Evaluation of nucleic acid sequencing of the D1/D2 region of the large subunit of the 28S rDNA and the internal transcribed spacer region using SmartGene IDNS [corrected] software for identification of filamentous fungi in a clinical laboratory.

Filamentous fungal infections have recently increased because of the increasing numbers of immunocompromised hosts. In this study, we evaluated DNA sequencing of the D1/D2 region of the large subunit of the 28S ribosomal RNA gene and the internal transcribed spacer (ITS) region using SmartGene (SG; SmartGene Inc., Raleigh, NC) for the identification of a broad range of commonly encountered filamentous fungi. The SG proofreaders were used to upload, align, and edit fragments, and the resultant sequences were interpreted using the quality-controlled SG database. The results were compared with reference identifications using conventional phenotypic methods or ITS DNA sequences obtained from GenBank if phenotypic identifications were inconclusive. A total of 146 clinical isolates were included in this study, representing 49 different genera. The overall agreements of the D1/D2 and the ITS sequencing methods to reference identification were 97.2% (95% CI, 93.1% to 98.9%) and 97.7% (95% CI, 92.8% to 99.4%), respectively. Of the 146 isolates, 18 (12.3%) did not amplify using the ITS universal primers after repeated attempts and, therefore, could not be sequenced using this target. Correct identification was achieved for 100% (95% CI, 97.4% to 100%) of the isolates when applying both the D1/D2 and ITS targets. In summary, DNA sequencing using SG software provides a rapid, accurate, and reliable tool for the identification of filamentous fungi in a clinical laboratory.

Evaluation of the detection of melanin by the Fontana-Masson silver stain in tissue with a wide range of organisms including Cryptococcus.

It is not uncommon for surgical pathologists to encounter yeast and yeast-like organisms in tissue sections, and correct identification is imperative for guiding therapy. The Fontana-Masson silver stain for detecting melanin has been accepted as a relatively specific stain for diagnosing cryptococcosis in tissue based on few studies with limited numbers of organisms. This study was designed to test the value of the Fontana-Masson silver by investigating a large collection of tissues with infections that may mimic cryptococcosis. Cases of cryptococcosis and other infections that can morphologically mimic it were identified in the pathology archives of The Johns Hopkins Hospital and The Armed Forces Institute of Pathology. Overall, Fontana-Masson silver was positive in 25 (56%) of 45 cases, including infections caused by Cryptococcus neoformans (9/9), Coccidioides immitis (7/7), Blastomyces dermatitidis (4/10), Paracoccidioides brasiliensis (2/2), Lacazia loboi (1/1), and Rhinosporidium seeberi (1/1). The percentage of organisms staining varied widely, from less than 1% to 100%. Fontana-Masson silver was negative in all infections caused by Histoplasma capsulatum (n = 10), Histoplasma duboisii (n = 1), Sporothrix schenckii (n = 1), and the alga genus Prototheca (n = 2). Fontana-Masson silver was 100% sensitive for cryptococcosis. The specificity was low, however, with 5 of 9 noncryptococcal species being positive in some cases. These results need to be confirmed and extended to other isolates and species but it is clear that many organisms in the morphological differential diagnosis of cryptococcosis can be Fontana-Masson silver stain positive. Accordingly, results of the Fontana-Masson silver stain, especially a positive, should be interpreted cautiously and only in the context of the organism's morphological features and host factors.

Prevalence and risk factors for recovery of filamentous fungi in individuals with cystic fibrosis.

BACKGROUND: Filamentous fungi are frequently recovered from respiratory cultures of individuals with CF. METHODS: A CF cohort database was utilized to determine filamentous fungal prevalence and risk factors. RESULTS: The prevalence of filamentous fungal isolation increased from 2.0% in 1997 to 28.7% in 2007. The odds of isolating filamentous fungi during a quarter was greater in CF adults [p<0.001], during chronic oral antibiotic use [p=0.002] and increased with each 10% drop in FEV(1) percent predicted [p=0.005], while inhaled corticosteroids surprisingly decreased the likelihood [p=0.012]. The direction of these effects persisted after excluding individuals with ABPA. A sub-analysis determined older age [p=0.019] and use of inhaled antibiotics [p=0.011] were independent risk factors for onset of fungal colonization. CONCLUSIONS: This study suggests that isolation of filamentous fungi in CF at JHH has increased and risk factors include older age, decreased lung function, and chronic oral antibiotics.

