The phageome in normal and inflamed human skin.

Dysbiosis of skin microbiota drives the progression of atopic dermatitis (AD). The contribution of bacteriophages to bacterial community compositions in normal and inflamed skin is unknown. Using shotgun metagenomics from skin swabs of healthy individuals and patients with AD, we found 13,586 potential viral contiguous DNA sequences, which could be combined into 164 putative viral genomes including 133 putative phages. The Shannon diversity index for the viral metagenome-assembled genomes (vMAGs) did not correlate with AD. In total, we identified 28 vMAGs that differed significantly between normal and AD skin. Quantitative polymerase chain reaction validation of three complete vMAGs revealed their independence from host bacterium abundance. Our data indicate that normal and inflamed skin harbor distinct phageomes and suggest a causative relationship between changing viral and bacterial communities as a driver of skin pathology.

Interlaboratory evaluation of Mucorales PCR assays for testing serum specimens: A study by the fungal PCR Initiative and the Modimucor study group.

Interlaboratory evaluations of Mucorales qPCR assays were developed to assess the reproducibility and performance of methods currently used. The participants comprised 12 laboratories from French university hospitals (nine of them participating in the Modimucor study) and 11 laboratories participating in the Fungal PCR Initiative. For panel 1, three sera were each spiked with DNA from three different species (Rhizomucor pusillus, Lichtheimia corymbifera, Rhizopus oryzae). For panel 2, six sera with three concentrations of R. pusillus and L. corymbifera (1, 10, and 100 genomes/ml) were prepared. Each panel included a blind negative-control serum. A form was distributed with each panel to collect results and required technical information, including DNA extraction method, sample volume used, DNA elution volume, qPCR method, qPCR template input volume, qPCR total reaction volume, qPCR platform, and qPCR reagents used. For panel 1, assessing 18 different protocols, qualitative results (positive or negative) were correct in 97% of cases (70/72). A very low interlaboratory variability in Cq values (SD = 1.89 cycles) were observed. For panel 2 assessing 26 different protocols, the detection rates were high (77-100%) for 5/6 of spiked serum. There was a significant association between the qPCR platform and performance. However, certain technical steps and optimal combinations of factors may also impact performance. The good reproducibility and performance demonstrated in this study support the use of Mucorales qPCR as part of the diagnostic strategy for mucormycosis.

Respiratory specimens and the diagnostic accuracy of Aspergillus lateral flow assays (LFA-IMMY™): real-life data from a multicentre study.

OBJECTIVES: Proper diagnosis of invasive aspergillosis is challenging because conventional methods lack sensitivity and are complicated by time-consuming incubation processes. To meet the requirement for early diagnosis the new Aspergillus-specific point-of-care test LFA-IMMY™ was evaluated with respect to the ability to accurately detect Aspergillus in bronchoalveolar fluids and sputa, and to clarify the potential of cross-reactivity with other fungal pathogens. METHODS: Respiratory specimens (n = 398) from non-selected patients (n = 390) underwent either fungal microscopy, culture or both before Aspergillus lateral flow assay (LFA-IMMY) testing. RESULTS: For Aspergillus culture- and microscopy-positive samples, sensitivity (48/52) and specificity (44/48) were 92% (95% CI 8.0%-9.7%) and 91% (95% CI 7.9%-9.7%), respectively; cross-reactivity was documented with non-Aspergillus pathogens. CONCLUSION: LFA-IMMY is a reliable diagnostic tool for the detection of Aspergillus in respiratory samples.

A prospective international Aspergillus terreus survey: an EFISG, ISHAM and ECMM joint study.

OBJECTIVES: A prospective international multicentre surveillance study was conducted to investigate the prevalence and amphotericin B susceptibility of Aspergillus terreus species complex infections. METHODS: A total of 370 cases from 21 countries were evaluated. RESULTS: The overall prevalence of A. terreus species complex among the investigated patients with mould-positive cultures was 5.2% (370/7116). Amphotericin B MICs ranged from 0.125 to 32 mg/L, (median 8 mg/L). CONCLUSIONS: Aspergillus terreus species complex infections cause a wide spectrum of aspergillosis and the majority of cryptic species display high amphotericin B MICs.

