Three clustered cases of candidemia caused by Candida quercitrusa and mycological characteristics of this novel species

Outbreaks of Fungal Infections in Hospitals: Epidemiology, Detection, and Management

Nosocomial clusters of fungal infections, whilst uncommon, cannot be predicted and are associated with significant morbidity and mortality. Here, we review reports of nosocomial outbreaks of invasive fungal disease to glean insight into their epidemiology, risks for infection, methods employed in outbreak detection including genomic testing to confirm the outbreak, and approaches to clinical and infection control management. Both yeasts and filamentous fungi cause outbreaks, with each having general and specific risks. The early detection and confirmation of the outbreak are essential for diagnosis, treatment of affected patients, and termination of the outbreak. Environmental sampling, including the air in mould outbreaks, for the pathogen may be indicated. The genetic analysis of epidemiologically linked isolates is strongly recommended through a sufficiently discriminatory approach such as whole genome sequencing or a method that is acceptably discriminatory for that pathogen. An analysis of both linked isolates and epidemiologically unrelated strains is required to enable genetic similarity comparisons. The management of the outbreak encompasses input from a multi-disciplinary team with epidemiological investigation and infection control measures, including screening for additional cases, patient cohorting, and strict hygiene and cleaning procedures. Automated methods for fungal infection surveillance would greatly aid earlier outbreak detection and should be a focus of research.

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.

Isolation, Identification, Optimization of Baker’s Yeast from Natural Sources, Scale-Up Production Using Molasses as a Cheap Carbohydrate Source, and Evaluation for Bread Production

(1) Background: Bangladesh must has to spend a large amount of foreign currency to import commercial baker’s yeast every year. We could save money by finding a potential Saccharomyces cerevisiae from natural sources compatible with commercial baker’s yeast production. (2) Methods: Grapes, rice, pineapples were collected, processed, and inoculated on YMA plates and incubated at 30 °C for 48 h. Then 11 single morphologically well-formed colonies were isolated, purified, and identified, three as S. cerevisiae, three as S. rouxii, three as S. bisporus, and two as S. exigus based on standard cultural, morphological, and biochemical characteristics. Identified S. cerevisiae (designated as G2, P5 and R3) were then assessed for CO2 production as a measure of their baking potential during bread production and compared with two commercial strains (designated as C1 and C2). (3) Results: Isolate-G2 produced the maximum of 1830 mm3 of gas, whereas C1, C2, R3, and P5 produced 1520, 1680, 770, and 610 mm3 gas, respectively. No strain produced H2S which is associated with an off-flavor and unpleasant taste. These isolates showed maximum cell density at a pH range of 4–5.5 in 4–16% molasses broth at 30 °C after 4 days of incubation and maximum 4.75 × 109, 7.9 × 108, 1.472 × 1010, 2.08 × 1010 and 5.24 × 109 CFU mL−1 were produced by C1, C2, G2, P5 and R3, respectively. Isolate-G2 was found to have the most potential, whereas isolate-R3 and P5 have satisfactory potential. (4) Conclusions: G2 could be a good candidate for commercial trials.

Isolation, characterization, and genome assembly of Barnettozyma botsteinii sp. nov. and novel strains of Kurtzmaniella quercitrusa isolated from the intestinal tract of the termite Macrotermes bellicosus

Bioconversion of hemicelluloses into simpler sugars leads to the production of a significant amount of pentose sugars, such as d-xylose. However, efficient utilization of pentoses by conventional yeast production strains remains challenging. Wild yeast strains can provide new industrially relevant characteristics and efficiently utilize pentose sugars. To explore this strategy, we isolated gut-residing yeasts from the termite Macrotermes bellicosus collected in Comoé National Park, Côte d'Ivoire. The yeasts were classified through their Internal Transcribed Spacer/Large Subunit sequence, and their genomes were sequenced and annotated. We identified a novel yeast species, which we name Barnettozyma botsteinii sp. nov. 1118T (MycoBank: 833563, CBS 16679T and IBT 710) and two new strains of Kurtzmaniella quercitrusa: var. comoensis (CBS 16678, IBT 709) and var. filamentosus (CBS 16680, IBT 711). The two K. quercitrusa strains grow 15% faster on synthetic glucose medium than Saccharomyces cerevisiae CEN.PKT in acidic conditions (pH = 3.2) and both strains grow on d-xylose as the sole carbon source at a rate of 0.35 h-1. At neutral pH, the yeast form of K. quercitrusa var. filamentosus, but not var. comoensis, switched to filamentous growth in a carbon source-dependent manner. Their genomes are 11.0-13.2 Mb in size and contain between 4888 and 5475 predicted genes. Together with closely related species, we did not find any relationship between gene content and ability to grow on xylose. Besides its metabolism, K. quercitrusa var. filamentosus has a large potential as a production organism, because of its capacity to grow at low pH and to undergo a dimorphic shift.

