Friday, 6 June 2014

Cheltenham Science Festival

Earlier this week members of the group represented the Nuffield Department of Medicine at the Cheltenham Science Festival with our Modernising Medical Microbiology stall, featuring the Antibiotic Resistance Coconut Shy and the Genome Evolution Dance Mat.

Antibiotic Resistance Coconut Shy
Antibiotic Resistance Coconut Shy: The children (and adults) visiting the stall were given five bean bags (antibiotics) to throw at the coconuts (bacterial pathogens) to try to knock them off. The front row of coconuts, representing bacteria more susceptible to antibiotics, were easier to knock off than the back row, which represented more resistant bacteria. The aim was to show the children that an unwanted side effect of using antibiotics is to increase the frequency of resistant bacteria, because they were usually the ones left standing.

The game was more difficult than it looks, and just one visitor knocked off all five coconuts. We gave out NDM pens to the sixty visitors who managed to knock off three or more.

Microscope and Top Trumps
Digital Microscope: We brought along a light microscope to show the children what bacteria really look like, which helps emphasize how small they are since they are difficult to see even under the highest magnification. We prepared slides for several Gram positive and Gram negative species, and provided a key to help identify them. We also brought along a number of games that have been used in previous departmental outreach activities, including Pathogen Top Trumps and Fact or Fiction.

Genome Evolution Dance Mat
Genome Evolution Dance Mat: In this game, the children had to copy a bacterial DNA sequence by replicating a sequence of dance moves (up=A, left=C, right=G, down=T) without introducing new errors (mutations). Any mutations that were introduced were passed on to the next template sequence. In this way we aimed to show how mutations occur by errors in DNA replication, and that they are inherited. This generates unique DNA fingerprints for bacteria, which we can use to track the spread of outbreaks.

Outbreak Map
The game, which was kindly programmed by Gareth Jenkin-Jones, included a form of natural selection, so that if too many errors were introduced at once, the sequence was considered inviable and did not survive to be passed on. There was also a speed control, which was handy since some people appear to have spent a lot more of their youth playing dance mats than others.

Outbreak Map: We made an Outbreak Map to show the reach of our stall over the day, with visitors that scored highly on the coconut shy pushing in pins to show where they had travelled from. Had we been handing out germs instead of pens, we could have started outbreaks as far afield as Edinburgh, France and Spain, as well as a large cluster in Cheltenham and the surrounding counties.

Other research groups are representing the department throughout the week.

NDM Microbiology Stall at the Cheltenham Science Festival (L-R): Sarah Earle, Louise Pankhurst, Danny Wilson, Liz Batty, Dilrini De Silva, Jess Hedge, Catrin Moore. Amy Mason, Gareth Jenkin-Jones and Jane Charlesworth also helped with the preparations, and Jen Bardsley co-ordinated all the NDM Stalls.

New paper: Mobile elements drive recombination hotspots in the core genome of Staphylococcus aureus

This week published in Nature Communications we have a new open access paper looking at what drives variability in rates of recombination (horizontal gene transfer, HGT) in the core genome of Staphylococcus aureus. HGT in the core genome is important for eliminating harmful mutations and promoting the spread of beneficial mutations, such as those that make the bacteria resistant to antibiotics.

Compared to recent work focusing on individual, highly-related strains of S. aureus, we found much higher rates of core HGT across the species as a whole. We saw that the frequency of HGT varies along the genome. At broad scales, core HGT is higher near the origin of replication, a pattern reminiscent of the one described by Eduardo Rocha and colleagues in E. coli, who hypothesized that the over-abundance of DNA near the origin during rapid growth could promote HGT.

At fine scales, we found more frequent HGT in regions of the core genome close to mobile elements. The hottest regions occurred near mobile regions called ICE6013, SCC and genomic island α. The insertion and excision of mobile elements from the genome represents a type of HGT, so our finding that nearby core regions also experience more HGT suggests there is some sort of "spill over". This idea is supported by work in Ashley Robinson's group that found similarities between ICE6013 and a class of mobile elements in Streptococcus agalactiae called TnGBS2. TnGBS2 was discovered by Phillipe Glaser's lab who showed it sometimes transfers large tracts of adjacent core material during conjugation.

Whether conjugation alone can explain the high levels of core HGT we saw in S. aureus is unclear - our results suggest there is detectable HGT even in core regions far from mobile elements. Transformation is another possible mechanism of core HGT, but S. aureus is generally thought to be naturally incapable of transformation. However, intriguing work published by Tarek Msadek and colleagues in 2012 indicates there may be cryptic mechanisms of transformation in S. aureus after all. It remains to be seen whether the relative contributions of transformation, transduction and conjugation to the long-term evolution of S. aureus can be disentangled.