Molecular epidemiology of apparent outbreak of invasive aspergillosis in a hematology ward

A single-source nosocomial outbreak of Aspergillus flavus uncovered by genotyping

During construction work (2017-2019), an increase in Aspergillus flavus infections was noted among pediatric patients, the majority of whom were receiving amphotericin B prophylaxis. Microsatellite genotyping was used to characterize the outbreak. A total of 153 A. flavus isolates of clinical and environmental origin were included. Clinical isolates included 140 from 119 patients. Eight patients were outbreak-related patients, whereas 111 were outbreak-unrelated patients from Danish hospitals (1994-2023). We further included four control strains. Nine A. flavus isolates were from subsequent air sampling in the outbreak ward (2022-2023). Typing followed Rudramurthy et al.(S. M. Rudramurthy, H. A. de Valk, A. Chakrabarti, J. Meis, and C. H. W. Klaassen, PLoS One 6:e16086, 2011, https://doi.org/10.1371/journal.pone.0016086). Minimum spanning tree (MST) and discriminant analysis of principal components (DAPC) were used for cluster analysis. DAPC analysis placed all 153 isolates in five clusters. Microsatellite marker pattern was clearly distinct for one cluster compared to the others. The same cluster was observed in an MST. This cluster included all outbreak isolates, air-sample isolates, and additional patient isolates from the outbreak hospital, previously undisclosed as outbreak related. The highest air prevalence of A. flavus was found in two technical risers of the outbreak ward, which were then sealed. Follow-up air samples were negative for A. flavus. Microsatellite typing defined the outbreak as nosocomial and facilitated the identification of an in-hospital source. Six months of follow-up air sampling was without A. flavus. Outbreak-related/non-related isolates were easily distinguished with DAPC and MST, as the outbreak clone's distinct marker pattern was delineated in both statistical analyses. Thus, it could be a variant of A. flavus, with a niche ability to thrive in the outbreak-hospital environment.

IMPORTANCE

Aspergillus flavus can cause severe infections and hospital outbreaks in immunocompromised individuals. Although lack of isogeneity does not preclude an outbreak, our study underlines the value of microsatellite genotyping in the setting of potential A. flavus outbreaks. Microsatellite genotyping documented an isogenic hospital outbreak with an internal source. This provided the "smoking gun" that prompted the rapid allocation of resources for thorough environmental sampling, the results of which guided immediate and relevant cleaning and source control measures. Consequently, we advise that vulnerable patients should be protected from exposure and that genotyping be included early in potential A. flavus outbreak investigations. Inspection and sampling are recommended at any site where airborne spores might disperse from. This includes rarely accessed areas where air communication to the hospital ward cannot be disregarded.

Development and application of a qPCR-based genotyping assay for Ophidiomyces ophidiicola to investigate the epidemiology of ophidiomycosis

Ophidiomycosis (snake fungal disease) is an infectious disease caused by the fungus Ophidiomyces ophidiicola to which all snake species appear to be susceptible. Significant variation has been observed in clinical presentation, progression of disease, and response to treatment, which may be due to genetic variation in the causative agent. Recent phylogenetic analysis based on whole-genome sequencing identified that O. ophidiicola strains from the United States formed a clade distinct from European strains, and that multiple clonal lineages of the clade are present in the United States. The purpose of this study was to design a qPCR-based genotyping assay for O. ophidiicola, then apply that assay to swab-extracted DNA samples to investigate whether the multiple O. ophidiicola clades and clonal lineages in the United States have specific geographic, taxonomic, or temporal predilections. To this end, six full genome sequences of O. ophidiicola representing different clades and clonal lineages were aligned to identify genomic areas shared between subsets of the isolates. Eleven hydrolysis-based Taqman primer-probe sets were designed to amplify selected gene segments and produce unique amplification patterns for each isolate, each with a limit of detection of 10 or fewer copies of the target sequence and an amplification efficiency of 90-110%. The qPCR-based approach was validated using samples from strains known to belong to specific clades and applied to swab-extracted O. ophidiicola DNA samples from multiple snake species, states, and years. When compared to full-genome sequencing, the qPCR-based genotyping assay assigned 75% of samples to the same major clade (Cohen's kappa = 0.360, 95% Confidence Interval = 0.154-0.567) with 67-77% sensitivity and 88-100% specificity, depending on clade/clonal lineage. Swab-extracted O. ophidiicola DNA samples from across the United States were assigned to six different clonal lineages, including four of the six established lineages and two newly defined groups, which likely represent recombinant strains of O. ophidiicola. Using multinomial logistic regression modeling to predict clade based on snake taxonomic group, state of origin, and year of collection, state was the most significant predictor of clonal lineage. Furthermore, clonal lineage was not associated with disease severity in the most intensely sampled species, the Lake Erie watersnake (Nerodia sipedon insularum). Overall, this assay represents a rapid, cost-effective genotyping method for O. ophidiicola that can be used to better understand the epidemiology of ophidiomycosis.

Aspergillus terreus Species Complex

Infections due to Aspergillus species are an acute threat to human health; members of the Aspergillus section Fumigati are the most frequently occurring agents, but depending on the local epidemiology, representatives of section Terrei or section Flavi are the second or third most important. Aspergillus terreus species complex is of great interest, as it is usually amphotericin B resistant and displays notable differences in immune interactions in comparison to Aspergillus fumigatus. The latest epidemiological surveys show an increased incidence of A. terreus as well as an expanding clinical spectrum (chronic infections) and new groups of at-risk patients being affected. Hallmarks of these non-Aspergillus fumigatus invasive mold infections are high potential for tissue invasion, dissemination, and possible morbidity due to mycotoxin production. We seek to review the microbiology, epidemiology, and pathogenesis of A. terreus species complex, address clinical characteristics, and highlight the underlying mechanisms of amphotericin B resistance. Selected topics will contrast key elements of A. terreus with A. fumigatus. We provide a comprehensive resource for clinicians dealing with fungal infections and researchers working on A. terreus pathogenesis, aiming to bridge the emerging translational knowledge and future therapeutic challenges on this opportunistic pathogen.

