Elaine McCulloch

Aspergillus PCR: one step closer to standardization.

ABSTRACT PCR has been used as an aid in the diagnosis of invasive aspergillosis for almost 2 decades. A lack of standardization has limited both its acceptance as a diagnostic tool and multicenter clinical evaluations, preventing its inclusion in disease-defining criteria. In 2006, the European Aspergillus PCR Initiative was formed. The aim of the initiative was to provide optimal standardized protocols for the widespread clinical evaluation of the Aspergillus PCR to determine its diagnostic role and allow inclusion in disease diagnosis criteria. Quality control panels were developed and circulated to centers for evaluation of the existing methodology before recommendations based on the initial results were proposed for further panels. The centers were anonymously classified as “compliant” or “noncompliant,” according to whether they had followed the proposed recommendations before the performance parameters were determined and meta-regression analysis was performed. Most PCR amplification systems provided similar detection thresholds, although positivity was a function of the fungal burden. When PCR amplification was combined with DNA extraction, 50% of the centers failed to achieve the same level of detection. Meta-regression analysis showed positive correlations between sensitivity and extraction protocols incorporating the proposed recommendations and the use of bead beating, white cell lysis buffer, and an internal control PCR. The use of elution volumes above 100 μl showed a negative correlation with sensitivity. The efficiency of the Aspergillus PCR is limited by the extraction procedure and not by PCR amplification. For PCR testing of whole blood, it is essential that large blood volumes (≥3 ml) be efficiently lysed before bead beating to disrupt the fungal cell and performance of an internal control PCR to exclude false negativity. DNA should be eluted in volumes of <100 μl.

Evaluation of Aspergillus PCR Protocols for Testing Serum Specimens

ABSTRACT A panel of human serum samples spiked with various amounts of Aspergillus fumigatus genomic DNA was distributed to 23 centers within the European Aspergillus PCR Initiative to determine analytical performance of PCR. Information regarding specific methodological components and PCR performance was requested. The information provided was made anonymous, and meta-regression analysis was performed to determine any procedural factors that significantly altered PCR performance. Ninety-seven percent of protocols were able to detect a threshold of 10 genomes/ml on at least one occasion, with 83% of protocols reproducibly detecting this concentration. Sensitivity and specificity were 86.1% and 93.6%, respectively. Positive associations between sensitivity and the use of larger sample volumes, an internal control PCR, and PCR targeting the internal transcribed spacer (ITS) region were shown. Negative associations between sensitivity and the use of larger elution volumes (≥100 μl) and PCR targeting the mitochondrial genes were demonstrated. Most Aspergillus PCR protocols used to test serum generate satisfactory analytical performance. Testing serum requires less standardization, and the specific recommendations shown in this article will only improve performance.

Pseudomonas aeruginosa and their small diffusible extracellular molecules inhibit Aspergillus fumigatus biofilm formation

Aspergillus fumigatus is often isolated from the lungs of cystic fibrosis (CF) patients, but unlike in severely immunocompromised individuals, the mortality rates are low. This suggests that competition from bacteria within the CF lung may be inhibitory. The purpose of this study was to investigate how Pseudomonas aeruginosa influences A. fumigatus conidial germination and biofilm formation. Aspergillus fumigatus biofilm formation was inhibited by direct contact with P. aeruginosa, but had no effect on preformed biofilm. A secreted heat-stable soluble factor was also shown to exhibit biofilm inhibition. Coculture of P. aeruginosa quorum-sensing mutants (PAO1:ΔLasI, PAO1:ΔLasR) did not significantly inhibit A. fumigatus biofilms (52.6-58.8%) to the same extent as that of the PA01 wild type (22.9-30.1%), both by direct and by indirect interaction (P<0.001). Planktonic and sessile inhibition assays with a series of short carbon chain molecules (decanol, decanoic acid and dodecanol) demonstrated that these molecules could both inhibit and disrupt biofilms in a concentration-dependent manner. Overall, this suggests that small diffusible and heat-stable molecules may be responsible for the competitive inhibition of filamentous fungal growth in polymicrobial environments such as the CF lung.

