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Spore production was determined by direct counts using a Petroff-Hauser chamber.
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Cell number was then determined by direct counting using a Neubauer chamber.
Allele frequencies were calculated by direct counting using the PyPop software [ 37].
The cell growth rate was determined by direct counting using randomly collected microscopic pictures.
The cell concentrations were ascertained by direct counting using Trypan blue.
Cell proliferation assays were performed by direct counting using a bacterial counting chamber (Hausser Scientific Partnership, PA, USA) and differential interference contrast microscopy.
The cell density (cells/mL) was determined by direct counting using a Neubauer chamber and a light microscope equipped with a 40× objective.
On the same days, faecal samples were also collected and the amount of Salmonella bacteria shed in faeces was quantified by direct counting using bacteriological methods as described by Uthe et al. [ 12].
Cell number was determined either by direct counting using a ViCell XR cell viability analyzer (Beckman Coulter, Miami, FL, USA) using trypan blue cell viability assay or by monolayer confluence readings as calculated from images acquired by Essen IncuCyte (Essen BioScience, Ann Arbor, MI, USA).
From this sample 10 µl was taken for direct counts using an epifluorescent microscope.
The distributions of allele and genotype frequencies for each polymorphism in the infected and control groups were estimated by direct counting and compared using the chi-square test or Fisher's exact test in cases where the sample size for a given genotype was lower than 5. Hardy-Weinberg equilibrium was tested using the chi-square test.
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