A multidimensional assessment of in-host fitness costs of drug resistance in the opportunistic fungal pathogen Candida glabrata

The global rise of antimicrobial resistance poses a serious threat to public health. Because drug-resistant (DR) pathogens typically carry mutations in genes involved in critical cellular functions, they may be less fit under drug-free conditions than their susceptible counterparts. As such, the limited use of antimicrobial drugs has been proposed as a practical strategy to diminish the prevalence of DR strains. However, in many cases the fitness of DR pathogens under host conditions is unknown. Candida (Nakaseomyces) glabrata is a prevalent opportunistic fungal pathogen notable for its high rate of fluconazole resistance (FLZR), echinocandin resistance (ECR), and multidrug resistance (MDR) relative to other Candida pathogens. Nonetheless, the fitness of C. glabrata MDR isolates is poorly characterized, and studies of FLZR isolate fitness have produced contradictory findings. Two important host niches for C. glabrata are macrophages, in which it can survive and proliferate, and the gut. Herein, by employing a comprehensive collection of clinical and isogenic C. glabrata isolates, we show that FLZR C. glabrata isolates are less fit inside macrophages than susceptible isolates and that this fitness cost is reversed by acquiring ECR mutations in FKS1/2 genes. Interestingly, dual-RNAseq revealed that macrophages infected with DR isolates mount an inflammatory response whereas the intracellular DR cells downregulate processes required for in-host adaptation. Consistently, DR isolates were outcompeted by their susceptible counterparts in the context of gut colonization and in the kidneys of systemically infected mice, whereas they showed comparable fitness in the spleen. Collectively, our study shows that macrophage-rich organs, such as the spleen, favor the retention of DR isolates, potentially reducing the utility of limited antifungal use to decrease the burden of DR C. glabrata in the context of candidemia. Author summary The rise of multidrug resistant (MDR) strains of fungal pathogens, notably Candida glabrata, poses a significant clinical challenge because of the limited number of antifungal drugs available for use. Thus, it is vital to minimize the prevalence of drug resistance in the clinic. Because in some bacterial and fungal species drug resistance is accompanied by a fitness cost, implementation of limited antibiotic or antifungal drug use in the clinic has been suggested as a practical way to favor the spread of susceptible isolates. However, it is not clear whether this strategy can work for MDR C. glabrata, as its fitness costs have not been systematically examined, particularly in the context of the host. Herein, we show that MDR C. glabrata isolates can replicate within macrophages as well as susceptible isolates, and this result was consistent with gene expression changes in the infected macrophages. In animal models, MDR strains were unfit in the context of the gastrointestinal tract and kidney, but their fitness in the spleen was comparable to that of susceptible strains. Accordingly, the potential of limited antifungal use to reduce the prevalence of MDR strains of C. glabrata strongly depends on the host reservoir of infection.