Molecular epidemiology of Aspergillus fumigatus isolates recovered from water, air, and patients shows two clusters of genetically distinct strains

Isolation and identification of Fusarium species from the water systems of ICUs and transplant wards of hospitals and determination of the in vitro susceptibilities of isolates to conventional antifungals

Background

The rising prevalence of nosocomial infections, particularly those caused by airborne fungal spores in operating rooms and intensive care units (ICUs), has become a significant public health concern. Fusarium species in water systems pose a severe threat to immunocompromised patients and can disseminate as aerosols through devices such as faucets and showers. This study aimed to isolate and identify Fusarium species from the water systems of the ICUs and transplant units at Imam Khomeini Hospital Complex and Shariati Hospital in Tehran, Iran, as potential sources of future outbreaks. Additionally, the study sought to determine the in vitro susceptibilities of the isolates to conventional antifungal agents.

Methods

Sterile swabs and open plates containing Sabouraud dextrose agar (SDA) with chloramphenicol were used to collect water samples from sink surfaces, shower trays, faucets, and around the drains of sinks, as well as from bathroom areas. Swab samples were cultured, and the open-plate samples were evaluated for the growth of Fusarium species. The validation of all Fusarium sp. isolates was performed using DNA sequencing of the translation elongation factor 1-alpha (TEF-1α) gene. The antifungal susceptibility patterns of each isolate were tested against voriconazole, itraconazole, posaconazole, caspofungin, and amphotericin B using the Clinical and Laboratory Standards Institute (CLSI) broth microdilution method for filamentous fungi.

Results

Fusarium species were recovered from six out of 362 water system samples, representing 1.65% of the total. Five isolates were identified as Fusarium oxysporum from the F. oxysporum complex, while one isolate was identified as Fusarium proliferatum from the Fusarium fujikuroi complex. All isolates were obtained from sinks (three isolates) and faucets (three isolates) at Imam Khomeini Hospital. Antifungal susceptibility testing revealed that posaconazole, voriconazole, and amphotericin B were the most effective drugs against all Fusarium isolates, with no instances of resistance to these antifungal agents observed. However, non-wild-type isolates were noted for the other drugs tested.

Discussion

The isolation of pathogenic Fusarium species from water samples collected in the ICU wards of the Imam Khomeini Hospital Complex underscores the urgent need to implement effective control and prevention measures in hospital water systems.

Monitoring the Occurrence of Aspergillus in the Air of Intensive Care Units

Poor air quality within hospitals can contribute to a range of health issues, collectively known as sick hospital syndrome, encompassing respiratory, skin, and nonspecific symptoms. Aspergillus poses a significant risk of severe respiratory infections, particularly within intensive care unit (ICU) patients often with compromised immune systems. This study was conducted in the intensive care units of three selected hospitals in Cracow, Poland. Air samples were obtained using the single-stage impactor MAS-100 NT Ex (Merck). The air samples were taken from each ward, seasonally, four times a year. Sampling of intensive care units' air for Aspergillus revealed the significant diversity in fungal concentration and unveiled seasonal fluctuations in culturable fungi levels. The highest concentration of Aspergillus species complexes was detected during autumn, while the lowest was in spring. The disturbing occurrence of Aspergillus in hospitals' air emphasizes the importance of monitoring fungal air bioburden and assessing air control efficiency and highlights the urgent need to develop and validate microbiological standards for fungal air contamination in hospitals.

Fungal presence and health implications in hospital water systems

Given the increasing occurrence of invasive fungal infections and the limited efficacy of modern antifungal medications, it is crucial to disseminate information regarding the potential sources of nosocomial mycoses through the One Health approach. This study investigated the presence and antifungal susceptibility of fungi in biofilm and water samples obtained from the drinking water distribution system (DWDS) of hospitals. The positivity rate for fungi in biofilm and water samples was 41% and 9%, respectively, with Aspergillus species, a significant causative agent of nosocomial mycoses, being the predominant fungi identified. Analysis of antifungal susceptibility test revelead a comparable resistance profile between some isolated species from the DWDS and those reported for certain clinical samples. While further research is required to determine the specific contribution of waterborne fungi to nosocomial fungal infections, our results emphasize the importance of controlling biofilm formation within DWDSs, particularly in high-risk hospital wards.

