Today’s post is the first guest post on Mostly Microbes. Dr. Adam Roberts at the University College London and one of his students, Tim Walker, share their initial findings from their citizen science project to isolate novel antibiotics – Swab and Send. Ever wonder what unusual bacteria might be lurking in your kid’s smelly, worn out shoes or under their fingernails? In your office fridge? On the dog’s paws? Donate to Swab and Send and the Roberts’ lab will send you materials to collect the samples, isolate the bacteria, and test them for novel antibacterial and fungicides! Photos of the swab isolates and their antimicrobial activity is posted on their Facebook page. For some of my favorites – see the Storify at the end of the post. I’m looking forward to purchasing a kit and setting the kids (and myself) loose with swabs. – Anne
Update 6/21/17 – The Atlantic has a great article about Swab and Send – Could the Answer to Our Most Urgent Health Crisis Be Found on a Toilet Seat?
Guest post by Tim Walker and Adam P. Roberts, PhD
University College London
What do horse manure, an asparagus bud, a garden trampoline, a refrigerator, a train station in London, and even the Nile Valley in Egypt have in common? They are all places where we have isolated bacteria producing antibiotics.
Setting the scene
Humans face many incredible challenges at the moment and one of them is antibiotic resistance. Quite simply, the wonderful chemicals (antibiotics) that we currently use to treat bacterial infections, and which also underpin much of modern day health care, are beginning to not work. The consequences of a world where the drugs don’t work are not very nice at all.
We can all do our bit to reduce the pressure of antibiotics on bacteria and slow down the development of resistance whether it is by reducing antibiotic consumption, finishing our antibiotics or not eating food which is grown or reared with the routine use of antibiotics. What we desperately need, in addition to better antibiotic stewardship, are new classes of antibiotics; different from the ones we have been relying on for the last 70 years. Most of our antibiotics come from bacteria in the soil which produce them naturally in order to compete in, what is, quite a harsh environment. Therefore there is an argument that maybe we just need to look harder.
Citizen science and Crowdfunding
We decided to use this urgent need to engage the public and increase awareness about the issues surrounding resistance and hopefully find some exciting new chemicals which we could use as drugs. The Swab and Send project, now in phase III allows individuals to pledge a small amount of money and embark on the hunt for novel antibiotics themselves. Individuals who participate in this citizen science project can swab anything and send it to our lab for analysis. As it is crowd funded, it means we get a good return rate on the swabs we send out. We have already received swabs from a wide range of different places which can be found on the Swab and Send Facebook site. When we plate out the swabs in the lab we grow a unique collection of bacteria from each one which we then screen for antibiotic production.
De-replication of discovery
A challenge in screening bacteria for antibiotics is that after sixty years of looking, the same old types of antibiotics tend to come up again and again. These are no longer useful to us because resistance has emerged and proliferated. We want to maximise our chances of finding something new and useful. Therefore we decided to initially screen our isolates against a clinical Escherichia coli that displays resistance to seventeen antibiotics from multiple different classes. This E. coli strain was originally isolated from blood of a patient at Alexandria Teaching Hospital in Egypt in 2009 and is part of another PhD project in the lab and also makes an ideal indicator strain for Swab and Send. We seek antimicrobial compounds that kill pathogenic, multi-drug resistant bacterial strains, such as this E.coli.
We have currently screened over 2000 Swab and Send isolates and have identified 52 that appear to inhibit the growth of our multi-resistant E. coli. Fifty-two isolates are too costly in time and reagents to study simultaneously. We rescreened these isolates against other nasty pathogens to shrink our list of candidate bacterial isolates. Those isolates inhibiting more than one pathogen are top priority as they may be producing an antibiotic with broad activity, or more than one antibiotic. We tested them against methicillin resistant Staphylococcus aureus (MRSA) – a multi-resistant bacteria known in the media as the ‘hospital superbug’, and Candida albicans. Candida isn’t a bacteria, but a fungus which causes candidiasis, commonly known as thrush. Fungal infections are becoming more common these days but are very difficult to treat. This is because fungal cells are very similar to our own, meaning current anti-fungal drugs can have very nasty side effects as they don’t discriminate against the fungal infection and our own bodies.
So far we have found that 10 of the isolates also inhibited the bacteria MRSA, while 5 inhibited the fungus Candida albicans, and 2 inhibited both of these as well as our E. coli. We determined what type of bacteria they are by sequencing a gene commonly used to identify bacteria called the 16S ribosomal RNA gene. All of these isolates were of the genus Bacillus, which is a group of bacteria known for having the capability to produce a lot of different antimicrobials. Potentially a lot of interesting chemicals are waiting to be found inside them! These isolates came from lots of weird and wonderful places including horse manure, an asparagus bud, a garden trampoline, a refrigerator, Charing Cross train station in London, and even the Nile Valley in Egypt. This just goes to show what exciting new discoveries might be under our very noises.
Isolation of the Antibiotics
The next step now is to try and extract and identify the chemicals these bacteria produce and see what they can do. We’re taking two approaches with this. Firstly, there is the traditional fermentation approach. This is where the bacterium is grown in liquid for a while to allow it to produce its chemicals and secrete them into the liquid. When we remove the bacteria from the liquid we test for the presence of any chemicals, purify them, and test them to see which one (if any) can kill. This is a tried and tested method; however, it’s not perfect. Sometimes bacteria can be stubborn and refuse to produce the chemicals freely because the exact nutrients which lead to production are not present in the media we use or certain environmental signals are absent when we grow them in the lab. Sometimes we know the bacteria have the capacity to produce some interesting chemicals as they have the required pathways in their DNA but we just can’t make them turn these on, we call these “cryptic pathways”. Additionally there is always the chance that we are rediscovering the same old stuff.
The second approach compliments the first and offers the chance to find chemicals that the bacteria won’t produce freely, and that is to sequence the entire genomes of the bugs. Every chemical the bacterium can produce is written into their genetic code. Using computer programmes we can ‘read’ this code and identify what chemicals the bugs can produce. This information can help us identify chemicals purified from fermentation liquid. But if the hypothetical chemicals our computers find aren’t being freely produced we can try and re-engineer the genes of the bacteria to force production.
Like any new drug, any novel antimicrobials we find still have a long road ahead of them with no guarantee they are suitable for human use. Clinical trials, large scale production, shelf-life, stability, and interactions with other drugs. However, new antibiotics can’t save lives if we don’t find them first! Swab and Send’s purpose is first finding as many potential new drugs as possible. The more drugs tested, the better chance we will find the next life-saving antibiotic.
About the Authors:
Tim Walker is a PhD student in Molecular Microbiology at UCL, funded by the BBSRC. He holds a MRes in Microbiology from Birkbeck College, University of London and a BSc in Biotechnology from The University of Edinburgh. He is interested in utilising microbially produced compounds for industrial and medical use.
Adam Roberts, PhD is a senior lecturer at UCL. He and his group investigate antimicrobial resistance, horizontal gene transfer and bacterial pathogenicity. They also search for new antibiotics and other interesting compounds produced by microbes. He is an advisor to the Longitude Prize and an award winning public outreach activist.