Azole Resistance of Aspergillus fumigatus Biofilms Is Partly Associated with Efflux Pump Activity

ABSTRACT This study investigated the phase-dependent expression and activity of efflux pumps in Aspergillus fumigatus treated with voriconazole. Fourteen strains were shown to become increasingly resistant in the 12-h (16- to 128-fold) and 24-h (>512-fold) phases compared to 8-h germlings. An Ala-Nap uptake assay demonstrated a significant increase in efflux pump activity in the 12-h and 24-h phases (P < 0.0001). The efflux pump activity of the 8-h germling cells was also significantly induced by voriconazole (P < 0.001) after 24 h of treatment. Inhibition of efflux pump activity with the competitive substrate MC-207,110 reduced the voriconazole MIC values for the A. fumigatus germling cells by 2- to 8-fold. Quantitative expression analysis of AfuMDR4 mRNA transcripts showed a phase-dependent increase as the mycelial complexity increased, which was coincidental with a strain-dependent increase in azole resistance. Voriconazole also significantly induced this in a time-dependent manner (P < 0.001). Finally, an in vivo mouse biofilm model was used to evaluate efflux pump expression, and it was shown that AfuMDR4 was constitutively expressed and significantly induced by treatment with voriconazole after 24 h (P < 0.01). Our results demonstrate that efflux pumps are expressed in complex A. fumigatus biofilm populations and that this contributes to azole resistance. Moreover, voriconazole treatment induces efflux pump expression. Collectively, these data may provide evidence for azole treatment failures in clinical cases of aspergillosis.

Phase-dependent antifungal activity against Aspergillus fumigatus developing multicellular filamentous biofilms

OBJECTIVES Aspergillus fumigatus undergoes morphological transition throughout its growth and development. These changes have direct implications for the effectiveness of antifungal treatment. Here we report the in vitro antifungal activity of voriconazole, amphotericin B and caspofungin against three specific phases of multicellular development of A. fumigatus. METHODS A. fumigatus conidia were propagated for 8, 12 and 24 h prior to antifungal challenge. The resultant activity of the three agents tested was determined using an XTT reduction assay to assess both endpoint and time-kill susceptibility profiles. RESULTS Endpoint susceptibility testing demonstrated a time-dependent decrease in efficacy for all three antifungal agents as the complexity of the A. fumigatus hyphal structure developed. Overall, amphotericin B exhibited the best spectrum of activity at each phase of growth, but was comparable to voriconazole against germinated conidial growth (8 h). Later, both voriconazole and caspofungin were ineffective against complex mycelial structures (12 and 24 h). Time-kill studies demonstrated that amphotericin B was significantly more efficacious at reducing A. fumigatus metabolism than both voriconazole and caspofungin for all three growth phases examined, most notably after 1 h of drug exposure (P < 0.001). CONCLUSIONS Overall, the data presented demonstrate that treatment of actively growing A. fumigatus cells with antifungal agents is more efficacious than treating mature structures in vitro. Amphotericin B was consistently more effective against each phase and displayed rapid effects, and therefore may be a suitable option for managing patient groups at risk from aspergillosis infections.

Critical Stages of Extracting DNA from Aspergillus fumigatus in Whole-Blood Specimens

ABSTRACT A standardized protocol for extracting DNA from Aspergillus fumigatus has been proposed by the European Aspergillus PCR Initiative (EAPCRI). Using meta-regression analysis, the EAPCRI showed certain stages of the process to be critical to providing a satisfactory analytical sensitivity. The study investigated each step of the EAPCRI protocol by elimination and monitored the influence on Aspergillus PCR performance.

Antifungal treatment affects the laboratory diagnosis of invasive aspergillosis

Aims The purpose of this study was to investigate the performance of non-invasive diagnostic tests such as galactomannan enzyme immunoassay and quantitative PCR in the early diagnosis of invasive aspergillosis (IA), and how these tests are impacted upon by the use of different classes of antifungal agents in an in-vivo model of IA. Methods A standardised rat inhalation model of IA was used to examine the effects of an azole, posaconazole, a polyene, amphotericin B and an echinocandin caspofungin. Daily blood samples were collected for subsequent analysis using a commercially available galactomannan assay and an inhouse qPCR assay. Results No significant differences were observed in the CE/g of Aspergillus fumigatus in the lungs of each group. qPCR was statistically more sensitive than galactomannan for both the early detection of infected controls (p=0.045) and for overall detection (p=0.018). However, antifungal treatment significantly reduced the overall sensitivity of qPCR (p=0.020); these effects were due to posaconazole and caspofungin. In the latter stages of infection (days 4 and 5) there were no significant differences in the numbers of infections detected by galactomannan and qPCR; however, the antifungal class used caused significant qualitative differences (p=0.041). Galactomannan showed improved detection in posaconazole-treated animals. Conclusions Previous exposure to antifungal therapy must be considered when interpreting either qPCR or galactomannan-based IA diagnostics as this study has shown that individual classes of antifungal agents impact upon the dynamics of antigen and DNA release into the circulation.