A practical approach to investigating nosocomial acquisition of Aspergillus

Invasive mould disease (IMD) has a high mortality in immunosuppressed patients. Invasive aspergillosis (IA) is the most common IMD. A guideline for preventing IA has been published jointly by the Centers for Disease Control and Prevention, the Infectious Disease Society of America, and the American Society of Blood and Marrow Transplantation. Use of high-efficiency particulate air filters, adequate air exchange rates, sealing of patient rooms, and preventing exposure to moulds by nursing patients in areas away from construction sites are recommended by the guideline. However, there is limited information in relation to the actions to be undertaken by infection prevention and control teams in the event of one or more cases of nosocomial aspergillosis. In this review, we describe a systematic approach to aspergillosis by defining possible and probable nosocomial acquisition based on the number of days since hospital admission. We advocate an incremental response to the investigation of nosocomial aspergillosis in patients in protective isolation taking into account the number of cases and the likelihood of nosocomial origin. For single cases of nosocomial IA, we suggest that infection control investigations should focus on case surveillance and walk-through inspection escalating in a stepwise manner to enhanced case surveillance, verification of environmental controls, environmental monitoring, genotyping of clinical and environmental isolates, and review of antifungal prophylaxis for multiple cases and outbreaks. Where applicable, the construction site should be inspected with the aim to reduce the dispersal of conidia. Surveillance systems need to be strengthened to better understand the epidemiology of IA.

Fungal contamination of the water distribution system of a tertiary hospital water supply system in a resource-limited setting

Background

Fungal contamination of hospital water distribution systems has been implicated in outbreaks of healthcare-associated infections.

Objectives

To evaluate the prevalence of fungi in the water distribution system of a tertiary hospital in Nigeria.

Design

This was a descriptive cross-sectional study.

Methods

Swabs and water samples were collected from taps and faucets in the hospital categorized into low (Accidents and Emergency Unit, Children Emergency Unit, Acute Stroke Unit and the 24 in-patient hospital wards) and high-risk (Renal Dialysis Unit, Central Sterile Services Department, Theatres and Intensive Care Units (ICUs)) units based on the vulnerability of patients being managed there. The membrane filtration method for water analysis was used. Where possible, isolates cultured were identified to species level. In total, 105 water and 49 swab samples were collected for analysis.

Results

All analysed water samples grew fungi. A total of 289 (high-risk; n = 178; low-risk; n = 111) and 76 fungi isolates were recorded from water and swab samples, respectively, with 31 different species identified. Aspergillus was the most predominant genus with five different species: Aspergillus niger (9.9%), terreus (4.4%), flavus (3.3%), fumigatus (8.8%) and versicolor (2.20%) isolated. Twenty-five and 18 species of fungi were identified in the low and high-risk units, respectively. The labour ward (n = 46; 25.8%) and modular theatre (n = 47; 42.3%) were the most contaminated units. Cladosporium spp. and Paecilomyces spp. were the most frequently isolated fungi in the low and high-risk units, respectively. The dialysis centre (n = 9; 8.1%) and renal transplant theatre (n = 7; 6.31%) had the lowest contamination rates in the high-risk units. Aspergillus niger, Cephalosporium curtipes, Penicillium chrysogenum and Penicillium glabrum were each identified in 4/6 units from which swabs were taken. The facility had no documented protocol for its water safety and quality.

Conclusion

Our data reveal a high rate of contamination of hospital water sources by fungi, some of which are known to cause life-threatening infections. For better water treatment and water tank cleaning and disinfection, a standard protocol is advised. Ensuring that the water distribution systems in hospital settings are free of fungal contaminants is important to prevent the possibility of waterborne mycosis outbreaks.

Drug-Resistant Aspergillus spp.: A Literature Review of Its Resistance Mechanisms and Its Prevalence in Europe

Infections due to the Aspergillus species constitute an important challenge for human health. Invasive aspergillosis represents a life-threatening disease, mostly in patients with immune defects. Drugs used for fungal infections comprise amphotericin B, triazoles, and echinocandins. However, in the last decade, an increased emergence of azole-resistant Aspergillus strains has been reported, principally belonging to Aspergillus fumigatus species. Therefore, both the early diagnosis of aspergillosis and its epidemiological surveillance are very important to establish the correct antifungal therapy and to ensure a successful patient outcome. In this paper, a literature review is performed to analyze the prevalence of Aspergillus antifungal resistance in European countries. Amphotericin B resistance is observed in 2.6% and 10.8% of Aspergillus fumigatus isolates in Denmark and Greece, respectively. A prevalence of 84% of amphotericin B-resistant Aspergillus flavus isolates is reported in France, followed by 49.4%, 35.1%, 21.7%, and 20% in Spain, Portugal, Greece, and amphotericin B resistance of Aspergillus niger isolates is observed in Greece and Belgium with a prevalence of 75% and 12.8%, respectively. The prevalence of triazole resistance of Aspergillus fumigatus isolates, the most studied mold obtained from the included studies, is 0.3% in Austria, 1% in Greece, 1.2% in Switzerland, 2.1% in France, 3.9% in Portugal, 4.9% in Italy, 5.3% in Germany, 6.1% in Denmark, 7.4% in Spain, 8.3% in Belgium, 11% in the Netherlands, and 13.2% in the United Kingdom. The mechanism of resistance is mainly driven by the TR34/L98H mutation. In Europe, no in vivo resistance is reported for echinocandins. Future studies are needed to implement the knowledge on the spread of drug-resistant Aspergillus spp. with the aim of defining optimal treatment strategies.

