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

• Published in: Euro surveillance : bulletin européen sur les maladies transmissibles Vol. 23; no. 13
• Main Authors: Morganti, Marina, Bolzoni, Luca, Scaltriti, Erika, Casadei, Gabriele, Carra, Elena, Rossi, Laura, Gherardi, Paola, Faccini, Fabio, Arrigoni, Norma, Sacchi, Anna Rita, Delledonne, Marco, Pongolini, Stefano
• Format: Journal Article
• Language: English
• Published: Sweden European Centre for Disease Prevention and Control (ECDC) 29-03-2018
• Subjects: Bacterial Typing Techniques - methods; Disease Outbreaks; DNA, Bacterial - genetics; Electrophoresis, Gel, Pulsed-Field; Endemic Diseases; Humans; Italy - epidemiology; Minisatellite Repeats - genetics; Molecular Epidemiology; Molecular Typing - methods; Polymorphism, Single Nucleotide; Retrospective Studies; Salmonella - classification; Salmonella - genetics; Salmonella - isolation & purification; Salmonella Infections - diagnosis; Salmonella Infections - epidemiology; Salmonella Infections - microbiology; Whole Genome Sequencing; Italy; Salmonella enterica 4,,12:i; Whole genome sequencing; clone; outbreak; salami; pulsed-field gel electrophoresis; Multiple- Locus VNTR Assay
• ISSN: 1560-7917; 1025-496X; 1560-7917
• DOI: 10.2807/1560-7917.ES.2018.23.13.17-00375

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
have shaped epidemiology of the disease at global level, as happened for serotype Enteritidis or, more recently, for
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
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.
we retrospectively investigated the outbreak through whole genome sequencing (WGS) and further monitored the outbreak clone for 2 years after its conclusion.
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
4,[5],12:i:-, namely lack of accuracy for MLVA and inadequate resolution power for PFGE to be reliably used for clone tracking.
: 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.