Primary treatment of zygomycosis with liposomal amphotericin B: analysis of 28 cases.

Lipid formulations of amphotericin B are increasingly used in lieu of deoxycholate amphotericin B for primary treatment of zygomycosis, but little is known about the efficacy of the former antifungal in treating this fungal disease. We therefore undertook an analysis of a case series of all patients with zygomycosis who received L-AMB for primary antifungal therapy in five major mid-Atlantic medical centers. Among the categories of variables studied were demographics, methods of diagnosis, microbiology, sites of infection, global responses, and survival. The median patient age was 44 years and 71% were male. Immunosuppressive hematological disorders (54%) were the most common underlying condition. Pulmonary disease constituted 50% of infections, sinus infection 29%, and cutaneous disease 18%. Members of the genus Rhizopus were the most common recovered agents. Success as defined by complete or partial positive response was noted in 32% of the cases. Concomitant surgery was performed in 46% of the cases, with similar response rates (31%). Overall survival was 39%. L-AMB was effective as primary therapy in only some patients in this cohort of highly immunocompromised individuals with invasive zygomycosis underscoring the importance of host response and the need for further advances for treatment of this lethal infection.

The epidemiology of Candida colonization and invasive candidiasis in a surgical intensive care unit where fluconazole prophylaxis is utilized: follow-up to a randomized clinical trial.

OBJECTIVE: To determine whether Candida glabrata colonization and invasive candidiasis (IC) increased among critically ill surgical patients 3 years after the introduction of fluconazole prophylaxis to a surgical intensive care unit (SICU). SUMMARY BACKGROUND DATA: Fluconazole prophylaxis has been shown in randomized clinical trials to reduce the occurrence of candidiasis in some patient populations, including high-risk SICU patients. One such trial was performed in The Johns Hopkins Hospital SICU in 1998. Whether the epidemiology of Candida colonization and IC has changed in SICUs where fluconazole prophylaxis is routinely utilized has not been adequately studied. METHODS: We conducted a prospective, observational study of subjects admitted for > or = 3 days to the SICU of a large, urban, academic medical center, where fluconazole prophylaxis had been utilized for approximately 3 years. Surveillance fungal cultures of rectal/fecal swabs, urine, and endotracheal aspirates were performed on admission to the SICU, once weekly, and upon discharge from the SICU. Demographic and clinical data were collected. C. glabrata colonization and IC prevalence among patients in the prospective cohort were compared with the prevalence among SICU patients enrolled in the 1998 clinical trial of fluconazole for the prevention of candidiasis that was performed at the same institution. RESULTS: C. glabrata colonization was not significantly more common among patients in the 2003 cohort as compared with patients in the 1998 trial (adjusted odds ratio [OR]: 0.90, 95% confidence interval [CI]: 0.57-1.41). Patients with IC in the 2003 cohort were not more likely than those in the 1998 trial to have IC due to C. glabrata (adjusted OR: 1.93, 95% CI: 0.20-18.98), while patients with IC in the 2003 cohort were less likely than patients in the 1998 trial to have acquired IC in the ICU (adjusted OR: 0.08, 95% CI: 0.009-0.82). CONCLUSIONS: There was no increase in C. glabrata colonization or in the proportion of IC due to C. glabrata after a 3-year period of routine fluconazole prophylaxis for selected SICU patients.

Identification of Candida nivariensis and Candida bracarensis in a large global collection of Candida glabrata isolates: comparison to the literature.

We analyzed 1,598 Candida glabrata isolates for the presence of the cryptic species Candida nivariensis and Candida bracarensis. Both species were very rare in this collection (0.2% prevalence), despite the number of isolates analyzed and the global distribution of the isolates. We saw no associated antifungal resistance in C. nivariensis.

