Infections due to Rare Cryptococcus Species. A Literature Review

An Unusual High Prevalence of Cryptococcus (Naganishia) diffluens Colonization in Neonates Hospitalized in a Referral Neonatal Intensive Care Unit

BACKGROUND

Although the Candida species continue to be the most frequent colonizer of neonatal skin, a clear increase of colonization due to rare yeast-like fungi has been reported. In this study, we report an unusual high prevalence of Cryptococcus diffluens colonization in neonates admitted to the neonatal intensive care unit (NICU) over a 1-month period.

METHODS

From January 2020 to June 2021, the study included all neonates who were admitted to the NICU of Bu Ali Sina Hospital at least 28 days old. Skin swabs from different anatomical areas were collected. Sampling was done 3 times/week. Each sample was inoculated into Sabouraud Dextrose Agar containing chloramphenicol and CHROMagar Candida, separately. The plates were incubated at 30 °C and 35 °C, respectively. Identification of the isolates was molecularly confirmed. In vitro antifungal susceptibility testing of the isolates was performed against different antifungal agents using the Clinical Laboratory Standards Institute protocol.

RESULTS

Among 1026 samples collected from 78 neonates, 213 yeast isolates were recovered, of which the Candida species were the most common (77.5%), followed by C. diffluens (16.9%). During the study, 55 isolated yeasts were collected from December 26, 2020, to January 26, 2021, of which 65.5% were C. diffluens , while Candida spp. constituted 100% and 98.3% of the isolates before and after this period, respectively. The most frequent sources of C. diffluens were genital regions (27.8%). Of 36 C. diffluens isolates, 13.9%, 22.2%, 52.8%, and 83.3% were non-wild type to fluconazole, amphotericin B, itraconazole and 5-flucytosine, respectively.

CONCLUSIONS

We reported for the first time an unusual high prevalence of C. diffluens colonization in neonates hospitalized in NICU. Our findings also showed the high minimum inhibitory concentration of amphotericin B and 5-flucytosine against C. diffluens .

A Vulvovaginal Yeast Infection Caused by Cryptococcus victoriae in Vietnam: A Rare Case Report

Cases of vulvovaginitis caused by Cryptococcus genus are exceedingly uncommon, with only a handful of instances having been described for this causative species. This report describes a rare case of vulvovaginitis suspected to be caused by Cryptococcus victoriae in a 58-year-old woman residing in an urban area of Hanoi city, Vietnam. The patient with a 10-year history of depression and type 2 diabetes mellitus was admitted to the hospital due to vulvar itching and vaginal discharge. Vaginal swabs confirmed the presence of a yeast infection by direct microscopic examination with 10% KOH and culture on CHROMagar Candida. The yeast was identified as C victoriae using genetic sequencing tools. The patient's treatment plan involved topical clotrimazole and a daily oral dose of 200 mg of itraconazole for 7 days. This comprehensive treatment approach resulted in the patient's full recovery. This is the first reported case of vulvovaginitis attributed to C victoriae in humans worldwide.

Temporal trends in antifungal susceptibility of Cryptococcus neoformans isolates from a reference laboratory in the United States, 2011-2021

BACKGROUND

There are no established clinical breakpoints for antifungal agents against Cryptococcus species; however, epidemiological cut-off values can help distinguish wild-type (WT) isolates without any acquired resistance from non-WT strains, which may harbour resistance mechanisms.

PATIENTS/METHODS

We describe the trends of antifungal MICs and percentages of WT C. neoformans species complex (CNSC) isolates processed in our reference laboratory from November 2011 to June 2021. There were only nine isolates in 2011, thus, we included them in the year 2012 for data analysis. Clinical data is also described when available.

RESULTS

We identified 632 CNSC, the majority collected from blood (n = 301), cerebrospinal fluid (n = 230), and respiratory (n = 71) sources. The overall percentage of WT isolates for amphotericin B (AMB), 5-flucytosine, and fluconazole was 77%, 98%, and 91%, respectively. We noticed a statistically significant change in the percentage of AMB WT isolates over the years, with 98% of isolates being WT in 2012 compared to 79% in 2021 (p < .01). A similar change was not observed for other antifungal agents. Clinical data was available for 36 patients, primarily non-HIV immunocompromised patients with disseminated cryptococcosis. There were no statistically significant differences in the clinical characteristics and outcomes between patients with WT (58.3%) versus non-WT (41.7%) isolates, but we noticed higher mortality in patients infected with an AMB non-WT CNSC isolate.

CONCLUSIONS

We observed an increase in the percentage of AMB non-WT CNSC isolates in the past decade. The clinical implications of this finding warrant further evaluation in larger studies.