Environmental monitoring for filamentous fungal pathogens in hematopoietic cell transplant units

The incidence of invasive fungal disease (IFD) is on the rise due to increasing numbers of highly immunocompromized patients. Nosocomial IFD remains common despite our better understanding of its risk factors and pathophysiology. High-efficiency particulate air filtration with or without laminar air flow, frequent air exchanges, a positive pressure care environment, and environmental hygiene, amongst other measures, have been shown to reduce the mould burden in the patient environment. Environmental monitoring for moulds in areas where high-risk patients are cared for, such as hematopoietic cell transplant units, has been considered an adjunct to other routine environmental precautions. As a collaborative effort between authors affiliated to the Infection Prevention and Control Working Group and the Fungal Infection Working Group of the International Society of Antimicrobial Chemotherapy (ISAC), we reviewed the English language literature and international guidance to describe the evidence behind the need for environmental monitoring for filamentous fungi as a quality assurance approach with an emphasis on required additional precautions during periods of construction. Many different clinical sampling approaches have been described for air, water, and surface sampling with significant variation in laboratory methodologies between reports. Importantly, there are no agreed-upon thresholds that correlate with an increase in the clinical risk of mould infections. We highlight important areas for future research to assure a safe environment for highly immunocompromized patients.

Culturable mycobiota of drinking water in Göteborg (Sweden) in comparison to Ljubljana (Slovenia) with implications on human health

The European Union currently has no specific regulations on fungi in water. The only country where fungi are listed as the parameter is Sweden, with the maximal number of 100 CFU per 100 mL. The present study thus compared culturable mycobiota from Swedish drinking water with Slovenian, which has no specific requirements for fungi. Fungi were isolated with up to 38 CFU/L from 75% of Swedish samples. The most common were the genera Varicosporellopsis (27.3%), Paracremonium (14.5%), and black yeasts Cadophora, Cyphellophora, and Exophiala (18.2%). Using the same sampling and isolation methods, 90% of tap water samples in Slovenia were positive for fungi, with Aspergillus spp. (46%), Aureobasidium melanogenum (36%), and Exophiala spp. (24%) being the most common. The observed differences between countries are likely the consequence of geographical location, the use of different raw water sources, and water treatment methods. However, the core species and emerging fungi Aspergillus fumigatus, Candida parapsilosis sensu stricto, Exophiala phaeomuriformis, Bisifusarium dimerum, and Rhodotorula mucilaginosa were isolated in both studies. These findings point out the relevance of tracking the presence of emerging fungi with known effects on health in drinking water and encourage further studies on their transmission from raw water sources to the end-users.

Comparison of Multi-locus Genotypes Detected in Aspergillus fumigatus Isolated from COVID Associated Pulmonary Aspergillosis (CAPA) and from Other Clinical and Environmental Sources

Background: Aspergillus fumigatus is a saprophytic fungus, ubiquitous in the environment and responsible for causing infections, some of them severe invasive infections. The high morbidity and mortality, together with the increasing burden of triazole-resistant isolates and the emergence of new risk groups, namely COVID-19 patients, have raised a crescent awareness of the need to better comprehend the dynamics of this fungus. The understanding of the epidemiology of this fungus, especially of CAPA isolates, allows a better understanding of the interactions of the fungus in the environment and the human body. Methods: In the present study, the M3 markers of the STRAf assay were used as a robust typing technique to understand the connection between CAPA isolates and isolates from different sources (environmental and clinical-human and animal). Results: Of 100 viable isolates that were analyzed, 85 genotypes were found, 77 of which were unique. Some isolates from different sources presented the same genotype. Microsatellite genotypes obtained from A. fumigatus isolates from COVID+ patients were all unique, not being found in any other isolates of the present study or even in other isolates deposited in a worldwide database; these same isolates were heterogeneously distributed among the other isolates. Conclusions: Isolates from CAPA patients revealed high heterogeneity of multi-locus genotypes. A genotype more commonly associated with COVID-19 infections does not appear to exist.

