New research has revealed that Escherichia coli (E. coli), a bacterium that normally lives in the human gut, can spread through populations at a rate comparable to the swine flu.
For the first time, researchers from the Wellcome Sanger Institute, the University of Oslo, the University of Helsinki, Aalto University in Finland, and their collaborators have been able to estimate how efficiently one person can pass gut bacteria to others. This kind of calculation, which measures transmission rates, has previously been possible mainly for viruses.
Tracking Dangerous Strains Across Populations
The study, published today (November 4) in Nature Communications, examined three key E. coli strains circulating in the UK and Norway. Two of these strains are resistant to several common classes of antibiotics. They are also the most frequent causes of urinary tract and bloodstream infections in both countries. The researchers suggest that better monitoring of these strains could guide public health responses and help prevent outbreaks of infections that are difficult to treat.
In the long term, gaining insight into the genetic factors that help E. coli spread could lead to more targeted therapies and reduce reliance on broad-spectrum antibiotics. The approach developed in this study could also be adapted to investigate other bacterial pathogens and improve strategies for managing invasive infections.
E. coli is one of the leading causes of infections around the world.1 While most strains are harmless and normally inhabit the gut, the bacteria can enter the body through direct contact such as kissing or indirect means like shared surfaces, food, or living spaces. When E. coli moves into areas such as the urinary tract, it can cause serious illness, including sepsis, especially in people with weakened immune systems.
Antibiotic resistance has made these infections even more concerning. In the UK, more than 40 percent of E. coli bloodstream infections are now resistant to a key antibiotic,2 reflecting a global trend of rising resistance levels.
Applying Viral-Style Transmission Metrics to Bacteria
Scientists often describe how infectious a pathogen is using the basic reproduction number, known as R0. This number estimates how many new cases a single infected person might cause. It is typically applied to viruses and helps predict whether an outbreak will expand or decline. Until now, researchers have been unable to assign an R0 value to bacteria that normally colonize the gut, since they often live in the body without triggering illness.
To overcome this, the team combined data from the UK Baby Biome Study with genomic information from E. coli bloodstream infection surveillance programs in the UK and Norway, previously compiled by the Wellcome Sanger Institute.
Using a software platform called ELFI3 (Engine for Likelihood-Free Inference), the researchers built a new model capable of estimating R0 for the three major E. coli strains studied.
Their results showed that one particular strain, known as ST131-A, can spread between people as rapidly as some viruses that have caused global outbreaks, including the swine flu (H1N1). This is particularly striking because E. coli is not spread through airborne droplets like flu viruses are.
The two other strains studied, ST131-C1 and ST131-C2, are resistant to multiple antibiotic classes but spread much more slowly among healthy individuals. However, in hospitals and other healthcare environments, where patients are more vulnerable and contact is frequent, these resistant strains could move through populations much faster.
Understanding R0 for Bacteria
Assigning an R0 value to bacteria opens the door to a clearer understanding of how bacterial infections spread. It also helps identify which strains pose the greatest threat and could inform public health strategies to better protect people with compromised immune systems.
Fanni Ojala, M.Sc., co-first author at Aalto University in Finland, explained: "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-lead of the UK Baby Biome Study, who was not involved in this research, noted: "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."
A New Lens on Bacterial Genetics
Professor Jukka Corander, senior author at the Wellcome Sanger Institute and the University of Oslo, added: "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."
The success of this study relied on extensive genomic data from the UK and Norway, all sequenced at the Wellcome Sanger Institute. This large-scale data made it possible to identify transmission patterns in detail. The datasets originated from earlier studies published in The Lancet Microbe,4,5 which laid the foundation for the modeling breakthrough achieved in this new research.
Notes
- Antimicrobial Resistance Collaborators. (2022) 'Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis.' The Lancet. DOI: 1016/S0140-6736(21)02724-0
- UK Health Security Agency. New data shows 148 severe antibiotic-resistant infections a day in 2021. Available at: https://www.gov.uk/government/news/new-data-shows-148-severe-antibiotic-resistant-infections-a-day-in-2021#:~:text=Over%20two-fifths%20of%20E,as%20cefiderocol%20to%20identify%20resistance[1]
- ELFI can be found: https://www.elfi.ai/[2]
- R. A. Gladstone, et al. (2021) ' Emergence and dissemination of antimicrobial resistance in Escherichia coli causing bloodstream infections in Norway in 2002-17: a nationwide, longitudinal, microbial population genomic study' Lancet Microbe. DOI: 10.1016/S2666-5247(21)00031-8.
- A. K. Pontinen, et al. (2024) 'Modulation of multidrug-resistant clone success in Escherichia coli populations: a longitudinal, multi-country, genomic and antibiotic usage cohort study' Lancet Microbe. DOI: 10.1016/S2666-5247(23)00292-6.