Invasive Candida infections in surgical patients in intensive care units: a prospective, multicentre survey initiated by the European Confederation of Medical Mycology (ECMM) (2006-2008).

A prospective, observational, multicentre study of invasive candidosis (IC) in surgical patients in intensive care units (ICUs) was conducted from 2006 to 2008 in 72 ICUs in 14 European countries. A total of 779 patients (62.5% males, median age 63 years) with IC were included. The median rate of candidaemia was 9 per 1000 admissions. In 10.8% the infection was already present at the time of admission to ICU. Candida albicans accounted for 54% of the isolates, followed by Candida parapsilosis 18.5%, Candida glabrata 13.8%, Candida tropicalis 6%, Candida krusei 2.5%, and other species 5.3%. Infections due to C. krusei (57.9%) and C. glabrata (43.6%) had the highest crude mortality rate. The most common preceding surgery was abdominal (51.5%), followed by thoracic (20%) and neurosurgery (8.2%). Candida glabrata was more often isolated after abdominal surgery in patients ≥60 years, and C. parapsilosis was more often isolated in neurosurgery and multiple trauma patients as well as children ≤1 year of age. The most common first-line treatment was fluconazole (60%), followed by caspofungin (18.7%), liposomal amphotericin B (13%), voriconazole (4.8%) and other drugs (3.5%). Mortality in surgical patients with IC in ICU was 38.8%. Multivariate analysis showed that factors independently associated with mortality were: patient age ≥60 years (hazard ratio (HR) 1.9, p 0.001), central venous catheter (HR 1.8, p 0.05), corticosteroids (HR 1.5, p 0.03), not receiving systemic antifungal treatment for IC (HR 2.8, p <0.0001), and not removing intravascular lines (HR 1.6, p 0.02).

Species and susceptibility distribution of 1062 clinical yeast isolates to azoles, echinocandins, flucytosine and amphotericin B from a multi-centre study.

Descriptive values were determined for eight antifungal agents within the course of a multi-centre study encompassing 1062 German and Austrian clinical yeast isolates. Candida albicans (54%) was the predominant species isolated followed by Candida glabrata (22%), Candida parapsilosis (6%), Candida tropicalis (5.7%), Candida krusei (4.3%), as well as eleven further candidal and four non-Candida yeast species. While 519 (48.9%) isolates were tested susceptible to all antifungals tested, no isolate was found to exhibit complete cross resistance. For C. albicans, the proportions of susceptible isolates were 93.2% (amphotericin B), 95.6% (flucytosine), 84.3% (fluconazole), 83.8% (posaconazole), 91.8% (voriconazole), 96.5% (anidulafungin), 96.2% (caspofungin) and 97.6% (micafungin). Patterns of complete parallel resistances were observed within azoles (8.8%) and echinocandins (1.7%). While a decreased susceptibility was found infrequently for echinocandins and flucytosine, it was more common for azoles with highest proportions for isolates of C. glabrata (fluconazole, 40.6%; posaconazole, 37.2%), Candida guilliermondii (fluconazole and posaconazole, each 25.0%), C. krusei (posaconazole, 28.3%; voriconazole, 60%), C. parapsilosis (fluconazole, 70.3%) and C. tropicalis (fluconazole, 62.3%). The descriptive values obtained in this study represent a valid basis for the comparison of recent and future epidemiological surveys to analyse the susceptibility of yeast isolates towards major antifungal substances.

Pulmonary, rhino-orbital and cutaneous mucormycosis caused by Rhizomucor pusillus in an immunocompromised patient.

