Comparison of four automated nucleic acid extraction platforms for the recovery of DNA from Aspergillus fumigatus

Invasive aspergillosis is a significant cause of morbidity and mortality within at-risk groups. Directed antifungal chemotherapy, guided by effective screening algorithms that incorporate reliable and validated molecular assays, reduces the morbidity associated with empirical administration and allows earlier diagnosis. The efficient extraction of nucleic acid from Aspergillus fumigatus is the main limiting factor for successful Aspergillus PCR from clinical specimens. With the integration of automated extraction platforms, assessment of the suitability of these platforms for specific targets is of paramount importance. In this study, four extraction robots (Applied Biosystems MagMAX, bioMérieux easyMAG, Qiagen EZ1 and Roche MagNA Pure LC) were evaluated for their ability to extract clinically significant levels of A. fumigatus from blood. All of the platforms could detect 10(1) c.f.u. ml(-1) from EDTA whole blood, although only the easyMAG, EZ1 and MagNA Pure had 100 % reproducibility at this level. Despite good analytical sensitivity, contamination associated with the easyMAG platform excluded its use for diagnostic Aspergillus PCR. The EZ1 and MagNA Pure platforms demonstrated equivalent high sensitivity and negative predictive values (97.4-100 %), essential for screening assays.

Scedosporium prolificans osteomyelitis following penetrating injury: A case report

Scedosporium prolificans are opportunistic moulds that can cause mycetoma following penetrating injuries. This fungus is more virulent than other species and treatment options are limited. Here we describe the first known case in the UK of S. prolificans osteomyelitis, in a 4 year old following penetrating injury. Successful outcome with limb salvage and foot function is achieved after repeated surgical debridement, and combination chemotherapy with voriconazole/terbinafine.

Therapeutic drug monitoring (TDM) of antifungal agents: guidelines from the British Society for Medical Mycology

The burden of human disease related to medically important fungal pathogens is substantial. An improved understanding of antifungal pharmacology and antifungal pharmacokinetics-pharmacodynamics has resulted in therapeutic drug monitoring (TDM) becoming a valuable adjunct to the routine administration of some antifungal agents. TDM may increase the probability of a successful outcome, prevent drug-related toxicity and potentially prevent the emergence of antifungal drug resistance. Much of the evidence that supports TDM is circumstantial. This document reviews the available literature and provides a series of recommendations for TDM of antifungal agents.

Infection in cancer and transplantation

The range of opportunist pathogens in cancer and transplant patients continues to increase. New treatment modalities and forms of immunosuppression following transplantation have improved survival from the underlying disease but can lead to prolonged immunosuppression and increased risk of infection. NICE guidelines for the management of neutropenic sepsis are now available but have aroused some controversy, particularly over the recommendation for quinolone prophylaxis in high-risk patient groups.

In addition to neutropenia, long-term defects in cell-mediated immunity are exposing patients to risk of chronic, viral, protozoal and fungal infection. Advances in diagnostic techniques have the potential to improve management and limit unnecessary empirical treatment, allowing a move towards a diagnosis-driven strategy. However, interpreting the clinical validity and utility of some of these assays can be difficult, particularly for low-prevalence infection where the positive predictive value of any diagnostic test is likely to be low and prompt empirical antibacterial therapy is still indicated in neutropenic patients.

Predictors of large and small for gestational age birthweight in offspring of women with gestational diabetes mellitus

AIM

To identify predictors of large and small for gestational age in women with gestational diabetes mellitus.

METHODS

A retrospective audit of clinical data analysed for singleton births in women diagnosed with gestational diabetes by Australasian Diabetes in Pregnancy Society guidelines from 1994 to 2009. Exclusions were: incomplete data, delivered at < 36 weeks gestation and/or last recorded weight > 4 weeks pre-delivery. We assessed: pre-pregnancy BMI, ethnicity, total maternal weight gain, weight gain before and after treatment initiation for gestational diabetes, HbA(1c) at gestational diabetes presentation and treatment modality (diet or insulin) and smoking. Birthweight was assessed using customized percentile charts (large for gestational age > 90th; small for gestational age < 10th percentile). Multiple regression analyses were undertaken; statistical significance was p < 0.05.