Sugar-seeking insects as a source of diverse bread-making yeasts with enhanced attributes

Insects represent a particularly interesting habitat in which to search for novel yeasts of value to industry. Insect-associated yeasts have the potential to have traits relevant to modern food and beverage production due to insect-yeast interactions, with such traits including diverse carbohydrate metabolisms, high sugar tolerance, and general stress tolerance. Here, we consider the potential value of insect-associated yeasts in the specific context of baking. We isolated 63 yeast strains from 13 species of hymenoptera from the United States, representing 37 yeast species from 14 genera. Screening for the ability to ferment maltose, a sugar important for bread production, resulted in the identification of 13 strains of Candida, Lachancea, and Pichia species. We assessed their ability to leaven dough. All strains produced baked loaves comparable to a commercial baking strain of Saccharomyces cerevisiae. The same 13 strains were also grown under various sugar and salt conditions relevant to osmotic challenges experienced in the manufacturing processes and the production of sweet dough. We show that many of these yeast strains, most notably strains of Lachancea species, grow at a similar or higher rate and population size as commercial baker's yeast. We additionally assessed the comparative phenotypes and genetics of insect-associated S. cerevisiae strains unable to ferment maltose and identified baking-relevant traits, including variations in the HOG1 signaling pathway and diverse carbohydrate metabolisms. Our results suggest that non-conventional yeasts have high potential for baking and, more generally, showcase the success of bioprospecting in insects for identifying yeasts relevant for industrial uses.

The fungal community associated with the ambrosia beetle Xylosandrus compactus invading the mediterranean maquis in central Italy reveals high biodiversity and suggests environmental acquisitions

In summer 2016 a severe infestation of the alien ambrosia beetle Xylosandrus compactus was recorded from the Mediterranean maquis in the Circeo National Park in Central Italy. Trees and shrubs were infested and displayed wilting and necrosis of terminal branches caused by the combined impact of the insect and associated pathogenic fungi. A preliminary screening carried out on captured adults resulted in the isolation of a discrete number of fungal taxa with different life strategies, ranging from true mutualist (e.g. Ambrosiella xylebori) to plant pathogens (Fusarium spp.). In the present study, high-throughput sequencing was applied to determine the total diversity and functionality of the fungal community associated with X. compactus adults collected in the galleries of three Mediterranean woody hosts, Quercus ilex, Laurus nobilis, and Ceratonia siliqua. The effect of season and host in determining the composition of the associated fungal community was investigated. A total of 206 OTUs composed the fungal community associated with X. compactus. Eighteen OTUs were shared among the three hosts, including A. xylebori and members of the Fusarium solani complex. All but two were previously associated with beetles. Sixty-nine out of 206 OTUs were resolved to species level, identifying 60 different fungal species, 22 of which already reported in the literature as associated with beetles or other insects. Functional guild assigned most of the fungal species to saprotrophs and plant pathogens. Effects of seasonality and host on fungal community assemblage were highlighted suggesting the acquisition by the insect of new fungal taxa during the invasion process. The consequences of enriched fungal community on the risk of the insurgence of novel threatful insect-fungus association are discussed considering direct and indirect effects on the invaded habitat.

Land Use Change and Water Quality Use for Irrigation Alters Drylands Soil Fungal Community in the Mezquital Valley, Mexico