The number of patients with haematopoietic malignancies receiving chemotherapy and stem-cell transplantation has increased the incidence of severe opportunistic infections. Systemic fungal infections are of major concern in immunocompromised patients, as these infections are often fatal. We report a case of a patient with acute myeloid leukaemia who developed multiple cutaneous plaques and necrotizing infiltrates in the lungs during chemotherapy. Using real-time PCR on a wax-embedded tissue sample, Rhizomucor pusillus was identified. We provide an overview of the literature on cutaneous mucormycosis and its diagnosis by PCR.

The Nationwide Austrian Aspergillus Registry: a prospective data collection on epidemiology, therapy and outcome of invasive mould infections in immunocompromised and/or immunosuppressed patients.

A prospective, observational, multicentre study was performed to assess the incidence, diagnosis, epidemiology and outcome of invasive mould infections (IMIs) reported to the Nationwide Austrian Aspergillus Registry. In total, 186 cases were recorded, corresponding to an annual incidence of 42 cases/1000 patients at risk or 2.36 cases/100000 inhabitants. Patients with acute myelogenous leukaemia (34%) and lung transplant recipients (17%) are currently at highest risk for IMI, followed by a mixed population with impaired immunity (14%). In total, 34%, 30% and 36% were proven, probable and possible cases of IMI. Predominant pathogens were Aspergillus spp. (67%), followed by the zygomycetes (28%). Voriconazole was the most frequently administered agent (38%), followed by caspofungin (20%) and posaconazole (19%). Eighty patients (43%) received antifungal prophylaxis for ≥7 days, 30% of whom (24 patients) suffered from a breakthrough infection. The overall crude 12-week mortality was 34%. Multivariate analysis showed that outcome and survival did not correlate with the status of fungal disease, breakthrough infection, fungal species or age (P>0.05). Aspergillosis remains the most commonly identified IMI amongst immunocompromised and/or immunosuppressed patients, but other moulds constitute a significant problem. Survival from IMIs appears to have improved and the main challenge is to overcome breakthrough fungal infections.

[Species diagnosis: From petri dish to molecular biology]. / Speziesdiagnostik: Von der Agarplatte zur Molekularbiologie.

During several decades microscopy and culture based methods have been the most important techniques for the detection of fungal infections. Culture, though often slow, sometimes insensitive and sometimes confusing with respect to contamination or colonization, may yield the specific aetiological agent, and may allow susceptibility testing to be performed. However, molecular detection and identification using PCR for the amplification of fungal DNA from tissue is being applied more and more frequently for the early diagnosis and identification of fungal pathogens. Other tools such as fluorescence in situ hybridization (FISH) or DNA microarrays have also been developed and their performance is currently being evaluated. Since standardization and validation for most of these newer techniques are still lacking the combination of various diagnostic tools is still mandatory to allow earlier diagnosis of systemic fungal infections.

Improved metabolic control after 12-week dietary intervention with low glycaemic isomalt in patients with type 2 diabetes mellitus.

The polyol isomalt (Palatinit) is a very low glycaemic sugar replacer. The effect of food supplemented with isomalt instead of higher glycaemic ingredients like sucrose and/or starch hydrolysates on metabolic control in patients with type 2 diabetes was examined in this open study. Thirty-three patients with type 2 diabetes received a diet with foods containing 30 g/d isomalt instead of higher-glycaemic carbohydrates for 12 weeks. Metformin and/or thiazolidindiones were the only concomitant oral antidiabetics allowed during the study. Otherwise, the participants maintained their usual diet during the test phase, but were instructed to refrain from additional sweetened foods. Before start, after 6 weeks and 12 weeks (completion of the study), blood samples were taken and analysed for clinical routine parameters, metabolic, and risk markers. Thirty-one patients completed the study. The test diet was well accepted and tolerated. After 12 weeks, significant reductions were observed for: glycosylated haemoglobin, fructosamine, fasting blood glucose, insulin, proinsulin, C-peptide, insulin resistance (HOMA-IR), and oxidised LDL (an atherosclerosis risk factor). In addition, significant lower nonesterified fatty acid concentrations were found in female participants. Routine blood measurements and blood lipids remained unchanged. The substitution of glycaemic ingredients by isomalt and the consequent on reduction of the glycaemic load within otherwise unchanged diet was accompanied by significant improvement in the metabolic control of diabetes. The present study is in agreement with findings of previous reported studies in human subjects demonstrating beneficial effects of low glycaemic diets on glucose metabolism in patients with diabetes mellitus type 2.

