  Multi-strain pathogens such as Group A Streptococcus, Streptococcus
pneumoniae, and Staphylococcus aureus cause millions of infections each year
with a substantial health burden. Control of multi-strain pathogens can be
complicated by the high strain diversity often observed in endemic settings. It
is not well understood how high strain diversity is maintained in populations,
given that they compete with each other both directly (within an individual
host) and indirectly (via host immunity). Previous modelling studies have
investigated how indirect competition affects the prevalence and diversity of
strains. However, these studies often make simplifying assumptions about the
direct competition that occurs within hosts. Currently, little data is
available to validate these assumptions, hence there is a need to clarify how
sensitive model outputs are to these assumptions. In this study, we compare the
dynamics of multi-strain pathogens under different assumptions about direct
competition between strains using an agent-based model. We find that the
assumptions made about direct competition can affect the epidemiological
dynamics, particularly when there is no long-term immunity following infections
and a low rate of importation of non-circulating strains. Our results suggest
that while direct and indirect competition can each decrease strain diversity
when they act in isolation, they may increase strain diversity when they act
together. This finding highlights the importance of examining sensitivity to
assumptions about strain competition. In particular, omitting consideration of
direct competition can lead to inaccurate estimates of the likely effectiveness
of control strategies as changes in strain diversity shift the level of direct
strain competition.
