Know your enemy

30th January 2014
By Maria Fookes

Pathogenic bacteria, like an army laying siege, represent a constant threat to human health. Salmonella is one such pathogen. Through evolution and diversification Salmonella has become an empire of more than 2,500 serovars (different types), an army of specialists and generalists with specific weapons, targets and signatures of attack.

To fight back we must know our enemies in fine detail, not only the tools of infection that they have developed but also their recent and distant evolutionary history. We hope this will give us the chance to predict their next move since as the way we live changes so do the opportunities to cause disease.

We aim to achieve this knowledge by spying on their genomes, analysing their genomic content and studying the mutations they accumulate in their genetic code (DNA). Some of the mutations will make these warriors (strains and isolates) strong and prevalent, often in patient populations already burdened by other diseases.

Recently, in Malawi, the main geographic focus of this study (reference 1), new Salmonella foot soldiers have emerged that, instead of the normal diarrhoea, cause an invasive blood infection called a non-typhoidal Salmonella infection. This infection occurs in both children and adults, particularly if they are HIV positive or have HIV positive parents (reference 3).

Within this attacking horde, there are three different types of Salmonella; namely, Salmonella Bovismorbificans (reference 2), Salmonella Typhimurium and Salmonella Enteritidis. These are considered the three main agents of non-typhoidal Salmonella infections in Sub-Saharan Africa.

Recent studies of Salmonella Typhimurium (called ST313), which is responsible for a large part of this invasive disease, have shown that there are signs in its genome that it has adapted to a new human niche. These include mutations that render genes dysfunctional, which we now recognise as key markers predicting the move towards a more severe and invasive disease. Resistance to antibiotics has also been shown to be a feature of these invasive Salmonella types (reference 4).

The question we asked in the current study was, has Salmonella Bovismorbificans also adapted to become a fighter, using the same weapons and strategies of evolution and attack as Salmonella Typhimurium? Or is it in the process of heading towards becoming one?

In order to answer this properly we prepared the ground by being the first to publish the blueprint of this type of Salmonella. Then we collected samples of Salmonella Bovismorbificans from different sources, geographical regions and years of isolation (UK veterinary samples) and compared them all, looking for anything in the array of genes that differentiated the arsenal of weapons in Salmonella Bovismorbificans, causing diarrhoea or symptoms associated with invasive disease. (See Figure).

Our findings showed that Malawian Salmonella Bovismorbificans was not in fact a specialist group and that its genetic blueprint was very similar to the other three main agents of non-typhoidal Salmonella infections in Sub-Saharan Africa. It appears that Salmonella Bovismorbificans was simply in the right place at the right time and were able to invade without the need for additional adaptation.

It may be that this is how other Salmonella in the past became invasive; they exploited a change in the human population, in this case associated with widespread HIV. S. Typhimurium ST313 has done this more successfully in the same region.

Surveillance within the region will tell us whether S. Bovismorbificans incidence will rise or fall; so far its weapons seem different than in the case of ST313. Clearly, we hope for the fall, and a similar reduction in immune-compromised patients.

Extended image caption: Isolates linked by long branches are more distantly related and isolates linked by short branches are more closely related. Colour-coded information on each strain is show to the right of the image, including origin (A = Adult, C = Child, V = Veterinary), year of isolation (ND refers to veterinary isolates where an exact year is not known but the collection is known to predate the 1980s), ST, antimicrobial resistance profile (RL = sulphamethoxazole, CXM =cefuroxime, RD = rifampicin, amoxicillin (AML), gentamicin (CN), trimethoprim (W), chloramphenicol (C), tetracycline (TET), streptomycin (S)) and presence or absence of the virulence plasimd pVIRBov. The shaded area (top right, coloured orange, blue and green) represents the whole genome of the reference strain and interesting parts of the genomes of the other strains we analysed that were not present in the reference strain. If the same DNA sequence was present in other S. Bovismorbificans we looked at, then below this we coloured that region on the appropriate line white, grey or black indicating whether it was absent, partially present or fully present.

Maria Fookes gained her Doctorate by immobilising pectic enzymes for juice clarification in her native Spain. She has worked at the Wellcome Trust Sanger Institute since 1999 and she enjoys looking into bacterial (mostly Salmonella) accessory and unique genomic regions. She is a Senior Research Assistant.

References

• 1. Gordon MA, Graham SM, Walsh AL, Wilson L, Phiri A, et al (2008). Epidemics of Invasive Salmonella enterica Serovar Enteritidis and S. enterica Serovar Typhimurium Infection Associated with Multidrug Resistance among Adults and Children in Malawi. Clinical Infectious Diseases. doi: 10.1086/529146.
• 2. Bronowsky, C, Fookes, MC et al (2013). Genomic Characterisation of Invasive Non-Typhoidal Salmonella enterica Subspecies enterica Serovar Bovismorbificans Isolates from Malawi. PLoS Neglected Tropical Diseases. DOI: 10.1371/journal.pntd.0002557.
• 3. Feasey NA, Dougan G, Kingsley RA et al (2012). Invasive non-typhoidal salmonella disease: an emerging and neglected tropical disease in Africa. The Lancet. DOI:10.1016/S0140-6736(11)61752-2
• 4. Okoro CK, Kingsley RA, Connor TR, Harris SR, Parry CM et al (2012). Nature Genetics. Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa. doi:10.1038/ng.2423
• 5. Wiersinga W and de Jong H. F1000 Prime Recommendation of ‘Genomic Characterisation of Invasive Non-Typhoidal Salmonella enterica Subspecies enterica Serovar Bovismorbificans Isolates from Malawi’. DOI: 10.3410/f.718178862.793488226

Related Links:

• Pathogen Genomics at the Sanger Institute