Invasive Aspergillosis by Aspergillus flavus: Epidemiology, Diagnosis, Antifungal Resistance, and Management

Aspergillus flavus is the second most common etiological agent of invasive aspergillosis (IA) after A. fumigatus. However, most literature describes IA in relation to A. fumigatus or together with other Aspergillus species. Certain differences exist in IA caused by A. flavus and A. fumigatus and studies on A. flavus infections are increasing. Hence, we performed a comprehensive updated review on IA due to A. flavus. A. flavus is the cause of a broad spectrum of human diseases predominantly in Asia, the Middle East, and Africa possibly due to its ability to survive better in hot and arid climatic conditions compared to other Aspergillus spp. Worldwide, ~10% of cases of bronchopulmonary aspergillosis are caused by A. flavus. Outbreaks have usually been associated with construction activities as invasive pulmonary aspergillosis in immunocompromised patients and cutaneous, subcutaneous, and mucosal forms in immunocompetent individuals. Multilocus microsatellite typing is well standardized to differentiate A. flavus isolates into different clades. A. flavus is intrinsically resistant to polyenes. In contrast to A. fumigatus, triazole resistance infrequently occurs in A. flavus and is associated with mutations in the cyp51C gene. Overexpression of efflux pumps in non-wildtype strains lacking mutations in the cyp51 gene can also lead to high voriconazole minimum inhibitory concentrations. Voriconazole remains the drug of choice for treatment, and amphotericin B should be avoided. Primary therapy with echinocandins is not the first choice but the combination with voriconazole or as monotherapy may be used when the azoles and amphotericin B are contraindicated.

Usefulness of Aspergillus Galactomannan Antigen Testing and the Prediction of an Outbreak during Hospital Reconstruction

Objective This study retrospectively evaluated fungal dissemination due to hospital reconstruction and explored effective methods of predicting an outbreak. Methods Patients suspected of having invasive aspergillosis were tested for Aspergillus galactomannan antigen before and after reconstruction, and the mean values of three months of testing for positive patients were determined. The characteristics of patients with aspergillosis during this period were also assessed. Results Forty-five patients were positive for Aspergillus antigen (>0.5 cut-off index) from January 2013 to December 2014. Mean Aspergillus antigen values significantly increased following reconstruction (p<0.05). Three patients developed pneumonia due to Aspergillus and were diagnosed with "probable" invasive aspergillosis according to the European Organization for Research and Treatment of Cancer and the National Institute of Allergy and Infectious Diseases Mycoses Study Group (EORTC/MSG) criteria. We also discovered that the anteroom to contain dust was not prefabricated and a negative pressure system to remove dust was not used. After construction of the unit, no new cases of aspergillosis were diagnosed. Conclusion Many Aspergillus spores may be transiently floating during hospital reconstruction. Therefore, monthly surveillance with frequent serum galactomannan antigen testing to predict outbreaks is necessary. Surveillance of all patients in the hematology ward is especially important. Reconsideration of prophylactic antifungals may also be necessary during hospital reconstruction.

Genome Sequences of Three Strains of Aspergillus flavus for the Biological Control of Aflatoxin

Aflatoxin is a carcinogenic contaminant of many commodities that are infected by Aspergillus flavus. Nonaflatoxigenic strains of A. flavus have been utilized as biological control agents. Here, we report the genome sequences from three biocontrol strains. This information will be useful in developing markers for postrelease monitoring of these fungi.

Cardiothoracic surgical site phaeohyphomycosis caused by Bipolaris mould, multiple US states, 2008-2013: a clinical description

Bipolaris mould surgical site infections (SSIs) are exceedingly rare. We describe 21 cases of Bipolaris SSIs in pediatric and adult cardiothoracic surgery patients at ten hospitals in Texas, Arkansas, and Florida during 2008-2013. Median case-patient age was 55 years (range: 3 days-82 years), and 19 (90%) were male. Ten (48%) had coronary artery bypass or valve surgery, and seven (33%) had heart transplantation. Fifteen (71%) had more than one cardiothoracic procedure (median: 3, range: 1-11). Thirteen (62%) case-patients (all 5 pediatric patients, and 8 (50%) of 16 adult patients) had delayed sternal closure (chest closed >1 day [median = 8 days; range: 2-22] following the initial cardiothoracic procedure). Thirteen (62%) had mediastinitis. Median time from initial surgery to positive Bipolaris culture was 20 days (range: 6-497). Sixteen (76%) case-patients died.

The roles of sexual and asexual reproduction in the origin and dissemination of strains causing fungal infectious disease outbreaks

Sexual reproduction commonly refers to the reproductive process in which genomes from two sources are combined into a single cell through mating and then the zygote genomes are partitioned to progeny cells through meiosis. Reproduction in the absence of mating and meiosis is referred to as asexual or clonal reproduction. One major advantage of sexual reproduction is that it generates genetic variation among progeny which may allow for faster adaptation of the population to novel and/or stressful environments. However, adaptation to stressful or new environments can still occur through mutation, in the absence of sex. In this review, we analyzed the relative contributions of sexual and asexual reproduction in the origin and spread of strains causing fungal infectious diseases outbreaks. The necessity of sex and the ability of asexual fungi to initiate outbreaks are discussed. We propose a framework that relates the modes of reproduction to the origin and propagation of fungal disease outbreaks. Our analyses suggest that both sexual and asexual reproduction can play critical roles in the origin of outbreak strains and that the rapid spread of outbreak strains is often accomplished through asexual expansion.

