DOI: 10.5061/dryad.j89d064
title: Data from: Mutations in bacterial genes induce unanticipated changes in the relationship between bacterial pathogens in experimental otitis media

description: Otitis media (OM) is a common polymicrobial infection of the middle ear in
 children under the age of fifteen years. A widely used experimental
 strategy to analyze roles of specific phenotypes of bacterial pathogens of
 OM is to study changes in co-infection kinetics of bacterial populations
 in animal models when a wild type bacterial strain is replaced by a
 specific isogenic mutant strain in the co-inoculating mixtures. Since
 relationships between the OM bacterial pathogens within the host are
 regulated by many interlinked processes, connecting the changes in the
 co-infection kinetics to a bacterial phenotype can be challenging. We
 investigated middle ear co-infections in adult chinchillas (Chinchilla
 lanigera) by two major OM pathogens: nontypeable Haemophilus influenzae
 (NTHI) and Moraxella catarrhalis (Mcat), as well as isogenic mutant
 strains in each bacterial species. We analyzed the infection kinetic data
 using Lotka-Volterra population dynamics, Maximum Entropy inference, and
 Akaike Information Criteria (AIC) based model selection. We found that
 changes in relationships between the bacterial pathogens that were not
 anticipated in the design of the co-infection experiments involving mutant
 strains are common and were strong regulators of the co-infecting
 bacterial populations. The framework developed here allows for a
 systematic analysis of host-host variations of bacterial populations and
 small sizes of animal cohorts in co-infection experiments to quantify the
 role of specific mutant strains in changing the infection kinetics. Our
 combined approach can be used to analyze the functional footprint of
 mutant strains in regulating co-infection kinetics in models of
 experimental OM and other polymicrobial diseases.
description: in vivo
 RawDataContains the data for
 bacterial counts in individual chinchilla earsRawData.xlsxMATLAB code used for analysisSet22A.mat This set of data provides the mapping from discretized alpha-space to a discretized N-space, as well as all the necessary information used to generate this particular mapping. This mapping was used throughout the data analysis in this manuscript (except as noted in Fig S5). Qa2Xmap – This matrix variable has 17,645,368 rows and 6 columns. This matrix is a map from alpha-space to N-space. For a given row, the first four columns are the alpha-matrix values {a11, a12, a21, a22}; the last two columns indicate the corresponding steady state N-values (in 106 CFU) {NTHi, Mcat}. See Eqn 3 in Methods B.1. X1, X2 – This column vector has the discretized values of N1, and N2 respectively (in 106 CFU). a11, a12, a21, a22 – These column vectors have the discretized values of a11, a12, a21, and a22 respectively. X1range, X2range – These variables contain the minimum and maximum of N1, and N2 respectively. Xbns – N1, and N2 were each discretized into this many number of bins. abns_diag – a11, and a22 were each discretized into this many number of bins. abns_offdiag – a12, and a21 were each discretized into this many number of bins. counts – this square matrix records the number of alpha matrices that correspond to steady state values in each bin of N-space. kappa – this square matrix is equal to “counts” / 17,645,368.Set22A.mat