Efflux pumps may play a role in tigecycline resistance in Burkholderia species

The purpose of this study was to investigate the role of multidrug resistance efflux pumps in relation to decreased susceptibility to tigecycline in clinical isolates of Burkholderia cepacia complex (BCC). The role of efflux pumps was analysed using the efflux pump inhibitor (EPI) MC-207,110. Minimum inhibitory concentrations (MICs) were determined for each strain against tigecycline alone and in the presence of 64 mg/L MC-207,110. The effect of efflux pump inhibition on the susceptibility of BCC isolates to tigecycline was assessed by a checkerboard titration assay. Ala-Nap uptake assay was performed to determine efflux pump activity in different strains. The checkerboard titration assay showed that the MIC decreased with increasing concentrations of EPI. MICs for tigecycline in the clinical isolates ranged between 8 mg/L and 32 mg/L, whereas in the presence of MC-207,110, MICs decreased significantly (range <0.125-1.0mg/L; 16 to >256 times reduction). Efflux pump activity was shown to be greatest in strains with the highest MIC and vice versa. In conclusion, BCC possess efflux pumps that influence their resistance to tigecycline. Use of an inhibitor of these pumps restored sensitivity to the antibiotic. Therefore, a combination of tigecycline and EPI to augment its efficacy may present an attractive therapeutic option.

Don’t throw your blood clots away: use of blood clot may improve sensitivity of PCR diagnosis in invasive aspergillosis

Background: The diagnosis of invasive aspergillosis (IA) remains challenging and frequently is not made until after death. Histopathological examination remains central to confirmation of diagnosis but often requires invasive procedures to obtain tissue for the examination. Detection of aspergillus DNA by quantitative PCR (qPCR) offers the potential for earlier diagnosis due to higher sensitivity, but PCR in clinical use is poorly reproducible, with different centres reporting variable results and often using different extraction and analytical methods. Aims: To optimise the performance of aspergillus PCR as a diagnostic modality. Methods: A rat inhalation model of invasive aspergillosis was used to optimise the methodology of diagnostic aspergillus PCR. Infected animals were terminally bled at 4 days post-infection; samples of EDTA blood, serum and the residual clot were pooled for subsequent analysis. DNA was extracted from each fraction using a variety of methods and an optimised qPCR reaction using an Aspergillus fumigatus primer set performed. Results: Significantly more aspergillus DNA was detected from the clot than EDTA and serum samples. Enzymatic and mechanical pretreatment reduced the yield of fungal DNA. There was some evidence that the average Ct values were greater for the EZ1 BioRobot than the MagNA Pure automated extractor, but this did not reach statistical significance at the 5% level (p = 0.078). Conclusions: Automated extraction from the clot present in a blood sample will increase DNA yield and improve the diagnostic sensitivity of the test.

Improved early diagnosis of Pseudomonas aeruginosa by real-time PCR to prevent chronic colonisation in a paediatric cystic fibrosis population

Early detection of Pseudomonas aeruginosa in children with cystic fibrosis is hampered by the need to process a sub-optimal specimen type, namely cough swabs, which are known to have a lower positive yield than sputa or more invasive samples. This delay in the detection of low levels of P. aeruginosa could potentially result in the loss of an opportunity to initiate early aggressive antibiotic therapy and result in chronic colonisation, with a poorer overall prognosis. Quantitative real-time PCR (qPCR) offers an opportunity to increase the detection rate of P. aeruginosa compared to traditional culture techniques. This study examined 500 cough swabs and 42 sputum samples from paediatric patients and showed that detection of P. aeruginosa could be increased in both sample types by 100% and 45% respectively. Overall the sensitivity was 100% and specificity of 58% when compared to culture as a gold standard. These results although initially promising require careful consideration both from a treatment and infection control standpoint as the significance of detection of very low levels of P. aeruginosa is unclear.