Molecular characterization of Aspergillus infections in an Iranian educational hospital using RAPD-PCR method

OBJECTIVES

The nosocomial infections by Aspergillus species are associated with constructions and increased dust loads in hospital indoors. Our main object was to find the environmental sources of Aspergillus species causing hospital acquired infections.

MATERIALS AND METHODS

The clinical and environmental samplings were performed during 18 months from spring 2010 to summer 2011 in Imam educational hospital, Urmia, Iran. A morphological diagnosis was performed including microscopic characterization of isolated aspergillus from cultured specimens and polymerase chain reaction - restriction fragment length polymorphism (PCR-RFLP) for the identification in the level of species. Random amplified polymorphic DNA - PCR RAPD-PCR using random primers for rDNA gene was performed to compare Aspergillus isolates of clinical cases with the relevant environmental sources.

RESULTS

Use of RAPD method resulted various differential patterns, so that some Aspergillus isolates from the clinical and hospital indoor were completely matched (matched pairs) and some other Aspergillus isolates were not matched. In the case of matched pairs, Aspergillus niger and A. flavus isolated from broncoalveolar lavage and sinus discharge were relevant to those of air conditioner and walls surfaces, respectively.

CONCLUSION

The hospital sources for the Aspergillus clinical isolates included air condition and walls. RAPD-PCR analysis can play a trivial role to find the hospital sources of Aspergillus clinical isolates.

Hospital environment and invasive aspergillosis in patients with hematologic malignancy

BACKGROUND

To determine whether there is a correlation between sources of Aspergillus spores in a high-efficiency particulate air (HEPA)-filtered environment and nosocomial invasive aspergillosis (IA), we performed a detailed environmental assessment and case review.

METHODS

From April to October 2004, 626 bioaerosol samples, 1,257 surface samples, and 607 water samples were obtained from 74 HEPA-filtered air hospital rooms occupied by 458 patients with hematologic malignancies. Samples were collected prospectively from the room before and after cleaning within 1 hour of patient admission or discharge. Aspergillus spp was isolated from 21 surface samples and 46 bioaerosol samples. Interestingly, Aspergillus spp was not isolated from any water samples.

RESULTS

Aspergillus spp was isolated from 21 surface samples and 46 bioaerosol samples. Interestingly, Aspergillus spp were not isolated from any water samples. The majority (90%) of the positive bioaerosol samples had ≤ 10 colony-forming units of Aspergillus/m3 of air. Only 2 patients developed nosocomial IA. No correlations were found between Aspergillus species isolated from the hospital rooms and those causing IA.

CONCLUSION

The risk of hematologic malignancy patients acquiring nosocomial aspergillosis from water or HEPA-filtered air is very low.

[Quantitative assessment of fungal risk in the case of construction works in healthcare establishments: Proposed indicators for the determination of the impact of management precautions on the risk of fungal infection]

Construction works in healthcare establishments produce airborne fungal spores and considerably increase the risk of exposure of immunosuppressed patients. It is necessary to reinforce protective measures, or even to implement specific precautions, during this critical phase. The aim of these precautions is to protect both those areas, which are susceptible to dust, and patients at risk of a fungal infection particularly invasive aspergillosis. When construction works are planned in healthcare establishments, the first step consists in the characterisation of the environmental fungal risk and the second one in proposing risk management methods. It is then essential to establish impact indicators in order to evaluate the risk management precautions applied. The working group promoted by the French societies of medical mycology and hospital hygiene (SFMM & SF2H) details here both environmental and epidemiological impact indicators that can be used.

Phylogeography of the cosmopolitan fungus Aspergillus flavus: is everything everywhere?

Aspergillus flavus is one of the most common fungal eukaryotes on the planet. It is notorious for production of aflatoxins, for causing aspergillosis in humans and animals, and as an opportunistic pathogen of animals and plants. Its role in marine habitats is unclear. Until now, little phylogeographic structure has been detected for the species, except at very local scales, and it appears to fit the classic dictum of microbial biogeography: Everything is everywhere. Here we use genetic relationships among isolates to determine phylogeographic structure, mating types, and differences in preferences for: marine vs. terrestrial habitats, various substrates, and clinical vs. nonclinical environments. Phylogenetic relationships among isolates were estimated using amplified fragment length polymorphisms (AFLPs) and mating types were determined for a worldwide sample of A. flavus isolates from diverse substrates and geographic locations. All isolates composed a single population, with no significant differentiation of marine vs. terrestrial isolates, clinical vs. environmental isolates, or association with substrate or geographic origin. There was evidence for local dominance of a single clade, probably clonal in origin and short-lived. The proportion of mating types was 1:1, supporting the hypothesis of recombination in natural populations. However, a high proportion of clinical isolates were MAT1-1 (85%), suggesting that a gene linked to the MAT1-1 idiomorph could play a role in pathogenicity. This study suggests that a more appropriate description of the phylogeography of A. flavus is 'everything is everywhere, but not all the time.'

Molecular epidemiology of Aspergillus fumigatus: an in-depth genotypic analysis of isolates involved in an outbreak of invasive aspergillosis

We recently reported an outbreak of invasive aspergillosis in the major heart surgery unit of Hospital Gregorio Marañón, Madrid, Spain (T. Peláez, P. Muñoz, J. Guinea, M. Valerio, M. Giannella, C. H. W. Klaassen, and E. Bouza, Clin. Infect. Dis., in press). Aspergillus fumigatus was isolated from clinical samples from 10 patients admitted to the unit during the outbreak period (surgical wound invasive aspergillosis, n = 2; probable pulmonary invasive aspergillosis, n = 4; colonization, n = 4). In the study described here, we have studied the genotypic diversity of the A. fumigatus isolates found in the air and clinical samples. We used short tandem repeats of A. fumigatus (STRAf) typing to analyze the genotypes found in the 168 available A. fumigatus isolates collected from the clinical samples (n = 109) from the patients and from the environmental samples taken from the air of the unit (n = 59). The genotypic variability of A. fumigatus was higher in environmental than in clinical samples. Intrasample variability was also higher in environmental than in clinical samples: 2 or more different genotypes were found in 26% and 89% of clinical and environmental samples, respectively. We found matches between environmental and clinical isolates in 3 of the 10 patients: 1 patient with postsurgical invasive aspergillosis and 2 patients with probable pulmonary invasive aspergillosis. A total of 7 genotypes from 3 different patients and the air grouped together in 2 clusters. Clonally related genotypes and microvariants were detected in both clinical and environmental samples. STRAf typing proved to be a valuable tool for identifying the source of invasive aspergillosis outbreaks and for studying the genotypic diversity of clinical and environmental A. fumigatus isolates.

