Day 98 – Poo studies

Here’s some news about poo studies! Yummy.

A few other facts first.

If you go for a Covid-19 test (which you actually can’t do now, because even our fancy schmancy, first world, private laboratories are completely overwhelmed), you will have a swab thrust into your head (hopefully through one of the holes in your nose) and that swab will be sent to the laboratory.

At the lab, they’ll wash the bits of stuff off the swab, apply a few chemicals to the juice, wave a  magic scientific wand over the little test tube and and put it into a machine which looks for a specific chunk of the RNA – one which is usually tucked inside the SARS-CoV-2 virus. The chunk of RNA that the machine looks for is only found in the SARS-CoV-2 virus, so it won’t detect any of your DNA or RNA, nor the genetic bits of anything that you’ve been snorting recently.


The thing is, you can find this section of RNA anywhere that the virus is (like up your nose), just by looking for it. And equally, because it’s so specific to this virus, you know that wherever you find these chunks of RNA, that’s indicative that the virus is there.

For the purposes of this post (and basically all of the scientific rationale behind Covid-19 testing):

Chunk of RNA = SARS-CoV-2 virus

Hold that thought.

Next up: one of the big problems with this pandemic stems from the fact that (even if you have enough tests to go around), we have people who don’t know that they have got the virus (because they show no symptoms), but who are passing it on. And because those people aren’t unwell, they don’t go to get tested (because why would you?), and so we actually have very little idea how many people in any given community actually have the virus. This makes it difficult to work out how many people are likely to be sick in that community and that makes if difficult to successfully and efficiently allocate resources. Ugh.

There’s some good news though: when we are infected with viruses (yes, including SARS-CoV-2) – whether or not we are showing symptoms – we poo out viruses (yes, including SARS-CoV-2). And, as we’ve already deduced above, we can look for SARS-CoV-2 anywhere, just by looking for that bit of RNA.

Are you going where I’m going here? Yes: down to the local sewage farm.

Mariana Matus has spent years studying what comes out of human bodies in order to better understand what is happening inside us. The computational biologist helped develop heavy-duty devices that are about the size of a milk crate and can be lowered into manholes to dangle over wastewater:steadily sucking up a stream of urine and feces through a straw-like tube.

Is it lunchtime yet?

The process in the lab is just about the same as if they were testing you, except that instead of doing the science with a swab from up your nose, they do it on some poo juice.

Even better news is that it seems that an uptick in the amount of RNA (and therefore the amount of virus) in the community’s sewage predicts an increase in local Covid-19 cases by about a week.

This environmental surveillance data were compared to declared COVID-19cases at municipality level, revealing that members of the community were shedding SARS-CoV-2 RNA in their stool even before the first cases were reported by local or national authorities in many of the citieswhere wastewaters have been sampled.


It’s early days, but this sewage screening technology has been used to predict other viral outbreaks such as Norovirus and Hepatitis A and could give us some important insights into how widespread the virus is and where we might be about to see one of those already infamous spikes – allowing us to get ready to deal with it by changing rules and/or providing extra healthcare resources. In turn, this might limit the extent of the local outbreak.

(And it works the other way, too: we can note a decrease in wastewater virus levels and predict when to lift lockdowns appropriately.)

This isn’t a substitute for testing people, obviously. We don’t know whose poos we’re testing. But as a epidemiology management tool, it could be hugely useful. It should also assist when (if?) a vaccine for Covid-19 is rolled out, as general community prevalence of the virus will be a good indicator of both vaccine uptake and success.

The only downside is that someone has to wander around your local sewage farm, sucking up the effluent and testing it each day to get these numbers. So just thank your given deity that there are people willing (and possibly even excited) to do this work for the good of humanity.

Stay home. Stay safe. Poo regularly. Microbiology will do the rest.

How long can a bacterium live?

Note: This is not a 5-second rule thing.

It’s ages. Really – an awfully long time.

But – can it manage to get to the ripe old age of 500 years?

Well, pop back in 2514 and researchers at Edinburgh University will be able to tell you. If there is still such a thing as a researcher by then. Or indeed a University in Edinburgh. Or indeed, an Edinburgh.

Who knows what the future holds? Other than our friend the Asparamancer, of course?

The experiment itself is really rather simple: at a given timepoint, take one of the hermetically sealed vials and crack it open, rehydrate the contents and plonk them onto an agar plate, incubate and see what grows.

A 10 year old could do that.

But not for 500 years. Because humans don’t live that long.

So the problem becomes not doing the experiment, but how to tell other people how to do the experiment. Paper won’t last. A fancy carved metal sheet might get nicked by some marauding invaders at some stage over the next 5 centuries: and technology?

The team left a USB stick with instructions, which Möller realizes is far from adequate, given how quickly digital technology becomes obsolete.

And if you think that is a bit over the top, please note that no-one had even heard about USB 25 years ago, because it hadn’t been invented then.

