Transcriptomic Analyses of Host Colonisation in Fungal Pathogens of Humans

The mammalian host environment presents a uniquely complex challenge to fungi, most of which have fine-tuned physiologies selected for and honed, in wider ecological niches. Survival, persistence, and proliferation in mammalian hosts require agile perception and adaptation to the multitude of stimuli, metabolic demands, and insults encountered. Therefore, pathogenicity requires not only the possession of inventories of virulence traits but also the capacity to regulate their expression with an exquisite degree of temporal precision. More than any other methodology applied to understand this process, transcriptomic approachestranscriptomic approaches have illuminated the critical events that initiate and substantiate successful host encounters, revealing that the sequence and timing of multiple biotic and abiotic influences, coupled with host immune status and pathogen responses determine the pathogenic identity of fungi in their hosts as well as disease outcomes. Given the plethora of studies that have focused upon responses to individual stresses and host immune cell types, the emphasis of this chapter will be upon the outputs and new insights gained from fungal transcriptomesfungal transcriptomes derived from mammalian host environments. Here, the power (but not the technical details that are excellently reviewed elsewhere (Hovhannisyan and Gabaldón. Transcriptome sequencing approaches to elucidate host–microbe interactions in opportunistic human fungal pathogens. In: Rodrigues (ed) Fungal physiology and immunopathogenesis. Springer, Cham, 2019)), of state-of-the-art methodologies are highlighted, with an emphasis upon the research questions and the different approaches that have led to new insights, and a look towards emerging technologiestechnologies that will enable us to address important unanswered questions.