When Reducing Transmission Is Not Enough: Carrier Dynamics and Backward Bifurcation in Influenza-Pneumococcal Co-infection

Abstract

Bacterial co-infection, particularly with \emph{Streptococcus pneumoniae}, is a major driver of morbidity during influenza epidemics, and this burden falls disproportionately on sub-Saharan Africa, where both pathogens circulate year-round at high levels and pneumococcal carriage remains common and persistent across the region. Yet existing mathematical models rarely track a host's bacterial carriage status jointly with their full influenza history through recovery. We develop a twelve-compartment ODE model that classifies each host by viral status (susceptible, infected, recovered) and bacterial status (susceptible, carrier, actively infected, recovered), allowing carrier-to-active progression to depend on prior influenza exposure. We establish positivity, boundedness, and a positively invariant region, then derive the basic reproduction number $\mathcal{R}_0$ and quasi-endemic equilibria of a single disease, together with invasion reproduction numbers $\mathbf{Inv}^{\mathbf{B}}$ and $\mathbf{Inv}^{\mathbf{V}}$ quantifying each pathogen's ability to invade a population where the other is already endemic. Center-manifold analysis shows that the bacterial subsystem and the full coexistence equilibrium undergo a backward bifurcation precisely when carrier transmission exceeds the carrier's total exit rate, $β_c>κ_S+θ+μ$, so that reducing $\mathcal{R}_0$ below one is not sufficient for elimination, while the viral subsystem bifurcates forward. A global sensitivity analysis (Latin Hypercube Sampling with partial rank correlation coefficients) shows that the viral and bacterial thresholds are governed by largely separate parameters, while the bacterial invasion potential is strongly shaped by viral transmission and recovery, giving a quantitative signature of cross-pathogen synergy.