So, the idea is to keep up to date by charging a human (a good choice because if there are no humans around, then there’s really no-one interested in the results anyway) to update the instructions every 25 years to some suitable format that will last until the next update.

I’ve done experiments that have lasted a couple of years, but they don’t have the same difficulties as this one, because I fully expected (correctly, as it happens) to still be alive when I finished it. There were occasional issues with remembering time points, but Google Calendar helped out with them. Will Google Calendar be around in 25, 50 or 500 years? I doubt it.
And it’s not like the lab staff will be working on this 24/7. This is an entirely  occasional thing.

I’m not sure how often data from this experiment are going to be shared, but I’ll keep an eye out, if only to give them a nudge if I think that they’ve forgotten to do their plating that year.

More micro in the news

I had literally an email about yesterday’s post, in which I lamented the frankly appalling image of microbiology in the news. And it turned out that the email was sent regarding a speling errer in the post, which I thought I had, and have now, corrected.

Still, despite the lack of support from the 6000 miles…  reading public, I set out with renewed vigour yesterday in an effort to find and document a better side of my favourite branch of science in the media.

I failed.

The most recent stories I could find which involved Microbiology were this one:

which included this line:

Staphylococcus aureus, which causes a range of conditions including MRSA, was found three times more often on the surfaces of air dryers compared to paper towel dispensers during an international study.

Well, MRSA is Staphylococcus aureus, it’s not ‘a condition caused by’ Staphylococcus aureus. It’s almost as if the S and the A in MRSA stand for… ag… you get my drift.

Gell-Mann Amnesia Effect anyone?

Anyway – the upshot of this whole thing is that there are fewer bacteria that are going to kill you while you’re in hospital if people use paper towels than if they use jet air dryers.

We found multiple examples of greater bacterial contamination on surfaces, including by faecal and antibiotic-resistant bacteria, when jet air dryers rather than paper towels were in use.

Nice. [dry heave]

And remember, folks: Hand dryers also terrorise the vulnerable.

… And this one:

No issues here though, because the chances of anyone picking up a virus and transmitting it to anywhere around the world in this scenario is… oh… is actually really high. Could there be a worse place for nasty viruses to be found? This is literally how pandemics start. Or at the very least, it’s how they become pandemics.

Not great.

The image that Sky News chose to illustrate this story is interesting.

Now, I’m not someone who travels an awful lot, but I’ve done my fair share of flying, and that looks highly illegal. I’m pretty sure that whoever’s plastic security tray that is, isn’t getting their stuff back.

But then, considering that it’s now all – from their Old Spice stick deodorant to their Maybelline foundation (mmm) – covered in nasty viruses from the tray anyway, maybe not getting it back is actually quite a good thing.

Perhaps the best professional advice I can give is for you to pick your hand luggage up from the plastic security tray, and then go and immediately wash your hands in the first public loo that you can find.

Unless there’s an air dryer in there, of course.
In which case, you’re already as good as dead.

Microbiology is bad news

Except it’s obviously really not.

Microbiology is great.

But when microbiology gets into the news, it’s rarely for happy happy joy joy reasons. Even the mention of words like Ebola, Listeriosis or Bacteroides melaninogenica twist the tongues and instill fear into the hearts – and horrendous infection into other major organs – of the population.

This isn’t how it should be, so to balance the bias, I went searching for some good news microbiology stories.

Rookie error. It’s all terrible.

A tiny beetle is is killing South Africa’s trees. But only because it’s introducing a tinier fungus into those trees.

According to Professor Marcus Byrne, an Ig Nobel prize winner and entomologist at the University of the Witwatersrand, the beetle bores tunnels into tree trunks where it spreads the fungus Fusarium euwallaceae, which effectively cuts off the trees’ vascular system, causing them to die.

So, it’s the fungus that is actually killing the trees. Not the beetle.
Entomology is only very slightly to blame here. Microbiology loses again.


Aside: Ig Nobel prize details here:

Byrne, an entomology lecturer, and his colleagues from Lund University in Sweden, designed caps and boots for dung beetles and dressed the beetles in their new apparel to prove, firstly, that dung beetles use the Milky Way to orientate.

The caps blocked light from reaching their eyes in order to experiment with how they use starlight to navigate. The boots, in a fashionable luminous green, blocked heat from reaching the dung beetles’ feet.


Next up: Virus kills pigs. Millions of pigs.

It’s African Swine Fever caused by… er… the African Swine Fever Virus.

Otto Saareväli lost his entire herd of 7000 pigs because of a case of ASF was diagnosed on his farm in Estonia.

“We have the strictest biosecurity measures here, and still no one is quite sure how the disease got in – it may have been a truck that wasn’t washed properly after visiting an infected farm,” says Saareväli. “But if you find just one pig, then everything has to go.”

