Lithgow was awarded an ARC Federation Fellowship to build capacity for studying host–pathogen interactions at Monash University, starting in 2008. In 2014, he took up an ARC Laureate Fellowship to build capacity in nanoscale imaging approaches to investigate bacterial cell biology. This included developing applications of single particle cryoEM, neutron reflectrometry, atomic force microscopy and super-resolution imaging of bacterial cells. The fundamental discoveries from this work include how bacterial outer membranes are assembled and the intracellular complexity of the bacterial cytoplasm and periplasm. Lithgow also led the NHMRC Program in Cellular Microbiology that used the fundamental knowledge of bacterial cell biology to better understand mechanisms of antimicrobial resistance (AMR), the mechanics driving entry of bacteriophage into bacteria and the mechanisms by which phages control host cell biology.