Imagine a harmless-seeming bacterium from your gut suddenly spreading through communities as swiftly as a deadly flu pandemic – that's the alarming scenario unfolding with a resilient strain of E. coli, and it's time we paid attention.
Escherichia coli, or E. coli for short, is a familiar type of bacteria that lives in the human digestive system, usually without causing trouble. But groundbreaking research now reveals that certain strains of this microbe could transmit from person to person at speeds rivaling those of viruses like the swine flu. This discovery comes from a collaborative team of scientists at the Wellcome Sanger Institute, the University of Oslo, the University of Helsinki, and Aalto University in Finland, who have cracked the code on measuring how gut bacteria spread – something previously doable only for viruses.
Published today, November 4th, in the journal Nature Communications, their study dives deep into three prevalent E. coli strains circulating in the UK and Norway. Two of these are notorious for resisting multiple types of antibiotics, making them particularly concerning. These strains rank among the top culprits behind urinary tract infections and severe bloodstream illnesses in both countries. By improving our ability to monitor these bacteria, experts believe we can better shape public health strategies to avert outbreaks of infections that shrug off standard treatments.
Looking ahead, unraveling the genetic secrets that enable some E. coli strains to proliferate so effectively could pave the way for more precise therapies. This might even allow us to cut back on the overuse of broad-spectrum antibiotics, which can wipe out beneficial microbes and fuel resistance. Plus, the innovative technique from this study could be tweaked for other bacterial threats, helping us grasp and contain a wider array of invasive diseases. For instance, think about how understanding the spread of one bacterium could inform efforts against similar ones causing foodborne illnesses or skin infections.
E. coli stands as one of the world's leading infection agents, though most varieties are innocent residents of our intestines. These colonizing bacteria enter our bodies via direct touch, like a shared kiss, or indirect means such as communal living spaces, shared items, or contaminated food. Normally benign, they can turn dangerous if they migrate to vulnerable areas, such as the urinary system, and escalate to life-threatening sepsis – especially in individuals with compromised immunity, like the elderly or those undergoing medical treatments.
And this is the part most people miss: the growing hurdle of antibiotic resistance complicates treatment immensely. Globally, and particularly in the UK, over 40% of E. coli bloodstream infections now defy a crucial antibiotic, turning routine fixes into battles. It's a reminder that while we rely on these drugs to fight infections, overuse is breeding superbugs that challenge modern medicine.
To quantify spread, scientists use a tool called the basic reproduction number, or R0, which calculates how many new cases one infected person typically generates in a susceptible group. It's a staple for viruses, helping predict if an outbreak will fizzle or explode. Until now, assigning an R0 to colonizing gut bacteria like E. coli was tricky because they often lurk silently without sparking symptoms.
In this pioneering work, the team scrutinized E. coli colonization data from the UK Baby Biome Study, merging it with genomic surveillance info on bloodstream infections from the UK and Norway, previously gathered by the Wellcome Sanger Institute. They employed a cutting-edge software called ELFI (Engine for Likelihood-Free Inference) to construct a model estimating R0 for the three key strains.
The results? One strain, ST131-A, zips through populations as fast as major viral epidemics, like the 2009 H1N1 swine flu, even though E. coli doesn't travel via airborne droplets. But here's where it gets controversial: the other two strains, ST131-C1 and ST131-C2, which are tough against several antibiotics, don't spread quickly in everyday settings among healthy folks. Yet, they ramp up transmission dramatically in hospitals and care facilities, posing a stark risk in those high-stakes environments. Is this a sign that healthcare settings are becoming breeding grounds for superbugs, or should we focus more on community prevention? It's a debate worth having.
Armed with R0 data, researchers can now dissect what drives transmission, pinpoint high-risk strains, and craft public health defenses to shield vulnerable populations, such as those with weakened immune systems.
As Fanni Ojala, M.Sc., co-first author at Aalto University in Finland, explains, “By having a large amount of systematically collected data, it was possible to build a simulation model to predict R0 for E. coli. To our knowledge, this was not just a first for E. coli, but a first for any bacteria that live in our gut microbiome. Now that we have this model, it could be possible to apply it to other bacterial strains in the future, allowing us to understand, track, and hopefully prevent the spread of antibiotic-resistant infections.”
Dr. Trevor Lawley, Group Leader at the Wellcome Sanger Institute and co-leader of the UK Baby Biome Study (though not part of this research), adds a personal touch: “E. coli is one of the first bacteria that can be found in a baby’s gut, and in order to understand how our bacteria shape our health, we need to know where we start – which is why the UK Baby Biome study is so important. It is great to see that our UK Baby Biome study data are being used by others to uncover new insights and methods that will hopefully benefit us all.”
Finally, Professor Jukka Corander, senior author at the Wellcome Sanger Institute and the University of Oslo, weighs in: “Having the R0 for E. coli allows us to see the spread of bacteria through the population in much clearer detail, and compare this to other infections. Now that we can see how rapidly some of these bacterial strains spread, it is necessary to understand their genetic drivers. Understanding the genetics of specific strains could lead to new ways to diagnose and treat these in healthcare settings, which is especially important for bacteria that are already resistant to multiple types of antibiotics.”
Reference: Ojala F, Pesonen H, Gladstone RA, et al. Basic reproduction number varies markedly between closely related pandemic Escherichia coli clones. Nat Commun. 2025;16(1):9490. doi:10.1038/s41467-025-65301-1 (https://doi.org/10.1038/s41467-025-65301-1)
This article has been republished from the following materials (https://www.sanger.ac.uk/news_item/advanced-disease-modelling-shows-some-gut-bacteria-can-spread-as-rapidly-as-viruses/). Note: material may have been edited for length and content. For further information, please contact the cited source. Our press release publishing policy can be accessed here (https://www.technologynetworks.com/tn/editorial-policies#republishing).
What do you think – should we be more alarmed about these bacterial threats than viral ones, or is antibiotic resistance the bigger crisis here? Do these findings change how you view everyday hygiene, like handwashing or food safety? Share your opinions in the comments below; I'd love to hear your take and spark a conversation!
