Changing face of health-care associated fungal infections

Clonal Spread of Candida glabrata Bloodstream Isolates and Fluconazole Resistance Affected by Prolonged Exposure: a 12-Year Single-Center Study in Belgium

Candida glabrata is a major cause of candidemia in immunocompromised patients and is characterized by a high-level of fluconazole resistance. In the present study, the acquisition of antifungal resistance and potential clonal spread of C. glabrata were explored at a single center over a 12-year period by analyzing 187 independent clinical C. glabrata bloodstream isolates. One strain was found to be micafungin resistant due to a mutation in the FKS2 gene. Fluconazole resistance remained stable throughout the period and was observed in 20 (10.7%) of the isolates. An analysis of the antifungal consumption data revealed that recent prior exposure to fluconazole increased the risk to be infected by a resistant strain. In particular, the duration of the treatment was significantly longer for patients infected by a resistant isolate, while the total and mean daily doses received did not impact the acquisition of resistance in C. glabrata No link between genotype and resistance was found. However, multilocus variable-number tandem-repeat analyses indicated a potential intrahospital spread of some isolates between patients. These isolates shared the same genetic profiles, and infected patients were hospitalized in the same unit during an overlapping period. Finally, quantitative real-time PCR analyses showed that, unlike that for other ABC efflux pumps, the expression of CgCDR1 was significantly greater in resistant strains, suggesting that it would be more involved in fluconazole (FLC) resistance. Our study provides additional evidence that the proper administration of fluconazole is required to limit resistance and that strict hand hygiene is necessary to avoid the possible spreading of C. glabrata isolates between patients.

Evaluation of mRNA Expression Levels of cyp51A and mdr1, Candidate Genes for Voriconazole Resistance in Aspergillus flavus

Background:

Voriconazole Resistance (VRC-R) in Aspergillus flavus isolates impacts the management of aspergillosis, since azoles are the first choice for prophylaxis and therapy. However, to the best of our knowledge, the mechanisms underlying voriconazole resistance are poorly understood.

Objectives:

The present study was designed to evaluate mRNA expression levels of cyp51A and mdr1 genes in voriconazole resistant A. flavus by a Real-Time Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) technique.

Materials and Methods:

Five A. flavus isolates with resistance to VRC were examined by a RT-PCR approach.

Results:

Four out of five isolates revealed cyp51A and mdr1 mRNA overexpression. Interestingly, the isolate, which was negative for cyp51A and mdr1 mRNA expression showed a high voriconazole Minimum Inhibitory Concentration (MIC). Furthermore, a computational-based analysis predicted that voriconazole resistance could be mediated through cooperation with a network protein interaction.

Conclusions:

Our experimental and in silico findings may provide new insight in the complex molecular pathways of drug resistance and also could assist design an efficient therapeutic strategy for aspergillosis treatment.

Rapid and reliable MALDI-TOF mass spectrometry identification of Candida non-albicans isolates from bloodstream infections

Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) fingerprinting has recently become an effective instrument for rapid microbiological diagnostics and in particular for identification of micro-organisms directly in a positive blood culture. The aim of the study was to evaluate a collection of 82 stored yeast isolates from bloodstream infection, by MALDI-TOF MS; 21 isolates were identified also directly from positive blood cultures and in the presence of other co-infecting micro-organisms. Of the 82 isolates grown on plates, 64 (76%) were correctly identified by the Vitek II system and 82 (100%) by MALDI-TOF MS; when the two methods gave different results, the isolate was identified by PCR. MALDI-TOF MS was unreliable in identifying two isolates (Candida glabrata and Candida parapsilosis) directly from blood culture; however, direct analysis from positive blood culture samples was fast and effective for the identification of yeast, which is of great importance for early and adequate treatment.

