Evolution of Fluconazole Resistance Mechanisms and Clonal Types of Candida parapsilosis Isolates from a Tertiary Care Hospital in South Korea

Resistance to Azoles in Candida parapsilosis Isolates from Spain Is Associated with an Impairment in Filamentation and Biofilm Formation

In recent years, there has been an increase in the incidence of fluconazole-non-susceptible (FNS) Candida parapsilosis. The reasons why these strains are able to colonize hospitals remain unknown. It is also unclear whether these strains exhibit resistance to the disinfectants used in hospitals, facilitating their spread. For these reasons, in this work, we aimed to investigate whether fluconazole resistance was associated with virulence traits and the resistance of these strains to common hospital disinfectants. The general conclusion of the study was that more than 95% of the FNS strains, regardless of the resistance mutation they carried, had filamentation problems, whereas around 75% of the susceptible strains formed pseudohyphae and were capable of filamentation. This 95% of the FNS strains did not form pseudohyphae, did not invade agar, and did not form biofilms, while the susceptible strains exhibited the opposite behaviour. Through microfluidics experiments, we observed that both the susceptible and FNS strains were capable of adhering to a plastic surface under dynamic conditions, but the FNS strains formed unstable aggregates that did not remain attached to the surface, confirming the filamentation defect of these strains. In the second part of the study, we observed that FNS strains are susceptible to clinical disinfectants, although they presented a slight resistance to some of them, such as chlorhexidine, compared to susceptible isolates. In this work, we address important aspects to understand the dissemination of FNS strains in clinical outbreaks.

Azole resistance: insights from Y132 substitutions in Candida sterol 14α-demethylase utilizing molecular dynamics simulations

Azole-resistant Candida infections are on the rise. Resistant substitutions at Y132 in sterol 14α-demethylase, the key target of azole drugs, are frequent. However, it is unclear why only some Y132 substitutions are favoured or how they exert differential effects on different azoles. Reported instances of Y132 substitutions were collected from the literature. Extensive molecular dynamics simulations of sterol 14α-demethylase bound to fluconazole or VT1161 (VT1) were performed using GROMACS, and the ligand-binding free energies were computed to quantify the effects of various Y132 substitutions on azole binding/interactions. Three azole-resistant substitutions, Y to C/F/H, were reported at residue position 132 in sterol 14α-demethylase. The Y132H was the most common substitution in C. albicans, while it was Y132F in other species. Ligand-binding free energies were -13.97 kcal/mol and -35.30 kcal/mol for fluconazole and VT1, respectively. There were differences in the ligand-binding free energies after substitutions compared to the wild type protein. Y132F and Y132H were the most frequent substitutions in Candida sterol 14α-demethylase. Far higher binding free energy of fluconazole in comparison with VT1 might partly explain its susceptibility to azole-resistant substitutions. The results give key insights into azole resistance, and antifungal drug discovery and optimization.

Phenotypic and genotypic characterization of Candida parapsilosis complex isolates from a Lebanese hospital

The opportunistic pathogen Candida parapsilosis is a major causative agent of candidiasis leading to death in immunocompromised individuals. Azoles are the first line of defense in their treatment. The purpose of this study was to characterize eight fluconazole-resistant and sensitive C. parapsilosis hospital isolates through a battery of phenotypic tests that target pathogenicity attributes such as virulence, biofilm formation, stress resistance, and ergosterol content. Whole genome sequencing was carried out to identify mutations in key pathogenicity and resistance genes. Phylogenetic comparison was performed to determine strain relatedness and clonality. Genomic data and phylogenetic analysis revealed that two isolates were C. orthopsilosis and C. metapsilosis misidentified as C. parapsilosis. Whole genome sequencing analysis revealed known and novel mutations in key drug resistance and pathogenicity genes such as ALS6, ALS7, SAPP3, SAP7, SAP9, CDR1, ERG6, ERG11 and UPC2. Phylogenetic analysis revealed a high degree of relatedness and clonality within our C. parapsilosis isolates. Our results showed that resistant isolates exhibited an increase in biofilm content compared to the sensitive isolates. In conclusion, our study is the first of its kind in Lebanon to describe phenotypic and genotypic characteristics of nosocomial C. parapsilosis complex isolates having a remarkable ability to form biofilms.

Genomic reconstruction of an azole-resistant Candida parapsilosis outbreak and the creation of a multi-locus sequence typing scheme: a retrospective observational and genomic epidemiology study

BACKGROUND

Fluconazole-resistant Candida parapsilosis has emerged as a significant health-care-associated pathogen with a propensity to spread patient to patient and cause nosocomial outbreaks, similar to Candida auris. This study investigates a long-lasting outbreak of fluconazole-resistant C parapsilosis that was initially detected in December, 2018, and January, 2019, and officially declared in November, 2019; lasted multiple years; and involved several health-care centres in Berlin, Germany.