Soil fungal communities provide important ecosystem services, however, some soil borne representatives damage agricultural productivity. Composition under land-use change scenarios, especially in drylands, is rarely studied. Here, the soil fungal community composition and diversity of natural shrubland was analyzed and compared with agricultural systems irrigated with different water quality, namely rain, fresh water, dam-stored, and untreated wastewater. Superficial soil samples were collected during the dry and rainy seasons. Amplicon-based sequencing of the ITS2 region was performed on total DNA extractions and used the amplicon sequence variants to predict specific fungal trophic modes with FUNGuild. Additionally, we screened for potential pathogens of crops and humans and assessed potential risks. Fungal diversity and richness were highest in shrubland and least in the wastewater-irrigated soil. Soil moisture together with soil pH and exchangeable sodium were the strongest drivers of the fungal community. The abundance of saprophytic fungi remained constant among the land use systems, while symbiotic and pathogenic fungi of plants and animals had the lowest abundance in soil irrigated with untreated wastewater. We found lineage-specific adaptations to each land use system: fungal families associated to shrubland, rainfed and part of the freshwater were adapted to drought, hence sensitive to exchangeable sodium content and most of them to N and P content. Taxa associated to freshwater, dam wastewater and untreated wastewater irrigated systems show the opposite trend. Additionally, we identified potentially harmful human pathogens that might be a health risk for the population.

Five-Year National Surveillance of Invasive Candidiasis: Species Distribution and Azole Susceptibility from the China Hospital Invasive Fungal Surveillance Net (CHIF-NET) Study

Data on the epidemiology of invasive candidiasis (IC) and the antifungal susceptibility of Candida isolates in China are still limited. Here we report on surveillance for IC from the China Hospital Invasive Fungal Surveillance Net (CHIF-NET) study. Sixty-five tertiary hospitals collected 8,829 Candida isolates from 1 August 2009 to 31 July 2014. Matrix-assisted laser desorption ionization-time of flight mass spectrometry supplemented by ribosomal DNA sequencing was used to define the species, and the fluconazole and voriconazole susceptibilities were determined by the Clinical and Laboratory Standards Institute disk diffusion method. A total of 32 Candida species were identified. Candida albicans was the most common species (44.9%), followed by the C. parapsilosis complex (20.0%), C. tropicalis (17.2%), and the C. glabrata complex (10.8%), with other species comprising <3% of isolates. However, in candidemia, the proportion of cases caused by C. albicans was only 32.3%. C. albicans and C. parapsilosis complex isolates were susceptible to fluconazole and voriconazole (<6% resistance), while fluconazole and azole cross-resistance rates were high in C. tropicalis (13.3% and 12.9%, respectively), C. glabrata complex (18.7% and 14%, respectively), and uncommon Candida species (44.1% and 10.3%, respectively) isolates. Moreover, from years 1 to 5 of the study, there was a significant increase in the rates of resistance to fluconazole among C. glabrata complex isolates (12.2% to 24.0%) and to both fluconazole (5.7% to 21.0%) and voriconazole (5.7% to 21.4%) among C. tropicalis isolates (P < 0.01 for all comparisons). Geographic variations in the causative species and susceptibilities were noted. Our findings indicate that antifungal resistance has become noteworthy in China, and enhanced surveillance is warranted.

Changing epidemiology of candidaemia in Australia

Objectives

Knowledge of contemporary epidemiology of candidaemia is essential. We aimed to identify changes since 2004 in incidence, species epidemiology and antifungal susceptibilities of Candida spp. causing candidaemia in Australia.

Methods

These data were collected from nationwide active laboratory-based surveillance for candidaemia over 1 year (within 2014-2015). Isolate identification was by MALDI-TOF MS supplemented by DNA sequencing. Antifungal susceptibility testing was performed using Sensititre YeastOne™.

Results

A total of 527 candidaemia episodes (yielding 548 isolates) were evaluable. The mean annual incidence was 2.41/105 population. The median patient age was 63 years (56% of cases occurred in males). Of 498 isolates with confirmed species identity, Candida albicans was the most common (44.4%) followed by Candida glabrata complex (26.7%) and Candida parapsilosis complex (16.5%). Uncommon Candida species comprised 25 (5%) isolates. Overall, C. albicans (>99%) and C. parapsilosis (98.8%) were fluconazole susceptible. However, 16.7% (4 of 24) of Candida tropicalis were fluconazole- and voriconazole-resistant and were non-WT to posaconazole. Of C. glabrata isolates, 6.8% were resistant/non-WT to azoles; only one isolate was classed as resistant to caspofungin (MIC of 0.5 mg/L) by CLSI criteria, but was micafungin and anidulafungin susceptible. There was no azole/echinocandin co-resistance.

Conclusions

We report an almost 1.7-fold proportional increase in C. glabrata candidaemia (26.7% versus 16% in 2004) in Australia. Antifungal resistance was generally uncommon, but azole resistance (16.7% of isolates) amongst C. tropicalis may be emerging.

