Genetic diversity and microevolution in clinical Cryptococcus isolates from Cameroon

Cryptococcal meningitis is the second most common cause of death in people living with HIV/AIDS, yet we have a limited understanding of how cryptococcal isolates change over the course of infection. Cryptococcal infections are environmentally acquired, and the genetic diversity of these infecting isolates can also be geographically linked. Here, we employ whole genome sequences for 372 clinical Cryptococcus isolates from 341 patients with HIV-associated cryptococcal meningitis obtained via a large clinical trial, across both Malawi and Cameroon, to enable population genetic comparisons of isolates between countries. We see that isolates from Cameroon are highly clonal, when compared to those from Malawi, with differential rates of disruptive variants in genes with roles in DNA binding and energy use. For a subset of patients (22) from Cameroon, we leverage longitudinal sampling, with samples taken at days 7 and 14 post-enrollment, to interrogate the genetic changes that arise over the course of infection, and the genetic diversity of isolates within patients. We see disruptive variants arising over the course of infection in several genes, including the phagocytosis-regulating transcription factor GAT204. In addition, in 13% of patients sampled longitudinally, we see evidence for mixed infections. This approach identifies geographically linked genetic variation, signatures of microevolution, and evidence for mixed infections across a clinical cohort of patients affected by cryptococcal meningitis in Central Africa.

Impact of pathogen genetics on clinical phenotypes in a population of Talaromyces marneffei from Vietnam

Talaromycosis, a severe and invasive fungal infection caused by Talaromyces marneffei, is difficult to treat and impacts those living in endemic regions of Southeast Asia, India, and China. While 30% of infections result in mortality, our understanding of the genetic basis of pathogenesis for this fungus is limited. To address this, we apply population genomics and genome-wide association study approaches to a cohort of 336 T. marneffei isolates collected from patients who enrolled in the Itraconazole vs Amphotericin B for Talaromycosis trial in Vietnam. We find that isolates from northern and southern Vietnam form two distinct geographical clades, with isolates from southern Vietnam associated with increased disease severity. Leveraging longitudinal isolates, we identify multiple instances of disease relapse linked to unrelated strains, highlighting the potential for multistrain infections. In more frequent cases of persistent talaromycosis caused by the same strain, we identify variants arising over the course of patient infections that impact genes predicted to function in the regulation of gene expression and secondary metabolite production. By combining genetic variant data with patient metadata for all 336 isolates, we identify pathogen variants significantly associated with multiple clinical phenotypes. In addition, we identify genes and genomic regions under selection across both clades, highlighting loci undergoing rapid evolution, potentially in response to external pressures. With this combination of approaches, we identify links between pathogen genetics and patient outcomes and identify genomic regions that are altered during T. marneffei infection, providing an initial view of how pathogen genetics affects disease outcomes.

Impact of pathogen genetics on clinical phenotypes in a population of Talaromyces marneffei from Vietnam

Talaromycosis, a severe and invasive fungal infection caused by Talaromyces marneffei , is difficult to treat and impacts those living in endemic regions of southeast Asia, India, and China. While 30% of infections result in mortality, our understanding of the genetic basis of pathogenesis for this fungus is limited. To address this, we apply population genomics and genome wide association study approaches to a cohort of 336 T. marneffei isolates collected from patients who enrolled in the Itraconazole versus Amphotericin B for Talaromycosis (IVAP) trial in Vietnam. We find that isolates from northern and southern Vietnam form two distinct geographical clades, with isolates from southern Vietnam associated with increased disease severity. Leveraging longitudinal isolates, we identify multiple instances of disease relapse linked to unrelated strains, highlighting the potential for multi-strain infections. In more frequent cases of persistent talaromycosis caused by the same strain, we identify variants arising over the course of patient infections that impact genes predicted to function in the regulation of gene expression and secondary metabolite production. By combining genetic variant data with patient metadata for all 336 isolates, we identify pathogen variants significantly associated with multiple clinical phenotypes. In addition, we identify genes and genomic regions under selection across both clades, highlighting loci undergoing rapid evolution, potentially in response to external pressures. With this combination of approaches, we identify links between pathogen genetics and patient outcomes and identify genomic regions that are altered during T. marneffei infection, providing an initial view of how pathogen genetics affects disease outcomes.

Genomic Variation across a Clinical Cryptococcus Population Linked to Disease Outcome