METHODS

In this retrospective, observational, and genomic epidemiology study, we used whole-genome sequencing (WGS) of isolates sent by German health-care facilities and laboratories to the National Reference Center for Invasive Fungal Infections (Jena, Germany) for antifungal susceptibility testing between Jan 1, 2016, and Dec 31, 2022. We included all potential outbreak samples (ie, isolates originating from Berlin that were resistant to fluconazole and voriconazole but susceptible to posaconazole) and all non-outbreak isolates that originated from outside of Berlin and were resistant to at least one azole. We also included a number of non-outbreak isolates from outside Berlin that were susceptible or resistant to azoles so that the total study dataset included a matching amount of outbreak and non-outbreak samples from Germany. We used admission and discharge records for patients involved in the outbreak and constructed a network of patient transfers in time and space. We used WGS data for included samples, complemented with WGS data for global samples obtained from the National Center for Biotechnology Information Sequence Read Archive, to construct single-nucleotide variant (SNV)-based phylogeny and perform SNV distance-based analyses. Additionally, we used the whole genomic dataset to identify loci with high discriminatory power to establish a multi-locus sequence typing (MLST) strategy for C parapsilosis.

FINDINGS

We identified 38 clonal, azole-resistant isolates of C parapsilosis causing 33 cases of invasive infection during a 2018-22 outbreak in multiple hospitals in Berlin. We also sequenced the genomes of 37 non-outbreak isolates. WGS revealed that outbreak strains were separated by a mean of 36 SNVs (SD 20), whereas outbreak strains differed from outgroup samples from Berlin and other regions of Germany by a mean of 2112 SNVs (828). Temporal and genomic reconstruction of the outbreak cases indicated that transfer of patients between health-care facilities was probably responsible for the persistent reimportation of the drug-resistant clone and subsequent person-to-person transmission. German outbreak strains were closely related to strains responsible for an outbreak in Canada and to isolates from Kuwait, Türkiye, and South Korea. Including the outbreak clone, we identified three distinct azole-resistant lineages carrying ERG11 Y132F in Germany. We identified four 750 bp loci in CPAR2_101400, CPAR2_101470, CPAR2_108720, and CPAR2_808110 for inclusion in our MLST strategy. Application of the MLST method to a global collection of 386 isolates identified 62 sequence types, with the outbreak strains all belonging to the same sequence type.

INTERPRETATION

This study underscores the emergence of drug-resistant C parapsilosis that can spread patient to patient within a health-care system, but also, possibly, internationally. Our findings highlight the importance of monitoring C parapsilosis epidemiology globally and of continuous surveillance and rigorous infection control measures at the local scale. We also developed a novel MLST scheme for genetic epidemiology and outbreak investigations, which could represent a faster and less expensive alternative to WGS.

FUNDING

German Federal Ministry for Education and Research, German Research Foundation, and German Ministry of Health.

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.

Clinical Characteristics of Candidemia Due to Candida parapsilosis with Serial Episodes: Insights from 5-Year Data Collection at a Tertiary Hospital in Korea

Candida parapsilosis is a common cause of non-albicans Candida species causing candidemia, particularly invasive candidiasis. This study aimed to characterize candidemia due to the C. parapsilosis complex with serial episodes, including clinical and mycological features.

METHODS

Blood isolates of the C. parapsilosis complex were collected from February 2019 to January 2023 at a tertiary Korean hospital. Species identification was performed using Vitek 2 or matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, and antifungal susceptibility testing was performed using the Sensititre YeastOne® system. Clinical information was collected, and characteristics were analyzed according to single or serial isolates.

RESULTS

A total of 586 blood isolates of the C. parapsilosis complex were recovered from 68 candidemia patients during the study period. Of them, only the first isolate per patient was investigated. The only two isolates were resistant to fluconazole and no isolate was resistant to echinocandins, amphotericin B, or 5-FC. A single episode of candidemia occurred in 35 patients, while serial episodes occurred in 33 patients. Underlying liver diseases, use of vasopressors, ICU admission, severe sepsis, and CVC use were more frequent in patients with serial episodes. There was no significant difference in the median MIC values of antifungal agents or the use of azoles or amphotericin B between single and serial episodes. However, patients with serial episodes more frequently received echinocandin therapy. Overall, there was no significant difference in the 30-day mortality rate between patients with single and serial episodes.

