Investigation of the Emerging Nosocomial Wickerhamomyces anomalus Infections at a Chinese Tertiary Teaching Hospital and a Systemic Review: Clinical Manifestations, Risk Factors, Treatment, Outcomes, and Anti-fungal Susceptibility

Detection and taxonomic identification of emerging pathogenic yeasts in surface waters from Lagoon Systems in Rio de Janeiro, Brazil

This study aimed to detect and identify emerging pathogenic yeasts in surface waters from two Lagoon Systems in Rio de Janeiro, Brazil, by polyphasic taxonomy. The monitoring of potentially pathogenic fungi in aquatic environments, especially in regions impacted by human actions, is highlighted in this study as one of the axes of the One Health approach. Water samples were collected, and after isolation, fungi were identified by polyphasic taxonomy, including MALDI-TOF-MS, which is also used for bacteria identification. Our results describe the physicochemical parameters of the surface water of these lagoons and reveal a significant diversity of yeast species, some of which are known to exhibit pathogenic potential and resistance to common antifungal treatments, as well as bacteria with resistance profiles to several currently used antibiotics. We conclude that Jacarepaguá Lagoon is the most impacted compared to Piratininga Lagoon; however, we highlight the urgent need for targeted interventions to mitigate pollution in both Lagoons, reinforcing the value of long-term surveillance in both ecosystems. We believe that monitoring emerging species is as critical as analyzing traditional water quality parameters. Early detection of resistant or invasive pathogens in aquatic ecosystems can prevent disease outbreaks, protect biodiversity, and mitigate public health risks, preventing loss of life, and optimizing public healthcare system expenditures.

Molecular identification and antifungal susceptibility profile of rare and emerging yeast species causing onychomycosis

OBJECTIVES

Onychomycosis is a nail infection caused by various fungal agents. In recent years, there has been an increase in cases of onychomycosis caused by rare fungi, which are often challenging to identify using conventional methods. Sometimes, these unusual species exhibit different antifungal susceptibility patterns compared to more common yeast species. Therefore, this study aimed to identify rare yeast species causing onychomycosis and assess their antifungal susceptibility profiles.

RESULTS

Nineteen rare and emerging yeast isolates, representing seven species, including Candida orthopsilosis (n = 9, 47.36%), Clavispora lusitaniae (formerly Candida lusitaniae) (n = 2, 10.52%), Wickerhamiella pararugosa (formerly Candida pararugosa) (n = 2, 10.52%), Naganishia diffluens (formerly Cryptococcus diffluens) (n = 2, 10.52%), Wickerhamomyces anomalus (n = 2, 10.52%), Cyberlindnera fabianii (n = 1, 5.26%), and Meyerozyma caribbica (formerly Candida fermentati) (n = 1, 5.26%), were identified. Most rare yeast agents exhibited high minimum inhibitory concentration (MIC) values for fluconazole.

Rare multi-fungal sepsis: a case of triple-impact immunoparalysis

Patients with burn injury and inhalation injury are highly susceptible to infectious complications, including opportunistic pathogens, due to the loss of skin cover and mucosal damage of respiratory tract as well as the disruption of homeostasis. This case report, a 34-year-old man suffered critical burns, provides the first literature description of triple-impact immunoparalysis (critical burns, inhalation injury, and SARS-CoV-2 infection), leading to a lethal multifocal infection caused by several fungi including very rare environmental representatives Metschnikowia pulcherrima and Wickerhamomyces anomalus. The co-infection by these common environmental yeasts in a human is unique and has not yet been described in the literature. Importantly, our patient developed refractory septic shock and died despite targeted antifungal therapy including the most potent current antifungal agent-isavuconazole. It can be assumed that besides immunoparalysis, effectiveness of therapy by isavuconazole was impaired by the large distribution volume in this case. As this is a common situation in intensive care patients, routine monitoring of plasmatic concentration of isavuconazole can be helpful in personalization of the treatment and dose optimization. Whatmore, many fungal species often remain underdiagnosed during infectious complications, which could be prevented by implementation of new methods, such as next-generation sequencing, into clinical practice.

