The genetic relationship of Lodderomyces elongisporus to other ascomycete yeast species as revealed by small-subunit rRNA gene sequences

Disseminated Lodderomyces elongisporus and Pantoea dispersa: A Rare Dual Infection in an Immunocompromised Patient

With the advancement of modern medicine and the prolonged survival of critically ill patients, unusual organisms are increasingly emerging. Initially found in the environment, these rare organisms started presenting as human pathogens, causing significant morbidity and mortality. Here, we present a rare case of disseminated Lodderomyces elongisporus fungemia and Pantoea dispersa bacteremia in a patient with parapneumonic effusion and ruptured liver abscess. This yeast was identified using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF). Although this organism has no antifungal breakpoint, the isolate shows low minimum inhibitory concentration (MIC) to a wide range of antifungals. The importance of effective communication between microbiologists and clinicians and early referral to the infectious disease team was also highlighted in this case for prompt treatment.

Lodderomyces elongisporus as causative organism of oropharyngeal infections - Two case reports

We report two cases of patients with oropharyngeal infection by Lodderomyces elongisporus. The identification of the two isolates was confirmed after sequencing the ITS1 and ITS4 regions. The antifungal susceptibility test revealed low MIC values for the different antifungals tested. This is the first reported case of L. elongisporus present during an oropharyngeal infection and describes the laboratory methodology employed in the diagnosis.

Three Successfully Treated Cases of Lodderomyces elongisporus Fungemia: Case Reports and a Review of the Literature

Fungemia is a fatal systemic infection that can occur in immunocompromised patients. Despite that, antifungal stewardship is spreading widely, but the mortality rate is extremely high, showing 40-60%. Loderomyces elongiporus is a newly morphologically detected pathogen, first described in 1994, followed by isolation in humans in 2008. It has been misrecognized as Candida parapsilosis. Recently, fever attributable to L. elongisporus fungemia cases has been reported, and the etiology and clinical features are still unknown. Here, we present three successfully treated L. elongisporus fungemia cases by echinocandin. In total, 11 cases were reviewed, including ours. Six of the eleven cases (55%) had external devices. All cases had some immunocompromised conditions or underlying diseases, such as diabetes mellitus, lung cancer, etc. Six patients survived, and the remaining five died. Seven patients who had received echinocandin initially survived. Risk factors for L. elongiporus fungemia overlap with those of candidemia. Even though there is no breakpoint for L. elongiporus, echinocandin can be a helpful treatment regimen for L. elongiporus fungemia.

The Flo Adhesin Family

The first step in the infection of fungal pathogens in humans is the adhesion of the pathogen to host tissue cells or abiotic surfaces such as catheters and implants. One of the main players involved in this are the expressed cell wall adhesins. Here, we review the Flo adhesin family and their involvement in the adhesion of these yeasts during human infections. Firstly, we redefined the Flo adhesin family based on the domain architectures that are present in the Flo adhesins and their functions, and set up a new classification of Flo adhesins. Next, the structure, function, and adhesion mechanisms of the Flo adhesins whose structure has been solved are discussed in detail. Finally, we identified from Pfam database datamining yeasts that could express Flo adhesins and are encountered in human infections and their adhesin architectures. These yeasts are discussed in relation to their adhesion characteristics and involvement in infections.

The first described case of Lodderomyces elongisporus meningitis

We describe the first documented case of meningitis caused by Lodderomyces elongisporus. Identification of L. elongisporus was made on the basis of an arachnoid biopsy with pathology samples sent for fungal internal transcribed spacer sequencing after multiple central nervous system (CNS) fungal culture specimens were negative. After final diagnosis, treatment was transitioned from amphotericin to fluconazole, which, combined with insertion of lumbar drain followed by a permanent ventriculopleural shunt, resulted in significant clinical improvement. Our report reviews the literature of (1) cases of L. elongisporus, which almost exclusively describe fungemia or endocarditis; (2) CNS infections caused by Candida parapsilosis, an organism with which L. elongisporus was previously conflated; and (3) management of fungal meningitis-associated hydrocephalus.

Concurrent bloodstream infection with Lodderomyces elongisporus and Candida parapsilosis

We report the case of a 54-year-old patient with central venous catheter related mixed candidaemia with Lodderomyces elongisporus and Candida parapsilosis, who responded to line removal and anidulafungin therapy.