CONCLUSION

Our data indicate that several factors related to the underlying conditions of the patients are associated with C. parapsilosis candidemia with serial episodes, rather than the characteristics of Candida itself.

Molecular Diagnostics for Invasive Fungal Diseases: Current and Future Approaches

Invasive fungal diseases (IFDs) comprise a growing healthcare burden, especially given the expanding population of immunocompromised hosts. Early diagnosis of IFDs is required to optimise therapy with antifungals, especially in the setting of rising rates of antifungal resistance. Molecular techniques including nucleic acid amplification tests and whole genome sequencing have potential to offer utility in overcoming limitations with traditional phenotypic testing. However, standardisation of methodology and interpretations of these assays is an ongoing undertaking. The utility of targeted Aspergillus detection has been well-defined, with progress in investigations into the role of targeted assays for Candida, Pneumocystis, Cryptococcus, the Mucorales and endemic mycoses. Likewise, whilst broad-range polymerase chain reaction assays have been in use for some time, pathology stewardship and optimising diagnostic yield is a continuing exercise. As costs decrease, there is also now increased access and experience with whole genome sequencing, including metagenomic sequencing, which offers unparalleled resolution especially in the investigations of potential outbreaks. However, their role in routine diagnostic use remains uncommon and standardisation of techniques and workflow are required for wider implementation.

Emergence of multiple fluconazole-resistant Candida parapsilosis sensu stricto clones with persistence and transmission in China

OBJECTIVES

We explored the epidemiological and molecular characteristics of Candida parapsilosis sensu stricto isolates in China, and their mechanisms of azole resistance.

METHODS

Azole susceptibilities of 2318 non-duplicate isolates were determined using CLSI broth microdilution. Isolates were genotyped by a microsatellite typing method. Molecular resistance mechanisms were also studied and functionally validated by CRISPR/Cas9-based genetic alterations.

RESULTS

Fluconazole resistance occurred in 2.4% (n = 56) of isolates, and these isolates showed a higher frequency of distribution in ICU inpatients compared with susceptible isolates (48.2%, n = 27/56 versus 27.8%, 613/2208; P = 0.019). Microsatellite-genotyping analysis yielded 29 genotypes among 56 fluconazole-resistant isolates, of which 10 genotypes, including 37 isolates, belonged to clusters, persisting and transmitting in Chinese hospitals for 1-29 months. Clusters harbouring Erg11Y132F (5/10; 50%) were predominant in China. Among these, the second most dominant cluster MT07, including seven isolates, characteristically harbouring Erg11Y132F and Mrr1Q625K, lent its carriage to being one of the strongest associations with cross-resistance and high MICs of fluconazole (>256 mg/L) and voriconazole (2-8 mg/L), causing transmission across two hospitals. Among mutations tested, Mrr1Q625K led to the highest-level increase of fluconazole MIC (32-fold), while mutations located within or near the predicted transcription factor domain of Tac1 (D440Y, T492M and L518F) conferred cross-resistance to azoles.

CONCLUSIONS

This study is the first Chinese report of persistence and transmissions of multiple fluconazole-resistant C. parapsilosis sensu stricto clones harbouring Erg11Y132F, and the first demonstration of the mutations Erg11G307A, Mrr1Q625K, Tac1L263S, Tac1D440Y and Tac1T492M as conferring resistance to azoles.

Fluconazole-resistant Candida parapsilosis complex candidemia and analysis of mutations in the ERG11 gene from Pakistan

BACKGROUND

Recent reports of the emergence of fluconazole resistance in Candida parapsilosis species complex poses a challenge, more specifically in settings where echinocandin-based treatment regime is not feasible.

OBJECTIVE

This study reported emergence of fluconazole resistance in C. parapsilosis species complex strains isolated from blood cultures.

MATERIALS AND METHODS

This retrospective observational study was conducted from 2018 to 2020 at a tertiary care laboratory from Pakistan. Fluconazole-resistant C. parapsilosis species complex fungemia cases were identified from laboratory database and clinical details were collected. Identification of C. parapsilosis species complex was done using API 20C AUX and Cornmeal Tween80 agar morphology. Minimum inhibitory concentrations (MICs) were determined using Sensititre YeastONE and interpretation was done with CLSI M60 ED1:2017. ERG11 gene region was amplified and sequenced by Sanger sequencing and analysed by MEGA 11 Software.

RESULTS

A total of 13 (8.5%) fluconazole-resistant isolates were identified from 152 C. parapsilosis species complex candidemia cases. Fluconazole MICs of resistant isolates ranged between 8 and 256 μg/mL. Analysis of ERG11 gene revealed nonsynonymous mutations at position Y132F in 86% of the fluconazole-resistant isolates. Diabetes and hospitalization were important risk factors for candidemia with fluconazole-resistant C. parapsilosis complex.

