Researchers in the United Kingdom have examined the emergence and spread of a strain of Salmonella common in pigs.

Scientists hope that understanding how and why new strains of Salmonella emerge in livestock will help develop improved strategies to reduce the incidence and make the food supply safer.

Work was led by the Quadram Institute and the University of East Anglia with Public Health England, the Animal and Plant Health Agency, the Earlham Institute, and the Teagasc Food Research Centre. It was funded by the Biotechnology and Biological Sciences Research Council and published in the journal Microbial Genomics.

Viruses are very small packages of genetic material that require cells to replicate this material and cause disease. There are also viruses, called bacteriophages, that use bacteria to replicate and in doing so kill the bacterium. However, some are able to hide inside the bacterial cell by merging with the bacteria’s genetic material.

Helping Salmonella spread
Researchers said this is what happened perhaps hundreds of times during the emergence of one strain which has helped the bacteria spread globally.

This gene is sporadically distributed within Salmonella and rare in Salmonella Typhimurium, but was acquired multiple times during clonal expansion of the currently dominant monophasic Salmonella Typhimurium sequence type (ST) 34 clone.

Monophasic Salmonella Typhimurium ST34 emerged in Europe around 2005, initially in pig populations. Half of all Salmonella infections in the European Union are linked to pigs.

In the UK, more than half of all Salmonella Typhimurium infections are caused by ST34. Salmonella Typhimurium has made up a growing proportion of all Salmonella infections for the past decade, largely due to the emergence of this new strain, according to the study.

Unlike Salmonella Enteritidis that has been largely controlled in layer hen flocks in the UK, little progress has been made on Salmonella Typhimurium. Occasional replacement of the dominant strain of Salmonella Typhimurium causing disease makes it a moving target. So, understanding why new strains emerge and what makes them distinct from previous ones is important to find ways of tackling this pathogen.

Growing dominance
Researchers found the common ancestor of the strain in UK pigs existed around 30 years ago but went unnoticed until 2005 when surveillance by the Animal and Plant Health Agency found ST34 in low numbers. Analysis of the genome sequence from human infections using data from Public Health England indicated that a bacterial virus called mTmV infected ST34 multiple times starting around 2002.

By analyzing the population structure of ST34 it was found that Salmonella harboring this virus in their genetic material became more numerous over time and gained a competitive advantage over those lacking the virus. The virus carries the sopE gene encoding a toxin known to help Salmonella infect their animal host species, cause diarrhea, and be passed on to new hosts in food and feed.

Researchers investigated the distribution of sopE in 1,697 Salmonella Typhimurium and monophasic variant Salmonella Typhimurium from human infections in England and Wales between 2012 and 2016 and found it was rare. They also looked at variation in the whole-genome sequences of Salmonella Typhimurium isolated from UK pigs between 2006 and 2015.

Of 442 monophasic Salmonella Typhimurium ST34 isolates from sources including humans, food, environment, livestock, companion and wild animals in 29 countries, 25 percent encoded the sopE gene.

The mTmV transfer to other Salmonella serovars in vitro was limited but included the common pig-associated Salmonella Derby. This may explain mTmV in Salmonella Derby co-circulating on farms with monophasic Salmonella Typhimurium ST34, highlighting the potential for further transfer of the sopE virulence gene in nature.

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