Basic reproduction number varies markedly between closely related pandemic Escherichia coli clones

Fanni Ojala; Henri Pesonen; Rebecca A. Gladstone; Tommi Mäklin; Gerry Tonkin-Hill; Pekka Marttinen; Jukka Corander

doi:10.1038/s41467-025-65301-1

Basic reproduction number varies markedly between closely related pandemic Escherichia coli clones

Fanni Ojala, Henri Pesonen, Rebecca A. Gladstone, Tommi Mäklin, Gerry Tonkin-Hill, Pekka Marttinen, Jukka Corander^*

^*Corresponding author for this work

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Abstract

Extra-intestinal pathogenic Escherichia coli ubiquitously colonize the human gut and represent clinically the most significant bacterial species causing urinary tract infections and bacteremia. During the last two decades clades of the ST131 lineage have spread globally, but it remains unknown how their transmission dynamics compare to the basic reproduction numbers (R₀) for viral pandemics. We develop a compartmental model for asymptomatic gut colonization and onward transmission coupled with an epidemiological observation model and fit it on the major ST131 clades. Our results indicate that the ST131-A transmission potential (R₀ = 1.47) can be comparable to pandemic influenza viruses, while the significantly lower transmissibility of ST131-C1 (R₀ = 1.18) and ST131-C2 (R₀ = 1.13) suggests that their dissemination has been aided by antibiotic selection pressure and healthcare facilities. Our results provide an advance in understanding the relative transmissibility of these opportunistic pathogens.

Original language	English
Article number	9490
Pages (from-to)	1-9
Number of pages	9
Journal	Nature Communications
Volume	16
Issue number	1
DOIs	https://doi.org/10.1038/s41467-025-65301-1
Publication status	Published - Dec 2025
MoE publication type	A1 Journal article-refereed

Funding

Research in this publication was supported by the Research Council of Norway through its Centre of Excellence Integreat - The Norwegian Centre for knowledge-driven machine learning, project number 332645 (H.P., J.C.), Trond Mohn Foundation (BATTALION grant, J.C., R.A.G.) and Academy of Finland (EuroHPC grant T.M., J.C.; Flagship programme: Finnish Center for Artificial Intelligence FCAI (J.C., P.M.); and grants 358246, 352986 (F.O., P.M.)) and EU (H2020 grant 101016775 and NextGenerationEU, F.O., P.M.). F.O. acknowledges travel support from the European Union’s Horizon 2020 research and innovation programme under ELISE Grant Agreement No 951847.

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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Basic_reproduction_number_varies_markedly_between_closely_related_pandemic_Escherichia_coli_clonesFinal published version, 812 KBLicence: CC BY

Cite this

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title = "Basic reproduction number varies markedly between closely related pandemic Escherichia coli clones",

abstract = "Extra-intestinal pathogenic Escherichia coli ubiquitously colonize the human gut and represent clinically the most significant bacterial species causing urinary tract infections and bacteremia. During the last two decades clades of the ST131 lineage have spread globally, but it remains unknown how their transmission dynamics compare to the basic reproduction numbers (R0) for viral pandemics. We develop a compartmental model for asymptomatic gut colonization and onward transmission coupled with an epidemiological observation model and fit it on the major ST131 clades. Our results indicate that the ST131-A transmission potential (R0 = 1.47) can be comparable to pandemic influenza viruses, while the significantly lower transmissibility of ST131-C1 (R0 = 1.18) and ST131-C2 (R0 = 1.13) suggests that their dissemination has been aided by antibiotic selection pressure and healthcare facilities. Our results provide an advance in understanding the relative transmissibility of these opportunistic pathogens.",

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T1 - Basic reproduction number varies markedly between closely related pandemic Escherichia coli clones

AU - Ojala, Fanni

AU - Pesonen, Henri

AU - Gladstone, Rebecca A.

AU - Mäklin, Tommi

AU - Tonkin-Hill, Gerry

AU - Marttinen, Pekka

AU - Corander, Jukka

N1 - | openaire: EC/H2020/101016775/EU//INTERVENE | openaire: EC/H2020/951847/EU//ELISE

PY - 2025/12

Y1 - 2025/12

N2 - Extra-intestinal pathogenic Escherichia coli ubiquitously colonize the human gut and represent clinically the most significant bacterial species causing urinary tract infections and bacteremia. During the last two decades clades of the ST131 lineage have spread globally, but it remains unknown how their transmission dynamics compare to the basic reproduction numbers (R0) for viral pandemics. We develop a compartmental model for asymptomatic gut colonization and onward transmission coupled with an epidemiological observation model and fit it on the major ST131 clades. Our results indicate that the ST131-A transmission potential (R0 = 1.47) can be comparable to pandemic influenza viruses, while the significantly lower transmissibility of ST131-C1 (R0 = 1.18) and ST131-C2 (R0 = 1.13) suggests that their dissemination has been aided by antibiotic selection pressure and healthcare facilities. Our results provide an advance in understanding the relative transmissibility of these opportunistic pathogens.

AB - Extra-intestinal pathogenic Escherichia coli ubiquitously colonize the human gut and represent clinically the most significant bacterial species causing urinary tract infections and bacteremia. During the last two decades clades of the ST131 lineage have spread globally, but it remains unknown how their transmission dynamics compare to the basic reproduction numbers (R0) for viral pandemics. We develop a compartmental model for asymptomatic gut colonization and onward transmission coupled with an epidemiological observation model and fit it on the major ST131 clades. Our results indicate that the ST131-A transmission potential (R0 = 1.47) can be comparable to pandemic influenza viruses, while the significantly lower transmissibility of ST131-C1 (R0 = 1.18) and ST131-C2 (R0 = 1.13) suggests that their dissemination has been aided by antibiotic selection pressure and healthcare facilities. Our results provide an advance in understanding the relative transmissibility of these opportunistic pathogens.

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Basic reproduction number varies markedly between closely related pandemic Escherichia coli clones

Abstract

Funding

UN SDGs

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Other files and links

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FCAI Flagship 2: Finnish Center for Artificial Intelligence (jatkohanke)

CLISHEAT/Marttinen: Green and digital healthcare

INTERVENE: International consortium for integrative genomics prediction

Cite this

Basic reproduction number varies markedly between closely related pandemic Escherichia coli clones

Abstract

Funding

UN SDGs

Access to Document

Other files and links

Fingerprint

Projects

FCAI Flagship 2: Finnish Center for Artificial Intelligence (jatkohanke)

CLISHEAT/Marttinen: Green and digital healthcare

INTERVENE: International consortium for integrative genomics prediction

Cite this