Inference of Pairwise Interactions from Strain Frequency Data Across Settings and Context-Dependent Mutual Invasibilities

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14310%2F25%3A00141251" target="_blank" >RIV/00216224:14310/25:00141251 - isvavai.cz</a>

Výsledek na webu

<a href="https://doi.org/10.1007/s11538-025-01450-0" target="_blank" >https://doi.org/10.1007/s11538-025-01450-0</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1007/s11538-025-01450-0" target="_blank" >10.1007/s11538-025-01450-0</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Inference of Pairwise Interactions from Strain Frequency Data Across Settings and Context-Dependent Mutual Invasibilities

Popis výsledku v původním jazyce

We propose a method to estimate pairwise strain interactions from population-level frequencies across different endemic settings. We apply the framework of replicator dynamics, derived from a multi-strain SIS model with co-colonization, to extract from 5 datasets the fundamental backbone of strain interactions. In our replicator, each pairwise invasion fitness explicitly arises from local environmental context and trait variations between strains. We adopt the simplest formulation for multi-strain coexistence, where context is encoded in basic reproduction number R0 and mean global susceptibility to co-colonization k, and trait variations αij capture pairwise deviations from k. We integrate Streptococcus pneumoniae serotype frequencies and serotype identities collected from 5 environments: epidemiological surveys in Denmark, Nepal, Iran, Brazil and Mozambique, and mechanistically link their distributions. Our results have twofold implications. First, we offer a new proof-of-concept in the inference of multi-species interactions based on cross-sectional data. We also discuss 2 key aspects of the method: the site ordering for sequential fitting, and stability constraints on the dynamics. Secondly, we effectively estimate at high-resolution more than 70% of the 92×92 pneumococcus serotype interaction matrix in co-colonization, allowing for further projections and hypotheses testing. We show that, in these bacteria, both within- and between- serotype interaction coefficients’ distribution emerge to be unimodal, their difference in mean broadly reflecting stability assumptions on serotype coexistence. This framework enables further model calibration to global data: cross-sectional across sites, or longitudinal in one site over time, - and should allow a more robust and integrated investigation of intervention effects in such biodiverse ecosystems.

Název v anglickém jazyce

Inference of Pairwise Interactions from Strain Frequency Data Across Settings and Context-Dependent Mutual Invasibilities

Popis výsledku anglicky

We propose a method to estimate pairwise strain interactions from population-level frequencies across different endemic settings. We apply the framework of replicator dynamics, derived from a multi-strain SIS model with co-colonization, to extract from 5 datasets the fundamental backbone of strain interactions. In our replicator, each pairwise invasion fitness explicitly arises from local environmental context and trait variations between strains. We adopt the simplest formulation for multi-strain coexistence, where context is encoded in basic reproduction number R0 and mean global susceptibility to co-colonization k, and trait variations αij capture pairwise deviations from k. We integrate Streptococcus pneumoniae serotype frequencies and serotype identities collected from 5 environments: epidemiological surveys in Denmark, Nepal, Iran, Brazil and Mozambique, and mechanistically link their distributions. Our results have twofold implications. First, we offer a new proof-of-concept in the inference of multi-species interactions based on cross-sectional data. We also discuss 2 key aspects of the method: the site ordering for sequential fitting, and stability constraints on the dynamics. Secondly, we effectively estimate at high-resolution more than 70% of the 92×92 pneumococcus serotype interaction matrix in co-colonization, allowing for further projections and hypotheses testing. We show that, in these bacteria, both within- and between- serotype interaction coefficients’ distribution emerge to be unimodal, their difference in mean broadly reflecting stability assumptions on serotype coexistence. This framework enables further model calibration to global data: cross-sectional across sites, or longitudinal in one site over time, - and should allow a more robust and integrated investigation of intervention effects in such biodiverse ecosystems.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10100 - Mathematics

Projekt

—

Návaznosti

S - Specificky vyzkum na vysokych skolach

Rok uplatnění

2025

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Bulletin of Mathematical Biology

ISSN

0092-8240

e-ISSN

1522-9602

Svazek periodika

87

Číslo periodika v rámci svazku

6

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

29

Strana od-do

1-29

Kód UT WoS článku

001492246600001

EID výsledku v databázi Scopus

2-s2.0-105005593428