Sunday, April 7

Ya mean the Doomsday Bug is a fungus?

Well well, three wells make a river, close your mouth Pundita you'll catch flies. But I can't help but be open-jawed; all these decades scanning the horizon for a freepin' supervirus then get a tap on the shoulder: 'Hi, how are ya? I'm a fungus.'

The good news is that the fungus Candida auris only kills about 45 percent of the people it infects, and most of those are just babies and old people. Oh right, and others with weak immune systems like diabetics and there are only 500 million or so cases of diabetes worldwide although this number is projected to skyrocket as more people in the 'developing' world get fat. 

The bad news is that the fungus seems to operate on the principle that whatever doesn't kill it makes it stronger. In other words, not only is it resistant to the top treatments for fungal infections, it thrives on them. 

Now before we ask how a garden-variety fungus morphed into a killer with global reach, we need to get our priorities in order. First and foremost, who can we blame? 

Right now it looks like a tie between (a) the CDC/WHO for not sounding the alarm earlier and wider; (b) hospitals that got hit by C. auris but kept their mouths shut so as not to scare off patients; and (c) the agriculture industry with emphasis on Big Ag, although this wouldn't absolve the little guys. From the bombshell April 6 report from The New York Times, A Mysterious Infection, Spanning the Globe in a Climate of Secrecywhich has already gone, uh, viral (c) may have the edge when it comes to parceling blame:
There are different theories as to what happened with C. auris. Dr. Meis, the Dutch researcher, said he believed that drug-resistant fungi were developing thanks to heavy use of fungicides on crops.
Dr. Meis became intrigued by resistant fungi when he heard about the case of a 63-year-old patient in the Netherlands who died in 2005 from a fungus called Aspergillus. It proved resistant to a front-line antifungal treatment called itraconazole. That drug is a virtual copy of the azole pesticides that are used to dust crops the world over and account for more than one-third of all fungicide sales.
A 2013 paper in Plos Pathogens said that it appeared to be no coincidence that drug-resistant Aspergillus was showing up in the environment where the azole fungicides were used.
The fungus appeared in 12 percent of Dutch soil samples, for example, but also in “flower beds, compost, leaves, plant seeds, soil samples of tea gardens, paddy fields, hospital surroundings, and aerial samples of hospitals.”
Dr. Meis visited the C.D.C. last summer to share research and theorize that the same thing is happening with C. auris, which is also found in the soil: Azoles have created an environment so hostile that the fungi are evolving, with resistant strains surviving.
This is similar to concerns that resistant bacteria are growing because of excessive use of antibiotics in livestock for health and growth promotion. As with antibiotics in farm animals, azoles are used widely on crops.
“On everything — potatoes, beans, wheat, anything you can think of, tomatoes, onions,” said Dr. Rhodes, the infectious disease specialist who worked on the London outbreak. “We are driving this with the use of antifungicides on crops.”
Dr. Chiller [yes, that's his real name] theorizes that C. auris may have benefited from the heavy use of fungicides. His idea is that C. auris actually has existed for thousands of years, hidden in the world’s crevices, a not particularly aggressive bug. But as azoles began destroying more prevalent fungi, an opportunity arrived for C. auris to enter the breach, a germ that had the ability to readily resist fungicides now suitable for a world in which fungi less able to resist are under attack.
On the other hand, I can't see Big Ag taking the fall for this; if push comes to shove they'll take an actuarial tack, arguing that many more people will die of starvation than would be killed by a germ if crops aren't blanketed with fungicides. If worst comes to worst they can always point the finger at Big Chem: Look, we just spray the stuff; we're not to blame if these companies make fungicides that make fungi stronger.

So the biggest blame might land on (b) and there is already an indication of how the winds are blowing in this regard. To return to the NYT report:
“Why the heck are we reading about an outbreak almost a year and a half later — and not have it front-page news the day after it happens?” said Dr. Kevin Kavanagh, a physician in Kentucky and board chairman of Health Watch USA, a nonprofit patient advocacy group. “You wouldn’t tolerate this at a restaurant with a food poisoning outbreak.”
He does have a point. There is no question that health care providers have to be more forthright with the public about outbreaks of all types of lethal infections in their facilities. The point would hold doubly true for dealing with killer fungi. Scientists are concerned that C. auris could make the jump from people with weak immune systems to a healthy population. The places ripe for this opportunity are health care facilities that provide services for healthy people in addition to caring for the sick, which covers just about all medical facilities.  

Another reason to fear C. auris in the medical-care setting is that the thing is well-nigh impossible to kill off even with extreme decontamination measures -- as you will see if you read the NYT report.

From here on out, medical clinics and hospitals must take special pains to keep reasonably healthy patients separated from the sick ones. At the least, they have to start issuing an alert to the public the moment they discover an outbreak of  C. auris in their facility.

Aso to whether C. auris or another fungus could become a doomsday bug -- I think there are too many variables, too many unknowns, to make a stab at the answer at this time. Much is still unknown about C. auris, which made its first known appearance in the USA in 2013, although it had probably been loose here before that. To return once more to the NYT report:
The C.D.C. investigators theorized that C. auris started in Asia and spread across the globe. But when the agency compared the entire genome of auris samples from India and Pakistan, Venezuela, South Africa and Japan, it found that its origin was not a single place, and there was not a single auris strain.
The genome sequencing showed that there were four distinctive versions of the fungus, with differences so profound that they suggested that these strains had diverged thousands of years ago and emerged as resistant pathogens from harmless environmental strains in four different places at the same time.
“Somehow, it made a jump almost seemingly simultaneously, and seemed to spread and it is drug resistant, which is really mind-boggling,” Dr. Vallabhaneni said.
But while much remains unknown about the fungus, I think it can be said with certainty that it doesn't bode well for humanity if our immune systems are becoming weaker; there is the concern that this is happening as we become cleaner. Discussion has been going on for years about what's been dubbed the "hygiene hypothesis."  See this 2015 BBC report for an overview of the discussion.

And there is concern that bottle-fed babies have weaker immune systems than breast-fed ones. 

We could be backing ourselves into a situation not unlike the one portrayed in "War of the Worlds," where invaders from a technologically advanced alien civilization were felled by ordinary germs on our planet.

All right; I've chopped up the New York Times report enough;  I think you'd be wise to go to their site and read the whole thing from start to finish.  The lead author of the report, Matt Richtel, is a Pulitzer Prize-winning journalist who specializes in translating some pretty dry subjects into a whale of a tale, and that's certainly the case with C. auris.


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