New research has revealed that Escherichia coli (E. coli), a bacterium that normally lives in the human gut, can spread through populations at a rate comparable to the swine flu.
For the first time, researchers from the Wellcome Sanger Institute, the University of Oslo, the University of Helsinki, Aalto University in Finland, and their collaborators have been able to estimate how efficiently one person can pass gut bacteria to others. This kind of calculation, which measures transmission rates, has previously been possible mainly for viruses.
Tracking Dangerous Strains Across Populations
The study, published today (November 4) in Nature Communications, examined three key E. coli strains circulating in the UK and Norway. Two of these strains are resistant to several common classes of antibiotics. They are also the most frequent causes of urinary tract and bloodstream infections in both countries. The researchers suggest that better monitoring of these strains could guide public health responses and help prevent outbreaks of infections that are difficult to treat.
In the long term, gaining insight into the genetic factors that help E. coli spread could lead to more targeted therapies and reduce reliance on broad-spectrum antibiotics. The approach developed in this study could also be adapted to investigate other bacterial pathogens and improve strategies for managing invasive infections.
E. coli is one of the leading causes of infections around the world.1 While most strains are harmless and normally inhabit the gut, the bacteria can enter the body through direct contact such as kissing or indirect means like shared surfaces, food, or living spaces. When E. coli moves into areas such as the urinary tract, it can cause serious illness, including sepsis, especially in people with weakened immune systems.
Antibiotic resistance has made these infections even more concerning. In the UK, more than 40 percent of E. coli bloodstream infections are now resistant to a key antibiotic,2 reflecting a global trend of rising resistance levels.
Applying Viral-Style Transmission Metrics to Bacteria
Scientists often describe how infectious a pathogen is using the basic reproduction number, known as R0. This number estimates how many new cases a single infected person might cause. It is typically applied to viruses and helps predict whether an outbreak will expand or decline. Until now, researchers have been unable to assign an R0 value to bacteria that normally colonize the gut, since they often live in the body without triggering illness.
To overcome this, the team combined data from the UK Baby Biome Study with genomic information from E. coli bloodstream infection surveillance programs in the UK and Norway, previously compiled by the Wellcome Sanger Institute.
Using a software platform called ELFI3 (Engine for Likelihood-Free Inference), the researchers built a new model capable of estimating R0 for the three major E. coli strains studied.
Their results showed that one particular strain, known as ST131-A, can spread between people as rapidly as some viruses that have caused global outbreaks, including the swine flu (H1N1). This is particularly striking because E. coli is not spread through airborne droplets like flu viruses are.
The two other strains studied, ST131-C1 and ST131-C2, are resistant to multiple antibiotic classes but spread much more slowly among healthy individuals. However, in hospitals and other healthcare environments, where patients are more vulnerable and contact is frequent, these resistant strains could move through populations much faster.
Understanding R0 for Bacteria
Assigning an R0 value to bacteria opens the door to a clearer understanding of how bacterial infections spread. It also helps identify which strains pose the greatest threat and could inform public health strategies to better protect people with compromised immune systems.
Fanni Ojala, M.Sc., co-first author at Aalto University in Finland, explained: "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-lead of the UK Baby Biome Study, who was not involved in this research, noted: "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."
A New Lens on Bacterial Genetics
Professor Jukka Corander, senior author at the Wellcome Sanger Institute and the University of Oslo, added: "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."
The success of this study relied on extensive genomic data from the UK and Norway, all sequenced at the Wellcome Sanger Institute. This large-scale data made it possible to identify transmission patterns in detail. The datasets originated from earlier studies published in The Lancet Microbe,4,5 which laid the foundation for the modeling breakthrough achieved in this new research.
Notes
- Antimicrobial Resistance Collaborators. (2022) 'Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis.' The Lancet. DOI: 1016/S0140-6736(21)02724-0
- UK Health Security Agency. New data shows 148 severe antibiotic-resistant infections a day in 2021. Available at: https://www.gov.uk/government/news/new-data-shows-148-severe-antibiotic-resistant-infections-a-day-in-2021#:~:text=Over%20two-fifths%20of%20E,as%20cefiderocol%20to%20identify%20resistance[1]
- ELFI can be found: https://www.elfi.ai/[2]
- R. A. Gladstone, et al. (2021) ' Emergence and dissemination of antimicrobial resistance in Escherichia coli causing bloodstream infections in Norway in 2002-17: a nationwide, longitudinal, microbial population genomic study' Lancet Microbe. DOI: 10.1016/S2666-5247(21)00031-8.
- A. K. Pontinen, et al. (2024) 'Modulation of multidrug-resistant clone success in Escherichia coli populations: a longitudinal, multi-country, genomic and antibiotic usage cohort study' Lancet Microbe. DOI: 10.1016/S2666-5247(23)00292-6.
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