MALDI-TOF mass spectrometry proteomic phenotyping of clinically relevant fungi

Proteomics is particularly suitable for characterising human pathogens with high life cycle complexity, such as fungi. Protein content and expression levels may be affected by growth states and life cycle morphs and correlate to species and strain variation. Identification and typing of fungi by conventional methods are often difficult, time-consuming and frequently, for unusual species, inconclusive. Proteomic phenotypes from MALDI-TOF MS were employed as analytical and typing expression profiling of yeast, yeast-like species and strain variants in order to achieve a microbial proteomics population study. Spectra from 303 clinical isolates were generated and processed by standard pattern matching with a MALDI-TOF Biotyper (MT). Identifications (IDs) were compared to a reference biochemical-based system (Vitek-2) and, when discordant, MT IDs were verified with genotyping IDs, obtained by sequencing the 25-28S rRNA hypervariable D2 region. Spectra were converted into virtual gel-like formats, and hierarchical clustering analysis was performed for 274 Candida profiles to investigate species and strain typing correlation. MT provided 257/303 IDs consistent with Vitek-2 ones. However, amongst 26/303 discordant MT IDs, only 5 appeared "true". No MT identification was achieved for 20/303 isolates for incompleteness of database species variants. Candida spectra clustering agreed with identified species and topology of Candida albicans and Candida parapsilosis specific dendrograms. MT IDs show a high analytical performance and profiling heterogeneity which seems to complement or even outclass existing typing tools. This variability reflects the high biological complexity of yeasts and may be properly exploited to provide epidemiological tracing and infection dispersion patterns.

Protein glycosylation in Candida

Candidiasis is a significant cause of invasive human mycosis with associated mortality rates that are equivalent to, or worse than, those cited for most cases of bacterial septicemia. As a result, considerable efforts are being made to understand how the fungus invades host cells and to identify new targets for fungal chemotherapy. This has led to an increasing interest in Candida glycobiology, with an emphasis on the identification of enzymes essential for glycoprotein and adhesion metabolism, and the role of N- and O-linked glycans in host recognition and virulence. Here, we refer to studies dealing with the identification and characterization of enzymes such as dolichol phosphate mannose synthase, dolichol phosphate glucose synthase and processing glycosidases and synthesis, structure and recognition of mannans and discuss recent findings in the context of Candida albicans pathogenesis.

Excess mortality, length of stay and cost attributable to candidaemia

BACKGROUND

There were 1967 reports of Candida species isolated from blood specimens in 2007 in the UK (excluding Scotland). Such infections are particularly common in the intensive care unit (ICU). The impact of candidaemia on mortality, length of stay (LOS) and cost in a UK hospital was examined.

METHODS

A retrospective analysis of candidaemia episodes and appropriate matched controls was undertaken based on data from the ICU, high dependency units and hospital wards at Wythenshawe Hospital in Manchester. The study covered the period November 2003-February 2007.

RESULTS

In total, 48 case-patients of candidaemia and 81 control-patients were identified. The attributable mortality due to candidaemia varied from 21.5% to 34.7%. Candidaemia patients spend on average 5.6 days more in the ICU than matched patients and generate mean additional costs of at least 8252 UK pounds per patient, 16,595 pounds in adults only.

CONCLUSION

Candidaemia remains a severe disease associated with high attributable mortality in the UK. In addition, candidaemia leads to additional ICU length of stay and costs. The implication is an attributable cost of at least 16.2 million UK pounds with 683 deaths attributable to candidaemia per year in the UK.

Invasive mycoses following trauma

Invasive fungal infection may afflict people with trauma in two ways: either by entry into tissue via penetrating trauma or by haematogenous spread in critically ill people with polytrauma. Penetrating injury allows the advance of ubiquitously present fungi into the human body. Miniscule foreign material fosters the establishment and growth of fungi within the traumatically changed tissue. The seriousness of the infection depends upon the type of injury, the body area and the person's general condition. Usually, the infection is confined to the cutis and subcutis; the fascia, muscles and bones are rarely affected. In the presence of immunocompromise, however, the fungus may spread rapidly and cause systemic disease. The following overview will focus on fungal infection associated with open wounds and fractures, particularly eye injury and with near-drowning, tropical mycetoma and nosocomial conditions. Post-traumatic invasive fungal infections are rare, but the surgeon should be alert to this possibility in cases with chronic inflammation and deferred healing of injuries, with or without systemic inflammatory response.

