In 1941 John Rex Whinfield and James Tennant Dickson of Calico Printers' Association of Manchester, England, patented a new compound that changed the way foods are packaged, the clothes we wear and many other manufacturing processes. The compound was poly(ethylene terephthalate) (PET), and is the most widely used polyester plastic worldwide. About 60% of the world’s PET is used to produce polyester often in the context of clothing production, with about 30% being used to produce plastic drinks bottles.

Whilst PET made a massive impact on the way we dressed or drank over the past decades it is perhaps only now that the full impact of the 1941 discovery is really being felt. PET takes hundreds of years to breakdown in the environment, and we are producing it at a rate that far outpaces its removal. PET has become one of the worst environmental pollutants of modern times. You only have to walk down the street to see the amount of plastic rubbish or watch the news to see the buildup in faraway villages and along our coastlines. There is also the unseen threat of so called “microplastics” (from the mechanical breakdown of these plastics) to our marine environments.
 
These microplastics are increasingly being seen as a major threat to environmental health, their accumulation is thought to be responsible for the death and destruction of marine life and is even being found in fish for human consumption. It is therefore suspected that we are eating microplastics and it is not yet known what effect that will have on our health; however it is unlikely to be good!
 
So what does this have to do with microbiology?
Well, I was getting to that!!
 
In 2016 a team in Japan lead by Yoshida discovered a new bacterium, Ideonella sakaiensis. This discovery was exciting for a number of reasons; firstly it is always exciting to us Microbiologists when a new bacterium is discovered (yep, it really is!), secondly of all the places this bacterium could be discovered it was in a waste reprocessing plant, and thirdly the bacterium was growing on and actually breaking down PET.
 
This is really exciting as it may represent a way of reprocessing PET without it being discharged into the environment and causing such massive concerns. Bacteria, you’ gotta love um!

How does I. sakaiensis breakdown PET?
I. sakaiensis is able to breakdown PET because it produces 2 enzymes which degrade the PET compound.
 
PET is made from ethylene glycol and terephthalic acid (TPA). The enzymes produced by I. sakaiensis reverse this process to produce the original parent compounds ethylene glycol and TPA. Of course science needs some long-winded compound names and lots of acronyms for this process when in fact it has just two-steps but I think the process is actually really quite neat.
 
The first enzyme is called PETase, or PET-digesting enzyme. This breaks PET into mono(2-hydroxyethyl)-TPA (MHET) with additional trace amounts of TPA and bis(2-hydroxyethyl)-TPA.  I did warn you about the names! The second enzyme MHETase, or MHET-digesting enzyme, breaks MHET down into TPA and ethylene glycol.
 
So the whole process from production of PET to its final breakdown results in the very same molecules that you started with, and that is very neat as there are no additional new compounds that might be of further harm to the environment.
 
In the original Japanese study a colony of I. Sakaiensis took about 6 weeks to degrade a thin film of PET; okay it’s not a rapid process at the moment but it’s a start and much better than the hundreds of years which it would normally take to breakdown plastics in the environment.
 
What happened next… a lucky accident?
Like all good scientific discoveries (think penicillin)… a mishap occurred! A group from Portsmouth University in the UK was trying to expand upon the Japanese discovery. Whilst studying the mechanism by which I. Sakaiensis breaks down PET and trying to establish the exact structure of the enzymes it produces using X-ray scanning, the team from Portsmouth “accidentally” created a mutant form of the PETase (first enzyme) which had enhanced activity against PET, although they don’t say by how much the activity was enhanced. I particularly like the quote from the Lead scientist, Professor John McGeehan, who said "serendipity often plays a significant role in fundamental scientific research, and our discovery here is no exception”. I would add that whilst the creation of the new enzyme might have been a lucky accident, the recognition of this mutation and its relevance was no accident and shows the skills of the researchers at Portsmouth; but humility is always a worthy trait.
 
The new enzyme created in Portsmouth not only had enhanced activity against PET but it was also active against poly(ethylene furanoate) (PEF). PEF is currently being pursued as the replacement for PET. It is hailed as the “environmentally friendly” version of PET as it is produced using a different starting block to TPA (which is a petroleum product) called 2,5-Furandicarboxylic acid. This is made from naturally occurring carbohydrates and, as it doesn’t use TPA, PEF is said to produce less greenhouse gases than PET hence its “green credentials”. As with many manmade things, it’s not really that “green”; a discarded plastic bottle made of PEF will still cause the same environmental pollution as PET but at least the PETase enzyme from Portsmouth can now also break this plastic down.
 
What does the future hold?
The researchers from Portsmouth say that their accidental creation of a more active PETase shows that there is more scope to further enhance the ability of PETase to breakdown PET. They believe with a more systematic and structured approach to modifying its structure the enzyme could become even more active. This might allow an industrial scale process whereby the PETase enzyme is used to breakdown PET in recycling centres in a more cost effective way. It may also allow for the processing of existing PET in the environment through the “deliberate contamination” with I. Sakaiensis to speed up the removal of PET. HOWEVER I’m not convinced by this last argument, from what I can see every time humans have tried to “modify” their surrounding it has almost always back-fired (e.g. the “planned” introduction of grey squirrels in the UK, rabbits in Australia, and ferrets, stoats and weasels in New Zealand).