CONCLUSION

This is the first report of the emergence and molecular mechanisms of fluconazole resistance in C. parapsilosis species complex from Pakistan. Y132F mutation in the ERG11 gene was the most common mutation in fluconazole-resistant strains. These findings are concerning and necessitate better diagnostics, newer antifungals, ongoing surveillance and further insights on resistance mechanisms in the country.

Candida parapsilosis complex in the clinical setting

Representatives of the Candida parapsilosis complex are important yeast species causing human infections, including candidaemia as one of the leading diseases. This complex comprises C. parapsilosis, Candida orthopsilosis and Candida metapsilosis, and causes a wide range of clinical presentations from colonization to superficial and disseminated infections with a high prevalence in preterm-born infants and the potential to cause outbreaks in hospital settings. Compared with other Candida species, the C. parapsilosis complex shows high minimal inhibitory concentrations for echinocandin drugs due to a naturally occurring FKS1 polymorphism. The emergence of clonal outbreaks of strains with resistance to commonly used antifungals, such as fluconazole, is causing concern. In this Review, we present the latest medical data covering epidemiology, diagnosis, resistance and current treatment approaches for the C. parapsilosis complex. We describe its main clinical manifestations in adults and children and highlight new treatment options. We compare the three sister species, examining key elements of microbiology and clinical characteristics, including the population at risk, disease manifestation and colonization status. Finally, we provide a comprehensive resource for clinicians and researchers focusing on Candida species infections and the C. parapsilosis complex, aiming to bridge the emerging translational knowledge and future therapeutic challenges associated with this human pathogen.

Detection and Characterization of Two Phenotypes of Candida parapsilosis in South Korea: Clinical Features and Microbiological Findings

We newly detected two (sinking and floating) phenotypes of Candida parapsilosis among bloodstream infection (BSI) isolates from Korean hospitals and assessed their microbiological and clinical characteristics. During the performance of a Clinical and Laboratory Standards Institute (CLSI) broth microdilution antifungal susceptibility testing, the sinking phenotype had a characteristic smaller button-like appearance because all yeast cells sank to the bottoms of the CLSI U-shaped round-bottom wells, whereas the floating phenotype comprised dispersed cells. Phenotypic analysis, antifungal susceptibility testing, ERG11 sequencing, microsatellite genotyping, and clinical analysis were performed on C. parapsilosis isolates from 197 patients with BSI at a university hospital during 2006 to 2018. The sinking phenotype was detected in 86.7% (65/75) of the fluconazole-nonsusceptible (FNS) isolates, 92.9% (65/70) of the isolates harboring the Y132F ERG11 gene substitution, and 49.7% (98/197) of all isolates. Clonality was more frequently observed for the Y132F-sinking isolates (84.6% [55/65]) than for all other isolates (26.5% [35/132]; P < 0.0001). Annual incidence of Y132F-sinking isolates increased 4.5-fold after 2014, and two dominant genotypes, persistently recovered for 6 and 10 years, accounted for 69.2% of all Y132F-sinking isolates. Azole breakthrough fungemia (odds ratio [OR], 6.540), admission to the intensive care unit (OR, 5.044), and urinary catheter placement (OR, 6.918) were independent risk factors for BSIs with Y132F-sinking isolates. The Y132F-sinking isolates exhibited fewer pseudohyphae, a higher chitin content, and lower virulence in the Galleria mellonella model than the floating isolates. These long-term results illustrate the increasing BSIs caused by clonal transmission of the Y132F-sinking isolates of C. parapsilosis. IMPORTANCE We believe that this is the first study describe the microbiological and molecular characteristics of bloodstream isolates of C. parapsilosis in Korea exhibiting two phenotypes (sinking and floating). An important aspect of our findings is that the sinking phenotype was observed predominantly in isolates harboring a Y132F substitution in the ERG11 gene (92.9%), fluconazole-nonsusceptible (FNS) isolates (86.7%), and clonal BSI isolates (74.4%) of C. parapsilosis. Although the increase in the prevalence of FNS C. parapsilosis isolates has been a major threat in developing countries, in which the vast majority of candidemia cases are treated with fluconazole, our long-term results show increasing numbers of BSIs caused by clonal transmission of Y132F-sinking isolates of C. parapsilosis in the period with an increased echinocandin use for candidemia treatment in Korea, which suggests that C. parapsilosis isolates with the sinking phenotype continue to be a nosocomial threat in the era of echinocandin therapy.