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.

Alien Invasion


Half the DNA on the NYC Subway Matches No Known Organism 

Indeed. But Don’t Panic!

We have (probably) not been invaded by aliens. This is merely a reminder that science still (and always will) have its limits. It’s not that half the DNA on the NYC Subway belongs to stuff from other planets, it’s just that we can’t match it against our genetic libraries right now because we simply don’t have enough books in them yet (he said, completely mangling the analogy).

As we continue to improve our knowledge of which bits of DNA come from which organisms (and we’re really just talking about bacteria here, because we’re kinda up to date with mammals and the like), so the next time we see that chunk of DNA on a subway (or anywhere else), we can attribute it to a given organism, and reduce that 50% bit by bit until there’s very little that’s unknown about the DNA on the NYC Subway.

In the meantime, there’s a really nice interactive map here, allowing you to look at which bacteria were found at which stations, or – better still –  to search by types of bacteria to see what they are associated with (from “heart valve infections” to “mozzarella cheese”) (no anthrax, though) and see whereabouts on the network they were found.

Let’s just say that I’m going to be avoiding 168th Street and East 149th Street for some time. Possibly forever.

I mean… Dysentery! Really?!?

Tenuous flesh-eating killer bug link

Usually, stories about flesh-eating killer bugs are enough to make the headlines all by themselves. Superstar disease, see?
But put yourself in the shoes of an online editor for a big News Corp and think how many clicks you could get if you tied it in with something else that also attracts a lot of attention.

Like a hurricane. That hurricane:

Yes. A man who was repairing homes flooded by Hurricane Harvey has died of necrotising fasciitis. By all accounts, he was a very nice man and this is a very sad story. But the Harvey link is rather tenuous at best.

Necrotising fasciitis (the ‘necrotising’ obviously has a Zee in America, by the way) is a nasty bacterial infection, caused by a range of different toxin-producing bacterial species. The infection gets into the body via a cut or wound, spreads quickly in the soft tissue between the skin and the muscle and can be lethal – as seen in the case of the unfortunate Mr Zurita above.


Hurricane Harvey has claimed another victim, about two months after making landfall in Texas.

But has it? Has it really?

The only connection between this death and Hurricane Harvey is that Josue Zurita was repairing houses which had been damaged in the recent storm. There’s not even any evidence that the wound which became infected was as a result of the work he was doing.
There are over a thousand cases of necrotising fasciitis in the USA every year, and the only reason that Harvey might increase the risk is that people sometimes hurt themselves while doing construction work and right now there’s more construction work going on than normal in Texas.

“We’re surprised we saw three of them in the region, but given the exposure to all the construction and potential injuries that people would have… it shouldn’t be surprising. It’s well within what we would expect given those numbers,” said Dr. Philip Keiser, the Galveston County local health authority.

So even the local doc says he’s not surprised. And nor should he be, because I’ve been doing some rudimentary calculations (rather unscientific ones, but still): 1,100 cases, divided by 50 states gives you an average of 22 cases per state per year or 1.83 per state per month. And in the 2 months since Harvey, there have been 3 cases in Texas.

So exactly what you’d expect, then.

So the stats say there’s nothing special about this, the experts say there’s nothing special about this, but you still go ahead and tell us that this guys died of this Hollywood bug, just to get clicks?

Donald was right: CNN is Fake News!*


* in this particular case, at least. 

Plague in Madagascar: not good, but not unusual either

Microbiology in the news again. This time it’s an outbreak of the plague in Madagascar, and it’s causing a bit of a stir.
Now, don’t get me wrong – an outbreak of plague is never a good thing – but once again, a little perspective is called for here. Surprise (and if I may be so bold) “surprise”.

Plague is one of those diseases which captures the public’s imagination, with historical tales about the Black Death sweeping across Europe in the Middle Ages and killing an awful lot of people in its path. And because of that history, plague has a cool nickname and a “superstar” disease status, and news outlets – desperate for clicks – are getting overly excited about it, just like they did with Ebola.

But the fact is that plague is not just a historical disease: yes, it was infamously around a few hundred years ago, but it never really went away. As with many diseases, its prevalence has merely declined due to better hygiene, better education, better pest control and better medical treatment. But even in (supposedly) developed countries like the USA, there are still up to 20 documented cases of plague each year. Worldwide, there are a few hundred reported cases each year, with a mortality rate of around 25%. However, it’s likely that there are many more unreported cases, given that it is now primarily a disease found in rural areas of less developed countries.

The bad news is that Madagascar is a less developed country than the USA (albeit that its gun control laws are somewhat better), and this makes outbreaks of plague (or any other infectious disease) more likely to occur there and more difficult to control once they do.

The better news is that while this is a terrible and potentially disastrous situation, at this point, it’s certainly not unusual. Madagascar is the plague capital of the world (look, it’s not a claim that they stick on their tourism posters) with around 80% of the world’s cases each year, and outbreaks occur almost annually around this time of year, as the temperatures start to rise and the rat and flea populations – vectors of the disease – start to increase.
Additionally, because of this recent history, the authorities will be better set up to deal with the outbreak, despite the challenges mentioned above. And as we saw with Ebola in West Africa in 2014, that’s really important. Also, as long as you can get treated promptly, as a bacterial disease, plague is eminently treatable with simple, basic, cheap antibiotics.

I’m in no way belittling a very serious situation, but if you didn’t get all panicky and excited about the plague outbreaks in Madagascar in, say, 2014 and 2015, then right now there’s really no reason to get carried away about this one either.

Bird Flu back

We have another outbreak of bird flu in the Western Cape. Officially, of course, it’s called Highly Pathogenic Avian Influenza (HPAI), but no-one knows what HPAI is, so let’s still with the vernacular, shall we? This latest outbreak, currently confined to two farms in the Heidelberg area, is type H5N8. Again, this means very little to the man (or womxn) on the street, but it is important to us scientists.

There have been 13 outbreaks of bird flu up north since June this year:

The outbreaks involved seven commercial chicken farms, two groups of backyard chickens, three sets of wild birds and one group of domestic geese.

But this is the Western Cape, and we like to do things a little differently. Thus, our outbreak is centred around two ostrich farms. Given that one of the primary symptoms of bird flu is a sore throat, contracting the disease if you’re an ostrich can’t be very nice – like an elephant getting earache or a narwhal suffering with horn rot.
That said, given that one of the other symptoms of bird flu is death, contracting the disease can’t be very nice full stop.

Fortunately, this outbreak seems to have been caught promptly during routine testing (which is what routine testing is all about, of course). The good news about this is that hopefully it won’t have the opportunity to spread. The bad news is that it’s still likely that all 1000 ostriches involved will have to be culled.

You might expect some sort of pithy comment to finish this informative post off, but the whole situation is actually potentially rather serious, so I think we’ll leave that for another time.