Nosocomial fungal infections: epidemiology, infection control, and prevention

Fungal infections are an increasing cause of morbidity and mortality in hospitalized patients. This article reviews the current epidemiology of nosocomial fungal infections in adult patients, with an emphasis on invasive candidiasis and aspergillosis. Recently published recommendations and guidelines for the control and prevention of these nosocomial fungal infections are summarized.

Aspergillosis: nosocomial or community-acquired?

Discrimination between nosocomial and community infections is important for investigation and prevention. Nosocomial and hospital-acquired infections require appropriate hospital control measures to avert additional cases. Nosocomial infections (NI) occur during hospitalization or are caused by microorganisms acquired during hospital stay. Such infections should not be evident when patients are admitted to the hospital. Furthermore, the definition of NI is based on epidemiological criteria, such as the time lapse between admission and onset, or microbiological criteria. This definition might be difficult to apply to invasive aspergillosis (IA) which often afflicts patients with severe immunosuppression or transplantation. Identification of the source may be difficult which could arise outside or inside the hospital. Another significant issue is the lack of valid and reproducible data on the incubation period. The incubation duration of IA is influenced by different individual or environmental determinants, including the severity of immunosuppression and air quality. The criteria of causality are also a means of discussing the contribution of hospital vs. community determinants of IA. The definition of nosocomial IA remains difficult. A better understanding of early events related to IA onset will help to prevent this disease for which the prognosis remains negative.

The first documented case of Aspergillus cardiac surgical site infection in Sweden: an epidemiology study using arbitrarily primed PCR

Here we report two rare cases of severe thoracic Aspergillus fumigatus infections after lung and heart surgery at the same thoracic intensive care unit at the same time. The main objective was to identify a possible source of transmission. With arbitrarily primed polymerase chain reaction a patient-to-patient transmission could rapidly be ruled out as the cause of the first documented case of aspergillosis after open-heart surgery in Sweden. Although no definitive source was identified, a genetically similar strain was found in a contaminated supply room.

[Aspergillus spp. in risk areas of transplant patients in a university hospital]

As a consequence of the increase in the number of immunocompromised patients, cases of aspergillosis, due to the opportunist character of this fungus, have increased considerably. Aspergillus fumigatus, Aspergillus flavus, and Aspergillus niger have been found in air and water samples of the majority of investigated hospitals. The aim of the present study was to investigate the presence of aspergilli in transplant patients areas at the Hospital Universitario of Bogotá, Colombia. Samples of air were collected using the MAS-100 Air Sampler from each of the investigated areas. A sample of 100 ml of water was also recovered from these areas. All samples were taken for triplicate and were cultured in 2% Sabouraud Dextrose Agar. The average of aspergilli in air samples was 2.8 CFU/l corresponding to A. flavus, A. niger, Aspergillus versicolor and Aspergillus terreus. In water samples, the average was 17.1 CFU/l corresponding to A. flavus and Aspergillus clavatus. Because potentially pathogenic Aspergillus species were found in the hospital areas were transplant patients are usually kept, active surveillance and a high clinical suspicion should be considered in those patients. Since Aspergillus infections haven't been found so far, a higher fungal load and other host factors might be needed to facilitate the infection.

Aspergillus flavus: an emerging non-fumigatus Aspergillus species of significance

Invasive aspergillosis is rare in immunocompetent people but contributes to significant morbidity and mortality in immunosuppressed patients. The majority (approximately 80%) of invasive Aspergillus infections is caused by Aspergillus fumigatus. The second most frequent (approximately 15-20%) pathogenic species is Aspergillus flavus and to a lesser extent, Aspergillus niger and Aspergillus terreus. Aspergillus flavus has emerged as a predominant pathogen in patients with fungal sinusitis and fungal keratitis in several institutions worldwide. To date, there has not been any publication exclusively reviewing the topic of A. flavus in the literature. This article reviews the microbiology, toxigenicity and epidemiology of A. flavus as well as describes the clinical characteristics, diagnosis and management of infections caused by this organism.

Reduction of Invasive Aspergillosis Incidence among Immunocompromised Patients after Control of Environmental Exposure

BACKGROUND

The objective of the study was to assess the impact of the relocation of an adult hematological intensive care unit on invasive aspergillosis (IA) incidence.

METHODS

A quasi-experimental study, including a control group and an intervention group that both underwent pretest and posttest evaluations, was conducted in the 3 adult hematological intensive care units (each composed of 14 single rooms) in a university hospital from 14 April 2005 through 1 February 2006. One of these units was relocated from the main building to an adjoining modular construction. In this unit, 4 rooms were equipped with laminar airflow before relocation; all rooms were equipped with positive pressure isolation after relocation. The 2 other units (control group), each containing 8 rooms with laminar airflow, did not undergo environmental modification. The diagnostic criteria for IA were based on the criteria of the European Organization for Research and Treatment of Cancer.