Cryptococcus neoformans is the causative agent of cryptococcosis, a disease with poor patient outcomes that accounts for approximately 180,000 deaths each year. Patient outcomes may be impacted by the underlying genetics of the infecting isolate; however, our current understanding of how genetic diversity contributes to clinical outcomes is limited. Here, we leverage clinical, in vitro growth and genomic data for 284 C. neoformans isolates to identify clinically relevant pathogen variants within a population of clinical isolates from patients with human immunodeficiency virus (HIV)-associated cryptococcosis in Malawi. Through a genome-wide association study (GWAS) approach, we identify variants associated with the fungal burden and the growth rate. We also find both small and large-scale variation, including aneuploidy, associated with alternate growth phenotypes, which may impact the course of infection. Genes impacted by these variants are involved in transcriptional regulation, signal transduction, glycosylation, sugar transport, and glycolysis. We show that growth within the central nervous system (CNS) is reliant upon glycolysis in an animal model and likely impacts patient mortality, as the CNS yeast burden likely modulates patient outcome. Additionally, we find that genes with roles in sugar transport are enriched in regions under selection in specific lineages of this clinical population. Further, we demonstrate that genomic variants in two genes identified by GWAS impact virulence in animal models. Our approach identifies links between the genetic variation in C. neoformans and clinically relevant phenotypes and animal model pathogenesis, thereby shedding light on specific survival mechanisms within the CNS and identifying the pathways involved in yeast persistence. IMPORTANCE Infection outcomes for cryptococcosis, most commonly caused by C. neoformans, are influenced by host immune responses as well as by host and pathogen genetics. Infecting yeast isolates are genetically diverse; however, we lack a deep understanding of how this diversity impacts patient outcomes. To better understand both clinical isolate diversity and how diversity contributes to infection outcomes, we utilize a large collection of clinical C. neoformans samples that were isolated from patients enrolled in a clinical trial across 3 hospitals in Malawi. By combining whole-genome sequence data, clinical data, and in vitro growth data, we utilize genome-wide association approaches to examine the genetic basis of virulence. Genes with significant associations display virulence attributes in both murine and rabbit models, demonstrating that our approach can identify potential links between genetic variants and patho-biologically significant phenotypes.

S2.5d Exploring multidrug resistance, fitness compensation, and collateral sensitivity in Candida auris : Fight fire with fire?

S2.5 Rare yeasts, September 21, 2022, 3:00 PM - 4:30 PM

Candida auris (C. auris) is a recently emerged human fungal pathogen of growing concern due to its ability to acquire extensive multidrug resistance (MDR) to all four antifungal drug classes. The unprecedented extent of MDR in C. auris, suggests accelerated resistance evolution, novel mechanisms of resistance, and/or potential fitness compensation. Despite being the first fungus to be officially considered an urgent antimicrobial resistance threat by the CDC (US), insights into the resistance mechanisms and evolutionary dynamics of C. auris are still scarce.

 

By using high-throughput in vitro experimental evolution with various antifungal drugs, we have obtained a library of resistant strains from four different clades. Through both genome and targeted sequencing, we have discovered novel mutations, especially for polyene resistance, which indicate new mechanisms of resistance and fitness compensation. For the validation of mutations, we have optimized a recyclable CRISPR/Cas9 tool for C. auris based on the C. albicans HIS-FLP system.

 

By mapping drug susceptibility responses of evolved strains across a library of several antifungals and repurposed drugs, we have discovered trends of cross-resistance and collateral sensitivity. Both phenomena have been extensively studied in tumors and bacteria but remain unexplored in fungi. In the light of these observations, we explore novel treatment schemes that prevent antifungal drug resistance development in C. auris and other pathogenic fungi.

738. A Novel Molecular Diagnostic Assay for Identification of Fungal Pathogens

Background

A rapid and accurate diagnostic method for invasive fungal infections remains a critical clinical need. We recently reported a rapid molecular method for bacterial species identification directly from clinical samples that targets highly abundant ribosomal RNA on a multiplexed hybridization platform called NanoString. Here we report an adaptation of this assay that accurately distinguishes common fungal pathogens with limit of detection at a single yeast cell.

Methods

Building on our bacterial approach, we computationally designed specific hybridization probes targeting species-specific variable regions of fungal 18S and 28S rRNA from 12 clinically relevant fungi: Aspergillus fumigatus, Cryptococcus neoformans, and 10 Candida species, including Candida auris. Following mechanical lysis of crude specimens, fungi were detected from laboratory culture or artificial cerebrospinal fluid via multiplexed hybridization on a NanoString (Seattle, WA) instrument which yielded results within 7 hours from sample collection. Assay sensitivity was probed using serial dilutions of lysed C. albicans in culture, and cell-equivalents were confirmed by plating.

Results

Our hybridization probes targeting fungal rRNA specifically recognized all species tested to date: A. fumigatus, C. neoformans, and C. albicans with no cross-reactivity (Fig 1a). Serial dilutions of C. albicans lysate demonstrated a limit of detection around 0.1 cell equivalents without rRNA amplification (Fig 1b), capitalizing on the intrinsic abundance of rRNA in fungal cells.

Figure 1.

Conclusion

We adapted a rapid, ultrasensitive hybridization-based diagnostic assay that has proven successful in bacteria, to fungi. Here we show the accurate detection of Aspergillus, Cryptococcus, and Candida species, including a computational design that will enable the distinction of 10 different Candida species, including C. auris, within hours from clinical specimen collection.

Disclosures

All Authors: No reported disclosures

Vomocytosis of live pathogens from macrophages is regulated by the atypical MAP kinase ERK5

Vomocytosis, or nonlytic extrusion, is a poorly understood process through which macrophages release live pathogens that they have failed to kill back into the extracellular environment. Vomocytosis is conserved across vertebrates and occurs with a diverse range of pathogens, but to date, the host signaling events that underpin expulsion remain entirely unknown. We use a targeted inhibitor screen to identify the MAP kinase ERK5 as a critical suppressor of vomocytosis. Pharmacological inhibition or genetic manipulation of ERK5 activity significantly raises vomocytosis rates in human macrophages, whereas stimulation of the ERK5 signaling pathway inhibits vomocytosis. Lastly, using a zebrafish model of cryptococcal disease, we show that reducing ERK5 activity in vivo stimulates vomocytosis and results in reduced dissemination of infection. ERK5 therefore represents the first host signaling regulator of vomocytosis to be identified and a potential target for the future development of vomocytosis-modulating therapies.