Identification of Candida albicans and Candida glabrata within 1.5 hours directly from positive blood culture bottles with a shortened peptide nucleic acid fluorescence in situ hybridization protocol.

Candida albicans and Candida glabrata can be identified in blood culture bottles within 2.5 h using peptide nucleic acid fluorescence in situ hybridization. A 1.25-h protocol was compared to the standard with 40 positive (clinical and spiked) blood culture bottles tested in batches of 5. All C. albicans (15) and C. glabrata (16) isolates, alone or mixed, were identified correctly using both protocols, whereas 18 isolates (five other species) were negative by both protocols. This shortened method will significantly reduce the time to identification.

Production of white colonies on CHROMagar Candida medium by members of the Candida glabrata clade and other species with overlapping phenotypic traits.

We hypothesized that species of the Candida glabrata clade and species with phenotypic traits that overlap those of C. glabrata would produce white colonies on CHROMagar Candida medium. Of 154 isolates (seven species) tested, C. bracarensis, C. nivariensis, C. norvegensis, C. glabrata, and C. inconspicua produced white colonies; the Pichia fermentans group and C. krusei did not. Many of these species are difficult to identify phenotypically; white colonies may signal the need for the use of molecular approaches.

An atypical case of fatal zygomycosis: simultaneous cutaneous and laryngeal infection in a patient with a non-neutropenic solid prostatic tumor.

We describe what we believe is the first reported case of simultaneous highly invasive cutaneous and laryngopharyngeal zygomycosis in a non-neutropenic, nondiabetic but immunosuppressed patient with prostate cancer. An invasive fungal process was not suspected until late in the patient's hospital course; when it was, a tracheotomy and direct laryngoscopic biopsies were performed. Unresectable invasive zygomycosis with Rhizopus rhizopodiformis was diagnosed. The patient was managed with liposomal amphotericin B initially and later with palliative medical therapy until he died. This case emphasizes the need for a rapid and specific diagnosis with timely introduction of appropriate antifungal management, particularly now that voriconazole is frequently used as empiric prophylaxis against aspergillosis in high-risk patients.

Multicenter evaluation of the Candida albicans/Candida glabrata peptide nucleic acid fluorescent in situ hybridization method for simultaneous dual-color identification of C. albicans and C. glabrata directly from blood culture bottles.

We evaluated the performance of the Candida albicans/Candida glabrata peptide nucleic acid fluorescent in situ hybridization (PNA FISH) method, a rapid two-color assay for detection of C. albicans and C. glabrata, in a multicenter study. The assay is designed for use directly from positive blood culture bottles in a FISH format. Intact, fixed cells are labeled fluorescent green (C. albicans) or fluorescent red (C. glabrata) by rRNA hybridization of fluorophore-labeled PNA probes. Results are available <3 h after cultures signal positive. An evaluation of 197 routine blood culture bottles newly positive for yeast by Gram staining was performed at five hospitals. The sensitivities of detection for C. albicans, and C. glabrata were 98.7% (78/79) and 100% (37/37), respectively, and the specificity for both components of the assay was 100% (82/82). The assay was also evaluated with 70 fungal reference strains and was challenged in the BacT/ALERT microbiological detection system with spiked blood culture bottles. These results support the use of the assay for rapid, simultaneous identification of C. albicans and C. glabrata in positive blood culture bottles. This rapid assay may aid in the selection of initial antifungal drugs, leading to improved patient outcomes.

Candida bracarensis detected among isolates of Candida glabrata by peptide nucleic acid fluorescence in situ hybridization: susceptibility data and documentation of presumed infection.