RESULTS

There were 1695 women first seen at (mean ± sd) 28.1 ± 5.3 weeks gestation (range 6-39). Ethnic mix was South-East Asian 36.7%, Middle Eastern 27.6%, European 22.4%, Indian/Pakistani 8.6%, Samoan 1.9%, African 1.5% and Maori 1.1%. Therapy was diet 69.1% and insulin 30.9%. Mean total weight gain was 12.3 ± 6.1 kg, the majority (10.6 ± 6.0 kg), gained before dietary intervention. There were 7.9% small for gestational age and 15.2% large for gestational age births. Significant independent large for gestational age predictors were: weight gain before intervention, pre-pregnancy BMI, weight gain after intervention and treatment type, but not HbA1c or smoking. Significant small for gestational age predictors were: weight gain before intervention, weight gain after intervention, but not pre-pregnancy BMI, HbA(1c) or smoking.

CONCLUSION

Conventional treatment for gestational diabetes mellitus concentrates on management of blood glucose levels. The trends identified here emphasize the need to also address pregnancy weight gain stratified by pre-pregnancy BMI.

Association of mannose-binding lectin deficiency with acute invasive aspergillosis in immunocompromised patients

BACKGROUND

Invasive aspergillosis is a devastating infection with attributable mortality of 40% despite antifungal therapy. In animal models of aspergillosis, deficiency of mannose-binding lectin (MBL), a pattern recognition receptor that activates complement, is a susceptibility factor. MBL deficiency occurs in 20%-30% of the population. We hypothesized that MBL deficiency may be a susceptibility factor for invasive aspergillosis in humans.

METHODS

Serum MBL concentrations were measured by enzyme-linked immunosorbent assay in 65 patients with proven or probable acute invasive aspergillosis and 78 febrile immunocompromised control subjects. MBL concentrations and the frequency of MBL deficiency were compared.

RESULTS

The median serum MBL level was significantly lower in patients with aspergillosis than in control subjects (281 ng/mL vs 835 ng/mL; P = .007). MBL deficiency (MBL concentration, <500 ng/mL) was significantly more common in patients with aspergillosis than control subjects (62% vs 32%; P < .001). Frequency of MBL deficiency was similar among patients with aspergillosis irrespective of response to antifungal therapy (P = .10).

CONCLUSIONS

This study is the first, to our knowledge, to show an association between MBL deficiency and acute invasive aspergillosis in humans. Further study is required to investigate the causal nature of this association and to define whether diagnosis of MBL deficiency may identify immunocompromised patients at increased risk of invasive aspergillosis.

Disseminated protothecosis following traumatic Hickman line removal in a patient with leukaemia

Human protothecosis is a rare infection caused by a member of the genus Prototheca, an ubiquitous alga. Traumatic inoculation can cause infections in the immunocompetent host while disseminated infection is mainly seen in patients with compromised immunity. We report here an unusual case of disseminated infection in a cancer patient. Traumatic removal of a Hickman catheter in this patient, led to the development of a severe skin and subcutaneous tissue infection with algaemia. These infections are often indolent and difficult to treat, with paucity of information available as to guidelines for diagnosis and effective therapeutic options.

Bacteraemia following single-stage percutaneous dilatational tracheostomy

OBJECTIVE

Surgical tracheostomy in critically ill adults has largely been replaced by physicians performing percutaneous dilatational tracheostomy (PDT) at the bedside. Complications associated with this technique include haemorrhage, wound infection, barotrauma, false passage, ruptured tracheal ring and bacteraemia. Prophylactic antibiotics are not generally used with this procedure, however the incidence of bacteraemia following PDT has not been extensively studied.

DESIGN

Prospective observational study.

SETTING

Adult intensive care unit of a university medical centre.

METHODS

Peripheral venous blood cultures were obtained immediately before and after PDT in 118 consecutive patients. Surveillance cultures of potential respiratory pathogens were also recorded using routine non-directed broncholalveolar lavage.

RESULTS

Forty-three female and 75 male patients underwent PDT. Fifty-seven patients (48.3%) were not receiving antibiotics on the day of PDT, whilst the remaining 61 individuals (51.7%) were on antibiotic therapy at the time of the procedure. Bacteraemia following PDT occurred in six out of 113 patients (5.3%), five of which occurred in patients not receiving antibiotics (9.2%). Unexpected bacteraemia (positive pre-and post PDT blood cultures) was identified in five patients, two of whom were on antibiotic therapy.

