Fluconazole-resistant Candida parapsilosis genotypes from hospitals located in five Spanish cities and one in Italy: Description of azole-resistance profiles associated with the Y132F ERG11p substitution

The S862C amino acid change in CpMrr1 confers fluconazole resistance in Candida parapsilosis

Background

Candida parapsilosis is an opportunistic pathogen with increasing rates of resistance to fluconazole and voriconazole. Recently, in an outbreak at the Azienda Ospedaliero-Universitaria Pisana, a new amino acid substitution, S862C in the CpMrr1 protein, was found only in azole-resistant strains. The contribution of this mutation to the acquisition of an azole-resistant phenotype was investigated in this study.

Methods

Antifungal resistance in C. parapsilosis clinical strains isolated from the outbreak (n = 16) was tested by the broth microdilution method and Etest strip. WGS and Sanger sequencing analyses were used for the detection of SNPs. A CRISPR-Cas9-based genome editing strategy was used to induce the C2585G substitution in the CpMRR1 gene of susceptible C. parapsilosis isolates to investigate its role in the acquisition of azole resistance.

Results

The A395T and the newly found C2585G substitution in the CpMRR1 gene were present in all resistant isolates, but not in the susceptible ones. Such mutations were later induced in the C. parapsilosis reference strain ATCC 22019 and in two azole-susceptible clinical isolates in homozygosis, and in heterozygosis only for ATCC 22019 and one azole-susceptible clinical isolate. Both heterozygous and homozygous mutants carrying the C2585G mutation were fluconazole resistant, with some clones also presenting intermediate susceptibility or resistance to voriconazole.

Conclusions

To the best of our knowledge, this is the first study to report the effect on azole resistance of a novel C2585G nucleotide substitution in the CpMRR1 gene found in clinical isolates recovered during an outbreak of azole-resistant C. parapsilosis in a healthcare setting.

Pharmacokinetic novelties of isavuconazole. Use in special situations

Isavuconazole, a next generation triazole, exhibits unique pharmacokinetic and pharmacodynamic properties that make it ideal for treating invasive fungal infections in critically ill and immunocompromised patients. This antifungal agent stands out for its broad spectrum of activity, which includes filamentous fungi such as Aspergillus and Mucorales, with an efficacy comparable to that of voriconazole and additional advantages against these pathogens. Its high oral bioavailability (close to 100%), prolonged half-life (>100h), and linear, predictable pharmacokinetic profile minimize the need for frequent dose adjustments and therapeutic monitoring. Its lipophilic structure facilitates penetration into key tissues, such as the central nervous system and pulmonary tissue, as validated by clinical studies showing survival rates exceeding 70% in patients with complicated invasive fungal infection. Its use is safe in populations with renal impairment, mild to moderate hepatic impairment, paediatrics, and obesity, although dose adjustment is recommended for severe hepatic impairment. Recent studies in critically ill patients undergoing extracorporeal membrane oxygenation or continuous renal replacement therapy have revealed moderate reductions in plasma concentration, without significant clinical impact. Adaptive dosing strategies have been proposed to optimize efficacy in these cases. Compared to other triazoles, isavuconazole demonstrates a robust safety profile, with lower incidences of hepatotoxicity and neurotoxicity. Its antifungal activity, favorable pharmacokinetics, and excellent safety profile underscore its role as a reference antifungal agent, particularly in challenging clinical scenarios.

Candida spp. colonization: a genotype source found in blood cultures that can become widespread

Objective

Our previous genotyping studies suggest that some anatomical locations act as reservoirs of genotypes that may cause further candidemia, since we found identical genotypes in gastrointestinal tract or catheter tip isolates and blood cultures, in contrast, we did not find blood culture genotypes in vagina samples. We observed that some genotypes can be found in blood cultures more frequently than others, some of them being called widespread genotypes because have been found in unrelated patients admitted to different hospitals. The presence of widespread genotypes may be more frequently found because of their predisposition to cause candidemia. It is unclear whether genotypes colonizing other anatomical sites different from the gastrointestinal tract can also be detected in this way; we studied C. albicans, C. parapsilosis, and C. tropicalis colonizing genotypes to assess what proportion could be found in blood cultures and the proportion of widespread genotypes.