Investigation of an unrecognized large-scale outbreak of Candida parapsilosis sensu stricto fungaemia in a tertiary-care hospital in China

A data analysis of yeast collections from the National China Hospital Invasive Fungal Surveillance Net (CHIF-NET) programme in 2013 revealed a sudden increase in the proportion of Candida parapsilosis complex isolates (n = 98) in one participating hospital (Hospital H). Out of 443 yeast isolates submitted to the CHIF-NET reference laboratory by Hospital H (2010–2014), 212 (47.9%) were identified as C. parapsilosis sensu stricto by sequencing analysis of the internal transcribed spacer region and D1/D2 domain of the 26S rRNA gene. Among the 212 C. parapsilosis sensu stricto isolates, 176 (83.0%) bloodstream-based isolates and 25 isolates from tip cultures of various vascular catheters from 25 patients with candidaemia, were subjected to microsatellite genotyping, and a phylogenetic relationship analysis was performed for 152 isolates. Among the 152 isolates, 45 genotypes (T01 to T45) were identified, and two prevalent genotypes (63.8%) were found: T15 (n = 74, 48.7%) and T16 (n = 23, 15.1%). These two main clones were confined mainly to three different wards of the hospital, and they persisted for 16–25 months and 12–13 months, respectively. The lack of proper coordination between the clinical microbiology laboratory and infection control staff as part of public health control resulted in the failure to timely identify an outbreak, which led to the wide and long-term dissemination of C. parapsilosis sensu stricto in Hospital H.

Sequencer-Based Capillary Gel Electrophoresis (SCGE) Targeting the rDNA Internal Transcribed Spacer (ITS) Regions for Accurate Identification of Clinically Important Yeast Species

Accurate species identification of Candida, Cryptococcus, Trichosporon and other yeast pathogens is important for clinical management. In the present study, we developed and evaluated a yeast species identification scheme by determining the rDNA internal transcribed spacer (ITS) region length types (LTs) using a sequencer-based capillary gel electrophoresis (SCGE) approach. A total of 156 yeast isolates encompassing 32 species were first used to establish a reference SCGE ITS LT database. Evaluation of the ITS LT database was then performed on (i) a separate set of (n = 97) clinical isolates by SCGE, and (ii) 41 isolates of 41 additional yeast species from GenBank by in silico analysis. Of 156 isolates used to build the reference database, 41 ITS LTs were identified, which correctly identified 29 of the 32 (90.6%) species, with the exception of Trichosporon asahii, Trichosporon japonicum and Trichosporon asteroides. In addition, eight of the 32 species revealed different electropherograms and were subtyped into 2–3 different ITS LTs each. Of the 97 test isolates used to evaluate the ITS LT scheme, 96 (99.0%) were correctly identified to species level, with the remaining isolate having a novel ITS LT. Of the additional 41 isolates for in silico analysis, none was misidentified by the ITS LT database except for Trichosporon mucoides whose ITS LT profile was identical to that of Trichosporon dermatis. In conclusion, yeast identification by the present SCGE ITS LT assay is a fast, reproducible and accurate alternative for the identification of clinically important yeasts with the exception of Trichosporon species.

Candida quercitrusa Candidemia in a 6-Year-Old Child

We present the first case of candidemia due to Candida quercitrusa in a pediatric patient. The identification of the isolate was protracted and ultimately dependent upon sequence analysis of the internal transcribed spacer region. To further define the antifungal susceptibility characteristics of this species, we performed antifungal susceptibility testing of clinical and type strains. In light of the antifungal susceptibility testing results, we caution against the use of fluconazole for treating C. quercitrusa infections.

Complementary amplicon-based genomic approaches for the study of fungal communities in humans

Recent studies highlight the importance of intestinal fungal microbiota in the development of human disease. Infants, in particular, are an important population in which to study intestinal microbiomes because microbial community structure and dynamics during this formative window of life have the potential to influence host immunity and metabolism. When compared to bacteria, much less is known about the early development of human fungal communities, owing partly to their lower abundance and the relative lack of established molecular and taxonomic tools for their study. Herein, we describe the development, validation, and use of complementary amplicon-based genomic strategies to characterize infant fungal communities and provide quantitative information about Candida, an important fungal genus with respect to intestinal colonization and human disease. Fungal communities were characterized from 11 infant fecal samples using primers that target the internal transcribed spacer (ITS) 2 locus, a region that provides taxonomic discrimination of medically relevant fungi. Each sample yielded an average of 27,553 fungal sequences and Candida albicans was the most abundant species identified by sequencing and quantitative PCR (qPCR). Low numbers of Candida krusei and Candida parapsilosis sequences were observed in several samples, but their presence was detected by species-specific qPCR in only one sample, highlighting a challenge inherent in the study of low-abundance organisms. Overall, the sequencing results revealed that infant fecal samples had fungal diversity comparable to that of bacterial communities in similar-aged infants, which correlated with the relative abundance of C. albicans. We conclude that targeted sequencing of fungal ITS2 amplicons in conjunction with qPCR analyses of specific fungi provides an informative picture of fungal community structure in the human intestinal tract. Our data suggests that the infant intestine harbors diverse fungal species and is consistent with prior culture-based analyses showing that the predominant fungus in the infant intestine is C. albicans.

