Echinocandin heteroresistance causes prophylaxis failure and facilitates breakthroughCandida parapsilosisinfection

Abstract

Antimicrobial drug resistance is a major problem in the prevention and treatment of infectious diseases. For patients on antimicrobial prophylaxis during cancer treatment and organ transplantation, breakthrough infections represent a significant and often unexplained cause of morbidity. Here, in high-risk patients on micafungin prophylaxis, we reveal that heteroresistance, the presence of a phenotypically unstable, low frequency subpopulation of resistant cells (~1 in 10,000), causes breakthrough bloodstream infections by Candida parapsilosis strains that were misclassified as susceptible by standard antimicrobial susceptibility testing. Genome-matched micafungin heteroresistant strains were isolated from the intestinal reservoir prior to invasive disease. To identify heteroresistance, we harnessed whole genome sequence analysis of 118 clinical C. parapsilosis strains and extracted six genetic features into a predictive machine learning model that distinguished heteroresistant strains with high accuracy. These data directly implicate heteroresistance in unexplained prophylaxis failure and highlight a proof-of-principle approach to detect this phenomenon and inform clinical decisions.

Macrophage internalization creates a multidrug-tolerant fungal persister reservoir and facilitates the emergence of drug resistance

“…Our group, however, has characterized a small subpopulation of C. glabrata persisters in vitro (which we referred to as "drug-tolerant cells") surviving supra-high MIC concentration of echinocandins 27,28 . Such subpopulations growing or surviving supra-high MIC concentrations of static or cidal antifungal drugs, respectively, have been observed in multiple fungal species and proposed to be involved in therapeutic failure, emergence of resistance, and poor clinical outcomes [29][30][31][32] . As described above, bacterial persisters are induced by environmental stress and internalization by host immune cells.…”

Candida parapsilosis Sensu Stricto Antifungal Resistance Mechanisms and Associated Epidemiology

“…The proposed underlying genetically based resistance mechanism for these two fungal pathogens is target drug/efflux pump gene aneuploidy, but still no consensus among researchers has been reached as aneuploidy could only partially explain the resistant phenotype [ 183 , 184 ]. Another clinically relevant issue related to heteroresistance is that it cannot be detected at standard antimicrobial susceptibility tests, this is caused by the reduced number of microorganisms constituting the heteroresistant population [ 185 , 186 ].…”

“…In the case of C. parapsilosis sensu stricto, heteroresistance to echinocandins was appointed by Zhai and colleagues to be correlated with prophylaxis failure, thus enhancing the risk of breakthrough infections [ 185 ]. Rates of C. parapsilosis echinocandin heteroresistance ranged between 0.1% and 0.01%, within an otherwise fully susceptible colony [ 92 , 185 ].…”

The challenges of the genome-based identification of antifungal resistance in the clinical routine

“…Fungal-specific and other tools have been already designed for this task, such as YMAP ( Abbey et al, 2014 ). Deep coverages are also adequate to find heteroresistant subpopulations ( Zhai et al, 2022 ). Homozygosity (~100% reads) and heterozygosity (~50% reads) are approachable using the proportion of mutated reads ( Spettel et al, 2019 ).…”