Species-specific identification of a wide range of clinically relevant fungal pathogens by use of Luminex xMAP technology.

In immunocompromised patients suffering from invasive fungal infection, rapid identification of the fungal species is a prerequisite for selection of the most appropriate antifungal treatment. We present an assay permitting reliable identification of a wide range of clinically relevant fungal pathogens based on the high-throughput Luminex microbead hybridization technology. The internal transcribed spacer (ITS2) region, which is highly variable among genomes of individual fungal species, was used to generate oligonucleotide hybridization probes for specific identification. The spectrum of pathogenic fungi covered by the assay includes the most commonly occurring species of the genera Aspergillus and Candida and a number of important emerging fungi, such as Cryptococcus, Fusarium, Trichosporon, Mucor, Rhizopus, Penicillium, Absidia, and Acremonium. Up to three different probes are employed for the detection of each fungal species. The redundancy in the design of the assay should ensure unambiguous fungus identification even in the presence of mutations in individual target regions. The current set of hybridization oligonucleotides includes 75 species- and genus-specific probes which had been carefully tested for specificity by repeated analysis of multiple reference strains. To provide adequate sensitivity for clinical application, the assay includes amplification of the ITS2 region by a seminested PCR approach prior to hybridization of the amplicons to the probe panel using the Luminex technology. A variety of fungal pathogens were successfully identified in clinical specimens that included peripheral blood, samples from biopsies of pulmonary infiltrations, and bronchotracheal secretions derived from patients with documented invasive fungal infections. Our observations demonstrate that the Luminex-based technology presented permits rapid and reliable identification of fungal species and may therefore be instrumental in routine clinical diagnostics.

Identification of fungal species by fragment length analysis of the internally transcribed spacer 2 region.

The rapid identification of fungal pathogens in clinical specimens is a prerequisite for timely onset of the most appropriate treatment. The aim of the present study was to develop a sensitive and rapid method for the species-specific identification of clinically relevant fungi. We employed fluorescent polymerase chain reaction (PCR)-fragment length analysis of the highly variable internally transcribed spacer 2 (ITS2) region to identify individual fungal species by their specific amplicon sizes. The specificity of the technique was ascertained by the detailed analysis of 96 strains derived from 60 different human-pathogenic fungal species. To achieve adequate sensitivity for species identification in patients with invasive fungal infection, who often display very low pathogen loads in peripheral blood, the ITS2 region was amplified by semi-nested PCR prior to amplicon-length analysis. Serial specimens from 26 patients with documented fungal infections were investigated. The fungal pathogens identified included different Aspergillus and Candida species, Rhizopus oryzae and Fusarium oxysporum. Fragment length analysis of the ITS2 region upon amplification by semi-nested PCR permits the sensitive identification of fungal species. The technique can be readily implemented in routine diagnostics.

Changing pattern of candidaemia 2001-2006 and use of antifungal therapy at the University Hospital of Vienna, Austria.