Diagnosis of clinically relevant fungi in medicine and veterinary sciences

This review focuses on the most economically and epidemiologically important fungi affecting humans and animals. This paper will also summarize the different techniques, either molecular, based on nucleic acid and antibody analysis, or nonmolecular such as microscopy, culture, UV Wood's lamp, radiology, and spectroscopy used to identify species or group of fungi assisting clinicians to take the best control approach to clear such infections. On the molecular side, the paper will review results on genome sequencing which can help colleagues to identify their own DNA/RNA tests if they are interested in the diagnostic of fungi in medicine and veterinary medicine.

Molecular characterisation of cyp51A and cyp51B genes coding for P450 14alpha-lanosterol demethylases A (CYP51Ap) and B (CYP51Bp) from voriconazole-resistant laboratory isolates of Aspergillus flavus

Aspergillus flavus is the second most common Aspergillus spp. causing invasive infections in immunocompromised patients. Extensive prophylactic use of voriconazole (VCZ) in immunocompromised patients may enhance the selection of VCZ-resistant clinical isolates of A. flavus, compromising the effectiveness of this antifungal drug against A. flavus infection. To study triazole resistance, we selected A. flavus isolates in the laboratory showing reduced in vitro susceptibility to VCZ. The cyp51A and cyp51B genes coding for P450 14alpha-sterol demethylases A (CYP51Ap) and B (CYP51Bp) were characterised to examine possible drug target modification-dependent resistance to VCZ in this fungus. High-molecular-weight DNA was isolated from 10 A. flavus isolates showing in vitro resistance to VCZ (minimum inhibitory concentration (MIC) range 4-32 microg/mL) as well as from the drug-susceptible parent isolate X26728 (MIC = 1 microg/mL). The cyp51A and cyp51B genes were cloned and the nucleotide sequences were determined. A comparison of the deduced amino acid sequences of CYP51Ap from 10 VCZ-resistant isolates with that of the drug-susceptible parent showed no amino acid variation in six of the ten isolates. CYP51Ap from isolates Afl-VCZ6 and Afl-VCZ46 showed a K197N change, CYP51Ap from isolate Afl-VCZ114 showed Y132N and T469S changes, whereas that from isolate Afl-VCZ45 showed K197N, D282E and M288L changes. These results suggest that VCZ-resistant A. flavus isolates can be readily isolated in the laboratory under selection pressure. Multiple mechanisms, including drug target modification, may be responsible for the in vitro resistance of A. flavus to VCZ.

Current status of antifungal susceptibility testing methods

Antifungal susceptibility testing is a very dynamic field of medical mycology. Standardization of in vitro susceptibility tests by the Clinical and Laboratory Standards Institute (CLSI) and the European Committee for Antimicrobial Susceptibility Testing (EUCAST), and current availability of reference methods constituted the major remarkable steps in the field. Based on the established minimum inhibitory concentration (MIC) breakpoints, it is now possible to determine the susceptibilities of Candida strains to fluconazole, itraconazole, voriconazole, and flucytosine. Moreover, utility of fluconazole antifungal susceptibility tests as an adjunct in optimizing treatment of candidiasis has now been validated. While the MIC breakpoints and clinical significance of susceptibility testing for the remaining fungi and antifungal drugs remain yet unclear, modifications of the available methods as well as other methodologies are being intensively studied to overcome the present drawbacks and limitations. Among the other methods under investigation are Etest, colorimetric microdilution, agar dilution, determination of fungicidal activity, flow cytometry, and ergosterol quantitation. Etest offers the advantage of practical application and favorable agreement rates with the reference methods that are frequently above acceptable limits. However, MIC breakpoints for Etest remain to be evaluated and established. Development of commercially available, standardized colorimetric panels that are based on CLSI method parameters has added more to the antifungal susceptibility testing armamentarium. Flow cytometry, on the other hand, appears to offer rapid susceptibility testing but requires specified equipment and further evaluation for reproducibility and standardization. Ergosterol quantitation is another novel approach, which appears potentially beneficial particularly in discrimination of azole-resistant isolates from heavy trailers. The method is yet investigational and requires to be further studied. Developments in methodology and applications of antifungal susceptibility testing will hopefully provide enhanced utility in clinical guidance of antifungal therapy. However, and particularly in immunosuppressed host, in vitro susceptibility is and will remain only one of several factors that influence clinical outcome.

