A nationwide survey of clinical laboratory methodologies for fungal infections

Candida auris: The recent emergence of a multidrug-resistant fungal pathogen

Candida auris is an emerging multidrug-resistant yeast that causes serious invasive infections with high mortality. It was first discovered in 2009, and since then, individual cases or outbreaks have been reported from over 20 countries on five continents. Controlling C. auris is challenging for several reasons: (1) it is resistant to multiple classes of antifungals, (2) it can be misidentified as other yeasts by commonly available identification methods, and (3) because of its ability to colonize patients perhaps indefinitely and persist in the healthcare environment, it can spread between patients in healthcare settings. The transmissibility and high levels of antifungal resistance that are characteristic of C. auris set it apart from most other Candida species. A robust response that involves the laboratory, clinicians, and public health agencies is needed to identify and treat infections and prevent transmission. We review the global emergence, biology, challenges with laboratory identification, drug resistance, clinical manifestations, treatment, risk factors for infection, transmission, and control of C. auris.

Rapid Isolation and Concentration of Pathogenic Fungi Using Inertial Focusing on a Chip-Based Platform

Systemic Candida infections remain a leading cause of nosocomial infections in the United States and worldwide. Many challenges remain in achieving rapid, direct diagnosis of fungal bloodstream infections due to limitations of conventional diagnostic methods that continue to demonstrate poor sensitivity, prolonged culture times that lead to delayed treatment, and detection variability between tests that compromises result reproducibility. Despite advancements in technology, mortality, and cost of care presented by blood stream infection with Candida spp. (candidemia) continues to rise and there is an urgent need for the development of novel methods to accurately detect Candida species present within the blood. This is especially true when patients are infected with drug resistant strains of Candida where accurate and immediate therapeutic treatment is of the importance. This study presents a method of separating fungal cells from lysed blood using inertial forces applied through microfluidics in order to abbreviate the time required to achieve a diagnosis by mitigating the need to grow blood cultures. We found that C. albicans can segregate into a focused stream distinct from white blood cells isolated within the Inertial Fungal Focuser (IFF) after red blood cell lysis. As a result of the focusing process, the collected cells are also concentrated 2.86 times. The same IFF device is applicable to non-albicans species: Candida parapsilosis, Candida glabrata, and Candida tropicalis, providing both isolation from lysed blood and a reduction in solution volume. Thus, the devised platform provides a means to isolate medically significant fungal cells from blood and concentrate the cells for further interrogation.

Rapid simultaneous detection and identification of six species Candida using polymerase chain reaction and reverse line hybridization assay

The aim of this study was to develop and evaluate PCR based reverse line blot (RLB) hybridization assay for rapid detection of the most common Candida isolates from clinical specimens. A pair of universal primers targeting the ITS2 region of the gene from 28S rRNA to 5.8S rRNA was designed for PCR amplification of DNA from 6 Candida species (C. albicans, C. tropicalis, C. krusei, C. glabrata, C. parapsilosis, C. dubliniensis), the reverse primer was biotin labeled. PCR products, which were 302-441 bp length, were hybridized with 6 specific oligonucleotides probes immobilized on a nylon membrane. These 6 probes proved specific (they hybridized with only their target molecules). The assay was shown to be sensitive in detecting yeast to a concentration of 10 CFU/ml. This method was used to test 100 isolates and 200 vaginal swabs. The results agreed with those of culture for all but 3 of 100 isolates. Sequencing was performed on these 3 samples and confirmed that the culture results were inaccurate. Our results show the PCR-RLB positive rate (49%) is higher than culture (39%) and smear microscopic screening (27%) (P<0.05). In conclusion, the PCR/RLB developed in this study is specific and offers increased sensitivity compared to culture for the detection of Candida species in swab specimens. Moreover, the improved detection of cases of polycandidal candidiasis is advantageous.

High-throughput identification of clinical pathogenic fungi by hybridization to an oligonucleotide microarray

Here we report the development of an oligonucleotide microarray method that can identify fungal pathogens in a single reaction. Specific oligonucleotide probes targeted to internal transcribed spacer 2 were designed and synthesized. Fungal DNA was amplified by universal primers, and the PCR product was hybridized with the oligonucleotide microarray. A series of specific hybridization profiles corresponding to species were obtained. The 122 strains of fungal pathogens, including standard and clinically isolated strains, used to test the specificity, stability, and sensitivity of the microarray system belonged to 20 species representing 8 genera. We found that the microarray system can successfully discriminate among the fungal pathogens to the species level, with high specificity and stability. The sensitivity was 15 pg/ml of DNA. This oligonucleotide microarray system represents a rapid, simple, and reliable alternative to conventional methods of identifying common clinical fungal isolates.

