Naming names

What's in a name? Well, if someone called you by the wrong name you wouldn't hesitate to correct them.
And humans do so love the naming of things. Whole books are written about those individuals who have come up with naming systems for different scientific areas such as Carolus Linnaeus for botany. 


Much effort is spent these days in testing and identifying the name of the bacteria that may have caused an infection. Once the doctor knows what it is then s/he feels able to prescribe the correct antibiotic. Or that's the theory.


But a new paper has shown how difficult it can be to put a name on something as shape-shifting as microbes. 
The genes from one microbe may be quite useful to another nearby microbe - especially if they convey antibiotic resistance - so they parcel it out in a generous way apparently. This is called horizontal gene transfer.


In Nature News magazine this week they reported on the important discovery of the mechanism by which microbes do this, and also revealed how amazingly quick it can happen. Overnight 47 per cent of marine bacteria had taken the genetic make-up of an introduced modified microbe in to their own genetic make-up. Now that makes naming microbes a bit tricky.


Evolutionary biologist Jeffrey Townsend at Yale University in New Haven, Connecticut, told the magazine: "In order to understand antibiotic resistance, pathogenicity, or the beneficial things that bacteria do for us, we need to understand how they evolve through horizontal gene transfer — knowing about this process can help us live in a world full of microbes."

And most of us want to carry on living in this microbe-crammed world, don't we? I think we need to pay less attention to naming things, and start applying our knowledge to understanding important processes in and around us.

Coalition thinking

Wow, what a week it's been for the English! Our first exciting experience of creating a real political coalition.
For it to continue, and work effectively, I believe we will have to change ourthinking. Maybe in the same way that microbiology experts have had to change their thinking recently about the human body and why it gets ill.
For so long we have talked of a sealed and protected physical body that has to wage war against any pathogens that threaten to infect us from the outside.
At the same time people have started to understand now that there are a lot of friendly bacteria on the inside (mainly because of that advert for a certain mini-drink).

So here we have a model depicting two tribes of bacteria, which suits our traditional way of thinking:there are these friendly, helpful bacteria that understand the needs of the human body; and there are those BAD bacteria (boo!) that we must never allow to have control over our body.
Suddenly we have a new third set of bacteria being mentioned and people are starting to say "D'you know, I never realised that they could look like that, or how they work exactly?" A bit like Nick Clegg.

Some microbiologists have named these bacteria existing inside our bodies pathobionts - a combination of pathogen and symbiont. A symbiont is a helpful organism which works in perfect synergy with its host.
Other experts are describing the human body now as a "superorganism" and conclude that the newly discovered microbes provide "metabolic functions far beyond the scope of our own physiological capabilities".
So how can we be sure if these pathobionts are going to work well together for our good, or if they might harm us instead?

We simply can't be sure.
That's right, we just have to try to get along with them.
We have to provide the right structure to work together in our body (a healthy immune system, well exercised muscles).
We have to limit the jobs that they do in our body to the ones we want them quietly to get on with (by not overfeeding them with any processed foods).
And we have to promise that we won't suddenly attack their tribal group (antibiotics are a dangerous weapon).

We are going to have to learn to live and work together with our pathobionts, otherwise we will see an even greater increase in chronic illness than we have already.
If you think my analogy is a bit far fetched then have a look at this scientific article (which focuses particularly on fungal infections like candida). University of North Carolina microbiologist William E. Goldman says that the infections are "not very good at causing disease in normal hosts with normal immune systems".
"But a growing population of people have not-so normal immune systems. Fungal infections are so deadly in part because most patients who become seriously ill are already weakened by AIDS, cancer, transplants or medications that handicap the body’s ability to mount a strong defense.
"More and more of these patients have taken high doses of anti biotics to prevent other infections, fundamentally changing the body’s ecology and allowing unnatural fungal growths to take over. More patients are also undergoing medical procedures that breach normal immune barriers with catheters and other devices."
He mentions catheters because we all have three parts to our immune system: the largest organ in our body, our skin; then our innate immune system which provides 24/7 security guards; and our adaptive system which attacks when danger is identified.
In these interesting times please give the microbial coalition a chance - a strong and stable agreement is the best option for your body's long term health.

Does your brain feel ill?

When we have been ill for a little while it is natural to feel "down", isn't it?
A bout of sickness, flu, or a bad flare-up of our chronic symptoms will often lead to feelings of lethargy and depression and we usually find our fellow humans' response to this is: "That's not surprising after being unable to do things normally - I would get depressed about it too!"
But this is a strange Western rationalisation of the brain as separate from the body. Obviously the brain is actually connected to the body, and the brain tissue can become ill as well.
New research has shown clearly that our brains actually respond to infection in the body to make us FEEL ill; it is not just a psychological after-effect of a physical event - the brain makes this happen.

