Detection of Echinocandin-Resistant Candida glabrata in Blood Cultures Spiked with Different Percentages of FKS2 Mutants

Genomic description of acquired fluconazole- and echinocandin-resistance in patients with serial Candida glabrata isolates

Candida glabrata is one of the most common causes of systemic candidiasis, often resistant to antifungal medications. To describe the genomic context of emerging resistance, we conducted a retrospective analysis of 82 serially collected isolates from 33 patients from population-based candidemia surveillance in the United States. We used whole-genome sequencing to determine the genetic relationships between isolates obtained from the same patient. Phylogenetic analysis demonstrated that isolates from 29 patients were clustered by patient. The median SNPs between isolates from the same patient was 30 (range: 7-96 SNPs), while unrelated strains infected four patients. Twenty-one isolates were resistant to echinocandins, and 24 were resistant to fluconazole. All echinocandin-resistant isolates carried a mutation either in the FKS1 or FKS2 HS1 region. Of the 24 fluconazole-resistant isolates, 17 (71%) had non-synonymous polymorphisms in the PDR1 gene, which were absent in susceptible isolates. In 11 patients, a genetically related resistant isolate was collected after recovering susceptible isolates, indicating in vivo acquisition of resistance. These findings allowed us to estimate the intra-host diversity of C. glabrata and propose an upper boundary of 96 SNPs for defining genetically related isolates, which can be used to assess donor-to-host transmission, nosocomial transmission, or acquired resistance. IMPORTANCE In our study, mutations associated to azole resistance and echinocandin resistance were detected in Candida glabrata isolates using a whole-genome sequence. C. glabrata is the second most common cause of candidemia in the United States, which rapidly acquires resistance to antifungals, in vitro and in vivo.

Evaluation of Inoculum Preparation for Etest and EUCAST Broth Dilution to Detect Anidulafungin Polyresistance in Candida glabrata

The influence of inoculum preparation in EUCAST broth dilution and Etest to detect the coexistence of resistant and susceptible Candida subpopulations (defined as polyresistance [PR]) was evaluated. Cocultures of two echinocandin-resistant and susceptible clinical C. glabrata strains were used to simulate the occurrence of mixed populations in clinical samples, and antifungal susceptibility testing was performed with standard and modified approaches of inoculum preparation. Polyresistant results manifested as microcolonies or double ellipses in Etest and in single reduced optical density (OD) values (dip in OD) in microdilution. The strict inclusion of five distinct colonies of 1:5 and 1:10 resistant and susceptible cocultures led to higher rates of PR and R results compared to including one to two colonies in inoculum preparation (30% and 26% for Etest and broth dilution, respectively). Modifying the inoculum preparation by increasing the turbidity from a 2 to a 4 McFarland standard before redilution to a 0.5 McFarland standard reliably enabled the detection of resistance, with better identification of PR by Etest than by broth dilution (82% versus 32%, respectively) and of resistant minimum inhibitory concentration (MIC) values in 18% of Etests and 67% of microdilutions. The highest identification of PR succeeded with Etest and a modified 3 McFarland standard approach of inoculum preparation. Our data demonstrate that inoculum preparation as recommended and practiced does not reliably identify resistant subpopulations in polyresistant Candida cultures. By increasing the inoculum size for Etest assays from a 2 to a 4 McFarland standard with subsequent redilution, we propose a simple adaptation to increase reliability.

In vitro activity of ibrexafungerp against Candida species isolated from blood cultures. Determination of wild-type populations using the EUCAST method

OBJECTIVES

Ibrexafungerp is a new oral glucan synthase inhibitor with in vivo and in vitro activity against Candida spp., including echinocandin- and azole-resistant isolates. We studied the in vitro activity of ibrexafungerp against Candida species isolated from blood cultures and assessed wild-type upper limits against the five Candida species most frequently associated to candidaemia.

METHODS

Isolates (n = 958) causing incident episodes of candidaemia in patients admitted to Gregorio Marañón hospital (Madrid, Spain) between January 2007 and April 2021 were studied. Antifungal susceptibility to ibrexafungerp, fluconazole, micafungin and anidulafungin was tested (EUCAST E.Def 7.3.2) and wild-type upper limits determined against C. albicans (n = 462), C. glabrata (n = 120), C. parapsilosis (n = 249), C. tropicalis (n = 73) and C. krusei (n = 24). fksgene sequencing was carried out in non-wild-type isolates.

RESULTS

Ibrexafungerp showed antifungal in vitro activity against the studied isolates. Wild-type upper limits for ibrexafungerp were >0.25 mg/L against C. albicans, >1 mg/L against C. parapsilosis, C. glabrata, and C. tropicalis, and >2 mg/L against C. krusei. Percentages of ibrexafungerp non-wild-type isolates were low (C. parapsilosis and C. krusei, 0%; C. albicans, 0.22% (1/462); C. glabrata, 0.83% (1/120); and C. tropicalis, 1.37% (1/73)). Ibrexafungerp proved in vitro activity against fluconazole- or echinocandin-resistant isolates.

DISCUSSION

We show in vitro activity of ibrexafungerp against the tested Candida species. Furthermore, we provide ibrexafungerp wild-type upper limits, which allows defining the wild-type populations of the five most relevant Candida species.

Pan-Echinocandin-Resistant Candida glabrata Bloodstream Infection Complicating COVID-19: A Fatal Case Report

Coinfections with bacteria or fungi may be a frequent complication of COVID-19, but coinfections with Candida species in COVID-19 patients remain rare. We report the 53-day clinical course of a complicated type-2 diabetes patient diagnosed with COVID-19, who developed bloodstream infections initially due to methicillin-resistant Staphylococcus aureus, secondly due to multidrug-resistant Gram-negative bacteria, and lastly due to a possibly fatal Candida glabrata. The development of FKS-associated pan-echinocandin resistance in the C. glabrata isolated from the patient after 13 days of caspofungin treatment aggravated the situation. The patient died of septic shock shortly before the prospect of receiving potentially effective antifungal therapy. This case emphasizes the importance of early diagnosis and monitoring for antimicrobial drug-resistant coinfections to reduce their unfavorable outcomes in COVID-19 patients.

Amphotericin B Induction with Voriconazole Consolidation as Salvage Therapy for FKS-Associated Echinocandin Resistance in Candida glabrata Septic Arthritis and Osteomyelitis

We report the case of a 61-year-old female with Crohn's disease dependent on total parenteral nutrition who developed a central venous catheter bloodstream infection and septic arthritis, complicated further by osteomyelitis and persistent Candida glabrata fungemia. Fluconazole treatment led to persistent infection, and micafungin therapy failed with development of FKS-associated resistance. Infection responded after initiation of amphotericin B plus voriconazole. Echinocandin resistance is increasingly recognized, suggesting a role for alternative antifungal therapies.