Species identification of medically important fungi by use of real-time LightCycler PCR

Invasive fungal infection has become a major cause of morbidity and mortality in immunocompromised patients. Rapid identification of pathogenic fungi to species level is critical for disease treatment. A real-time LightCycler assay aiming at rapid detection and species identification of pathogenic fungi from clinical isolates was developed. Template DNAs of different species were amplified and detected in real time by employing SYBR Green fluorescent dye. The target sequences for species-level detection were located between the 18S and 28S rDNA. Seven fungal species encountered frequently in the clinical setting, Candida albicans, Candida glabrata, Candida krusei, Candida parapsilosis, Candida tropicalis, Candida guilliermondii and Cryptococcus neoformans, could be discriminated by species-specific primers and confirmed by melting-curve analyses. The range of linearity was from 1 ng to 1 pg (microl(-1) water) and the sensitivity was 1 pg fungal DNA microl(-1). Identification by this real-time PCR method matched biochemical identification for all 58 clinical strains. Therefore, the method is simple, rapid and sensitive enough for detection and identification of several fungal species.

Antifungal susceptibility testing in teaching hospitals

BACKGROUND

An assessment of antifungal susceptibility testing (AST) has not been conducted since the introduction of the National Committee for Clinical Laboratory Standards (NCCLS) M27-A document.

OBJECTIVE

To determine AST practices in teaching hospitals.

METHODS

A questionnaire was mailed to the heads of 386 randomly assigned microbiology departments from teaching hospitals identified through the 2000 American Hospital Association Guide. Identifiers were used to delineate responders from nonresponders. A reminder letter was mailed 3 weeks after the initial mailing to all nonresponders. The hospital bed-size and number of inpatient days for respondents were obtained through the American Hospital Directory.

RESULTS

The questionnaire was returned by 171 (44.3%) institutions. The total and median (range) number of candida isolates were 137,088 and 8.5 (1-145)/1000 inpatient days for the year 2000, respectively. Approximately 1% (1300) of candida isolates, from predominantly blood specimens, underwent AST. AST was reported by 115 (67.2%) hospitals, with testing on site at 27 hospitals and off site for 88 hospitals. NCCLS methodology (80% broth microdilution) was used by 75% of the hospitals performing on-site AST. The median time to obtain AST results was significantly lower when testing was performed on site (3 d) compared with off site (7-10 d).

SUMMARY

A large number of candida bloodstream isolates undergoes AST annually. AST results are obtained sooner when performed on site compared with off site.

Rapid identification of pathogenic fungi directly from cultures by using multiplex PCR

A multiplex PCR method was developed to identify simultaneously multiple fungal pathogens in a single reaction. Five sets of species-specific primers were designed from the internal transcribed spacer (ITS) regions, ITS1 and ITS2, of the rRNA gene to identify Candida albicans, Candida glabrata, Candida parapsilosis, Candida tropicalis, and Aspergillus fumigatus. Another set of previously published ITS primers, CN4 and CN5, were used to identify Cryptococcus neoformans. Three sets of primers were used in one multiplex PCR to identify three different species. Six different species of pathogenic fungi can be identified with two multiplex PCRs. Furthermore, instead of using templates of purified genomic DNA, we performed the PCR directly from yeast colonies or cultures, which simplified the procedure and precluded contamination during the extraction of DNA. A total of 242 fungal isolates were tested, representing 13 species of yeasts, four species of Aspergillus, and three zygomycetes. The multiplex PCR was tested on isolated DNA or fungal colonies, and both provided 100% sensitivity and specificity. However, DNA from only about half the molds could be amplified directly from mycelial fragments, while DNA from every yeast colony was amplified. This multiplex PCR method provides a rapid, simple, and reliable alternative to conventional methods to identify common clinical fungal isolates.

Aspergillus species isolated from clinical specimens: suggested clinical and microbiological criteria to determine significance