Estonia is just the tip of the iceberg though. China is home to half the pigs in the world, so it’s vital that the virus doesn’t get a trotterhold there… oh… too late:

“The key thing that makes us very conscious of the threat that ASF poses is that China represents half the pigs in the world,” says Dr Matthew Stone, deputy director general of science at the World Organisation for Animal Health (OIE), which coordinates international monitoring of diseases. “It’s extremely important for food security and the economy of China and in the absence of a vaccine, stamping-out policies are crucial.”

And it’s not under control.

“At the moment because it’s on the move and undergoing a period of pandemic spread it’s very important.”

Still – at least that’s just a virus of pigs. There’s worse news when it comes to (very human) Measles Virus.

The annoying… no… the INFURIATING! thing about hearing about cases of, and deaths from, measles is that we have a very, very effective vaccine for measles. It’s entirely preventable.

Simply: there is no need for any child, any human, to suffer from, let alone die of, measles. So why is it happening?

Well, in Western Europe because “Dr” Andrew Wakefield is a corrupt twat, and because people chose – and continue to choose – to believe his lies.


Oh, and because misinformation and fake news is a big deal these days:

A new study showing that Russian-linked trolls and social media bots have been heavily promoting misinformation on vaccines shows just how far Putin’s government is prepared to go in its worldwide effort to sow mistrust and division. The study follows rapidly on the heels of earlier reports that Russian-owned media sites had been among the most prominent proponents of anti-GMO stories and memes, again aiming to undermine scientific consensus and public trust in academic institutions.

Both anti-vaccine and anti-GMO groups appeal to prejudices against modern science and conspiracy thinking to spread fear and misinformation. Like the tobacco lobby of old, doubt itself is their product.

We live in a truly sick (no pun intended), truly bizarre world.

And, as if it couldn’t get any worse, this:

In which, the Indonesian Ulama Council (MUI) declared the vaccine haram – religiously forbidden, despite also commenting that:

…the religious organisation understood the dangers associated with not getting children immunised.

So they do understand that the vaccine works, they do understand the need for it and they do understand the implications of children not being vaccinated, but they’re still going ahead and railing against it anyway.


And why would you do that?

It’s entirely possible Amin is using this fatwa and the MUI in general as political tools to impact the election. The group receives funding from the government of Indonesia, and Amin has used it to impact politics in the past.

Ah – personal gain at the expense of others. Pretty sure that’s unlikely to be top of the list at the Things I Learnt From the Quran Symposium later this year.

To be fair to Microbiology, it might be Fusarium spp. killing the trees and not the beetle, but it’s Ma’ruf Amin killing Indonesian kids and not the measles virus.

Science is doing everything it can, but in Indonesia, it’s Religion 1-0 Microbiology.

Microbiology will still get the blame, though.

I will go on looking for good news Microbiology stories, but I’m not going to waste too much time over it, because I don’t think that there are any of them out there.

Wash the duck up

OK. We’re still not supposed to have baths in Cape Town and many people have seen that as a bad thing, but given this new research from Swiss and American researchers, maybe it’s not so unwelcome after all.

How could we ever have expected that something which is dark, constantly moist and regularly warmed to somewhere around body temperature could be a place that bacteria and other nasty bugs might like to live?

It’s almost like that old research from Swiss and American researchers from a few years ago which suggested that His Holiness the Supreme Pontiff, Bishop of Rome and apostolic successor to Saint Peter… might be Catholic.

Who knew?

They also did something about bears… I think that one might have been disproved though.

Swiss and American researchers counted the microbes swimming inside the toys and say the murky liquid released when ducks were squeezed contained “potentially pathogenic bacteria” in four out of the five toys studied.

The bacteria found included Legionella and Pseudomonas aeruginosa, a bacterium that is “often implicated in hospital-acquired infections.”

Well, at least it’s not penguicidal avian flu.
Still, not great, but really not very surprising either. Create near perfect conditions for microbes to thrive and microbes will thrive.

Lots of them:

They turned up a strikingly high volume – up to 75 million cells per square centimetre – and variety of bacteria and fungus in the ducks.

As a microbiologist, I’m used to seeing big numbers when it comes to the number of cells in any given place, so yes, that’s a big number, but microbes like to grow in big numbers.

Still, multiply it up for the internal area of this big boy…

…and you’ve got enough bacteria to wipe out the entire planet several times over. Perhaps that’s Florentijn Hofman‘s secret plan.

Anyway, if you’re a parent and you have concerns (or even if you’re not a parent and you have concerns), you have a few options:

Ditch the duck.
Clean the duck.
Buy a watertight rubber duck to prevent internal growth of nasty bugs.

It’s worth noting that actual, real ducks are also watertight, and most of them aren’t full of Legionella and Pseudomonas spp. – lessons from Mother Nature, ne?

But perhaps the best way to avoid diseases transmitted by rubber ducks is not to bath with a rubber duck in the first place. Or – as I mentioned at the start of this post – not to bath at all.