In addition to the classical phagosome maturation pathway, the cell content recycling pathway of autophagy has been implicated in the response to a number of pathogens particularly those that can escape the phagosome (Cemma and Brumell, 2012). Components of the autophagy pathway were first implicated in the handling of cryptococci in a Drosophila S2 cell RNAi screen (Qin et al., 2011) and the autophagy effector LC3 has been observed associated with cryptococcal phagosomes (Nicola et al., 2012). Conditional macrophage ATG5 deficient mice showed no difference in survival, although histology of lung lesions showed reduced inflammation (Nicola et al., 2012). There are multiple routes into activation of autophagy and the lack of strong phenotype may be explained by compensation of alternative autophagy activation pathways (Cemma and Brumell, 2012).