RESULTS

In total, 356 hospitalized patients were included. Of the 21 cases of IA, 18 were nosocomial, and 3 were of undetermined origin. In the relocated unit, the incidence of IA decreased from 13.2% (9 patients) before relocation to 1.6% (1 patient) after relocation (P=.018). Eight of the 9 patients with IA before relocation stayed in rooms without specific air treatment. The rate of IA did not change in the control group. Patient characteristics were similar in each unit before and after relocation.

CONCLUSION

We detected a straightforward association between environmental modification and decreased IA incidence, which emphasizes the use of an environmental strategy, including high-efficiency air filtration, in the prevention of IA.

Characterization of a novel gene for strain typing reveals substructuring of Aspergillus fumigatus across North America

Fifty-five epidemiologically linked Aspergillus fumigatus isolates obtained from six nosocomial outbreaks of invasive aspergillosis were subtyped by sequencing the polymorphic region of the gene encoding a putative cell surface protein, Afu3g08990 (denoted as CSP). Comparative sequence analysis showed that genetic diversity was generated in the coding region of this gene by both tandem repeats and point mutations. Each unique sequence in an outbreak cluster was assigned an arbitrary number or CSP sequence type. The CSP typing method was able to identify "clonal" and genotypically distinct A. fumigatus isolates, and the results of this method were concordant with those of another discriminatory genotyping technique, the Afut1 restriction fragment length polymorphism typing method. The novel single-locus sequence typing (CSP typing) strategy appears to be a simple, rapid, discriminatory tool that can be readily shared across laboratories. In addition, we found that A. fumigatus isolates substructured into multiple clades; interestingly, one clade consisted of isolates predominantly representing invasive clinical isolates recovered from cardiac transplant patients from two different outbreak situations. We also found that the A. fumigatus isolate Af293, whose genome has been sequenced, possesses a CSP gene structure that is substantially different from those of the other A. fumigatus strains studied here, highlighting the need for further taxonomic study.

Comparison of two highly discriminatory molecular fingerprinting assays for analysis of multiple Aspergillus fumigatus isolates from patients with invasive aspergillosis

Two highly discriminatory fingerprinting assays, short tandem repeat typing and amplified fragment length polymorphism (AFLP), were compared to determine the genetic relatedness between 55 isolates of Aspergillus fumigatus obtained from 15 different patients suffering from proven invasive aspergillosis. Both techniques showed that interpatient isolates belonged to different genotypes and that intrapatient isolates from deep sites were all of the same genotype. By contrast, multiple genotypes were found among isolates originating from respiratory samples. Both techniques have specific advantages and disadvantages. AFLP is more universally applicable, but short tandem repeat analysis offers better discriminatory power and should be the preferred method for standardizing typing of clinical isolates of Aspergillus fumigatus.

Nosocomial aspergillosis in outbreak settings

Nosocomial aspergillosis represents a serious threat for severely immunocompromised patients and numerous outbreaks of invasive aspergillosis have been described. This systematic review summarizes characteristics and mortality rates of infected patients, distribution of Aspergillus spp. in clinical specimens, concentrations of aspergillus spores in volumetric air samples, and outbreak sources. A web-based register of nosocomial epidemics (outbreak database), PubMed and reference lists of relevant articles were searched systematically for descriptions of aspergillus outbreaks in hospital settings. Fifty-three studies with a total of 458 patients were included. In 356 patients, the lower respiratory tract was the primary site of aspergillus infection. Species identified most often were Aspergillus fumigatus (154 patients) and Aspergillus flavus (101 patients). Haematological malignancies were the predominant underlying diseases (299 individuals). The overall fatality rate in these 299 patients (57.6%) was significantly greater than that in patients without severe immunodeficiency (39.4% of 38 individuals). Construction or demolition work was often (49.1%) considered to be the probable or possible source of the outbreak. Even concentrations of Aspergillus spp. below 1 colony-forming unit/m(3) were sufficient to cause infection in high-risk patients. Virtually all outbreaks of nosocomial aspergillosis are attributed to airborne sources, usually construction. Even small concentrations of spores have been associated with outbreaks, mainly due to A. fumigatus or A. flavus. Patients at risk should not be exposed to aspergilli.

Molecular typing of aspergilli: Recent developments and outcomes

Aspergillus spp. have been the subject of numerous epidemiological studies. The most useful typing techniques are DNA based methods including the random amplified polymorphic DNA technique, microsatellite length polymorphisms, restriction fragment length polymorphism (RFLP) analysis using retrotransposon-like sequences as probes, and multilocus sequence typing. The results of typing clinical isolates indicate that most of the invasive aspergillosis (IA) patients were infected by a single strain. Genetic analysis could not discriminate between clinical and environmental isolates of Aspergillus. fumigatus, indicating that every strain present in the environment is a potential pathogen if it encounters the appropriate host. The source of infection can also be monitored by typing. Typing studies led to the discovery of a new pathogenic species, A. lentulus, and to the identification of several species not known previously to be pathogenic. Typing studies revealed the existence of two genetically isolated groups within a global A. fumigatus population. Aspergillus fumigatus was found to be the first example of a true cosmopolitan fungus. Additionally, the results obtained in several studies support the premise that recombination played an important role in A. fumigatus populations. The discovery of functional mating type genes in A. fumigatus indicates that past or recent sexual processes could be responsible for the observed recombining population structure.

Clinical implications of environmental sources for Aspergillus

Invasive aspergillosis presents a formidable problem for both diagnosis and therapy. Therefore, prevention is a very important strategy in controlling this disease. Preventing invasive aspergillosis demands a clear understanding of the environmental sources of Aspergillus spp. and how this mould is transmitted to patients. Insight into the sources of exposure, mechanisms of transmission, and host susceptibility to infection are vital to appropriately direct preventive strategies to those settings where the risk of infection is the highest and consequently the impact of prevention the greatest.