Fungemia by Wickerhamomyces anomalus-A Narrative Review

Wickerhamomyces anomalus has been previously classified as Hansenula anomala, Pichia anomala, and Candida pelliculosa and was recently reclassified in the genus Wickerhamomyces after phylogenetic analysis of its genetic sequence. An increasing number of reports of human infections by W. anomalus have emerged, suggesting that this microorganism is an emerging pathogen. The present review aimed to provide data on the epidemiology, antifungal resistance, clinical characteristics, treatment, and outcomes of fungemia by W. anomalus by extracting all the available information from published original reports in the literature. PubMed/Medline, Cochrane Library, and Scopus databases were searched for eligible articles reporting data on patients with this disease. In total, 36 studies involving 170 patients were included. The age of patients with fungemia by W. anomalus ranged from 0 to 89 years; the mean age was 22.8 years, the median age was 2.2 years, with more than 37 patients being less than one month old, and 54% (88 out of 163 patients) were male. Regarding patients' history, 70.4% had a central venous catheter use (CVC), 28.7% were on total parenteral nutrition (TPN), 97% of neonates were hospitalized in the neonatal ICU (NICU), and 39.4% of the rest of the patients were hospitalized in the intensive care unit (ICU). Previous antimicrobial use was noted in 65.9% of patients. The most common identification method was the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) in 34.1%, VITEK and VITEK 2 in 20.6%, and ID32 C in 15.3%. W. anomalus had minimal antifungal resistance to fluconazole, echinocandins, and amphotericin B, the most commonly used antifungals for treatment. Fever and sepsis were the most common clinical presentation noted in 95.8% and 86%, respectively. Overall mortality was 20% and was slightly higher in patients older than one year. Due to the rarity of this disease, future multicenter studies should be performed to adequately characterize patients' characteristics, treatment, and outcomes, which will increase our understanding and allow drawing safer conclusions regarding optimal management.

Emergence of rare and uncommon yeast-like pathogens causing neonatal sepsis at a tertiary care center, North India

Introduction

Neonatal candidemia is a life-threatening event in babies requiring ICU admission. Prompt diagnosis and appropriate treatment reduce mortality and morbidity. Worldwide, there is an emergence of drug-resistant rare Candida species causing neonatal sepsis that necessitates antifungal susceptibility testing in each case.

Methods

We did a prospective study to isolate Candida species causing neonatal sepsis and to determine the predisposing risk factors and time to positivity for flagged positivity. We also determined fluconazole, itraconazole and amphotericin B minimum inhibitory concentration (MIC) against isolated Candida species by broth microdilution method using CLSI M27-A3 guidelines.

Results

A total of 107 neonatal candidemia events were noted. Prematurity was the most common predisposing risk factor. Most isolates were non-albicans Candida. Candida utilis, C. pelliculosa, C. tropicalis and K. ohmeri were the predominant fungi causing neonatal candidemia. A varied antifungal MIC against isolated Candida species was noted. However, 90% of the isolated Candida strains had <8 µg/mL fluconazole MIC. Moreover, ≥8 and ≥2 µg/mL MIC for fluconazole and amphotericin B respectively were also noted.

Conclusions

Rare Candida species having varied fluconazole and amphotericin B MIC cause neonatal candidemia. Therefore, culture isolation and antifungal susceptibility testing should be done in each case of neonatal candidemia.

Fungemia With Wickerhamomyces anomalus: A Case Report and Literature Review

We report the case of an 84-year-old man with a history of IgG4-related sclerosing cholangitis who was diagnosed with advanced esophageal cancer and underwent radiation and chemotherapy. An implantable central venous access port was placed for chemotherapy and total parenteral nutrition. The patient presented with a fever and received antimicrobial therapy for acute cholangitis but remained febrile, and subsequently, yeast was detected in the aerobic bottle of blood culture obtained from the central venous line. The yeast was identified as Wickerhamomyces anomalus. Liposomal amphotericin B was administered, and the central line access port was removed. After confirmation of negative blood cultures and 14 days post treatment, he underwent reinsertion of the central line access port. Due to persistent pain at the insertion site, fluconazole was added for an additional 14 days, and the patient was discharged and transferred to another hospital. Wickerhamomyces anomalus is a rare fungal infection with other synonyms including Pichia anomala, Hansenula anomala, and Candida pelliculosa. A literature review of 53 case reports of Wickerhamomyces anomalus, Pichia anomala, Hansenula anomala, and Candida pelliculosa was conducted, with a total of 211 cases reviewed. Fungemia was reported in 94% of cases, with central venous catheterization, parental feeding, low birth weight, and immunocompromised status identified as major risk factors. The majority of cases were pediatric, particularly neonatal, and there were reports of nosocomial infections causing outbreaks, with some cases involving the eye such as endophthalmitis or keratitis.