Molecular taxonomic studies have revealed new Candida species among phenotypically delineated species, the best example being Candida dubliniensis. This study was designed to determine the occurrence of two new molecularly defined species, Candida bracarensis and Candida nivariensis, which are closely related to and identified as Candida glabrata by phenotypic assays. A total of 137 recent clinical isolates of C. glabrata identified by phenotypic characteristics was tested with C. bracarensis and C. nivariensis species-specific peptide nucleic acid fluorescence in situ hybridization probes. Three of 137 (2.2%) isolates were positive with the C. bracarensis probe, whereas the control strain, but none of the clinical isolates, was positive with the C. nivariensis probe. D1/D2 sequencing confirmed the identification of the three isolates as representing C. bracarensis. Clinically, one C. bracarensis isolate was recovered from a presumed infection, a polymicrobial pelvic abscess in a patient with perforated diverticulitis. The other two isolates were recovered from two adult oncology patients who were only colonized. C. bracarensis was white on CHROMagar Candida, had variable API-20C patterns that overlapped with C. nivariensis and some C. glabrata isolates, and had variable results with a rapid trehalose assay. Interestingly, an isolate from one of the colonized oncology patients was resistant to fluconazole, itraconazole, voriconazole, and posaconazole in vitro. In summary, C. bracarensis was detected among clinical isolates of C. glabrata, while C. nivariensis was not. One C. bracarensis isolate causing a presumed deep infection was recovered, and another isolate was azole resistant. Whether clinical laboratories should identify C. bracarensis will require more data.

Use of peptide nucleic acid-fluorescence in situ hybridization for definitive, rapid identification of five common Candida species.

We investigated a 2.5-h peptide nucleic acid-fluorescence in situ hybridization (PNA-FISH) assay with five Candida species-specific probes to identify Candida colonies and compared it to standard 2-h to 5-day phenotypic identification methods. Suspensions were made and slides were prepared and read for fluorescence per the manufacturer's instructions. Sensitivity was 99% (109/110), and specificity was 99% (129/130). PNA-FISH can rapidly identify those Candida species isolated most frequently.

Isolation of Trichophyton violaceum and Trichophyton soudanense in Baltimore, Maryland.

Tinea capitis is of public health importance because of its transmissibility. Trichophyton violaceum and Trichophyton soudanense, which are common causes of tinea capitis in parts of Africa and West Asia, have only rarely been reported to cause dermatophytoses in the United States. We identified 24 patients with 25 positive cultures for T. violaceum or T. soudanense that were processed in a single hospital laboratory in Baltimore, Maryland, between 1 January 2000 and 30 June 2006. Most patients for whom clinical information was available had tinea capitis. There was a marked increase in the isolation of these organisms between the period from 2000 to 2002 and the period from 2003 to 2006, possibly associated with changes in immigration to the Baltimore metropolitan area. The changing epidemiology of this transmissible fungal infection not only is of public health interest as an example of the introduction of a "new" pathogen to an area where it traditionally was not endemic but also is of clinical and microbiological importance given reports suggesting an increasing incidence of tinea capitis in some areas and increasing clinical failure rates of current therapies.

Rapid identification of ascomycetous yeasts from clinical specimens by a molecular method based on flow cytometry and comparison with identifications from phenotypic assays.

This study was designed to compare the identification of ascomycetous yeasts recovered from clinical specimens by using phenotypic assays (PA) and a molecular flow cytometric (FC) method. Large-subunit rRNA domains 1 and 2 (D1/D2) gene sequence analysis was also performed and served as the reference for correct strain identification. A panel of 88 clinical isolates was tested that included representatives of nine commonly encountered species and six infrequently encountered species. The PA included germ tube production, fermentation of seven carbohydrates, morphology on corn meal agar, urease and phenoloxidase activities, and carbohydrate assimilation tests when needed. The FC method (Luminex) employed species-specific oligonucleotides attached to polystyrene beads, which were hybridized with D1/D2 amplicons from the unidentified isolates. The PA identified 81 of 88 strains correctly but misidentified 4 of Candida dubliniensis, 1 of C. bovina, 1 of C. palmioleophila, and 1 of C. bracarensis. The FC method correctly identified 79 of 88 strains and did not misidentify any isolate but did not identify nine isolates because oligonucleotide probes were not available in the current library. The FC assay takes approximately 5 h, whereas the PA takes from 2 h to 5 days for identification. In conclusion, PA did well with the commonly encountered species, was not accurate for uncommon species, and takes significantly longer than the FC method. These data strongly support the potential of FC technology for rapid and accurate identification of medically important yeasts. With the introduction of new antifungals, rapid, accurate identification of pathogenic yeasts is more important than ever for guiding antifungal chemotherapy.