Use of a novel panel of nine short tandem repeats for exact and high-resolution fingerprinting of Aspergillus fumigatus isolates

Here we describe a new panel of short tandem repeats (STRs) for a novel exact typing assay that can be used to discriminate between Aspergillus fumigatus isolates. A total of nine STR markers were selected from available genomic A. fumigatus sequences and were divided into three multicolor multiplex PCRs. Each multiplex reaction amplified three di-, tri-, or tetranucleotide repeats, respectively. All nine STR markers were used to analyze 100 presumably unrelated A. fumigatus isolates. For each marker, between 11 and 37 alleles were found in this population. One isolate proved to be a mixture of at least two different isolates. With the remaining 99 isolates, 96 different fingerprinting profiles were obtained. The Simpson's diversity index for the individual markers ranged from 0.77 to 0.97. The diversity index for the multiplex combination of di-, tri-, and tetranucleotide repeats ranged from 0.9784 to 0.9968. The combination of all nine markers yielded a Simpson's diversity index of 0.9994, indicative of the high discriminatory power of these new loci. In theory, this panel of markers is able to discriminate between no less than 27 x 10(9) different genotypes. The multicolor multiplex approach allows large numbers of markers to be tested in a short period of time. The exact nature of the assay combines high reproducibility with the easy exchange of results and makes it a very suitable tool for large-scale epidemiological studies.

Development of a method to detect and quantify Aspergillus fumigatus conidia by quantitative PCR for environmental air samples

Exposure to Aspergillus fumigatus is linked with respiratory diseases such as asthma, invasive aspergillosis, hypersensitivity pneumonitis, and allergic bronchopulmonary aspergillosis. Molecular methods using quantitative PCR (qPCR) offer advantages over culture and optical methods for estimating human exposures to microbiological agents such as fungi. We describe an assay that uses lyticase to digest A. fumigatus conidia followed by TaqMan qPCR to quantify released DNA. This method will allow analysis of airborne A. fumigatus samples collected over extended time periods and provide a more representative assessment of chronic exposure. The method was optimized for environmental samples and incorporates: single tube sample preparation to reduce sample loss, maintain simplicity, and avoid contamination; hot start amplification to reduce non-specific primer/probe annealing; and uracil-N-glycosylase to prevent carryover contamination. An A. fumigatus internal standard was developed and used to detect PCR inhibitors potentially found in air samples. The assay detected fewer than 10 A. fumigatus conidia per qPCR reaction and quantified conidia over a 4-log10 range with high linearity (R2 >0.99) and low variability among replicate standards (CV=2.0%) in less than 4 h. The sensitivity and linearity of qPCR for conidia deposited on filters was equivalent to conidia calibration standards. A. fumigatus DNA from 8 isolates was consistently quantified using this method, while non-specific DNA from 14 common environmental fungi, including 6 other Aspergillus species, was not detected. This method provides a means of analyzing long term air samples collected on filters which may enable investigators to correlate airborne environmental A. fumigatus conidia concentrations with adverse health effects.

Use of random amplified microsatellites to type isolates from an outbreak of nosocomial aspergillosis in a general medical ward

Numerous patients were diagnosed with aspergillosis in a nosocomial outbreak caused by Aspergillus fumigatus and Aspergillus flavus. Thirty-three isolates of the former and 28 isolates of the latter were collected from the hospital environment and from the patients and studied for genetic relatedness by random amplified microsatellites (RAMS) analysis, in which two polymorphic regions were tested. Twenty-eight genotypes of A. fumigatus and 23 genotypes of A. flavus were identified. Four patients were infected by two isolates with the same genotype as the environmental isolates. One clinical genotype was shared by three patients and another was shared by two patients. We found that RAMS was useful for fingerprinting Aspergillus spp.

Identification to the species level and differentiation between strains of Aspergillus clinical isolates by automated repetitive-sequence-based PCR

A commercially available repetitive-sequence-based PCR (rep-PCR) DNA fingerprinting assay adapted to an automated format, the DiversiLab system, enables rapid microbial identification and strain typing. We explored the performance of the DiversiLab system as a molecular typing tool for 69 Aspergillus isolates (38 A. fumigatus, 15 A. flavus, and 16 A. terreus isolates) had been previously characterized by morphological analysis. Initially, 27 Aspergillus isolates (10 A. fumigatus, 9 A. flavus, and 8 A. terreus isolates) were used as controls to create a rep-PCR-based DNA fingerprint library with the DiversiLab software. Then, 42 blinded Aspergillus isolates were typed using the system. The rep-PCR-based profile revealed 98% concordance with morphology-based identification. rep-PCR-based DNA fingerprints were reproducible and were consistent for DNA from both hyphae and conidia. DiversiLab dendrogram reports correctly identified all A. fumigatus (n = 28), A. terreus (n = 8), and A. flavus (n = 6) isolates in the 42 blinded Aspergillus isolates. rep-PCR-based identification of all isolates was 100% in agreement with the contiguous internal transcribed spacer (ITS) region (ITS1-5.8S-ITS2) sequence-based identification of the respective isolates. Additionally, the DiversiLab system could demonstrate strain-level differentiation of A. flavus and A. terreus. Automated rep-PCR may be a time-efficient, effective, easy-to-use, novel genotyping tool for identifying and determining the strain relatedness of fungi. This system may be useful for epidemiological studies, molecular typing, and surveillance of Aspergillus species.

Environmental investigations and molecular typing of Aspergillus flavus during an outbreak of postoperative infections

After an outbreak of sternal surgical-site infections (SSSI) with Aspergillus flavus following cardiac surgery, a mycological survey of air and surfaces (41 and 149 samples, respectively) was performed throughout the surgical ward (SW) and in other areas of the hospital. Results showed massive contamination by A. flavus: more than 100 cfu per contact plate were frequently observed in some areas of the SW. The distribution of the A. flavus spores in the building, and especially in the SW, enabled the location of a possible source within the non-medical part of the SW, but the true source could not be identified. Four other surveys were made to follow up the decontamination process; the contamination level did not fall rapidly, needing repetitive cleaning operations. Strains from patients and from the hospital environment selected all over the SW were typed by random amplification of polymorphic DNA (RAPD), using two different primers (ERIC-1, BG-2). All these strains showed the same genotype, proving the clonal single-source of the environmental contamination and the intra-operative acquisition of A. flavus in the SSSI outbreak.