The role of fruits as reservoirs for resistant and virulent strains of opportunistic yeasts

Strains of the Candida parapsilosis and Meyerozyma guilliermondii species complexes isolated from the internal tissues of 26 fruit species from 21 countries were evaluated for their susceptibility to conventional antifungal compounds (fluconazole, voriconazole, amphotericin B) and hydrolytic activity. A total of 144 strains were studied. Resistance to at least one of the antifungal compounds tested was found in 26.4% of the endophytic strains examined. Most of the strains were insensitive to fluconazole. Multiresistance was detected only in two strains of C. parapsilosis sensu stricto from tropical apples. Phospholipase production and proteolytic and hemolytic activities were significantly higher in endophytes from tropical fruits. Resistant and virulent strains of opportunistic yeasts can thus spread worldwide via purchased fruit, which can harm people with a weakened immune status and children whose immune systems are not yet fully developed.

Wickerhamomyces Anomalus Postoperative Endophthalmitis

INTRODUCTION

We describe the case of a postoperative fungal endophthalmitis caused by Wickerhamomyces anomalus, an opportunistic yeast common in nature but rare as a causative agent in ocular infections. This would be the second reported case of W. anomalus endophthalmitis.

CASE REPORT

A patient came to our hospital with a dense hemovitreous caused by an inadvertent ocular perforation and retinal detachment during a cataract surgery. In the days following the first vitreoretinal surgery a chronic postoperative endophthalmitis was evidenced. Only after several surgeries as well as intravitreal antibiotics and sample takings, Wickerhamomyces was detected. The treatment with oral voriconazole and an intraocular lens extraction controlled the infection.

DISCUSSION

Wickerhamomyces anomalus, despite not being particularly aggressive in our case, was resistant to various consequent vitreoretinal surgeries. The unresponsiveness to treatment led us to contemplate the fungal etiology, and fortunately the cultures were positive for this yeast. In conjunction to antifungal therapy, it is possible that the IOL explantation played an important role in the treatment.

CONCLUSION

A high index of suspicion must be held in cases of fungal endophthalmitis. Both IOL explantation and oral antifungal therapy are useful treatment options in cases of W. anomalus endophthalmitis.

Microbiota is structured by gut regions, life stage, and diet in the Black Soldier Fly (Hermetia illucens)

The larvae of the Black Soldier Fly (Hermetia illucens) provide numerous ecological benefits, leading to significant commercial advancements. These benefits include the bioconversion of low-value waste into high-value feed and soil amendments. Understanding how the bacterial and eukaryotic microbiota communities affect host performance becomes vital for the optimization and specialization of industrial-scale rearing. This study investigates H. illucens-associated microbiota taxonomic composition and dynamics across the developmental cycle (eggs, neonates, larvae, prepupae, and imago X0 to second generation X1) when reared on two substrates: (i) plant-based (Housefly Gainesville diet) and (ii) animal-based (poultry hatchery waste). By using the 16S gene amplicon metataxonomic approach, we found that the results revealed that bacterial microbiota inherited from parents reared on a different substrate may have induced dysbiosis in the progeny. Specifically, the interaction networks of individuals reared on hatchery waste showed a high prevalence of negative interactions and low connectivity. Proteobacteria (39-92%), Firmicutes (4-39%), Bacteroidota (1-38%), and Actinobacteria (1-33%). In animal feed-reared individuals, Firmicutes reached the highest relative abundance (10-80%), followed by Proteobacteria (6-55%), Actinobacteria (1-31%), and Bacteroidota (0-22%). The rearing substrate was the main driver of microbiota composition, while the developmental stage influenced only the whole individual's bacterial microbiota composition. Gut regions were associated with distinct bacterial composition and richness, with diversity decreasing along the digestive tract. For the first time, microeukaryotes of the microbiota other than Fungi were investigated using 18S genetic marker amplicon sequencing with novel blocking primers specific to the Black Soldier Fly. Microeukaryotes are a neglected part of multitrophic microbiota communities that can have similar effects on their hosts as bacterial microbiota. Microeukaryotes from seven orders were identified in black soldier flies, including potential pathogens (e.g., Aplicomplexa group). Nucletmycea were the dominant class throughout development, followed by Holozoa and Stramenophiles. The eukaryote microbiota was structured by developmental stages but not by gut regions. Insights from this study are a stepping stone toward the microbiological optimization of black soldier flies for industrial rearing, highlighting how a synthetic microbiota assembly should be tailored to the rearing environment of the larvae at a targeted developmental stage.