Methods

The isolates (n= 640 Candida isolates from 323 patients) studied herein were obtained from samples processed at the Clinical Microbiology and Infectious Diseases Department of the Gregorio Marañón Hospital (Madrid, Spain) from July 1, 2016, to June 30, 2019. C. albicans (n=486), C. parapsilosis (n=94), and C. tropicalis (n=60) isolates were genotyped using species-specific microsatellite markers and sourced from blood (n=120) and colonized anatomical sites (n=520; catheter [n=50], lower respiratory tract [n=227], skin/mucosa [n=132], and urinary tract [n=111]). Isolates with identical genotypes were those presenting the same alleles for all markers or with only differences at one locus of a given marker. Identical genotypes were further classified as a match (identical genotype found in different groups of samples from a given patient) or as a cluster (identical genotype found in ≥2 patients). Finally, singletons were genotypes detected once. The genotypes found were then compared with our in-house database containing 587 blood genotypes from patients admitted to the Gregorio Marañón Hospital (2007-2023) to assess the proportion of genotypes found in colonized samples that were also found in blood cultures. Moreover, since some of our in-house database genotypes had been tagged as widespread genotypes, we compared the proportions of widespread genotypes as well as the proportions of matches, clusters, and patients involved in clusters found among exclusively colonizing genotypes, exclusively blood culture genotypes, and both colonizing and blood culture genotypes using a standard binomial method.

Results

Intra-patient analysis was conducted exclusively on those patients (n=225; 69.7%) who had ≥2 isolates from a given species; the proportion of patients with matches was lower in exclusively colonized patients than in patients with candidemia and colonizing genotypes (87.3% vs. 94.1%; p = 0.126). Inter-patient analysis was conducted considering all patients (n=323) and isolates from groups 1, 2, and 3 (n=640). Overall, we detected 341 genotypes, of which 320 were singletons and 21 were clusters (6.16%). Clusters involving blood cultures and colonizing isolates sourced from catheter tips (14.6%), skin and mucosa (7.5%), urine (7.4%), and lower respiratory tract (4.6%). Cluster-involved patients had not been admitted to the same ward at the same time. Of the 290 colonizing genotypes, 91 (31.1%) were also found in blood cultures, the highest proportion being C. parapsilosis (p < 0.05); proportions of identical genotypes found in blood cultures and catheter tips were higher than those found in blood cultures and other colonized samples (79.2% vs. 26.7%; p < 0.001). Widespread genotype ratios were significantly higher among genotypes found in both blood and colonized samples than among genotypes found exclusively in either blood culture or other colonizing genotypes (31.9% vs. 7.1% vs. 3.7%, respectively; p < 0.001).

Conclusion

We observed that 94% of patients with candidemia were colonized by a genotype causing the infection; likewise, a total of 31% of colonizing genotypes were detectable in blood cultures. Finally, identical genotypes found in both colonized samples and blood cultures had a higher probability of being widespread.

Fluconazole-resistant Candida parapsilosis: fast detection of the Y132F ERG11p substitution, and a proposed microsatellite genotyping scheme

OBJECTIVES

We propose fast and accurate molecular detection of the Y132F ERG11p substitution directly on pure-cultured Candida parapsilosis isolates. We also assessed a discriminative genotyping scheme to track circulating genotypes.

METHODS

A total of 223 C. parapsilosis isolates (one patient each) from 20 hospitals, located in Spain and Italy were selected. Isolates were fluconazole-resistant (n = 94; harbouring the Y132F ERG11p substitution [n = 85], the G458S substitution [n = 6], the R398I substitution [n = 2], or the wild-type ERG11 gene sequence) or fluconazole-susceptible (n = 129). Two targeted-A395T-mutation PCR formats (conventional and real-time) were engineered and optimized on fluconazole-susceptible and fluconazole-resistant pure-cultured isolates, thus skipping DNA extraction. Two genotyping schemes were compared: Scheme 1 (CP1, CP4a, CP6, and B markers), and Scheme 2 (6A, 6B, 6C, CP1, CP4a, and CP6 markers).

RESULTS

The screening performed using both PCR formats showed 100% specificity (fluconazole-susceptible isolates; n = 129/129) and sensitivity (Y132F isolates; n = 85/85) values; however, results were available in 3 and 1.5 hours with the conventional and real-time PCR formats, respectively. Overall, Scheme 1 showed higher genetic diversity than Scheme 2, as shown by the number of alleles detected (n = 98; mean 23, range 13-38), the significantly higher observed and expected heterozygosity, and the probability of identity index (2.5 × 10-6). Scheme 2 markers did not provide further genotypic discrimination of Y132F fluconazole-resistant genotypes.

