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. 2018 Mar;23(13):17-00375.
doi: 10.2807/1560-7917.ES.2018.23.13.17-00375.

Rise and fall of outbreak-specific clone inside endemic pulsotype of Salmonella 4,[5],12:i:-; insights from high-resolution molecular surveillance in Emilia-Romagna, Italy, 2012 to 2015

Marina Morganti  1 , Luca Bolzoni  2 , Erika Scaltriti  1 , Gabriele Casadei  1 , Elena Carra  3 , Laura Rossi  4 , Paola Gherardi  4 , Fabio Faccini  4 , Norma Arrigoni  5 , Anna Rita Sacchi  4 , Marco Delledonne  4 , Stefano Pongolini  1   2
Affiliations

Rise and fall of outbreak-specific clone inside endemic pulsotype of Salmonella 4,[5],12:i:-; insights from high-resolution molecular surveillance in Emilia-Romagna, Italy, 2012 to 2015

Marina Morganti et al. Euro Surveill. 2018 Mar.

Abstract

Background and aimEpidemiology of human non-typhoid salmonellosis is characterised by recurrent emergence of new clones of the pathogen over time. Some clonal lines of Salmonella have shaped epidemiology of the disease at global level, as happened for serotype Enteritidis or, more recently, for Salmonella 4,[5],12:i:-, a monophasic variant of serotype Typhimurium. The same clonal behaviour is recognisable at sub-serotype level where single outbreaks or more generalised epidemics are attributable to defined clones. The aim of this study was to understand the dynamics of a clone of Salmonella 4,[5],12:i:- over a 3-year period (2012-15) in a province of Northern Italy where the clone caused a large outbreak in 2013. Furthermore, the role of candidate outbreak sources was investigated and the accuracy of multilocus variable-number tandem repeat analysis (MLVA) was evaluated. Methods: we retrospectively investigated the outbreak through whole genome sequencing (WGS) and further monitored the outbreak clone for 2 years after its conclusion. Results: The study showed the transient nature of the clone in the population, possibly as a consequence of its occasional expansion in a food-processing facility. We demonstrated that important weaknesses characterise conventional typing methods applied to clonal pathogens such as Salmonella 4,[5],12:i:-, namely lack of accuracy for MLVA and inadequate resolution power for PFGE to be reliably used for clone tracking. Conclusions: The study provided evidence for the remarkable prevention potential of whole genome sequencing used as a routine tool in systems that integrate human, food and animal surveillance.

Keywords: Multiple- Locus VNTR Assay; Salmonella enterica 4,[5],12:i:-; Whole genome sequencing; clone; outbreak; pulsed-field gel electrophoresis; salami.

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Conflict of interest statement

Conflict of interest: None declared.

Figures

Figure 1
Figure 1
Number of isolates per week of Salmonella 4,[5],12:i:- pulsotype STYMX.0131 in Piacenza province, Italy, 2012–2015 (n = 158)
Figure 2
Figure 2
Phylogenetic Bayesian tree of Salmonella 4,[5],12:i:- isolates sequenced in this study, Emilia-Romagna, Italy, 2012–2015
Figure 3
Figure 3
Probability of occurrence of variant multilocus variable-number tandem repeat analysis profiles (panel A) and single nucleotide polymorphisms to the consensus (panel B) in outbreak isolates as a function of the isolation date
See this image and copyright information in PMC

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