Bench-to-bedside review: Candida infections in the intensive care unit

Invasive mycoses are life-threatening opportunistic infections and have emerged as a major cause of morbidity and mortality in critically ill patients. This review focuses on recent advances in our understanding of the epidemiology, diagnosis and management of invasive candidiasis, which is the predominant fungal infection in the intensive care unit setting. Candida spp. are the fourth most common cause of bloodstream infections in the USA, but they are a much less common cause of bloodstream infections in Europe. About one-third of episodes of candidaemia occur in the intensive care unit. Until recently, Candida albicans was by far the predominant species, causing up to two-thirds of all cases of invasive candidiasis. However, a shift toward non-albicans Candida spp., such as C. glabrata and C. krusei, with reduced susceptibility to commonly used antifungal agents, was recently observed. Unfortunately, risk factors and clinical manifestations of candidiasis are not specific, and conventional culture methods such as blood culture systems lack sensitivity. Recent studies have shown that detection of circulating β-glucan, mannan and antimannan antibodies may contribute to diagnosis of invasive candidiasis. Early initiation of appropriate antifungal therapy is essential for reducing the morbidity and mortality of invasive fungal infections. For decades, amphotericin B deoxycholate has been the standard therapy, but it is often poorly tolerated and associated with infusion-related acute reactions and nephrotoxicity. Azoles such as fluconazole and itraconazole provided the first treatment alternatives to amphotericin B for candidiasis. In recent years, several new antifungal agents have become available, offering additional therapeutic options for the management of Candida infections. These include lipid formulations of amphotericin B, new azoles (voriconazole and posaconazole) and echinocandins (caspofungin, micafungin and anidulafungin).

The Pan-AC assay: a single-reaction real-time PCR test for quantitative detection of a broad range of Aspergillus and Candida species

In view of the growing incidence and the high mortality of invasive aspergillosis and candidiasis, adequate diagnostic techniques permitting timely onset of treatment are of paramount importance. More than 90 % of all invasive fungal infections in immunocompromised individuals can be attributed to Candida and Aspergillus species. To date, standardized techniques permitting rapid, sensitive and, no less importantly, economic screening for the clinically most relevant fungi are lacking. In the present report, a real-time quantitative PCR assay, developed for the detection of the most common pathogenic Candida and Aspergillus species, is described. The single-reaction PCR assay targets a judiciously selected region of the 28S subunit of the fungal rDNA gene. The unique design of the universal primer/probe system, including a pan-Aspergillus and pan-Candida (Pan-AC) hydrolysis probe, facilitates the detection of numerous Aspergillus species (e.g. Aspergillus fumigatus, Aspergillus flavus, Aspergillus niger, Aspergillus terreus, Aspergillus versicolor and Aspergillus nidulans) and Candida species (e.g. Candida albicans, Candida glabrata, Candida krusei, Candida tropicalis, Candida parapsilosis, Candida kefyr, Candida guilliermondii, Candida lusitaniae and Candida dubliniensis). The assay permits highly reproducible detection of 10 fg fungal DNA, which corresponds to a fraction of a fungal genome, and facilitates accurate quantification of fungal load across a range of at least five logs. Upon standardization of the technique using cultured fungal strains, the applicability in the clinical setting was assessed by investigating a series of clinical specimens from patients with documented fungal infections (n=17). The Pan-AC assay provides an attractive and economic approach to the screening and monitoring of invasive aspergillosis and candidiasis, which is readily applicable to routine clinical diagnosis.

