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This simple graph shows how sewage water might predict COVID-19 outbreaks — but it also shows how statistics can trick you

The bad news? COVID-19 can be transmitted through poop. The good news? We can use that to our advantage and track the outbreak. The caveat? The science is somewhat debated.

Virus RNA concentrations in sewage sludge almost perfectly predicts COVID-19 new cases. Image credits: Peccia et al.

Prior research has shown that when people are infected with SARS-CoV-2, it shows up in their stool samples. Recent research has even confirmed that these are active, infectious viral pieces. So poop can, at least in theory, be capable of passing the disease (at least in people suffering from a severe infection). But this is unlikely to make a significant difference in the grand scheme of things, at least not directly.

Poop is, thankfully, not an important means of transmission for this particular virus, but it could be a way to monitor it. Several teams have already pointed out that sewage water might be a useful and non-invasive tool to track COVID-19 spread in a community and detect clusters.

The downside of it is pretty obvious: you don’t know who has the disease, or exactly how many people have it, but it’s still very useful: you follow the amount of virus in the water, and when you see a sudden rise, you might be alerted of an emerging infection cluster.

Having an alert system could be of great help — and poop could be that alert system.

Infection with SARS-CoV-2 is accompanied by the shedding of the virus in stool. That might be a good thing, because it could give researchers a way to track the spread and concentration of the virus in a population.

Here’s a common scenario: the government is looking at ways to relax the pandemic lockdown. At the same time, it is vital to make sure that the number of COVID-19 cases doesn’t spiral out of control. But there’s a catch: there’s a lag between when people contract the disease and when they start manifesting the disease. If you wait for people to start developing symptoms, you may already be too late to nip the outbreak in the bud.

What we flush down ultimately ends up in the sewage system, and that includes viruses. The idea is not new. Sewage water can tell us a lot of things about the community, from how rich people are to what type of diseases the community has.

Several research groups have already shown data suggesting that sewage water could be used for this purpose, and a new study at Yale backs that idea up. The study, which features the chart at the top of the article, has stirred a lot of debate.

Unlike other studies, this study utilized primary sewage sludge instead of raw wastewater for virus RNA measurements (sewage sludge being comprised of solids that are removed during primary sedimentation steps and typically gravity thickened). Sludge was preferred because it tends to have a higher concentration of viruses, which makes it easier to detect the trends.

While the study only analyzed data from one plant (and the researchers caution that there may be significant differences in different plants), the results are very encouraging, suggesting that sewage is indeed a good predictor of COVID-19 infections.

“Raw wastewater and sludge-based surveillance is particularly useful for low and middle-income countries where clinical testing capacity is limited,” the study concludes.

But there’s a caveat: the chart looks almost too good. In the real world, nothing is correlated this well, and even if sewage sludge can predict coronavirus infection, this is too perfect to be believed at face value.

So a couple of researchers took a look at the data behind the graph and found a few issues with it. Nick Brown, self-appointed data police cadet who often comments on statistics on Twitter analyzed the data from the study, and found that the original study authors did a bit of statistical trickery.

What the chart does is that it correlates the trend lines for smoothed data presented in the study. Let’s break it down in simpler terms. The data looks like this:

Image credits: Peccia et al.

Scatter plots such as this one often deploy a trend line, which is basically a way to visualize the approximate trend followed by the data. This line itself is an approximation — as you can see above, it can’t correlate perfectly.

Then, this is smoothed, which is another approximation. Sure, the smoothed data trend-lines fit perfectly, but the real data doesn’t fit quite as smoothly. There’s still a correlation between the actual data (as was revealed by Brown and several other researchers commenting on the study, but it’s not nearly as spectacular. It’s still exciting and warrants further investigation, but the statistical artifice is unfortunate and disappointing.

The bottom line

This study has not yet been officially peer-reviewed (although unofficially, it was truly put to the gauntlet). Alexander Danvers published an excellent write-up of why researchers sometimes do this: there is a perverse incentive for researchers to publish as much as possible and as stand-out-y as possible. It’s almost certainly not ill-intent, but rather sloppiness, Danvers writes. The study is valuable and creative, and shows a plausible, cheap, and non-invasive way of predicting COVID-19 infections. With a bit more attention, we wouldn’t have spent the past few paragraphs diving into this whole issue.