Relationship between metabolism and biomass of medically important zygomycetes.

Little is known about the relationships between metabolic activity and fungal biomass or time of incubation for medically important fungal pathogens. Understanding these relationships may be especially relevant for rapidly growing organisms, such as zygomycetes. A range of inocula of five clinical isolates of zygomycetes (one each of Rhizopus oryzae,Rhizopus microsporus, Cunninghamella bertholletiae, Mucor circinelloides and Absidia corymbifera) were incubated for 6, 8, 12, 24 and 48 h, after which hyphal mass was assessed spectrophotometrically and metabolic activity was measured using various concentrations of XTT and menadione. Both linear regression and the Boltzmann sigmoid model were used and compared for description of relationships between metabolic activity, biomass and time of incubation. Modeling was further applied to eleven additional zygomycete isolates. The relationships of biomass or metabolic activity as a function of time of incubation were well described with the Boltzmann sigmoid model. The latter was superior to linear regression in describing the relationship between metabolic activity and fungal biomass. For all isolates of zygomycetes, increases in metabolic activity preceded increases in biomass. Inter-species differences in growth patterns were observed, with Rhizopus microsporus and Mucor spp. reaching the plateau of growth earlier compared to other species. These findings on the temporal relationship and inter-species differences of hyphal growth and metabolic activity for zygomycetes may be useful in the design and interpretation of in vitro studies of these emerging pathogens.

The association between anatomic site of Candida colonization, invasive candidiasis, and mortality in critically ill surgical patients.

We evaluated whether the likelihood of developing invasive candidiasis (IC) differed depending upon the anatomic site of Candida colonization in 182 surgical intensive care unit (SICU) patients who participated in a randomized trial of fluconazole to prevent candidiasis. We also determined the impact of Candida colonization of different anatomic sites on all-cause SICU and hospital mortality. A total of 2851 surveillance fungal cultures collected from 5 anatomic sites were analyzed. There was a statistically significant difference in the frequency of IC comparing patients with and without urinary (13.2% versus 2.8%, P = .02), respiratory (8.0% versus 1.2%, P = .04), and rectum/ostomy (8.4% versus 0%, P = .01) colonization. Patients with negative rectum/ostomy cultures and patients with both negative urine and respiratory tract cultures did not develop IC. Candiduria detected at any time in the SICU was independently associated with SICU mortality (odds ratio, 2.86; 95% confidence interval, 1.05-7.74). Surveillance fungal cultures of particular anatomic sites may help differentiate patients at higher risk of developing IC from those at low risk.

Phenotypic switching in Candida lusitaniae on copper sulfate indicator agar: association with amphotericin B resistance and filamentation.

Candida lusitaniae is an opportunistic yeast pathogen that has the ability to develop resistance to amphotericin B (AmB). The mechanism(s) for this resistance is not well understood, although there are data supporting mutations in sterol pathways and other data supporting phenotypic switching (PS). The goal of this study was to determine whether C. lusitaniae has a PS system and to characterize any phenotypes, including any changes in AmB MICs. When 10(4) CFU of an AmB-resistant (MIC of 16 to 32 microg/ml) clinical strain was plated on yeast-peptone-dextrose (YPD) agar with 1 mM CuSO(4), three colony colors were observed: light brown (LB) >> dark brown (DB) > white (W), similar to the result for Candida glabrata. Switching did occur with high AmB resistance (MIC of 256 microg/ml) being associated with W, whereas LB and DB colonies had MICs of 2 to 8 microg/ml and 2 to 16 microg/ml, respectively. Filamentation (pseudohyphae) was associated with DB colonies. All phenotypes occurred spontaneously with greater frequency ( approximately 10(-2) to 10(-4)) than spontaneous mutations, and all phenotypes were reversible, fulfilling the two PS criteria. High AmB MICs were always associated with W colonies but not with all W colonies. Detection of PS on YPD-CuSO(4) is also similar to that in Candida glabrata, and we hypothesize that this is due to similarities in metallothionein gene expression. Phenotypic switching represents a key strategy in C. lusitaniae that confers a selective advantage during environmental challenges, including the ability to switch to AmB resistance.