Now some clear research studies have shown the process involved. The innate (initial defensive) immune system produces proteins called cytokines whenever they encounter a bacterial challenge.
This then signals to the brain, then the entire balance of "mini" hormones and different chemicals in the endocrine system undergoes a change. These signals run through the neurotransmitters and alter our mood and behaviour.
There is already enough evidence to show that the root of depression is in something called the subgenual cingulate of the brain.
When researchers watched the subgenual cingulate with an MRI scanner they found that patients who had mild inflammation from a typhoid injection showed activity here. And those who had the largest inflammatory cytokine response had the greatest problems with their mood and a slowing down of their normal responses.

Dr Neil Harrison of Sussex University told the World Service's Healthcheck programme that many different illnesses with a bacterial element and immune response cause this real physical action in the brain:"Cytokines can cross the blood brain barrier but can also bind to nerve endings and be signalled in the brain."

One thing he didn't touch on was why the body might want the brain to make it feel so bad. If your body feels confused, withdraws from social situations, suffers depression and slows right down, according to this research, that's because it is busy mounting an immune response to infection.
So, may I suggest, it might at times be healthy (for all concerned) to stay at home in bed and avoid others, instead of taking some tablets and making a psychological effort to get back in to the swing of things.

Dig deeper

Pandemic flu may have fallen off the news agenda but over the summer more scientific evidence has been gathering of how our underlying health could be a crucial factor in its severity.
Most people know about MRSA - and some avoid hospital out of fear they may get it there - but few people are aware of community associated MRSA.
CA-MRSA infections are known to be circulating among healthy members of the community and yet they have never been tested for in the UK population. The USA has undertaken studies and found that one in every 100 people carries CA-MRSA.
The SA in the abbreviation is Staphylococus aureus, a rather nasty family of microbes.
When the lungs of the young victims of the 1918 Spanish flu were studied, they were found to have been destroyed by a pneumonia which killed them within 72 hours. The weight of evidence since then has led infectious disease specialists to conclude that the extra factor in these swift deaths was Staph aureus.
One study by epidemiologists Noymer and Garenne of US 1918 flu deaths postulated that the Staph infection could have taken hold in the chest because apparently healthy people had undiagnosed tuberculosis, which makes little 'pockets' in the lungs.
Now two brand new studies by virologists - in Rotterdam, and Atlanta, Georgia - have found out exactly how different the pandemic H1N1 virus is from seasonal influenza virus - it particularly attacks the lungs.
Seasonal flu virus bound to the cells in the nose but they observed that pandemic H1N1 binds much deeper, in the trachea, bronchi and bronchioles of the lungs.
The US team also found the virus bound to cells in the intestine, explaining the nausea and vomiting associated with swine flu.
New Scientist magazine reported on this discovery: 'Individuals differ in the way they react to viruses. A virus that binds deep in the lungs can trigger potentially fatal pneumonia if the person infected mounts a strong inflammation in response to it.'
So where does that leave people with an autoimmune disease, like sarcoidosis or rheumatoid arthritis, where the immune system is apparently overreacting? Or people who always have sudden and severe reactions in the chest or gut whenever they take antibiotics?
These unknowns are part of the 'evolving threat' from community infections, and the NHS is ill-prepared for it, according to an expert.
Professor Richard James, director of the Centre for Healthcare Associated Infections at the University of Nottingham, said last month: 'It took the UK over 10 years to start to get to grips with the problems of hospital MRSA infections and we are still fighting this war. We are not yet ready to fight the next one against CA-MRSA infections.'
He complains that the NHS is: not testing for this known community health risk factor; has not got enough intensive care beds to cope with even a low number of cases of swift-acting pneumonia in swine flu patients; and has failed to invest in laboratories and advanced diagnostic testing.
He is trying to raise £1.4m in charitable donations to fund new research in to infections because of the lack of public funding.
Meanwhile 37,000 people have died in the last ten years from MRSA or another serious infection C.diff. That's twice as many deaths as those from road traffic accidents - and the extra treatment costs incurred by these infections in the NHS is £1 billion each and every year.
Infectious disease specialists have been asking for UK investment in advanced laboratory testing for a long time now.
Emeritus Professor at the University of Aberdeen, Hugh Pennington warned in a Radio 4 investigation last year that the current system of two main laboratories for the whole country, with results delivered at a snail's pace, was inadequate. The national Health Protection Agency lacks enough resources to track infections.
He told File on Four: "The scandal here is that we know what to do, the technology's there to spot these things as they are appearing and we know how to react to them. It would be quite wrong if we allow these things to develop and of course history tells us that if we do neglect these bugs, we neglect them at our peril."
Can someone in charge of NHS resources please wake up and smell the coffee?