Epidemiology of Aspergillus terreus at a university hospital

Invasive fungal infections due to Aspergillus species have become a major cause of morbidity and mortality among immunocompromised patients. Aspergillus terreus, a less common pathogen, appears to be an emerging cause of infection at our institution, the University of Alabama hospital in Birmingham. We therefore investigated the epidemiology of A. terreus over the past 6 years by using culture data; antifungal susceptibility testing with amphotericin B, voriconazole, and itraconazole; and molecular typing with random amplification of polymorphic DNA-PCR (RAPD-PCR). During the study period, the percentage of A. terreus isolates relative to those of other Aspergillus species significantly increased, and A. terreus isolates frequently were resistant to amphotericin B. Molecular typing with the RAPD technique was useful in discriminating between patient isolates, which showed much strain diversity. Further surveillance of A. terreus may better define epidemiology and determine whether this organism is becoming more frequent in relation to other Aspergillus species.

Molecular epidemiology of invasive stomatitis due to Aspergillus flavus in patients with acute leukemia

BACKGROUND

Invasive oral aspergillosis is a rare complication and only little information on the epidemiology of Aspergillus flavus infection is available. We present here the molecular analysis of the epidemiology of invasive stomatitis due to Aspergillus flavus in patients with acute leukemia.

METHODS

During a 5-year period (1992-1996), six isolates of A. flavus were obtained from leukemic patients with invasive Aspergillus stomatitis. Random amplification of polymorphic DNA (RAPD) with three different PCR primers was carried out to investigate the DNA typing of the isolates.

RESULTS

The molecular analysis using RAPD revealed that three isolates of A. flavus obtained in 1992 from three patients were of the same type, whereas each of the isolates from the other three patients had a distinct unique band, resulting in four groups of A. flavus.

CONCLUSION

As the three patients with invasive oral aspergillosis detected in 1992 were infected by a single strain of A. flavus, the strain was suspected to have caused a nosocomial outbreak of invasive oral aspergillosis in the hematology unit.

Are plants vectors for transmission of infection in acute care?

This article reviews relevant research that sheds light on the role of plants and flowers in hospital-acquired infections. After a review of a survey of acute care hospital policies, evidence-based practice recommendations intended to reduce nosocomial infections in acute and critical care are provided.

Microsatellite analysis of environmental and clinical isolates of the opportunist fungal pathogen Aspergillus fumigatus

Microsatellite analysis was used to examine the genetic relatedness of 111 clinical and environmental isolates of the opportunist human pathogenic fungus Aspergillus fumigatus from Ontario, Canada. Forty-three A. fumigatus isolates were from clinical sources and 68 from environmental sources. Phylogenetic analysis of the genotypes revealed that there were no geographical or temporal associations of clinical or environmental genotypes. In fact, several of the environmental and clinical isolates showed identical (clonal) genotypes from disparate geographical areas. However, a locus by locus examination revealed that there were several significant differences in allele frequencies between clinical and environmental isolates. There may be linkage of certain microsatellite loci with genes affecting virulence in A. fumigatus. A susceptible individual may be equally predisposed to infection by any isolate of A. fumigatus. However, under transient selection as a pathogen, genes encoding alleles for enhanced virulence may not assort independently from microsatellite loci. A dynamic equilibrium may exist between random recombination of loci in the natural environment and selection for virulence factors during host infection cycles.

Evaluation of performance of four genotypic methods for studying the genetic epidemiology of Aspergillus fumigatus isolates

In the present investigation, 49 Aspergillus fumigatus isolates obtained from four nosocomial outbreaks were typed by Afut1 restriction fragment length polymorphism (RFLP) analysis and three PCR-based molecular typing methods: random amplified polymorphic DNA (RAPD) analysis, sequence-specific DNA primer (SSDP) analysis, and polymorphic microsatellite markers (PMM) analysis. The typing methods were evaluated with respect to discriminatory power (D), reproducibility, typeability, ease of use, and ease of interpretation to determine their performance and utility for outbreak and surveillance investigations. Afut1 RFLP analysis detected 40 types. Thirty types were observed by RAPD analysis. PMM analysis detected 39 allelic types, but SSDP analysis detected only 14 types. All four methods demonstrated 100% typeability. PMM and RFLP analyses had comparable high degrees of discriminatory power (D = 0.989 and 0.988, respectively). The discriminatory power of RAPD analysis was slightly lower (D = 0.971), whereas SSDP analysis had the lowest discriminatory power (D = 0.889). Overall, SSDP analysis was the easiest method to interpret and perform. The profiles obtained by PMM analysis were easier to interpret than those obtained by RFLP or RAPD analysis. Bands that differed in staining intensity or that were of low intensity were observed by RAPD analysis, making interpretation more difficult. The reproducibilities with repeated runs of the same DNA preparation or with different DNA preparations of the same strain were high for all the methods. A high degree of genetic variation was observed in the test population, but isolates were not always similarly divided by each method. Interpretation of band profiles requires understanding of the molecular mechanisms responsible for genetic alternations. PMM analysis and Afut1 RFLP analysis, or their combination, appear to provide the best overall discriminatory power, reproducibility, ease of interpretation, and ease of use. This investigation will aid in planning epidemiologic and surveillance studies of A. fumigatus.