CONCLUSION

The incidence of bacteraemia following a single stage PDT was similar to other manipulations of the aerodigestive tract such as intubation, insertion of an LMA or tooth brushing. We suggest that routine antibiotic prophylaxis is unnecessary for this procedure.

An update on the molecular diagnosis of invasive fungal disease

Despite improvements in medical technology, the definitive diagnosis of invasive fungal disease (IFD) is limited. The prevalence of disease is relatively low but many cases are undiagnosed. With the diagnosis of proven IFD dependent on histopathology or culture from a sterile site, clinicians have become more reliant on noninvasive nonculture diagnostic techniques. PCR technology has the capacity to overcome classical limitations but has its own drawbacks, resulting from an incomplete knowledge of the various disease processes and subsequent shortage of optimal specimens, leading to a lack of methodological standardization. This review will consider the general principles and limitations of fungal PCR before discussing genus-specific PCR applications. It is by no means a systematic review of the literature but is intended, where possible, to provide the reader with access to assays with proficient clinical performance.

Use of PCR for diagnosis of invasive aspergillosis: systematic review and meta-analysis

A systematic review and meta-analysis was done on the use of PCR tests for the diagnosis of invasive aspergillosis. Data from more than 10000 blood, serum, or plasma samples obtained from 1618 patients at risk for invasive aspergillosis were retrieved from 16 studies. Overall, the mean diagnostic odds ratios (DORs) of PCR for proven and probable cases were similar whether two consecutive positive samples were required to define positivity (DOR 15.97 [95% CI 6.83-37.34]) or a single positive PCR test was required (DOR 16.41 [95% CI 6.43-41.88]). Sensitivity and specificity of PCR for two consecutive positive samples were 0.75 (95% CI 0.54-0.88) and 0.87 (95% CI 0.78-0.93), respectively, and if only a single positive sample was required, these values were 0.88 (95% CI 0.75-0.94) and 0.75 (95% CI 0.63-0.84), respectively. Whereas specificity based on a single positive test was significantly lower (p=0.027) than two positive tests, the sensitivity and DOR did not differ significantly. A single PCR-negative result is thus sufficient to exclude a diagnosis of proven or probable invasive aspergillosis. However, two positive tests are required to confirm the diagnosis because the specificity is higher than that attained from a single positive test. Populations at risk varied and there was a lack of homogeneity of the PCR methods used. Efforts are underway to devise a standard for Aspergillus sp PCR for screening, which will help enable formal validation of PCR and estimate its use in patients most likely to benefit.

Antifungal susceptibility of Candida species using the Clinical and Laboratory Standards Institute disk diffusion and broth microdilution methods

There are conflicting reports on the agreement between the Clinical and Laboratory Standards Institute disk diffusion (M44-A) and reference broth microdilution (M27-A) methods for determination of antifungal susceptibility of yeasts. The antifungal susceptibility of 541 yeasts, the majority of which were from the oral cavity, was determined using these two methods and the accuracy of the disk diffusion method assessed for clinical testing of various Candida species. Of the strains tested, Candida albicans predominated (390 out of 541). The classification of susceptibility determined by the disk diffusion method was largely in concordance with that obtained using the broth dilution method, regardless of species within Candida genus. The overall observed agreement between these two methods was 94.7% for fluconazole and 96.7% for voriconazole was with a 'very major' discrepancy level of 1.5% and 1.7% respectively. This study demonstrates a strong agreement of the simple disk diffusion method with the more labour intensive 'gold standard' broth microdilution method. These findings would support the use of the disk diffusion method in a routine mycology service.

A consensus on fungal polymerase chain reaction diagnosis?: a United Kingdom-Ireland evaluation of polymerase chain reaction methods for detection of systemic fungal infections

The limitations of classical diagnostic methods for invasive fungal infections (IFIs) have led to the development of molecular techniques to aid in the detection of IFIs. Despite good published performance, interlaboratory reproduction of these assays is variable, and no consensus has been reached for an optimal method. This publication describes the first multicenter study of polymerase chain reaction methods, for the detection of Aspergillus and Candida species, currently used in the UK and Ireland by distribution and analysis of multiple specimen control panels. All three Candida methods were comparable, achieving a satisfactory level of detection (10 cfu), and the method of preference was dependent on the requirements of the particular laboratory. The results for the five Aspergillus assays were more variable, but two methods (2Asp and 4Asp) were superior (10(1) conidia). Formally, the overall performances of the two Aspergillus assays were comparable (kappa statistic = 0.77). However, on the Roche LightCycler, there was a clear sample-type effect that greatly reduced the detection limit of the 4Asp method when testing whole blood samples. Therefore, the preferred Aspergillus method relied on the amplification platform available to the user. This study represents the initial process to achieve a consensus method for the diagnosis of IFIs.