Mixed candidaemia was detected on Candida chromogenic agar. Identification of the two isolates was confirmed by MALDI-TOF MS (Bruker). Antifungal susceptibility testing revealed different antifungal MICs. This is the first reported case of mixed Lodderomyces candidaemia and outlines laboratory methodology to aid diagnosis and management.

Lodderomyces elongisporus: a bloodstream pathogen of greater clinical significance

The true clinical significance of Lodderomyces elongisporus remains underestimated as a result of problems associated with its identification by the VITEK 2 yeast identification system. Here we describe a case of L. elongisporus primary progressive fungaemia in a woman with no known risk factors for invasive fungal infections. The isolate was identified by PCR sequencing of the internally transcribed spacer region of ribosomal DNA. Despite treatment with caspofungin, the patient died within 3 days of onset of fungaemia. Our literature review highlights this organism's emerging role as a bloodstream pathogen. A need for application of molecular methods for its accurate identification is emphasized.

Gene editing in clinical isolates of Candida parapsilosis using CRISPR/Cas9

Candida parapsilosis is one of the most common causes of candidiasis, particularly in the very young and the very old. Studies of gene function are limited by the lack of a sexual cycle, the diploid genome, and a paucity of molecular tools. We describe here the development of a plasmid-based CRISPR-Cas9 system for gene editing in C. parapsilosis. A major advantage of the system is that it can be used in any genetic background, which we showed by editing genes in 20 different isolates. Gene editing is carried out in a single transformation step. The CAS9 gene is expressed only when the plasmid is present, and it can be removed easily from transformed strains. There is theoretically no limit to the number of genes that can be edited in any strain. Gene editing is increased by homology-directed repair in the presence of a repair template. Editing by non-homologous end joining (NHEJ) also occurs in some genetic backgrounds. Finally, we used the system to introduce unique tags at edited sites.

MTL genotypes, phenotypic switching, and susceptibility profiles of Candida parapsilosis species group compared to Lodderomyces elongisporus

Reference isolates of Candida parapsilosis (n = 8), Candida metapsilosis (n = 6), Candida orthopsilosis (n = 7), and Lodderomyces elongisporus (n = 11) were analyzed to gain insight into their pathobiology and virulence mechanisms. Initial evaluation using BBL Chromagar Candida medium misidentified L. elongisporus isolates as C. albicans. Polymerase chain reaction analysis of isolate MTL idiomorphs revealed that all C. parapsilosis isolates were MTLa homozygous and no MTL α1, α2, a1, or a2 gene was detected in L. elongisporus isolates. For C. orthopsilosis, two isolates were MTLa homozygous and five were MTL-heterozygous. Similarly, one C. metapsilosis isolate was MTLα homozygous whereas five were MTL-heterozygous. Isolate phenotypic switching analysis revealed potential phenotypic switching in the MTLα homozygous C. metapsilosis isolate, resulting in concomitant elongated cell formation. Minimum inhibitory concentrations of fluconazole (FLC) and FK506, alone or in combination, were determined by checkerboard assay, with data analyzed using the fractional inhibitory concentration index model. Synergistic or additive effects of these compounds were commonly observed in C. parapsilosis and L. elongisporus isolates. No killer activity was observed in the studied isolates, as determined phenotypically. No significant difference in virulence was seen for the four species in a Galleria mellonella model (P > 0.05). In conclusion, our results demonstrated phenotypic switching of C. metapsilosis CBS 2315 and that FLC and FK506 represent a promising drug combination against C. parapsilosis and L. elongisporus. The findings of the present study contribute to our understanding of the biology, diagnosis, and new possible treatments of the C. parapsilosis species group and L. elongisporus.

Catheter-Related Bloodstream Infection Due to Lodderomyces elongisporus

Lodderomyces elongisporus infrequently causes bloodstream infections and has been isolated from Asia and Mexico. We encountered a catheter-related bloodstream infection, which involved some risk factors, due to L. elongisporus masquerading as Candida parapsilosis. A 39-year-old man who received a total arch and thoracoabdominal aortic replacement was admitted with a diagnosis of aorto-esophageal fistula. After thoracic drainage for the aorto-esophageal fistula, a catheter-related bloodstream infection was diagnosed. Micafungin (100 mg/day) was successfully administered to treat the catheter-related bloodstream infection for 42 days in total. The bloodstream and catheter tip yeast was grown on Candida agar medium and produced dark green colonies indicating Candida albicans. We performed sequencing analysis using a GenBank BLAST search. The sequence of the internal transcribed spacer region was 99.9% identical with that of the type strain L. elongisporus. This yeast organism has frequently been technically mistaken for non-albicans Candida spp. Furthermore, the prognosis and risk factors of L. elongisporus infection remain unclear owing to the scarcity of reported cases. Catheter-related bloodstream infection caused by this organism has not been described to date.