Application of Novel Short Tandem Repeat Typing for Wickerhamomyces anomalus Reveals Simultaneous Outbreaks within a Single Hospital

Wickerhamomyces anomalus, previously known as Candida pelliculosa, occasionally causes candidemia in humans, primarily infecting neonates, and infants. The mortality rate of these invasive infections is high, and isolates with a reduced susceptibility to fluconazole have been reported. W. anomalus outbreaks are regularly reported in healthcare facilities, especially in neonatal intensive care units (NICUs). In order to rapidly genotype isolates with a high-resolution, we developed and applied a short tandem repeat (STR) typing scheme for W. anomalus. Six STR markers were selected and amplified in two multiplex PCRs, M3 and M6, respectively. In total, 90 W. anomalus isolates were typed, leading to the identification of 38 different genotypes. Four large clusters were found, unveiling simultaneous outbreak events spread across multiple units within the same hospital. STR typing results of 11 isolates were compared to whole-genome sequencing (WGS) single nucleotide polymorphism (SNP) calling, and the identified genotypic relationships were highly concordant. We performed antifungal susceptibility testing of these isolates, and a reduced susceptibility to fluconazole was found for two (2.3%) isolates. ERG11 genes of these two isolates were examined using WGS data, which revealed a novel I469L substitution in one isolate. By constructing a homology model for W. anomalus ERG11p, the substitution was found in close proximity to the fluconazole binding site. In summary, we showed multiple W. anomalus outbreak events by applying a novel STR genotyping scheme.

A pseudo-outbreak of Cyberlindnera fabianii funguria: Implication from whole genome sequencing assay

Background

Although the yeast Cyberlindnera fabianii (C. fabianii) has been rarely reported in human infections, nosocomial outbreaks caused by this organism have been documented. Here we report a pseudo-outbreak of C. fabianii in a urology department of a Chinese hospital over a two-week period.

Methods

Three patients were admitted to the urology department of a tertiary teaching hospital in Beijing, China, from Nov to Dec 2018, for different medical intervention demands. During the period Nov 28 to Dec 5, funguria occurred in these three patients, and two of them had positive urine cultures multiple times. Sequencing of rDNA internal transcribed spacer (ITS) region and MALDI-TOF MS were applied for strain identification. Further, sequencing of rDNA non-transcribed spacer (NTS) region and whole genome sequencing approaches were used for outbreak investigation purpose.

Results

All the cultured yeast strains were identified as C. fabianii by sequencing of ITS region, and were 100% identical to the C. fabianii type strain CBS 5640T. However, the MALDI-TOF MS system failed to correctly identify this yeast pathogen. Moreover, isolates from these three clustered cases shared 99.91%-100% identical NTS region sequences, which could not rule out the possibility of an outbreak. However, whole genome sequencing results revealed that only two of the C. fabianii cases were genetically-related with a pairwise SNP of 192 nt, whilst the third case had over 26,000 SNPs on its genome, suggesting a different origin. Furthermore, the genomes of the first three case strains were phylogenetically even more diverged when compared to a C. fabianii strain identified from another patient, who was admitted to a general surgical department of the same hospital 7 months later. One of the first three patients eventually passed away due to poor general conditions, one was asymptomatic, and other clinically improved.

Conclusion

In conclusion, nosocomial outbreaks caused by emerging and uncommon fungal species are increasingly being reported, hence awareness must be raised. Genotyping with commonly used universal gene targets may have limited discriminatory power in tracing the sources of infection for these organisms, requiring use of whole genome sequencing to confirm outbreak events.

Role of Guinea Pigs (Cavia porcellus) Raised as Livestock in Ecuadorian Andes as Reservoirs of Zoonotic Yeasts

Guinea pigs (Cavia porcellus) have been reared for centuries in the Andean region for ceremonial purposes or as the main ingredient of traditional foods. The animals are kept in close proximity of households and interact closely with humans; this also occurs in western countries, where guinea pigs are considered pets. Even though it is acknowledged that domestic animals carry pathogenic yeasts in their tissues and organs that can cause human diseases, almost nothing is known in the case of guinea pigs. In this work we used traditional microbiological approaches and molecular biology techniques to isolate, identify, and characterize potentially zoonotic yeasts colonizing the nasal duct of guinea pigs raised as livestock in Southern Ecuador (Cañar Province). Our results show that 44% of the 100 animals studied were colonized in their nasal mucosa by at least eleven yeast species, belonging to eight genera: Wickerhamomyces, Diutina, Meyerozyma, Candida, Pichia, Rhodotorula, Galactomyces, and Cryptococcus. Noticeably, several isolates were insensitive toward several antifungal drugs of therapeutic use, including fluconazole, voriconazole, itraconazole, and caspofungin. Together, our results emphasize the threat posed by these potentially zoonotic yeasts to the farmers, their families, the final consumers, and, in general, to public and animal health.