References
1.    A bacterium that degrades and assimilates poly(ethylene terephthalate) Yoshida S, Hiraga K, Takehana T, et al. Science  11 Mar 2016:Vol. 351, Issue 6278, pp. 1196-1199
2.    Characterization and engineering of a plastic-degrading aromatic polyesterase Austin H, Allen M, Donohue B, et al. PNAS published ahead of print April 2018.

The Microbiology Consultant was waiting for the new Microbiology Registrar to finish the authorisation before going through any problems or questions they had. They started with their first question, a urine isolate which was identified as Pseudomonas aeruginosa but the antibiotic sensitivities didn’t make sense. The bacterium was sensitive to Co-amoxiclav and Ceftriaxone but resistant to Gentamicin and Amikacin. Pseudomonas aeruginosa is normally resistant to Co-amoxiclav and Ceftriaxone and sensitive to Gentamicin and Amikacin. A “nonsensical” or “incorrect” result like this should normally prompt further investigation as to what might be wrong before it is authorised or released.

The patient’s mother was at her wits end. Her little boy’s head was covered in scaly skin. At first she thought his scaly hair was dandruff so she had washed his hair in medicated shampoo but this was met with screams and tears. She thought he was being a bit extreme “it’s only dandruff” but guessed kids can be funny about having soap in their eyes. He just kept saying “mummy my head is really sore”. Tonight he had refused to have his hair washed and while trying to get him into bed, she noticed he was going bald! She was so alarmed that she brought him in to the Emergency Department for help.

Gosh nearly 2,000 of you read last weeks’ blog on cholera (that’s a record) and it sparked a couple of really good questions to Nuts & Bolts.
 
One from Virginia related to the use of TCBS agar to grow Vibrio cholerae, so I thought that this week I would cover some “old fashioned” microbiology and talk about agar. Really! I hear you cry “that’s not very interesting”! Well, as “interesting” is banned when discussing microbiology, I’ll use “actually very clever” to describe the reasons why we use different types of agar in the laboratory… here goes…

​Looking through the positive blood cultures in the morning, the Microbiology Registrar noticed a set positive for Staphylococcus lugdenensis. There were no clinical details on the request form but checking the patient’s blood tests showed a high white blood cell count and C-reactive protein. There was clearly something going on so the registrar gave the ward team a call. The team said the patient was being treated for pyelonephritis with Gentamicin but further questioning revealed that they also had a prosthetic aortic valve. The registrar wondered whether the patient might have infective endocarditis but the team weren’t convinced at first. The registrar explained the risks and suggested repeating the blood cultures as well as asking the Cardiologists for an opinion about the possible diagnosis.

​The Microbiologist recently received a letter from a colleague asking for advice about how to manage a patient with Helicopter pylon. After a little pondering, it was decided that in fact advice was really required for a patient with Helicobacter pylori who had had failed two courses of treatment and was still symptomatic for peptic ulcer disease. It was clear that the automatic spell checker had made its own diagnosis! Spell checkers are a nightmare in medicine but often lead to some interesting questions. The colleague was asking whether the microbiology laboratory could perform culture and sensitivity on a biopsy sample and if so how the sample should be sent. There was also a question about what antibiotics to use next to treat the patient.

​​​We are so pleased you all enjoy reading the bug blogs and are delighted to announce that we have been ranked 3rd in the "top 25 Microbiology blogs". Your continued support is much appreciated.

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Good luck with the puzzle and Merry Christmas. See you in the New Year!

​An elderly diabetic man presents to hospital with a fever, tachycardia and hypotension. He is septic and so blood cultures are taken and he is started on IV Piptazobactam as per the hospitals empirical guidelines for sepsis. There is no obvious focus and therefore source control (e.g. draining of an abscess) at this time is not possible.
 
The next day his blood cultures signal positive and a beta-haemolytic streptococcus is isolated. What does this mean? What is the significance?
 
Does the terminology around beta-haemolytic streptococci confuse you? It did me when I was a student and junior doctor; I couldn’t understand why beta-haemolytic streptococcus wasn’t the Group B streptococcus! They both have a “B” in them just one is the Latin letter while the other is Greek; surely they are the same thing? Well no, they’re not so how did I eventually get to grips with them.

Previously I blogged about the use of antibiotics in pancreatitis and I mentioned procalcitonin as an exciting new marker of infection. I have little experience of this laboratory test but have heard many others talk about how useful it is. But what is it? What is it useful for? Can it help in the diagnosis and management of infection?
 
What is procalcitonin?
Procalcitonin (PCT) is a protein produced by the thyroid, lungs and intestine in response to inflammation, especially when the inflammation is caused by bacterial infection. In contrast, levels of PCT do not increase much when inflammation is caused by viruses or most non-infectious causes. Levels increase quickly (within 2-4 hours) and have a half-life of 24-36 hours. It is suggested (by the manufacturers of the PCT assay machines) that PCT can therefore be used to identify septic patients and predict who is at risk of developing severe sepsis. The amount of PCT is said to be related to the amount of inflammation therefore in theory the level of PCT can also be used to monitor response to treatment; a decrease in PCT corresponding to a favourable response to treatment.