A retrospective survey of candidaemia between 2001 and 2006 was performed at the University Hospital of Vienna, a 2200-bed centre with large organ transplantation and haematology-oncology units. The incidence rate of Candida spp. in blood cultures increased from 0.27 cases/1000 admissions in 2001 to 0.77 cases/1000 admissions in 2006 (p <0.005). The incidence of candidaemia caused by Candida albicans and by non-albicans Candida spp. both increased during this period; although there was a trend towards an increased incidence (37%) of non-albicans Candida spp., particularly Candida glabrata, in surgical wards, C. albicans remained the predominant pathogen (63%). In the haematology-oncology unit, C. albicans remained the leading pathogen (23/29 isolates, 79%), followed by Candida tropicalis and C. glabrata (2/29, 7% each), Candida sake and Candida lusitaniae (1/29, 3% each). The overall survival rate was 43.8%, ranging from 32.8% in 2004 to 63.6% in 2002. In total, 108 (33.2%) patients died within 4 weeks of the first isolation of Candida spp. from blood; 58 (54%) of these patients died within the first 7 days, and a further 34 patients died within the next 3 months. Fluconazole was used extensively (24 701.5 defined daily doses), followed by amphotericin B (8981.4 defined daily doses), during 2005. The consumption of antifungal agents increased continuously (p <0.05) because of increased use of voriconazole and caspofungin. Although the numbers of susceptible patients remained unchanged, the net increase in the number of cases of candidaemia warrants a re-evaluation of the risk-factors and the use of improved diagnostic procedures for invasive fungal infections.

Laboratory diagnosis and therapy of invasive fungal infections.

Diagnosing fungal infections remains a problem, particularly in the immunocompromised patient. Symptoms are mostly non-specific and colonization is difficult to distinguish from invasive disease. Existing diagnostic tools often lack sensitivity. Thus, the combination of various diagnostic tools is mandatory to allow earlier diagnosis of systemic fungal infections. Microscopy, culture based methods, antigen detection, and PCR may help to facilitate and accelerate the diagnosis. Galactomannan and glucan are two promising antigens that may be useful for early detection of the infection, but also for therapeutic monitoring. Sensitive and specific PCR assays to detect fungal DNA are an important part of the diagnostic approach. But extensive validation and standardization is strongly needed, before PCR assays can be used in a routine laboratory. The tremendous increase in invasive fungal infections has led to an increased interest in new antifungal agents and the field of antifungal chemotherapy evolved even more rapidly than diagnostic assays. The development of less toxic formulations of amphotericin B, the introduction of improved azoles and the availability of the echinocandins are opening new opportunities for the treatment of fungal infections. However, continuing efforts in the laboratory and well-designed clinical trials are still needed.

PCR based identification and discrimination of agents of mucormycosis and aspergillosis in paraffin wax embedded tissue.

BACKGROUND: Invasive fungal infections are often diagnosed by histopathology without identification of the causative fungi, which show significantly different antifungal susceptibilities. AIMS: To establish and evaluate a system of two seminested polymerase chain reaction (PCR) assays to identify and discriminate between agents of aspergillosis and mucormycosis in paraffin wax embedded tissue samples. METHODS: DNA of 52 blinded samples from five different centres was extracted and used as a template in two PCR assays targeting the mitochondrial aspergillosis DNA and the 18S ribosomal DNA of zygomycetes. RESULTS: Specific fungal DNA was identified in 27 of 44 samples in accordance with a histopathological diagnosis of zygomycosis or aspergillosis, respectively. Aspergillus fumigatus DNA was amplified from one specimen of zygomycosis (diagnosed by histopathology). In four of 16 PCR negative samples no human DNA was amplified, possibly as a result of the destruction of DNA before paraffin wax embedding. In addition, eight samples from clinically suspected fungal infections (without histopathological proof) were examined. The two PCR assays detected a concomitant infection with Absidia corymbifera and A fumigatus in one, and infections with Rhizopus arrhizus and A fumigatus in another two cases. CONCLUSIONS: The two seminested PCR assays described here can support a histopathological diagnosis of mucormycosis or aspergillosis, and can identify the infective agent, thereby optimising antifungal treatment.

In vitro activity of fosfomycin alone and in combination with amoxicillin, clarithromycin and metronidazole against Helicobacter pylori compared with combined clarithromycin and metronidazole.