Triazole cross-resistance among Candida spp.: case report, occurrence among bloodstream isolates, and implications for antifungal therapy.

Candida spp. are common causes of bloodstream infections among hospitalized patients. Fluconazole (FLC) remains a first-line therapy for candidemia; and voriconazole (VRC), an expanded-spectrum triazole, was recently approved for the treatment of candidemia in nonneutropenic patients. In vitro studies have suggested that VRC has potent activity against Candida spp. with reduced susceptibilities to FLC. We present a case report of invasive candidiasis and candidemia due to a Candida glabrata isolate that developed resistance to all currently available triazole antifungals after a course of FLC treatment. This case prompted us to determine the frequency of cross-resistance among bloodstream Candida isolates collected during a recent 12-month period at a large, academic medical center. FLC MICs were determined for 125 of 153 isolates (81.7%). Thirty of 125 isolates (24%) were resistant or showed reduced susceptibilites to FLC (MICs >/= 16 microg/ml). When 28 of these 30 isolates were tested for their VRC susceptibilities, 9 (32%) had MICs that were >/=2 microg/ml. Five of these nine isolates were C. glabrata, two isolates were Candida tropicalis, one isolate was Candida albicans, and one isolate was Candida parapsilosis. All five Candida krusei isolates tested had VRC MICs

Use of green fluorescent protein-expressing Aspergillus fumigatus conidia to validate quantitative PCR analysis of air samples collected on filters.

This study used green fluorescent protein (GFP)-expressing Aspergillus fumigatus conidia to compare quantitative PCR (qPCR) enumeration with direct epifluorescent microscopic filter counts of conidia collected on filters in a test chamber. In separate experiments this study initially compared white versus fluorescent light microscopy for counting A. fumigatus conidia, then compared fluorescent microscopy counting of corresponding filter halves, and finally compared qPCR enumeration to counting by fluorescent light microscopy. The use of GFP-expressing conidia with epifluorescent microscopy yielded significantly higher conidia counts (p = 0.026, n = 41, mean of 4.1 conidia per counting field) and 40% faster counting times when compared to conventional counting using white light microscopy. GFP-expressing conidia were aerosolized in a test chamber and collected onto filters. Filters were divided in half and GFP-expressing conidia enumerated. There was no significant difference in the average conidia count per field between corresponding filter halves (p = 0.3, n = 9 filters, mean of 7.8 conidia per counting field). Thus, one filter half could be counted optically and would provide a reliable estimate of filter loading of the corresponding half, which could then be analyzed by qPCR. Filters (n = 38) loaded with GFP conidia in the aerosol chamber were divided in half and analyzed by either fluorescent microscopy or qPCR. The estimated filter loadings ranged from 15-30,000 conidia per filter. There was a linear relationship with a nearly 1:1 ratio between qPCR and direct microscopic estimates of filter loading (y = 1.06x + 404; R(2) = 0.91) showing that the outlined qPCR analysis method is in agreement with an external reference method and is reliable for enumerating A. fumigatus conidia collected on filters. The comparative data derived using GFP-expressing conidia confirmed that qPCR provides sensitive and accurate quantification of DNA from airborne conidia collected on filters.

Use of a commercial reagent leads to reduced germ tube production by Candida dubliniensis.

The goal of this study was to determine the factor(s) explaining our inability to detect Candida dubliniensis. When germ tube-positive yeasts were tested for C. dubliniensis, no C. dubliniensis was detected; however, 58 C. dubliniensis strains were detected when germ tube-negative Candida albicans strains were tested further. Since all 58 C. dubliniensis strains detected were germ tube negative, these data implied that false-negative germ tube tests occurred with germ tube solution (GTS; Remel, Lenexa, KS). All 41 known C. dubliniensis strains tested were negative with GTS, whereas 40 were positive with rabbit serum (RS; Sigma-Aldrich, St. Louis, MO). Results for C. albicans were equivalent in GTS and RS. In conclusion, GTS cannot be used for the detection of C. dubliniensis, and switching from yeast to hyphae in C. dubliniensis is more restricted than in C. albicans.