Molecular identification, antifungal susceptibility, and resistance mechanisms of pathogenic yeasts from the China antifungal resistance surveillance trial (CARST-fungi) study

To have a comprehensive understanding of epidemiology and antifungal susceptibilities in pathogenic yeasts, the China Antifungal Resistance Surveillance Trial (CARST-fungi) study was conducted. All yeast isolates were identified by ribosomal DNA sequencing. Antifungal susceptibilities were performed using CLSI M27-A4 broth microdilution method. Sequence and expression level of resistant-related genes in resistant/non-wide-type (NWT) Candida isolates were analyzed. Totally 269 nonduplicate yeast isolates from 261 patients were collected. About half of the yeast isolates (127, 47.2%) were recovered from blood, followed by ascetic fluid (46, 17.1%). C. albicans remained the most prevalent (120, 44.6%), followed by C. parapsilosis complex (50, 18.6%), C. tropicalis (40, 14.9%), and C. glabrata (36, 13.4%). Fourteen (11.7%) C. albicans isolates and 1 (2.0%) C. parapsilosis isolate were resistant/NWT to triazoles. Only 42.5% (17/40) C. tropicalis were susceptible/WT to all the triazoles, with 19 (47.5%) isolates NWT to posaconazole and 8 (20%) cross-resistant to triazoles. Among C. glabrata, 20 (55.6%) and 8 (22.2%) isolates were resistant/NWT to voriconazole and posaconazole, respectively, and 4 (10.3%) isolates were cross-resistant to triazoles. Isavuconazole was the most active triazole against common Candida isolates. Except for 2 isolates of C. glabrata cross-resistant to echinocandins which were also NWT to POS and defined as multidrug-resistant, echinocandins exhibit good activity against common Candida species. All isolates were WT to AMB. For less common species, Rhodotorula mucilaginosa exhibited high MICs to echinocandins and FLC, and 1 isolate of Trichosporon asahii showed high MICs to all the antifungals except AMB. Among triazole-resistant Candida isolates, ERG11 mutations were detected in 10/14 C. albicans and 6/23 C. tropicalis, while 21/23 C. tropicalis showed MDR1 overexpression. Overexpression of CDR1, CDR2, and SNQ2 exhibited in 14, 13, and 8 of 25 triazole-resistant C. glabrata isolates, with 5 isolates harboring PDR1 mutations and 2 echinocandins-resistant isolates harboring S663P mutation in FKS2. Overall, the CARST-fungi study demonstrated that although C. albicans remain the most predominant species, non-C. albicans species accounted for a high proportion. Triazole-resistance is notable among C. tropicalis and C. glabrata. Multidrug-resistant isolates of C. glabrata and less common yeast have been emerging.

Effect of Dough-Related Parameters on the Antimold Activity of Wickerhamomyces anomalus Strains and Mold-Free Shelf Life of Bread

The aim of the present study was to assess the antimold capacity of three Wickerhamomyces anomalus strains, both in vitro and in situ, and to identify the responsible volatile organic compounds. For that purpose, two substrates were applied; the former included brain heart infusion broth, adjusted to six initial pH values (3.5, 4.0, 4.5, 5.0, 5.5, 6.0) and supplemented with six different NaCl concentrations (0.0%, 0.5%, 1.0%, 1.5%, 2.0%, 2.5%), while the latter was a liquid dough, fortified with the six aforementioned NaCl concentrations. After a 24 h incubation at 30 °C, the maximum antimold activity was quantified for all strains at 5120 AU/mL, obtained under different combinations of initial pH value and NaCl concentration. A total of twelve volatile compounds were detected; ethanol, ethyl acetate, isoamyl alcohol and isoamyl acetate were produced by all strains. On the contrary, butanoic acid-ethyl ester, acetic acid-butyl ester, ethyl caprylate, 3-methyl-butanoic acid, 2,4-di-tert-butyl-phenol, benzaldehyde, nonanal and octanal were occasionally produced. All compounds exhibited antimold activity; the lower MIC was observed for 2,4-di-tert-butyl-phenol and benzaldehyde (0.04 and 0.06 μL/mL of headspace, respectively), while the higher MIC was observed for butanoic acid-ethyl ester and ethyl caprylate (5.14 and 6.24 μL/mL of headspace, respectively). The experimental breads made with W. anomalus strains LQC 10353, 10346 and 10360 gained an additional period of 9, 10 and 30 days of mold-free shelf life, compared to the control made by commercially available baker’s yeast. Co-culture of the W. anomalus strains with baker’s yeast did not alter the shelf-life extension, indicating the suitability of these strains as adjunct cultures.