In July 2008, Australian microbiologists braved wintry Melbourne weather to attend the Annual Scientific Meeting of the Australian Society for Microbiology. The meeting attracted more than 1100 delegates from around the Asia–Pacific region and offered over 400 scientific presentations covering the latest research findings from leading local and international research and clinical laboratories. The theme of the meeting, ‘Changing Times’, highlighted the immense challenges ahead for the microbiology community in responding quickly and appropriately to often unpredictable environmental, political, public health and regulatory changes in the face of microbes that are changing just as rapidly. Keynote speakers addressed many of these issues within their presentations including Nobel Laureate, Peter Doherty (Department of Microbiology & Immunology, University of Melbourne, Australia) who delivered the opening address. Mike Levine (Center for Vaccine Development, Baltimore, USA) gave the Commonwealth Serum Laboratory-sponsored Bazeley Oration and used his invaluable clinical insight to discuss the history and future development of typhoid vaccines as well as the use of Salmonella as a vaccine carrier, and the construction and testing of new-generation Salmonella vaccines. Alan Cowman (Walter and Eliza Hall Institute, Australia) gave the prestigious Rubbo Oration and presented a stunning overview of malaria biology as well as recent progress on mechanisms to control this devastating infectious disease. The meeting also hosted a special ‘Infection Control Day’, which comprised a series of workshops and presentations designed to draw attention to the problems of antibiotic resistance and the measures needed to reduce hospital-acquired infections and their transmission. In the area of microbial and molecular pathogenesis, a major topic of the meeting was the secretion of bacterial proteins and their trafficking within infected cells. There are now at least six recognized bacterial systems (Type I–VI) dedicated to the export of bacterial proteins that often play a direct role in the interaction of pathogens with their hosts. The study of these secretion systems and their substrates is therefore an essential part of understanding how a pathogen causes disease. In some cases, the export of a protein leads to the construction of zones within the bacterial membranes that serve as an adhesive organelle to contact host surfaces. In other cases, the secreted factors are translocated directly into a eukaryotic cell, where they interfere with host cell function. In this instance, a bacterial protein may need to cross two bacterial membranes and one or more mammalian cell membranes to reach a target site. The substrate specificity of secretion systems is remarkable and a single secretion system may be dedicated to a single substrate, only a few substrates or, in the case of Legionella, more than 150 proteins. Current work on the function of bacterial secretion systems and their substrates at the molecular and structural level is driven by the expectation of greater insight into how pathogens evolve and cause disease.