Identification and typing of the Candida parapsilosis complex: MALDI-TOF MS vs. AFLP

In this study we compare the capability of amplification fragment-length polymorphism (AFLP) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to identify and subtype isolates of members of the Candida parapsilosis complex (C. parapsilosis, C. orthopsilosis, C. metapsilosis) and Lodderomyces elongisporus, which cannot be differentiated with biochemical methods. Both techniques correctly identified all isolates included in this study and clustered isolates within the different species. DNA-based and mass spectrum-based dendrograms yielded similar outcomes with regard to phylogenetic distance within C. orthopsilosis and C. parapsilosis species. However, a different clustering was obtained for C. metapsilosis for which AFLP was highly effective in differentiating. While MALDI-TOF MS was found to be a reliable method for species-level identification, further studies are required to assess its value as a fungal typing tool.

Isolation of Lodderomyces elongisporus from the Catheter Tip of a Fungemia Patient in the Middle East

Lodderomyces elongisporus is phenotypically closely related to Candida parapsilosis and has recently been identified as an infrequent cause of bloodstream infections in patients from Asia and Mexico. We report here the isolation of Lodderomyces elongisporus from the catheter of a suspected case of fungemia. The identity of the isolate was confirmed by phenotypic characteristics and ribosomal DNA sequencing.

Differentiation of Candida parapsilosis, C. orthopsilosis, and C. metapsilosis by specific PCR amplification of the RPS0 intron

Although Candida parapsilosis is the most prevalent among the 3 species of the *psilosis group, studies applying DNA-based diagnostic techniques with isolates previously identified as C. parapsilosis have revealed that both C. orthopsilosis and C. metapsilosis account for 0-10% of all these isolates, depending on the geographical area. Differences in the degrees of antifungal susceptibility and virulence have been found, so a more precise identification is required. In a first approach, we reidentified 38 randomly chosen clinical isolates, previously identified as C. parapsilosis, using the RPO2 (CA2) RAPD marker. Among them, we reclassified 4 as C. metapsilosis and 5 as C. orthopsilosis. We previously developed a method to identify different pathogen yeast species, including C. parapsilosis, based on the amplification of the RPS0 gene intron. In this work, we extend this approach to the new *psilosis species by partially sequencing their RPS0 gene, including the intron sequence. Based on intron sequences, we designed specific primers capable of identifying C. orthopsilosis and C. metapsilosis species, and we reidentified species among the initial isolates. These new primers have allowed a specific and rapid identification of C. orthopsilosis and C. metapsilosis.

Fungal sex and pathogenesis

Human fungal pathogens are associated with diseases ranging from dandruff and skin colonization to invasive bloodstream infections. The major human pathogens belong to the Candida, Aspergillus, and Cryptococcus clades, and infections have high and increasing morbidity and mortality. Many human fungal pathogens were originally assumed to be asexual. However, recent advances in genome sequencing, which revealed that many species have retained the genes required for the sexual machinery, have dramatically influenced our understanding of the biology of these organisms. Predictions of a rare or cryptic sexual cycle have been supported experimentally for some species. Here, I examine the evidence that human pathogens reproduce sexually. The evolution of the mating-type locus in ascomycetes (including Candida and Aspergillus species) and basidiomycetes (Malassezia and Cryptococcus) is discussed. I provide an overview of how sex is suppressed in different species and discuss the potential associations with pathogenesis.

