Super-speed Salmonella evolution

DATE: 28/01/16

By Elizabeth Klemm

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Development of host-adaptatation by gastrointestinal bacteria. Credit E Klemm

Being sick from food poisoning for a week sounds bad enough to most people, but what if the infection lasted 15 years?  This was the experience of one unlucky patient with a severe and prolonged infection with the bacterium Salmonella Enteritidis. The rare combination of an immunocompromised individual and a hyper-mutating bacterium produced a remarkably fast example of host-adaptation by the Salmonella bacterium.

By sequencing the S. Enteritidis bacterial genome from the patient over time we learned how other host-adapted strains of Salmonella may have evolved, such as S. Typhi, which causes typhoid fever. The genomic information also helped doctors treat the patient.

The patient first came to the hospital with a high fever and rash in 1995, and doctors diagnosed a blood-bourne bacterial infection. The bacterium was identified as S. Enteritidis using antibodies that recognise different Salmonella serotypes. Right away the doctors knew something was unusual about this case: S. Enteritidis typically stays in the gut and causes gastroenteritis, but this Salmonella was found in the blood.

Testing of the patient’s DNA revealed that the patient was deficient for a subunit of the IL-12 receptor (IL-12R-β1). This is a key receptor involved in stimulating the production of IFN-γ (interferon-γ), which revs up the immune system to fight infection. Deficiency of IL-12R-β1 would account for why the Salmonella was able to escape from the gut into the blood stream and cause a systemic infection.

The patient was given IFN-γ and antibiotics, a treatment that has been effective for other patients with the same condition. Unfortunately, this patient did not respond to the treatment and made over 50 return visits to the hospital. At each episode S. Enteritidis was isolated from the patient’s blood, although the symptoms became less severe.

At this stage, the doctors from Addenbrooke’s Hospital approached our group at the Wellcome Trust Sanger Institute to shed some light on the problem. We conducted whole genome sequencing on the Salmonella isolates collected over 10 years from this patient. Expecting the isolates to be genetically very similar to each other, we were surprised to see that they were mutating at an extremely high rate. We were able to trace back the bacterial “family tree” to a single infection of S. Enteritidis from a strain called PT4. This is the same strain linked to the Salmonella epidemic in the UK in the 1990s caused by contaminated eggs.

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Mutations in isolates from gastrointestinal S. Enteritidis and from the patient. Credit E. Klemm

In fact, the genomes of these patient isolates differed from one another by as many as 600 single nucleotide polymorphisms (SNPs) and from the most recent common ancestor by nearly 1,000 SNPs. For reference, isolates of “normal” S. Enteritidis only differed by around 80 SNPs. We were able to show that the hyper-mutating phenotype was due to a loss-of-function mutation in the mutS mismatch DNA repair gene in the patient isolates. The remarkable level of mutation is similar to the number of SNPs acquired by Salmonella Typhi since divergence from its most recent common ancestor thousands of years ago – compared to just 15 years in this patient.

Looking more closely at the genetic differences in the patient isolates, we found numerous genes with severe mutations that would render them inactive: “pseudogenes”. Gene inactivation and deletion, called genome degradation, is commonly observed during host adaptation. Indeed, we were able to observe genome degradation in the Salmonella from this patient and we defined the specific repertoire of pseudogenes as a signature of host adaptation.

The selective pressures to maintain gastrointestinal-specific genes disappeared once the bacterium had moved into the blood and other organs. Hence, many of the genes involved in pathways required for the bacterium to survive in the gastrointestinal tract had been disrupted in these patient isolates, as in other host-adapted Salmonellae, including S. Typhi.

This unique set of conditions could never be replicated in a lab experiment. The self-limiting gastroenteritis S. Enteritidis evolved rapidly to a host-adapted, phenotypically and genetically distinct bacteria within a single host. Not only were we able to use this opportunity to observe evolution in real-time, this research also had great benefits for the patient. Realising that the hypermutating phenotype made the bacterium a moving target, the doctors tried alternative treatments.  After the patient received a bone marrow transplant, the Salmonella infection was resolved, and has not recurred since.

Elizabeth Klemm is a post doctoral fellow at the Wellcome Trust Sanger Institute, who is working in the group of Gordan Dougan.

References:

  • Elizabeth J. Klemm et al. (2016) Emergence of host-adapted Salmonella Enteritidis through rapid evolution in an immunocompromised host. Nature Microbiology. DOI: 10.1038/NMICROBIOL.2015.23

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