Multilocus Sequence Typing as a Replacement for Serotyping in Salmonella enterica

Abstract

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.

Patterns of genome evolution that have accompanied host adaptation in Salmonella

“…The phylogeny of these serotypes is largely consistent with previous studies showing that S. Dublin represents an independent clade (9,11). Our data show that there are ∼23,000 SNPs differentiating S. Dublin from the most recent common ancestor of S. Enteritidis and the avian-adapted salmonellae, S. Gallinarum and S. Pullorum.…”

“…Somatic serogrouping and MLST have identified a single lineage with closely related members that exhibit a range of different host specializations (6)(7)(8)(9). These include two of the most important Salmonella pathogens: S. Enteritidis and S. Gallinarum.…”

Molecular typing of bacteria for epidemiological surveillance and outbreak investigation / Molekulare Typisierung von Bakterien für die epidemiologische Überwachung und Ausbruchsabklärung

“…Owing to the slow mutation rate of housekeeping genes, MLST often does not display the resolution of PFGE or MLVA, but is the method of choice for long-term epidemiological and phylogenetic investigations. In our laboratory, MLST was used for typing of particular S. enterica serovars (Zeinzinger et al, 2012) and we were able to confirm that MLST has the discriminatory power to type isolates beneath serotype level (Achtman et al, 2012;Zeinzinger et al, 2012).…”

“…A methodical exception to the shift from conventional to molecular typing techniques is the classical serotyping of S. enterica. Although it has been shown that many Salmonella serotypes comprise strains that have completely different genotypes because of lateral gene transfer of flagella genes (Achtman et al, 2012), implementation of suitable molecular methods is still an issue. Several molecular methods such as PFGE, MLVA, MLST, and HRM have been proposed as alternatives for serotyping but all are hindered by the fact that a one-to-one comparability between serotyping and molecular typing results is impossible.…”

Molecular Characterization of Antibiotic-Resistant Bacteria in Contaminated Chicken Meat Sold at Supermarkets in Bangkok, Thailand

“…enterica subtyping by Wattiau et al emphasizes the importance of DNA-based typing schemes (44). Furthermore, the latest MLST findings can demonstrate evolutional grouping better than serotyping, which sometimes can mislead an epidemiological investigation (45).…”