DNA microarray-based detection and identification of fungal pathogens in clinical samples from neutropenic patients

The increasing incidence of invasive fungal infections (IFI) in immunocompromised patients emphasizes the need to improve diagnostic tools. We established a DNA microarray to detect and identify DNA from 14 fungal pathogens (Aspergillus fumigatus, Aspergillus flavus, Aspergillus terreus, Candida albicans, Candida dubliniensis, Candida glabrata, Candida lusitaniae, Candida tropicalis, Fusarium oxysporum, Fusarium solani, Mucor racemosus, Rhizopus microsporus, Scedosporium prolificans, and Trichosporon asahii) in blood, bronchoalveolar lavage, and tissue samples from high-risk patients. The assay combines multiplex PCR and consecutive DNA microarray hybridization. PCR primers and capture probes were derived from unique sequences of the 18S, 5.8S, and internal transcribed spacer 1 regions of the fungal rRNA genes. Hybridization with genomic DNA of fungal species resulted in species-specific hybridization patterns. By testing clinical samples from 46 neutropenic patients with proven, probable, or possible IFI or without IFI, we detected A. flavus, A. fumigatus, C. albicans, C. dubliniensis, C. glabrata, F. oxysporum, F. solani, R. microsporus, S. prolificans, and T. asahii. For 22 of 22 patients (5 without IFI and 17 with possible IFI), negative diagnostic results corresponded with negative microarray data. For 11 patients with proven (n = 4), probable (n = 2), and possible IFI (n = 5), data for results positive by microarray were validated by other diagnostic findings. For 11 of 11 patients with possible IFI, the microarray results provided additional information. For two patients with proven and probable invasive aspergillosis, respectively, microarray results were negative. The assay detected genomic DNA from 14 fungal pathogens from the clinical samples, pointing to a high significance for improving the diagnosis of IFI.

Active surveillance for candidemia, Australia

This infection has a high death rate and is predominantly associated with healthcare.

Population-based surveillance for candidemia in Australia from 2001 to 2004 identified 1,095 cases. Annual overall and hospital-specific incidences were 1.81/100,000 and 0.21/1,000 separations (completed admissions), respectively. Predisposing factors included malignancy (32.1%), indwelling vascular catheters (72.6%), use of antimicrobial agents (77%), and surgery (37.1%). Of 919 episodes, 81.5% were inpatient healthcare associated (IHCA), 11.6% were outpatient healthcare associated (OHCA), and 6.9% were community acquired (CA). Concomitant illnesses and risk factors were similar in IHCA and OHCA candidemia. IHCA candidemia was associated with sepsis at diagnosis (p<0.001), death <30 days after infection (p<0.001), and prolonged hospital admission (p<0.001). Non–Candida albicans species (52.7%) caused 60.5% of cases acquired outside hospitals and 49.9% of IHCA candidemia (p = 0.02). The 30-day death rate was 27.7% in those >65 years of age. Adult critical care stay, sepsis syndrome, and corticosteroid therapy were associated with the greatest risk for death. Systematic epidemiologic studies that use standardized definitions for IHCA, OHCA, and CA candidemia are indicated.

Genomic analysis of allergen genes inAspergillusspp.: the relevance of genomics to everyday research

Full genomic sequencing of Aspergillus fumigatus and other genomes has allowed correction of Aspergillus allergen gene sequences and requires revision of Genbank and IUIS sequences of allergens. In addition allergens in other fungal species may be found in the aspergilli. We compared the published sequences of numerous allergens with recently available genome sequences. This analysis suggests that Aspf 56KD, Asp f 15 and Asp f 16 should be removed from the approved allergen list and that Asp f 17 is a larger protein than published. Additionally we propose likely gene candidates for Asp f GST (Afu6g09690) and Asp o lipase (AO090701000644). We suggest that the heat shock allergens should be re-classified: Asp f 12 should be classified as HSP90 (Asp f 12), HSP88 (Mala s 10) and HSP70 (Alt a 3, Cla h 4 and Pen c 19) according to human gene nomenclature. Comparison of fungal allergen databases with genome sequences suggests the presence of a core set of allergen - like proteins in all fungi. We also analysed allergens in the 3 sequenced aspergilli to look for internal homologies and this suggests that multi gene families may produce numerous cross-reactive allergens.