“The key takeaway here isn’t that the Yale researchers who conducted the poop study are bad. The work is thoughtful and creative, and even being able to predict COVID-19 outbreaks with 15% accuracy is useful. The takeaway is that the behavior of scientists is governed by incentives, and these need to be better aligned with the production of high-quality science,” writes Danvers.

It’s definitely not perfect, and there is a lot of fine-tuning, but sewage water is still pretty much on the table when it comes to predicting outbreaks.

The loosening of restrictions has had mixed results, with some places continuing to see declining infection rates, while others reporting a dramatic rise in cases. While things like mandatory face masks and contact tracing are believed to play a role here, at this point, it’s impossible to say where the disease will make a resurgence and where it won’t. Having access to a cheap and non-invasive way to raise the alarm when COVID-19 cases are on the rise could make all the difference in the world.

We’d be crazy not to use this.

Credit: Wikimedia Commons.

Purple bacteria turns sewage waste into clean energy

Wastewater is not something you usually want to be around — but that doesn’t mean it can’t be valuable. Your typical household sewage is rich in bioplastics, organic compounds that can be turned into energy, or even proteins for animal feed. The challenge lies in separating contaminants from the valuable organic compounds — the gold from the trash, so to speak. Now, researchers say they’ve found a new cost-effective and environmentally-friendly method that does just that using purple bacteria.

Credit: Wikimedia Commons.

Credit: Wikimedia Commons.

In most people’s minds, photosynthesis is associated with the color green. However, photosynthetic pigments come in all sorts of colors (think of yellow, orange, and red leaves in the autumn), but also in a variety of different organisms. For instance, a group phototrophic bacteria use energy from the sun via a variety of different pigments, such as orange, red, brown, but also purple — they’re even called purple bacteria.

However, it’s not their color that interests scientists but rather their unique metabolism. In the presence of light, these microbes use organic molecules and nitrogen gas to make carbon and nitrogen, all while releasing electrons. A byproduct of this metabolic reaction is hydrogen gas, which can be used to generate electricity in a fuel cell.

Dr. Daniel Puyol and colleagues at King Juan Carlos University, Spain designed a biorefinery process that harvests green energy from wastewater using a mixture of purple bacteria species. In a new study published in the Frontiers in Energy Researchthe research team analyzed the optimal conditions for maximizing hydrogen product and found a nutrient blend that not only outputs the highest rate of hydrogen, but also minimizes the production of CO2.

One of the biggest environmental problems associated with wastewater treatment is its significant carbon emissions which warm up the planet’s atmosphere. So, having a technical solution that not only removes this excess carbon from the atmosphere but also produces a useful, clean fuel is a great combo.

“Our group manipulates these conditions to tune the metabolism of purple bacteria to different applications, depending on the organic waste source and market requirements,” says co-author Professor Abraham Esteve-Núñez of University of Alcalá, Spain.

“But what is unique about our approach is the use of an external electric current to optimize the productive output of purple bacteria.”

The most interesting result, however, was obtained when the Spanish researchers found that purple bacteria are capable of using electrons from the cathode (negative electrode) to capture CO2 via photosynthesis. The bioelectrochemical system is the first demonstration of any phototroph shifting metabolism due to interaction with a cathode.

“Recordings from our bioelectrochemical system showed a clear interaction between the purple bacteria and the electrodes: negative polarization of the electrode caused a detectable consumption of electrons, associated with a reduction in carbon dioxide production,” Esteve-Núñez said in a statement.

“This indicates that the purple bacteria were using electrons from the cathode to capture more carbon from organic compounds via photosynthesis, so less is released as CO2.”

Capturing CO2 is useful not only to reduce carbon emissions but also for refining biogas for use as a fuel. What’s more, the researchers say that there may be even more surprises in store.

“One of the original aims of the study was to increase biohydrogen production by donating electrons from the cathode to purple bacteria metabolism. However, it seems that the PPB bacteria prefer to use these electrons for fixing CO2 instead of creating H2,” Puyol said in a statement.