Effects of Anthropogenic Disturbance and Seasonal Variation on Aerobiota in Highly Visited Show Caves in Slovenia

Aerosols in caves are natural tracers and, together with climatic parameters, provide a detailed insight into atmospheric conditions, responses to climatic changes and anthropogenic influences in caves. Microbiological air monitoring in show caves is becoming increasingly useful to understand changes in cave ecosystems and to implement and review measures for sustainable cave use and tourism development. In 2017 and 2018, air along tourist trails in caves Postojnska jama and Škocjanske jame (Slovenia) was sampled before and after tourist visits. Samples were analysed using culture-dependent methods, flow cytometry, detection of β-D-glucan and lipopolysaccharide and compared with CO2 and temperature data to measure anthropogenic influences and seasonality on aerobiota. While the presence of tourists significantly increased concentrations of airborne microorganisms (p < 0.05), β-D-glucan and CO2 did not show such a trend and were more dependent on seasonal changes. Locally, concentrations of cultivable microorganisms above 1000 CFU/m3 were detected, which could have negative effects on the autochthonous microbiota and possibly on human health. A mixture of bacteria typically associated with humans was found in the air and identified with MALDI-TOF MS. Using MALDI-TOF MS, we achieved a 69.6% success rate in identification. Micrococcus luteus, Streptococcus mitis, Staphylococcus epidermidis and Moraxella spp. were recognized as good indicators of cave anthropisation.

Draft genome sequence of yeast Vanrija sp. strain TS01, isolated from leukemia patient's urine

Vanrija sp. strain TS01 was isolated from urine sample from a leukemia patient in Nanjing, China. The closest known relative strain is Vanrija humicola with average nucleotide identity value of 93.1. The draft genome comprises 22.0 Mb in 52 contigs, with G + C content of 62.57%.

Fungal Whole-Genome Sequencing for Species Identification: From Test Development to Clinical Utilization

Using next-generation sequencing (NGS), we developed and validated a whole-genome sequencing (WGS)-based clinical test for fungal species identification on clinical isolates. The identification is mainly based on the fungal ribosomal internal transcribed spacer (ITS) region as the primary marker, and additional marker and genomic analysis applied for species within the Mucorales family (using the 28S rRNA gene) and Aspergillus genus (using the beta-tubulin gene and k-mer tree-based phylogenetic clustering). The validation study involving 74 unique fungal isolates (22 yeasts, 51 molds, and 1 mushroom-forming fungus) showed high accuracy, with 100% (74/74) concordance on the genus-level identifications and 89.2% (66/74) concordance on the species level. The 8 discrepant results were due to either the limitation of conventional morphology-based methodology or taxonomic changes. After one year of implementation in our clinical laboratory, this fungal NGS test was utilized in 29 cases; the majority of them were transplant and cancer patients. We demonstrated the utility of this test by detailing five case studies, in which accurate fungal species identification led to correct diagnosis, treatment adjustment or was ruled out for hospital acquired infection. This study provides a model for validation and implementation of WGS for fungal identification in a complex health system that serves a large immunocompromised patient population.

Humicola Trauma-related Invasive Fungal Infection in an Immunocompetent Patient

The majority of invasive fungal infections arise in immunocompromised patients; however, there exist many clinical interventions and physiologic phenomena in the setting of traumatic injury that induce immunosuppressant states. Enhanced clinical suspicion and early detection of invasive fungal infections has played an increasingly pertinent role in clinical management of patients admitted for traumatic injury, given its substantial morbidity and mortality rates. In this case report, we discuss a case of trauma-related invasive fungal infection by a rare humicola pathogen in a previously immunocompetent patient. We present this case in hopes of instilling a high index of clinical suspicion for trauma-related invasive fungal infections. We also discuss the role of negative pressure wound therapy and aggressive surgical management, including debridement and various levels of amputation to optimize patient outcomes. Clinical management of trauma-related IFI has adopted increasingly aggressive approaches with respect to its formidable morbidity and mortality rates. Multidisciplinary discussions and patient-centered care are essential when making surgical decisions that impact quality of life such as amputation level.

Central Nervous System Cryptococcosis in Patients With Sarcoidosis: Comparison With Non-sarcoidosis Patients and Review of Potential Pathophysiological Mechanisms

Introduction

Cryptococcus spp. infection of the central nervous system (CINS) is a devastating opportunistic infection that was historically described in patients with acquired immunodeficiency syndrome (AIDS). Cryptococcus spp. infections are also associated with sarcoidosis; the impairment of cell-mediated immunity and long-term corticosteroid therapy being evoked to explain this association. Nevertheless, this assertion is debated and the underlying pathophysiological mechanisms are still unknown. The aims of this study were (i) to describe the clinical and biological presentation, treatments, and outcomes of CINS patients with and without sarcoidosis and (ii) to review the pathophysiological evidence underlying this clinical association.