Molecular differentiation and antifungal susceptibilities of Candida parapsilosis isolated from patients with bloodstream infections

The genetic heterogeneity and antifungal susceptibility patterns of Candida parapsilosis isolated from blood cultures of patients were investigated in this study. Randomly amplified polymorphic DNA (RAPD) analysis generated 5 unique profiles from 42 isolates. Based on the major DNA fragments of the RAPD profiles, the isolates were identified as RAPD type P1 (29 isolates), P2 (6 isolates), P3 (4 isolates), P4 (2 isolates) and P5 (1 isolate). Sequence analysis of the internal transcribed spacer (ITS) gene of the isolates identified RAPD type P1 as C. parapsilosis, P2 and P3 as Candida orthopsilosis, P4 as Candida metapsilosis, and P5 as Lodderomyces elongisporus. Nucleotide variations in ITS gene sequences of C. orthopsilosis and C. metapsilosis were detected. Antifungal susceptibility testing using Etests showed that all isolates tested in this study were susceptible to amphotericin B, fluconazole, ketoconazole, itraconazole and voriconazole. C. parapsilosis isolates exhibited higher MIC(50) values than those of C. orthopsilosis for all of the drugs tested in this study; however, no significant difference in the MICs for these two Candida species was observed. The fact that C. orthopsilosis and C. metapsilosis were responsible for 23.8 and 4.8 % of the cases attributed to C. parapsilosis bloodstream infections, respectively, indicates the clinical relevance of these newly described yeasts. Further investigations of the ecological niche, mode of transmission and virulence of these species are thus essential.

Lodderomyces elongisporus masquerading as Candida parapsilosis as a cause of bloodstream infections

Ten yeast bloodstream isolates identified as Candida parapsilosis by conventional methods grew as turquoise blue colonies on Chromagar media. Subsequent sequence analysis showed that these isolates were the species Lodderomyces elongisporus. To our knowledge, this is the first published report of L. elongisporus as a cause of human disease.

A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis

BACKGROUND

To date, most fungal phylogenies have been derived from single gene comparisons, or from concatenated alignments of a small number of genes. The increase in fungal genome sequencing presents an opportunity to reconstruct evolutionary events using entire genomes. As a tool for future comparative, phylogenomic and phylogenetic studies, we used both supertrees and concatenated alignments to infer relationships between 42 species of fungi for which complete genome sequences are available.

RESULTS

A dataset of 345,829 genes was extracted from 42 publicly available fungal genomes. Supertree methods were employed to derive phylogenies from 4,805 single gene families. We found that the average consensus supertree method may suffer from long-branch attraction artifacts, while matrix representation with parsimony (MRP) appears to be immune from these. A genome phylogeny was also reconstructed from a concatenated alignment of 153 universally distributed orthologs. Our MRP supertree and concatenated phylogeny are highly congruent. Within the Ascomycota, the sub-phyla Pezizomycotina and Saccharomycotina were resolved. Both phylogenies infer that the Leotiomycetes are the closest sister group to the Sordariomycetes. There is some ambiguity regarding the placement of Stagonospora nodurum, the sole member of the class Dothideomycetes present in the dataset. Within the Saccharomycotina, a monophyletic clade containing organisms that translate CTG as serine instead of leucine is evident. There is also strong support for two groups within the CTG clade, one containing the fully sexual species Candida lusitaniae, Candida guilliermondii and Debaryomyces hansenii, and the second group containing Candida albicans, Candida dubliniensis, Candida tropicalis, Candida parapsilosis and Lodderomyces elongisporus. The second major clade within the Saccharomycotina contains species whose genomes have undergone a whole genome duplication (WGD), and their close relatives. We could not confidently resolve whether Candida glabrata or Saccharomyces castellii lies at the base of the WGD clade.

CONCLUSION

We have constructed robust phylogenies for fungi based on whole genome analysis. Overall, our phylogenies provide strong support for the classification of phyla, sub-phyla, classes and orders. We have resolved the relationship of the classes Leotiomyctes and Sordariomycetes, and have identified two classes within the CTG clade of the Saccharomycotina that may correlate with sexual status.

Mitochondrial telomeres as molecular markers for identification of the opportunistic yeast pathogen Candida parapsilosis

Recent studies have demonstrated that a large number of organisms carry linear mitochondrial DNA molecules possessing specialized telomeric structures at their ends. Based on this specific structural feature of linear mitochondrial genomes, we have developed an approach for identification of the opportunistic yeast pathogen Candida parapsilosis. The strategy for identification of C. parapsilosis strains is based on PCR amplification of specific DNA sequences derived from the mitochondrial telomere region. This assay is complemented by immunodetection of a protein component of mitochondrial telomeres. The results demonstrate that mitochondrial telomeres represent specific molecular markers with potential applications in yeast diagnostics and taxonomy.