A case of sepsis caused by Acidovorax

This report documents a case of sepsis caused by a recently recognized environmental organism and demonstrates the pathogenicity of this bacterium in the clinical setting.

Prospective Study of Amphotericin B Formulations in Immunocompromised Patients in 4 European Countries

BACKGROUND

Amphotericin B is a widely used broad-spectrum antifungal agent, despite being associated with significant adverse events, including nephrotoxicity.

METHODS

The present prospective study collected data on outcomes for 418 adult patients treated consecutively with polyenes in hematology and oncology wards in 20 hospitals in Europe.

RESULTS

Patients initially received amphotericin B deoxycholate (62% of patients), liposomal amphotericin B (27%), or other lipid formulations of amphotericin B (11%). Of the patients initially treated with amphotericin B deoxycholate, 36% had therapy switched to lipid formulations of amphotericin B, primarily because of increased serum creatinine levels (in 45.7% of patients) or other amphotericin B-attributable adverse events (in 41.3% of patients). Nephrotoxicity, which was defined as a > or = 50% increase in the serum creatinine level, developed in 57% of patients with normal kidney function at baseline. Predictors of nephrotoxicity included formulation type and duration of treatment. Compared with patients without nephrotoxicity, patients with nephrotoxicity had a higher mortality rate (24%), and their mean length of stay in the hospital was prolonged by 8.6 days. Slight increases in the serum creatinine level (i.e., > or = 50%) were associated with a significantly longer stay in the hospital. Severe nephrotoxicity (i.e., a > or = 200% increase in the serum creatinine level) was a significant predictor of death, as were severe underlying medical conditions and documented fungal infection.

CONCLUSION

This prospective study confirmed that, in European hospitals, amphotericin B formulations have a major influence on the length of stay in the hospital and nephrotoxicity-associated mortality.

The evolution and evaluation of a whole blood polymerase chain reaction assay for the detection of invasive aspergillosis in hematology patients in a routine clinical setting

BACKGROUND

Invasive aspergillosis (IA) is associated with high mortality. Successful outcome with treatment is linked to early diagnosis. The utility of classic diagnostic methods, however, is limited.

METHODS

To aid in the diagnosis of IA, we retrospectively assessed our diagnostic service, using real-time polymerase chain reaction (PCR) and galactomannan sandwich enzyme-linked immunosorbent assay (ELISA).

RESULTS

A total of 203 patients at risk of invasive fungal infection were screened by PCR, and 116 of the patients were also tested by ELISA. The patient group comprised 176 patients with hematological malignancy and 28 control patients with evidence of invasive candidal infection. Consensus European Organisation for Research and Treatment of Cancer and Mycoses Study Group criteria were used to classify fungal infection, which, by definition, excluded the PCR result. The PCR method was sensitive (up to 92.3% sensitivity) and specific (up to 94.6% specificity) and had good agreement with the galactomannan ELISA (76.7%) and high-resolution computed tomography scan results.

CONCLUSIONS

A negative PCR result can be used to rule out IA and to limit the need for empirical antifungal therapy; thus, it has a role in diagnosing IA infections, especially in combination with antigen testing. PCR-positive cases classified as "false positives" regularly reflect the limitations of classic microbiological procedures or restricted use of consensus clinical methods employed to classify infection.

Aspergillus PCR - Platforms, strengths and weaknesses

PCR is a useful tool to aid in the diagnosis of invasive aspergillosis. However, it is essential that an optimal method be agreed to allow inclusion in future consensus diagnosis criteria. It should be used in conjunction with other methods (e.g., galatomannan (GM) ELISA and high resolution computed tomography (HRCT)) to enhance the opportunity for detection of this devastating infection. This manuscript will try to highlight the benefits but mainly the limitations occurring throughout the process of molecular testing. It will focus on real-time methods although many of the points will be relevant to block-based amplification.