Patients and Methods

Every patient with positive cerebrospinal fluid (CSF) cryptococcal antigen testing, India ink preparation, and/or culture from January 2015 to December 2020 at a tertiary university hospital were included, and patients with sarcoidosis were compared with non-sarcoidosis patients. Quantitative variables are presented as mean ± SD and are compared using the Mann-Whitney Wilcoxon rank-sum test. Categorical variables are expressed as the number of patients (percentage) and compared using the χ² or Fisher's tests.

Results

During the study period, 16 patients experienced CINS, of whom 5 (31%) were associated with sarcoidosis. CINS symptoms, biological, and CSF features were similar between CINS patients with and without sarcoidosis except regarding CD4 cells percentages and CD4/CD8 ratio that was higher in those with sarcoidosis (47 ± 12 vs. 22 ± 18, p = 0.02 and 2.24 ± 1.42 vs. 0.83 ± 1.10, p = 0.03, respectively). CINS patients with sarcoidosis had less often positive blood antigen testing than those without sarcoidosis (2/5 vs. 11/11, p = 0.02). CINS patients with and without sarcoidosis were treated with similar drugs, but patients with sarcoidosis had a shorter length of treatment. CD4 cell levels do not seem to explain the association between sarcoidosis and cryptococcosis.

Conclusion

Sarcoidosis was the most frequently associated condition with CINS in this study. CINS patients associated with sarcoidosis had overall similar clinical and biological presentation than CINS patients associated with other conditions but exhibited a lower rate of positive blood cryptococcal antigen testing and higher CD4/CD8 T cells ratio. Pathophysiological mechanisms underlying this association remain poorly understood but B-1 cell deficiency or lack of IgM could be a part of the explanation. Another plausible mechanism is the presence of anti-granulocyte-macrophage colony-stimulating factor (GM-CSF) antibodies in a subset of patients with sarcoidosis, which could impair macrophage phagocytic function. Further studies are strongly needed to better understand those mechanisms and to identify at-risk patients.

Search for Cryptococcus neoformans/gattii Complexes and Related Genera (Filobasidium, Holtermanniella, Naganishia, Papiliotrema, Solicoccozyma, Vishniacozyma) spp. Biotope: Two Years Surveillance of Wild Avian Fauna in Southern France

Fungi belonging to the Cryptococcus genus and related genera (Filobasidium, Holtermanniella, Naganishia, Papiliotrema, Solicoccozyma, Vishniacozyma) are encapsulated yeasts found in either the environment or animal sources. However, the precise biotopes of most species remain poorly defined. To assess whether wild birds from southern France can carry or spread the most pathogenic species (i.e., species belonging to the C. neoformans and C. gattii complexes), as well as lesser-studied species (non-neoformans/gattii Cryptococcus and former Cryptococcus spp.), 669 birds belonging to 89 species received for care over a two-year period at the Centre de Protection de la Faune Sauvage of Villeveyrac (Bird Protection League nongovernmental organization (NGO) care center) were sampled. Samples were cultured, and Cryptococcus and former Cryptococcus yeasts were identified by PCR sequencing. The purpose was to evaluate whether there was any health risk to local populations or care personnel in aviaries and gather new data on the ecological niches of lesser-known species. One hundred and seven birds (16%) were found to be positive for at least one Cryptococcus or former Cryptococcus species. No yeasts belonging to the highly pathogenic C. neoformans or C. gattii complexes were isolated. However, diversity was notable, with 20 different Cryptococcus or former Cryptococcus species identified. Furthermore, most bird–yeast species associations found in this study have never been described before.

Airborne Fungi in Show Caves from Southern Spain

The aerobiology of caves in Southern Spain possesses special characteristics, different from caves located in Northern Spain. Previous studies demonstrated the influence of outdoor air on caves in the north and the existence of two different patterns, depending on the season. In summer there is an abundance of Ascomycota, whereas in winter Basidiomycota predominates, which are related to the periods of stagnation and ventilation, respectively. In caves in Southern Spain the presence of airborne Basidiomycota is scarce and Ascomycota represents the main group of fungi widely distributed across the caves in all seasons. The most characteristic features were the abundant presence of entomopathogenic fungi (Beauveria bassiana, Parengyodontium album, Pochonia chlamydosporia, Leptobacillium symbioticum, Leptobacillium leptobactrum) and Cladosporium cladosporioides in Cueva del Tesoro, Cueva de Ardales and Gruta de las Maravillas. However, the presence of yeasts of the genera Cutaneotrichosporon, Trichosporon, Cryptococcus, Naganishia, Cystobasidium, Microstroma and Phragmotaenium was exclusive to Gruta de las Maravillas. Fungal hazard in the three show caves were determined using an ecological indicator based on the concentration of spores in cave air.