Antifungal susceptibilities of Candida glabrata species complex, Candida krusei, Candida parapsilosis species complex and Candida tropicalis causing invasive candidiasis in China: 3 year national surveillance

OBJECTIVES

To define the antifungal susceptibility patterns of the most common non-albicans Candida spp. in China.

METHODS

We evaluated the susceptibilities to nine antifungal drugs of Candida parapsilosis species complex, Candida tropicalis, Candida glabrata species complex and Candida krusei isolates from patients with invasive candidiasis at 11 hospitals over 3 years. Isolates were identified by MALDI-TOF MS supplemented by DNA sequencing. MICs were determined by Sensititre YeastOne(TM) using current clinical breakpoints/epidemiological cut-off values to assign susceptibility (or WT), and by CLSI M44-A2 disc diffusion for fluconazole and voriconazole.

RESULTS

Of 1072 isolates, 392 (36.6%) were C. parapsilosis species complex. C. tropicalis, C. glabrata species complex and C. krusei comprised 35.4%, 24.3% and 3.7% of the isolates, respectively. Over 99.3% of the isolates were of WT phenotype to amphotericin B and 5-flucytosine. Susceptibility/WT rates to azoles among C. parapsilosis species complex were ≥97.5%. However, 11.6% and 9.5% of C. tropicalis isolates were non-susceptible to fluconazole and voriconazole, respectively (7.1% were resistant to both). Approximately 14.3% of C. glabrata sensu stricto isolates (n = 258) were fluconazole resistant, and 11.6% of C. glabrata sensu stricto isolates were cross-resistant to fluconazole and voriconazole. All C. krusei isolates were susceptible/WT to voriconazole, posaconazole and itraconazole. Overall, 97.7%-100% of isolates were susceptible to caspofungin, micafungin and anidulafungin, but 2.3% of C. glabrata were non-susceptible to anidulafungin. There was no azole/echinocandin co-resistance. Disc diffusion and Sensititre YeastOne(TM) methods showed >95% categorical agreement for fluconazole and voriconazole.

CONCLUSIONS

In summary, reduced azole susceptibility was seen among C. tropicalis. Resistance to echinocandins was uncommon.

A rare fungal species, Quambalaria cyanescens, isolated from a patient after augmentation mammoplasty--environmental contaminant or pathogen?

Some emerging but less common human fungal pathogens are known environmental species and could be of low virulence. Meanwhile, some species have natural antifungal drug resistance, which may pose significant clinical diagnosis and treatment challenges. Implant breast augmentation is one of the most frequently performed surgical procedures in China, and fungal infection of breast implants is considered rare. Here we report the isolation of a rare human fungal species, Quambalaria cyanescens, from a female patient in China. The patient had undergone bilateral augmentation mammoplasty 11 years ago and was admitted to Peking Union Medical College Hospital on 15 September 2011 with primary diagnosis of breast infection. She underwent surgery to remove the implant and fully recovered thereafter. During surgery, implants and surrounding tissues were removed and sent for histopathology and microbiology examination. Our careful review showed that there was no solid histopathologic evidence of infection apart from inflammation. However, a fungal strain, which was initially misidentified as “Candida tropicalis” because of the similar appearance on CHROMagar Candida, was recovered. The organism was later on re-identified as Q. cyanescens, based on sequencing of the rDNA internal transcribed spacer region rather than the D1/D2 domain of 26S rDNA. It exhibited high MICs to 5-flucytosine and all echinocandins, but appeared more susceptible to amphotericin B and azoles tested. The possible pathogenic role of Q. cyanescens in breast implants is discussed in this case, and the increased potential for misidentification of the isolate is a cause for concern as it may lead to inappropriate antifungal treatment.