Echinocandins in the management of invasive fungal infections, part 1

PURPOSE

The chemistry, pharmacology, spectrum of activity, resistance, pharmacokinetics, pharmacodynamics, clinical efficacy, adverse effiects, drug interactions, dosage and administration, cost, and place in therapy of echinocandins are reviewed.

SUMMARY

Three echinocandins are currently available: caspofungin, micafungin, and anidulafungin. The principal mechanism of action of the echinocandins is the noncompetitive inhibition of beta-(1,3)-dglucan synthase, an essential component of the cell wall of many fungi that is not present in mammalian cells. Echinocandins exhibit fungicidal activity against Candida species, including triazole-resistant isolates, and fungistatic activity against Aspergillus species. While fungistatic against mold, echinocandins may hold promise for the treatment of these pathogens when given in combination with amphotericin B or broad-spectrum triazoles, such as voriconazole. To date, resistance to echinocandins has been reported in only two patients. Echinocandins exhibit concentration- dependent activity against Candida species. In clinical trials, caspofungin has demonstrated efficacy in treating candidemia, esophageal candidiasis, and febrile neutropenia. Micafungin has demonstrated efficacy as antifungal prophylaxis in hematopoietic stem cell transplant recipients and in the treatment of esophageal candidiasis. Anidulafungin received approved labeling from the Food and Drug Administration in February 2006. Clinical efficacy data will be forthcoming.

CONCLUSION

Echinocandins are fungicidal against yeast and fungistatic against mold. Their limited toxicity profile and minimal drug-drug interactions make them an attractive new option for the treatment of invasive fungal infections. Their cost may limit their use as initial therapy for patients with fungemia in medical centers or intensive care units with a high rate of triazoleresistant Candida infections.

Primer R108 performs best in the RAPD strain typing of three Aspergillus species frequently isolated from patients

We evaluated the suitability of various primers for the RAPD (random amplified polymorphic DNA) accurate species identification and strain typing of Aspergillus clinical isolates. Five primers described previously were tested for their discriminatory power in three Aspergillus species (A. fumigatus, A. niger agg. and A. flavus - 23 clinical isolates and 2 reference strains). Clustering of RAPD fingerprints corresponded well with the identification based on morphological features. All isolates were resolved as different strains using the primer R108 and the RAPD protocol optimized for a Robocycler thermal cycler. RAPD with the primer R108 thus can be considered to be a valuable, simple and powerful tool for identification and strain delineation of Aspergillus spp.

Role of the dual interaction of fungal pathogens with pattern recognition receptors in the activation and modulation of host defence

Recognition of pathogen-associated molecular patterns (PAMPs) of microorganisms by pathogen recognition receptors induces signals responsible for the activation of genes important for an effective host defence, especially those of pro-inflammatory cytokines. Toll-like receptors (TLRs) and lectin-like receptors are the most important classes of pattern-recognition receptors. In addition to their effects on the activation of host defence, recent studies suggest that pathogenic fungi can modulate or interfere with the pattern recognition mechanisms of innate immunity, and can use pattern recognition receptors as mechanisms of escape from host defence. Two major recognition receptor-mediated escape mechanisms have been identified during infection with fungal pathogens: immunosuppression induced by activation of certain pattern recognition receptors, especially induction of IL-10 release through TLR2; and the blockade of TLR recognition by antigen modification during the germination of yeasts into hyphae. Thus, signals mediated by recognition receptors are not only beneficial to the host, but in certain situations can be used by pathogenic fungi to escape immune recognition and promote infection.

The long hard road to a completed Candida albicans genome

After almost a decade of work, the sequencing, assembly, and annotation of the genome of the fungal pathogen Candida albicans is finally close at hand. This review covers the early history of the C. albicans genome project, from the release of early assemblies that provided the impetus for an explosion in functional genomics research, to a community-based annotation and a preview of the work that was necessary for the production of a final genome assembly.