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Strain typing of pathogens: how do Salmonella emerge in poultry?

By Tim Johnson 
Associate Professor at the University of Minnesota

Editor's note:  This is part 3 of a 3-part series written for Gobbles, the official publication of the Minnesota Turkey Growers Association.  It is being published here prior to printing of Gobbles because of the current events involving Salmonella in the poultry industries.

Salmonella is on everyone’s mind, with recent declared outbreaks by the CDC of Salmonella Reading in turkeys and Salmonella Infantis in chickens. It can be a bit perplexing for the producer to understand why the ecology of Salmonella changes so dramatically, when nothing has changed from a management perspective. In order to understand what might have changed, we first have to consider basic Salmonella ecology and how it impacts into our understanding of what has happened.

1. Salmonella can change very quickly through gene transfer.

What is the fastest way for Salmonella populations to change? The answer lies in its genome. Salmonella, like E. coli, are very good at picking up extra pieces of DNA in the genome. Most often, these “extra pieces” of DNA ride on genetic elements called plasmids. The most important thing to remember about plasmids is that they are mobile – meaning, they can move from one bacteria to another naturally when these bacteria come into close contact. There are some very good examples of this happening in Salmonella, but perhaps the best example occurred with Salmonella Kentucky. We discussed avian pathogenic E. coli in a previous issue of Gobbles, and that is possesses a unique plasmid that makes it more successful in the poultry environment. Salmonella Kentucky emerged as a dominant serovar in broilers about 15 years ago. Through genetic work, it was determined that coinciding with this emergence was the acquisition of the avian pathogenic E. coli plasmid by Salmonella Kentucky, making it better at colonizing the bird and persisting in the barn environment.


2. Salmonella can change more slowly, through mutation.

A “slower” mechanism for Salmonella to evolve is by acquiring mutations within its chromosome. This happens naturally as Salmonella grows – its DNA sometimes has errors when it replicates, and the new cell has a single change (mutation) in its genome. Most times, these are mutations that do not survive because they are not beneficial to the Salmonella. However, rarely these mutations are beneficial to the bacteria. For example, it takes several mutations acquired in a stepwise fashion to make a Salmonella resistant to the antibiotic ciprofloxacin. This is an extremely rare event; however, when it happens the bacteria now has an advantage because it is resistant to an important antibiotic.

3. A new strain of Salmonella can be introduced which is better adapted to poultry.

Instead of a Salmonella evolving within a system to become poultry-adapted, sometimes a new strain can be introduced that is already poultry-adapted. With Salmonella Reading, this appears to be the case. Prior to the outbreak in turkeys, meat and live turkey isolates belonged to a circulating cluster of strains which apparently did not display high prevalence in flocks (green cluster below). Since 2017, a new strain appears to have emerged (blue below). This strain displays higher prevalence in turkey flocks and coincides both in terms of timing of isolation, and genetic similarity, to strains from humans in the recently declared outbreak (blue below). 

Whether change in Salmonella occurs as a result of gene acquisition, mutation, or new strain introduction, the end result is the same: a modified/new strain with enhanced ability to persist in poultry. As a result, more of these strains will spill over into humans, where they are subsequently detected by our public health agencies, which are excellent at detecting changing patterns in human Salmonella. While Salmonella Reading is the current problem in turkeys, there will undoubtedly be another serovar and another problem tomorrow. In order to tackle these emerging strains, it is critical to understand what changes make them successful and then to identify strategies for controlling them based upon their successful traits.

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