From loo to lab: the fascinating journey of a wastewater sample

It’s not every day you think about what happens after you flush the toilet – but maybe you should. Because that trip to the bathroom might just set off a chain of events with a surprisingly important outcome. What starts as a simple flush can turn into a journey of discovery, as scientists take a closer look at what we leave behind to unlock valuable insights into public health. 

You heard that right. Your poo is a goldmine of information. By studying what goes down the s-bend, ESR scientists can catch early signs of disease outbreaks, monitor the effectiveness of vaccines and detect emerging health threats. The next time you flush, remember: your contribution might just help keep your community healthier! 

So, buckle up (or better yet, plug your nose) as we dive into the fascinating world of wastewater-based epidemiology, tracing the path from loo to lab. 

Collection 

Our journey begins in bowels. Our faeces are fascinating: alive and teeming with billions of microbes. Around three quarters of poo is made up of water, the rest is organic solids. Mixed in there are a whole lot of bacteria. In fact, it’s been estimated there are nearly 100 billion bacteria in every gram of wet stool. Most of these are helpful – for example they help to soften the stool. But not all of them are friendly. Because ‘bad’ bacteria as well as viruses (taken together they’re known as pathogens) can also be found in human waste.  

Exactly how these pathogens ‘shed’ into our faeces depends a lot on the type of bacterial or viral infection. In some cases, like with SARS-CoV-2 (the virus that causes COVID-19), virus particles can end up in our faeces without a person even knowing they were infected. 

Now imagine we have a fresh stool, let’s say with traces of a recent bout of COVID-19, swimming in the toilet bowel. How does its sloshy secrets make it to a lab? 

Once flushed, the wastewater travels through small pipes in the home to larger pipes under the street. These larger pipes, called sewer mains, carry the wastewater from many different sources. The sewer mains lead to even larger pipes that carry the combined wastewater from neighbourhoods, towns, and cities. This entire network of pipes forms an area’s sewer system. 

Gravity and pumps guide the flow towards wastewater treatment plants. Here, the sewerage goes through an initial screening – essentially pumping the wastewater through a giant sieve – that removes solids, like wet wipes, tampons and rubbish. The liquid that makes it through is known as influent, and it’s at this stage samples are collected. 

In most cases, the wastewater is collected using a clever piece of technology called an autosampler. The device, which resembles a drum with a plastic tube sticking out the top, is programmed to suck up small volumes of influent at regular intervals. For example, it might be set to collect 60 millilitres (that’s about four tablespoons) every 15 minutes over 24 hours. 

At the end of a sampling period, the contents of the drum are emptied into sterile bottles, which are packed on ice and sent to ESR for testing. 

Analysis 

Upon arrival at the lab the sample undergoes preparation. What this looks like depends on what’s being tested for. For pathogens, it involves a concentration step to increase the likelihood of detection. The first step is centrifugation – a sort of supercharged washing machine cycle. With our wastewater sample spinning at high speed, the dense particles move away from the axis of rotation, while lighter ones to move toward it.

Dense particles sediment at the bottom of a tube into what’s known as a pellet, to which pathogens become stuck. That pellet and the remaining solution, the supernatant, are processed further before pathogens are further concentrated.  

Now the magic really happens. For viruses, the sample undergoes a process to extract its nucleic acid. Nucleic acids are like the instruction manuals for living things. These manuals use DNA and RNA as their building blocks. The nucleic acid of our concentrated SARS-CoV-2 sample is of the RNA variety. 

This RNA can be detected using a polymerase chain reaction (PCR) test, which allows scientists to makes multiple copies of this genetic material – like making photocopies of a small piece of paper until you have a giant stack – even when there was only a tiny amount in the original sample.

Here’s where it gets really mind-blowing. A PCR test can only detect DNA – so the viral RNA is first converted to DNA using an enzyme called reverse transcriptase. This ‘complementary’ DNA is then used to measure how much viral RNA was present. From that, the concentration is calculated, with this number converted into genome copies per litre of wastewater.  

Interpretation and reporting 

Following analysis, the raw data from around New Zealand is collected and interpreted by ESR’s scientists. By knowing how much water is flowing through a given wastewater treatment plant, as well as the population size for that area, the levels of the examined pathogens can be determined. 

This information allows the number of genome copies per person per day to be calculated, which can in turn be used to understand trends in infections in the community. Generally, the higher the number, the more infections there will be. In the case of COVID, this data is inputted as part of ESR’s COVID-19 Wastewater Dashboard. 

Sometimes we don’t need to count the number of genome copies. What’s important is knowing whether they show up. For example, ESR tests wastewater samples for different types of poliovirus – some of which are disease causing and some of which are not. About three-quarters of poliovirus infections are asymptomatic, allowing the disease to spread undetected- sometimes for years. This makes wastewater surveillance a powerful tool for protecting community health. 

A behind-the-scenes superhero of public health

Wastewater monitoring might not be glamorous, but it’s a vital, behind-the-scenes superhero, helping us catch health trends before they become big problems – and doing so in a non-invasive and non-biased way. This information in turn is used to inform policy, and to efficiently allocated limited resources.  

Importantly, it can be quickly adjusted to search for different pathogens, and is cost effective, allowing us to cover huge populations – from rural towns to metropolitan centres. As we continue to face challenges such as urbanisation, industrialisation, and climate change, understanding and monitoring wastewater remains essential for building healthier communities.