EEA1 and infection: In support of the hypothesis that early events in infection and intracellular growth are crucial events in Ct survival and pathogenicity, we identified SNPs within genes that are expressed from the beginning of the chlamydial developmental cycle including CTA0156 (encoding early endosomal antigen 1 (EEA1) [73]), CTA0498 (encoding translocated actin-recruiting phosphoprotein (tarP) [94]) and CTA0884 (encoding polymorphic membrane protein D (PmpD) [95]), which have identified roles in entry to and initial interactions with host cells.