many eBGs contained more than one serovar. Furthermore, most serovars were polyphyletic and are distributed across multiple unrelated eBGs. Thus, serovar designations confounded genetically unrelated isolates and failed to recognize natural evolutionary groupings. An inability of serotyping to correctly group isolates was most apparent for Paratyphi B and its variant Java. Most Paratyphi B were included within a sub-cluster of STs belonging to eBG5, which also encompasses a separate sub-cluster of Java STs. However, diphasic Java variants were also found in two other eBGs and monophasic Java variants were in four other eBGs or STs, one of which is in subspecies salamae and a second of which includes isolates assigned to Enteritidis, Dublin and monophasic Paratyphi B. Similarly, Choleraesuis was found in eBG6 and is closely related to Paratyphi C, which is in eBG20. However, Choleraesuis var. Decatur consists of isolates from seven other, unrelated eBGs or STs. The serological assignment of these Decatur isolates to Choleraesuis likely reflects lateral gene transfer of flagellar genes between unrelated bacteria plus purifying selection. By confounding multiple evolutionary groups, serotyping can be misleading about the disease potential of S. enterica. Unlike serotyping, MLST recognizes evolutionary groupings and we recommend that Salmonella classification by serotyping should be replaced by MLST or its equivalents.
Subfields: Ecology, Endocrinology, Food Science
View Paper: https://www.semanticscholar.org/paper/d68e9e18cdebbd65d3839c9da6e538f9b16ffc4a
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Citations in the corpus
- MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies (2018, neutral): “However, the use of codes outside of a local user ’ s database is limited due to the need for centralization of cluster assignment, which is analogous to the centralized allele and sequence type assignments for multilocus sequence typing approaches [30 – 33].”
- GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens (2017, methodology): “Each node corresponds to a single ST, with diameter scaled to the number of assemblies, and was colour-coded according to the dominant serovar of the corresponding eBURST group (Achtman et al., 2012).”
- The Salmonella In Silico Typing Resource (SISTR): An Open Web-Accessible Tool for Rapidly Typing and Subtyping Draft Salmonella Genome Assemblies (2016, methodology): “[33], and the ribosomal MLST (rMLST) scheme described by Jolley et al.”