OBJECTIVE: To test a case-definition score for its usefulness in the diagnosis of pulmonary aspergillosis and to determine microbiological criteria useful in assessing the significance of isolating Aspergillus species from lower respiratory tract specimens (LRTS). METHODS: With the exception of cystic fibrosis patients, all patients with Aspergillus isolated from LRTS were classified according to a clinical case-definition ratio as: (i) colonized patients; (ii) patients with isolates of undetermined significance; (iii) patients with proven or probable pulmonary aspergillosis. Retrospective review of pathology records led to the identification of additional patients with histologically compatible pulmonary aspergillosis. Microbiological variables were compared between aspergillosis and colonization groups. RESULTS: Seventy-six isolates of Aspergillus species were obtained from 73 patients. For patients with proven (n=2) or histologically compatible pulmonary aspergillosis (n=5), the case definition ratio was always higher than 0.3; no patient with proven disease was classified into the colonized group. Compared to patients considered to be colonized (n=26), patients with proven or probable pulmonary aspergillosis showed a significant difference in the total number of Aspergillus colonies cultured per episode. In addition, for bronchoalveolar lavage specimens, the mean number of Aspergillus colonies/agar plate was also significantly higher in the latter group. The sensitivity and specificity of Aspergillus spp. detection by culture of LRTS for proven or probable pulmonary aspergillosis was 35.7% and 70.4%, respectively. CONCLUSION: The case-definition ratio used in this study helps interpret the clinical significance of Aspergillus isolated from LRTS. Data for assessment should include the absolute number of colonies recovered from culture of any LRTS and, for bronchoalveolar lavage, the mean number of Aspergillus colonies per agar plate.

Detection of Aspergillus ribosomal RNA using biotinylated oligonucleotide probes

Aspergillosis continues to be a devastating disease entity that results in significant mortality in immunosuppressed patients. Rapid diagnosis is often required to initiate appropriate therapy. Although the histopathologist may be able to visualize fungal organisms in tissue specimens, the histology of Aspergillus species may overlap with a variety of fungi, so diagnosis often relies on fungal cultures that can take weeks to complete. Recently, an in situ hybridization assay targeting Aspergillus 5S ribosomal RNA (rRNA) was reported. This assay proved to be useful when fungal cultures were negative or not performed but when fungi compatible with Aspergillus species were identified in tissue sections. That study was performed to compare the probe described in the previous study (5S-1 probe) with two other probes specific for Aspergillus. Two customly designed 21- and 23-base oligonucleotide probes complementary to 5S (5S-2 probe) and 18S (18S-1 probe) rRNA of Aspergillus were synthesized and labeled with multiple biotin moieties at the 3' termini. By GenBank analysis, the sequence of the 18S-1 probe was shown to have 90% to 100% homology to Aspergillus fumigatus group, Aspergillus flavus, Aspergillus niger, Aspergillus terreus, Aspergillus parasiticus, Aspergillus tamarii, and Aspergillus glaucus group; the 5S-2 probe was homologous to Aspergillus flavus, Aspergillus niger, Aspergillus nidulans, Aspergillus awamori, and Aspergillus wentii. In situ hybridization was performed on 43 cases of Aspergillus infection including 41 localized aspergillomas in the lung, brain, sinonasal tract, and ear, and 2 cases of invasive aspergillosis involving pleura and soft tissue of the scapular region. The results were compared with those obtained using a previously reported 5S-1 probe. In situ hybridization was positive in 38, 38, and 40 cases with the 5S-1, 5S-2, and 18S-1 probes, respectively. The 18S-1 probe was most useful because of a wider detection spectrum. In situ hybridization for Aspergillus rRNA provides a useful means for rapidly and accurately identifying Aspergillus in tissues and may be useful if fungal organisms suggestive of Aspergillus species are present but if cultures are negative or have not been performed.

Treatment and serological studies of an Italian case of penicilliosis marneffei contracted in Thailand by a drug addict infected with the human immunodeficiency virus

A case of disseminated penicilliosis marneffei, the first to be diagnosed in Italy, is described in a male HIV-positive drug addict. The patient had visited Thailand several times in the two years prior to his hospitalization. The presenting signs were fever, productive cough, facial skin papules and pustules, nodules on both thumbs and oropharyngeal candidiasis. Penicillium marneffei was isolated from a series of blood specimens with the lysis centrifugation procedure. Septate, yeast-like cells were observed in histological sections of the nodules and sputum smears. The patient was treated for 6 weeks with amphotericin B (total dosage 1,400 mg) and flucytosine (150 mg/kg/die) for the first 3 weeks. Prompt clinical improvement and sterilization of all biological specimens were attained. Itraconazole was administered as maintenance therapy (400 mg/die for the first month and 200 mg afterward). During the follow-up period, no relapse was observed. The patient, however, did succumb to a variety of non-mycotic infections and died nine months after start of therapy. At autopsy, P. marneffei was not detected in his tissues. Serological studies were performed with a micro-immunodiffusion procedure using a mycelial culture filtrate antigen of P. marneffei. Sera taken early in the course of the disease gave positive antibody reactions. Whereas sera taken 3-5 months following therapy were negative. All known cases of penicilliosis marneffei in bamboo rats and in humans among the inhabitants and visitors to the endemic areas of P. marneffei in South East Asia and Indonesia are summarized.