“We recently obtained funding to pursue this aim with further research, and will work on this for the following years. Stay tuned for more metabolic tuning.”

British surfers are more prone to be antibiotic resistant bacteria carriers

A new study shows that surfers are three times more likely to harbor very resistant types of E.coli.

Surfers swallow almost ten times more seawater than the average swimmer, researchers at the University of Exeter report. Since many sewage collections drain into the sea, they sometimes bring along various types of Antibiotic-Resistant Bacteria (ARB). Researchers suspected that surfers ingest a worrying amount of such bacteria.

Source: Pixabay/andyperdana69

Dr Anne Leonard, lead author of the paper said: “This research is the first of its kind to identify an association between surfing and gut colonisation by antibiotic resistant bacteria.”

Unfit antibiotic treatments for viral infections and not respecting the full length and dosage of such treatments, are catalysts for bacterial resistance, a problem which is becoming more and more worrisome.

Bacteria are living organisms and the laws of evolution apply to them just like other creatures. When you take a treatment that kills most but not all bacteria, you’re accelerating their evolution. The survivors will be super trained to resist treatment. In a way, antibiotic resistance is their only way of surviving and adapting.

Via Pixabay/geralt

Surfing with the bugs

Scientists isolated many genes responsible for allowing Enterobacteriae (the family which includes E. coli) to survive antibiotics. One group, the blaCTX-M genes, confers resistance to multiple beta-lactam antibiotics.

Researchers analyzed 97 bathing water samples from England and Wales, noting the proportion of E. coli harboring blaCTX-M.They discovered that 11 out of the 97 bathing water samples were contaminated with the super-bug.

After they identified surfers as being at risk of exposure to ARB, scientists compared surfers and non-surfers to see whether there was an association between surfing and gut colonization by blaCTX-M- bearing E. coli.

The scientists discovered that 9 out of 143 (6.3%) surfers were colonized by blaCTX-M-bearing E. coli, as compared with 2 out of 130 (1.5%) of non-surfers.

Professor Colin Garner, founder and manager of Antibiotic Research UK — the only charity in the world set-up to tackle antibiotic resistance — said this was a “pioneering finding”.

He said that antibiotics enter the environment from farms or sewage. Environmental samples “have higher antibiotic concentrations than patients being administered antibiotics”.

“Research into new medicines to replace our archaic antibiotics has stagnated and unless new treatments are found, this could be potentially devastating for human health,” Professor Garners added.

“We know very little about the spread of antibiotic resistant bacteria and resistance genes between our environment, farm animals, wild animals and humans.”

Source: Pixabay/n4pgw

“This research helps us understand better the movement of resistant bacteria in surfers,” he said, but the next step should be testing if surfers and those in close contact with them are at greater risk of serious infection.

Fourth Day of Montreal’s 7-Day Sewage Dump

Raw human sewage isn’t in the news often enough. But infrastructure repair in Montreal has given sewage world attention.  Starting Wednesday night, Montreal began dumping 8 billion litres of raw toilet flushings, garburator grindings, and shower stall drippings into the St. Lawrence River. The mayor says they had to do it. It’s not such a big deal. The sewage, which will by-pass treatment for one week, may even bring fresh nutrients to the beautiful river’s fish, flora, and fauna. Or maybe it will kill them.

MontrealMontreal.  Eventually every city must do it. Upgrade its infrastructure, that is. (Credit: Wiki)

Montreal’s raw sewage dump is temporary. When the story caught international attention, Montreal Mayor Denis Coderre grew impatient with questions from American reporters. At a news conference  on Thursday, he suggested to American reporters that it might be “appropriate to take a look at some cities in the United States before talking against Montreal.”  Indeed. But American cities generally score well on sewage treatment. Unlike Canada, the USA has a national policy on sewage standards and it’s enforced (more or less) by the country’s Environmental Protection Agency. Two Canadian provincial capitals – Halifax and Victoria – dumped all their effluent directly into the ocean for centuries. In 2008, Halifax ended 250 years of ocean dumping, built a proper treatment plant, and then opened beaches to swimming.  Victoria – one of the loveliest cities in the world – still dumps raw. Canada’s biggest city, Toronto, handles its sewage well, except when it rains. Then, the wastes of its 3 million people swamp Toronto’s treatment plants. The excess flows directly into Lake Ontario.