Epidemiology and Prevention of Invasive Aspergillosis

Aspergillus species are the most common causes of invasive mold infections in immunocompromised persons. This review examines the available information regarding the rising incidence of invasive aspergillosis in different high-risk groups, including persons with acute leukemia, hematopoietic stem cell transplant recipients, and liver and lung transplant recipients. The risk factors for infection in these groups are discussed. Because Aspergillus species are widespread in the environment, it is difficult to link specific sources and exposures to the development of human infections. However, molecular strain typing and other studies indicate that a significant number of Aspergillus infections are now being acquired outside the health care setting, either before patients are admitted to hospital, or after they have been discharged. The role of environmental control measures and antifungal drug prophylaxis in the prevention of hospital- and community-acquired aspergillosis is discussed.

Counterpoint: invasive aspergillosis and the environment--rethinking our approach to prevention

Preventive measures are important in the control of invasive aspergillosis (IA) because diagnosis is difficult and the outcome of treatment is poor. If effective strategies are to be devised, it will be essential to have a clearer understanding of the sources and routes of transmission of Aspergillus species. Nosocomial outbreaks of IA highlight the fact that Aspergillus spores are common in the hospital environment. However, in general, such outbreaks are uncommon. Most cases of IA are sporadic in nature, and many of them are now being acquired outside of the hospital setting. Housing patients in high-energy particulate air-filtered hospital rooms helps prevent IA, but it is feasible and cost-effective only for the highest-risk groups and for limited periods. Control measures, which are designed to protect patients from exposure to spores outside the hospital, are even more difficult. Nevertheless, now that high-risk patients are spending more time outside of the hospital, the cost benefits of antifungal prophylaxis and other preventive measures require careful evaluation.

Comparison of restriction fragment length polymorphism, microsatellite length polymorphism, and random amplification of polymorphic DNA analyses for fingerprinting Aspergillus fumigatus isolates

Aspergillus fumigatus fingerprints generated by random amplification of polymorphic DNA (RAPD), restriction fragment length polymorphism (RFLP) upon hybridization with repeated DNA sequences, and PCR detection of microsatellite length polymorphism (MLP) were compared among 67 isolates. In contrast to RAPD, RFLP and MLP gave discriminating and significantly concordant genotyping results.

Relationship between environmental fungal contamination and the incidence of invasive aspergillosis in haematology patients

Invasive aspergillosis (IA) is a major opportunistic infection in haematology patients. Spore inhalation is the usual route of Aspergillus infection, suggesting a determining role of environmental contamination by spores in the epidemiology of IA. We prospectively examined the relationship between environmental contamination by Aspergillus and other fungal species and the incidence of invasive nosocomial aspergillosis (INA) in a bone marrow transplantation unit and two haematology wards. During a four-year period, levels of air and surface fungal contamination were determined bi-monthly in patients' rooms (some equipped with HEPA filters and LAF systems), and various common sites in each ward (corridors, nursing stations, etc.). Results were compared to the incidence of INA. A total of 3100 air and 9800 surface samples were collected, and 79 cases of IA were diagnosed, of which 64 were probably or possibly INA. Patterns of fungal contamination were comparable in the three wards, with a gradient ranging from high levels in common sites to a virtual absence in rooms equipped with HEPA filters and LAF systems. Using a regression model, a significant relationship was found between the incidence of INA and the degree of fungal contamination of air and surfaces in conventional patient rooms (not equipped with HEPA) and common sites. This study shows that in a non-epidemic setting, there is a significant relationship between environmental fungal contamination in haematology wards and the incidence of INA. Our findings underline the importance of environmental surveillance and strict application of preventive measures.

New restriction fragment length polymorphism (RFLP) markers for Aspergillus fumigatus

In this study, we isolated and tested restriction fragment length polymorphism (RFLP) markers for Aspergillus fumigatus based on PCR products amplified by the random amplified polymorphic DNA (RAPD) primer R108. Four DNA fragments, Afd, Af5, Af4, and Af4A, were amplified. Fragments Afd and Af5 were 85% and 88% identical at the DNA level to part of the Afut1 retrotransposon from A. fumigatus. Fragment Af4A is a duplication of fragment Af4 and both showed similarity at the amino acid level with endonucleases from other fungal retrotransposons. We used both RAPD with primer R108 and RFLP assays with Afut1, Afd, and Af4A, to determine the genetic relatedness of clinical isolates of A. fumigatus isolated sequentially from four patients colonized with A. fumigatus. The combination of these different methods suggested that the isolates infecting the four patients were not identical.

Genetic polymorphism of Aspergillus fumigatus in clinical samples from patients with invasive aspergillosis: investigation using multiple typing methods

The genotypes of 52 strains of Aspergillus fumigatus isolated from 12 patients with invasive aspergillosis were investigated using three typing methods (random amplified polymorphic DNA, sequence-specific DNA polymorphism, and microsatellite polymorphism) combined with multilocus enzyme electrophoresis. Isolates were from patients hospitalized in three different geographic areas (Lyon, France; Grenoble, France; and Milan, Italy). In each case, the genetic polymorphism of several colonies (two to five) within the first respiratory clinical sample was studied. For the 52 isolates tested, random amplified polymorphic DNA identified 8 different genotypes, sequence-specific DNA polymorphism identified 9 different types, and microsatellite polymorphism identified 14 types. A combination of these results with multilocus enzyme electrophoresis study identified 25 different types within the sample studied. We identified 3 patients (of the 12 studied) who carried a single genotype; 6 patients were infected by two genotypes, 1 patient had four genotypes, while the last patient had five. A combination of typing methods provided better discrimination than the use of a single method. Typing methods revealed a population structure within each geographical site, suggesting that the epidemiology of A. fumigatus should be considered separately for each of these geographic areas. This study demonstrates the usefulness of combining several typing methods in reaching an understanding of the epidemiology of A. fumigatus and clarifies whether it is sufficient to type one isolate from each specimen to determine the strain involved in invasive aspergillosis.