CONCLUSION

Both proposed PCR formats allow us to speed up the accurate detection of substitution Y132F ERG11p in C. parapsilosis isolates with 100% specificity and sensitivity. In addition, we recommend CP1, CP4a, CP6, and B microsatellite markers for genotyping fluconazole-resistant isolates.

High-Resolution Melting Assay to Detect the Mutations That Cause the Y132F and G458S Substitutions at the ERG11 Gene Involved in Azole Resistance in Candida parapsilosis

BACKGROUND

Candida parapsilosis is a pathogenic yeast that has reduced susceptibility to echinocandins and ranks as the second or third leading cause of candidaemia, depending on the geographical region. This yeast often causes nosocomial infections, which are frequently detected as outbreaks. In recent years, resistance to azoles in C. parapsilosis has increased globally, primarily due to the accumulation of mutations in the ERG11 gene.

OBJECTIVES

In this study, we have developed an assay based on real-time PCR and high-resolution melting (HRM) curve analysis to detect two of the most prevalent mutations at ERG11 that confer resistance to fluconazole (Y132F and G458S).

METHODS

We designed allele-specific oligonucleotides that selectively bind to either the wild type or mutated sequences and optimised the conditions to ensure amplification of the specific allele, followed by detection via high-resolution melting (HRM) analysis.

RESULTS

The designed oligonucleotides to detect the Erg11Y132F and Erg11G458S mutations produced specific amplification of either WT or mutated alleles. We conducted a duplex real-time PCR combining oligonucleotides for the wild-type sequences in one mix, and oligonucleotides for the mutated alleles in another. Following this, we performed an analysis of the HRM curve to identify the amplified allele in each case. This technique was blindly evaluated on a set of 114 C. parapsilosis isolates, all of which were unequivocally identified using our approach.

CONCLUSION

This technique offers a new method for the early detection of azole resistance mechanism in C. parapsilosis.

Short Tandem Repeat Genotyping of Medically Important Fungi: A Comprehensive Review of a Powerful Tool with Extensive Future Potential

Fungal infections pose an increasing threat to public health. New pathogens and changing epidemiology are a pronounced risk for nosocomial outbreaks. To investigate clonal transmission between patients and trace the source, genotyping is required. In the last decades, various typing assays have been developed and applied to different medically important fungal species. While these different typing methods will be briefly discussed, this review will focus on the development and application of short tandem repeat (STR) genotyping. This method relies on the amplification and comparison of highly variable STR markers between isolates. For most common fungal pathogens, STR schemes were developed and compared to other methods, like multilocus sequence typing (MLST), amplified fragment length polymorphism (AFLP) and whole genome sequencing (WGS) single nucleotide polymorphism (SNP) analysis. The pros and cons of STR typing as compared to the other methods are discussed, as well as the requirements for the development of a solid STR typing assay. The resolution of STR typing, in general, is higher than MLST and AFLP, with WGS SNP analysis being the gold standard when it comes to resolution. Although most modern laboratories are capable to perform STR typing, little progress has been made to standardize typing schemes. Allelic ladders, as developed for Aspergillus fumigatus, facilitate the comparison of STR results between laboratories and develop global typing databases. Overall, STR genotyping is an extremely powerful tool, often complimentary to whole genome sequencing. Crucial details for STR assay development, its applications and merit are discussed in this review.

The Impact of the Fungal Priority Pathogens List on Medical Mycology: A Northern European Perspective

Fungal diseases represent a considerable global health concern, affecting >1 billion people annually. In response to this growing challenge, the World Health Organization introduced the pivotal fungal priority pathogens list (FPPL) in late 2022. The FPPL highlights the challenges in estimating the global burden of fungal diseases and antifungal resistance (AFR), as well as limited surveillance capabilities and lack of routine AFR testing. Furthermore, training programs should incorporate sufficient information on fungal diseases, necessitating global advocacy to educate health care professionals and scientists. Established international guidelines and the FPPL are vital in strengthening local guidance on tackling fungal diseases. Future iterations of the FPPL have the potential to refine the list further, addressing its limitations and advancing our collective ability to combat fungal diseases effectively. Napp Pharmaceuticals Limited (Mundipharma UK) organized a workshop with key experts from Northern Europe to discuss the impact of the FPPL on regional clinical practice.