A hundred years ago, the United States was lauded for its fine sewage system. By the 1940s, 80% of its city water was treated. Rural areas enjoyed a mix of efficient septic tanks and cesspools that handled wastes with dignity. But in recent years, American infrastructure has suffered budget cuts and things are beginning to leak and wreak. Many systems in the States have gone a hundred years without major repairs. Most recent USA sewage spills have been in the mere millions (not billions) of litres and have generally involved ruptured pipes (Pennsylvania) or tanks overflows (California).  But without infrastructure investment, a big spill is inevitable.

Even when wastewater is treated in modern sewage plants, the refreshed fluid contains a host of ugly modern chemicalsincluding pharmaceuticals, along with grit and grizz of all sorts.  A 2012 study by the United States Geological Survey working in Iowa found that treated wastewater went from streams to groundwater, carrying biologically active carbamazepine, sulfamethoxazole, and immunologically-related compounds. These biotics joined other known contaminants flowing from cleansed effluent. Other contaminants may include heavy metals, phthalates that mimic hormones, and industrial chemicals. Even when sewage is properly scrubbed, some chemicals evade removal. Arguably, those invisible chemicals smell OK, but are far more dangerous to the environment than highly noticeable human droppings.

Port-au-Prince – a city the size of Toronto – is one of the world’s largest cities without a sewage system. Most of the city’s raw waste runs through streets, into streams, rivers, and finally the sea. You’d think this could lead to disease. It does. Cholera erupted after the 2010 earthquake and has led to 9,000 deaths.  Brigades of Haitians are employed by the city to scoop cholera-infested waste into buckets. Every night, those bayakou crawl into latrine pits and pull out human waste. They dump it into the ditches and canals which ooze along with the day’s garbage, reaching Port-au-Prince Bay within a few days. In recent decades, the percentage of untreated sewage in Haiti has actually increased – it’s now just 17%. In 1990, 26% of wastewater was treated.

'Poor sanitation in Cap-Haitien' by Rémi Kaupp - Self-photographed. Licensed under CC BY-SA 3.0 via CommonsOpen sewer in Haiti.   (Attribution: Poor-sanitation-by-Rémi-Kaupp-Licensed-under-CC-BY-SA-3.0-via-Commons.jpg)

Other cities, such as Peru’s capital, have efficient collection systems, but sewage from the city’s 10 million people is untreated. It’s dumped directly into the Pacific. In Lima, I went to a pleasant beach where families splashed in the green water. I didn’t wade in the water – it looked much too green. And stuff was floating in it. I saw something similar in Vietnam’s capital, Hanoi. In the heart of the city, iconic lake Hoàn Kiếm with Turtle Tower on its small center island was awash in waste when was there.  Another big developing city, Rio de Janeiro, is trying to clean up its open sewers ahead of the 2016 Olympics.

peru and vietnamLima, Peru, left and Hanoi, Vietnam, right: Two beautiful cities that could use a bit of infrastructure. (Photos: Miksha)

Meanwhile, the city of Montreal is quickly – very quickly – fixing its infrastructure. In a few days, treated water will again flow into the St. Lawrence River. Until then, 8 billion litres of raw sewage will merge into the river’s flow. That’s 12,000 litres every second. However, each second 7,500,000 litres of clean water flow past Montreal. Merging in the sewage means mixing in one-tenth of one percent into the other 99.9% river water. The fish will hardly notice, except for the parts that are synthetic hormones, heavy metals, and microscopic carcinogens from plastics and industrially produced food scraps. But that stuff is in every city’s wastewater – even after sewage treatment.

warning signActually, it’s not that bad. (French inscription might be on the sign’s reverse side.)

golden toilet paper

You’re flushing a goldmine down the toilet, literally

At a recent meeting of the of the American Chemical Society, researchers proposed a novel source of valuable metals: waste water. They proposed a method that could be used to extract valuable metals like gold, silver or titanium which end up in waste water plants via the city’s sewage.

golden toilet paper

Who the heck throws gold down the toilet, you might ask. Well, you’ve done it plenty of times without knowing it, most likely.