In order to evaluate the suitability of fosfomycin in combination with other agents for the treatment of Helicobacter pylori infections, the susceptibility profiles of 65 H. pylori strains were determined against multiple antimicrobial agents and combinations thereof using the agar dilution method. For fosfomycin alone, the range of minimum inhibitory concentration (MIC) results and the MICs at which 50% and 90% of strains were inhibited were 0.5-32 microg/ml and 2 and 4 microg/ml, respectively. For the combination of fosfomycin with amoxicillin, clarithromycin or metronidazole, the means calculated for the minimum and maximum fractional inhibitory concentration index were 0.70-1.17 and 1.15-2.03, respectively, suggesting partial synergy or indifference in the majority of strains. The combination of clarithromycin and metronidazole showed synergistic activity against 14 of 28 H. pylori strains tested. The in vitro activity results suggest the combination of fosfomycin with either amoxicillin or clarithromycin may be a promising alternative for the treatment of H. pylori infection. However, the clinical efficacy of these regimens remains to be investigated.

Routine use of a commercial test, GLABRATA RTT, for rapid identification of Candida glabrata in six laboratories.

When evaluated in six clinical laboratories from six countries with 1,174 fresh isolates, including 715 Candida glabrata and 459 non-C. glabrata strains, GLABRATA RTT (Fumouze Diagnostics, Levallois Perret, France) yielded an overall sensitivity and an overall specificity of 95.8 and 98.9%, respectively. The results were consistent from one laboratory to another. The five false-positive results corresponded to C. parapsilosis (n = 2), C. tropicalis, C. guilliermondii, and C. lusitaniae. GLABRATA RTT allows a rapid, cost-effective, and reliable presumptive identification of C. glabrata.

[Antigen detection in invasive aspergillosis and candidosis: the Austrian experience]. / Erfahrungen zum Antigennachweis bei invasiver Aspergillose und Candidose in Osterreich.

In order to assess the performance of different methods for the detection of fungal antigens, data of five Austrian hospitals were evaluated. The enzyme immunoassay (EIA) Platelia Aspergillus Antigen (Bio-Rad, USA) was used for the diagnosis of invasive aspergillosis and compared with clinical data. It could be shown that it is more effective to investigate at least two sequential sera than only one sole serum. For several high-risk patients diagnosis could be improved or confirmed by investigating other body fluids such as cerebrospinal fluid or bronchoalveolar lavage fluid in addition to sera. For invasive Candida infections several diagnostic kits detecting antigens are commercially available. The performance of the EIA Platelia Candida Antigen (Bio-Rad, USA), the latexagglutination test Cand-Tec (Ramco, USA) and the detection of (1-3)-Beta-D-Glucan using the test kit Glucatell (CAPE COD, USA) were evaluated. The detection of (1-3)-Beta-D-Glucan by means of Glucatell showed the highest sensitivity as all sera of 15 patients with invasive candidosis showed positive results. The other tests showed positive and negative results independently of the occurrence of an invasive infection. However, the number of tested sera is too small to decide which test is the most appropriate for establishing an early and definite diagnosis. Prospective studies in combination with clinical data are still needed for definite evaluation.

Application of blood-based polymerase chain reaction for detection of Chlamydia pneumoniae in acute respiratory tract infections.

The aim of this study was to investigate whether blood-based polymerase chain reaction could serve as a diagnostic tool to identify individuals with acute respiratory Chlamydia pneumoniae infection. Respiratory specimens and peripheral blood mononuclear cells of 58 patients were analyzed using nested polymerase chain reaction and cell culture. Fifteen patients were polymerase chain reaction-positive for Chlamydia pneumoniae. Nine patients were positive in only the respiratory specimen; two in both the respiratory and blood sample (time intervals between onset of symptoms and sample collection, 3-10 days and 3-4 weeks, respectively); and four in only the blood sample. Detection of Chlamydia pneumoniae DNA in peripheral blood mononuclear cells does not seem to be a suitable marker for acute respiratory Chlamydia pneumoniae infection.