“There are metals everywhere,” Kathleen Smith of the U.S. Geological Survey (USGS) says, noting they are “in your hair care products, detergents, even nanoparticles that are put in socks to prevent bad odors.” Whatever their origin, the wastes containing these metals all end up being funneled through wastewater treatment plants, where she says many metals end up in the leftover solid waste.

According to Smith, more than 7 million tons of biosolids come out of U.S. wastewater facilities each year. Half of that is used as fertilizer, while the rest is sent to landfills or is incinerated. One man’s trash, is another’s treasure, and with this in mind Smith and colleagues are currently working on ways to value solid waste, particularly rare metals. At first glance, you might think this isn’t worth it, considering the energy (money) you need to pump in the system to extract, but the waste from 1 million Americans might contain metal worth $13 million. In some places, the concentration of gold is about the same or more than that found in natural mine deposits currently being exploited.

This image shows microscopic gold-rich and lead-rich particles in a municipal biosolids sample. Image credit: Heather Lowers, USGS Denver Microbeam Laboratory

This image shows microscopic gold-rich and lead-rich particles in a municipal biosolids sample. Image credit: Heather Lowers, USGS Denver Microbeam Laboratory

To extract metals, the researchers propose methods commonly in use by the mining industry. This involves using chemicals called leachates, which this industry uses to pull metals out of rock. Typically, these are very harmful to the environment, but at the American Chemical Society meeting, the researchers claim that these can be contained to waste water plants only, with no adverse effects to the environment or the population.

So far, Smith’s group has collected samples from small towns in the Rocky Mountains, rural communities and big cities. They found traces of platinum, silver and gold, and on a case by case basis, these could be found in a high enough concentration for extraction to become economically feasible.

Elsewhere, the city of Suwa in Japan is already working on extracting the gold from its sewers. They installed a treatment plant near a large number of precision equipment manufacturers reportedly collected nearly 2 kilograms of gold in every metric ton of ash left from burning sludge, making it more gold-rich than the ore in many mines.

 

Sewage waster

Sewage is virus haven to a myriad of unknown strains

Sewage waster

Well, it’s pretty obvious that the rotten, insalubrious sewage environment is perfect for fostering infectious diseases and virus cultures. What’s surprising however is actually the sheer number of viruses, most of them unknown, which biologists at University of Pittsburgh have described in a recently published study in the journal mBio.

According to the researchers, there are around 1.8 million species of organisms on Earth each host untold numbers of unique viruses yet only about 3,000 have been identified to date. Actually, genomic studies have shown that it’s probably only a tiny fraction of the number that actually exist, a hypothesis backed up by the Pittsburgh researchers find consisted of a myriad of unknown viruses in the raw sewage.

The scientists analyzed a sample of untreated wastewater. What they found was 234 known viruses that can infect people, plants, animals and other organisms, along with unknown viruses representing more than 50 different virus families. The researchers have noted that the raw sewage holds the most diverse array of bacteria of any place collected from so far.

“What was surprising was that the vast majority of viruses we found were viruses that had not been detected or described before,” Pittsburgh researcher Roger Hendrix said.

“The big question we’re interested in is, ‘Where do emerging viruses come from?'” Hendrix said.

Their findings suggest the viruses stem from a variety of sources, including animal and human feces and urine and plant material from domestic and agricultural settings. DNA sequencing of the viruses from the wastewater lead scientists to believe many are yet to be discovered. By examining specific points on the samples’ genomes, the team could determine whether a specific virus had similar genes to other known types.

“First you have to see the forest before you can pick out a particular tree to work on,” researcher James Pipas said. “If gene exchange is occurring among viruses, then we want to know where those genes are coming from, and if we only know about a small percentage of the viruses that exist, then we’re missing most of the forest.”