Occurrence of fungal spores in drinking water: A review of pathogenicity, odor, chlorine resistance and control strategies

Fungi in drinking water have been long neglected due to the lack of convenient analysis methods, widely accepted regulations and efficient control strategies. However, in the last few decades, fungi in drinking water have been widely recognized as opportunity pathogens that cause serious damage to the health of immune-compromised individuals. In drinking water treatment plants, fungal spores are more resistant to chlorine disinfection than bacteria and viruses, which can regrow in drinking water distribution systems and subsequently pose health threats to water consumers. In addition, fungi in drinking water may represent an ignored source of taste and odor (T&O). This review identified 74 genera of fungi isolated from drinking water and presented their detailed taxonomy, sources and biomass levels in drinking water systems. The typical pathways of exposure of water-borne fungi and the main effects on human health are clarified. The fungi producing T&O compounds and their products are summarized. Data on free chlorine or monochloramine inactivation of fungal spores and other pathogens are compared. At the first time, we suggested four chlorine-resistant mechanisms including aggregation to tolerate chlorine, strong cell walls, cellular responses to oxidative stress and antioxidation of melanin, which are instructive for the future fungi control attempts. Finally, the inactivation performance of fungal spores by various technologies are comprehensively analyzed. The purpose of this study is to provide an overview of fungi distribution and risks in drinking water, provide insight into the chlorine resistance mechanisms of fungal spores and propose approaches for the control of fungi in drinking water.

Molecular typing of clinical and environmental Aspergillus fumigatus isolates from Iran using microsatellites

Background and Purpose

Because of the growing incidence of Aspergillus infection, typing methods of Aspergillus species are increasingly being used. Accordingly, studying the spread and population dynamics of strains isolating from clinical and environment, from a single host to large-scale ecosystems is definitely needed. In the current study, we carried out a genetic analysis of nine microsatellite loci in isolates from different regions of Iran to compare and explore the genetic diversity between environmental and clinical A. fumigatus strains.

Materials and Methods

Sixty-six clinical (n=43) and environmental (n= 23) isolates of A. fumigatus, have collected from six cities of Iran. All A. fumigatus isolates identified based on macroscopic and microscopic characters, the ability to grow at above 45°C, and confirmed using DNA sequencing of the partial b-tubulin gene. Sixty-six A. fumigatus isolates were subjected by microsatellite typing using three separate multiplex PCRs with a panel of nine short tandem repeats (STR) to evaluate the genetic relatedness.

Results

The STR typing of 66 A. fumigatus isolates revealed 38 distinct genotypes distributed among environmental and clinical isolates. We identified 12 clones including 40 different isolates representing 60% of all isolates tested, which each clone included 2-7 isolates.

Conclusion

The STR typing is considered as a valuable tool with excellent discriminatory power to study the molecular epidemiology and genotypic diversity of A. fumigatus isolates. These findings show that the high genetic diversity observed of Iranian A. fumigatus isolates with those outside Iran and formed a separate cluster.

Aspergillus fumigatus and aspergillosis: From basics to clinics

The airborne fungus Aspergillus fumigatus poses a serious health threat to humans by causing numerous invasive infections and a notable mortality in humans, especially in immunocompromised patients. Mould-active azoles are the frontline therapeutics employed to treat aspergillosis. The global emergence of azole-resistant A. fumigatus isolates in clinic and environment, however, notoriously limits the therapeutic options of mould-active antifungals and potentially can be attributed to a mortality rate reaching up to 100 %. Although specific mutations in CYP 51A are the main cause of azole resistance, there is a new wave of azole-resistant isolates with wild-type CYP 51A genotype challenging the efficacy of the current diagnostic tools. Therefore, applications of whole-genome sequencing are increasingly gaining popularity to overcome such challenges. Prominent echinocandin tolerance, as well as liver and kidney toxicity posed by amphotericin B, necessitate a continuous quest for novel antifungal drugs to combat emerging azole-resistant A. fumigatus isolates. Animal models and the tools used for genetic engineering require further refinement to facilitate a better understanding about the resistance mechanisms, virulence, and immune reactions orchestrated against A. fumigatus. This review paper comprehensively discusses the current clinical challenges caused by A. fumigatus and provides insights on how to address them.

Exploring genetic diversity, population structure, and phylogeography in Paracoccidioides species using AFLP markers

Paracoccidioidomycosis (PCM) is a life-threatening systemic fungal infection acquired after inhalation of Paracoccidioides propagules from the environment. The main agents include members of the P. brasiliensis complex (phylogenetically-defined species S1, PS2, PS3, and PS4) and P. lutzii. DNA-sequencing of protein-coding loci (e.g., GP43, ARF, and TUB1) is the reference method for recognizing Paracoccidioides species due to a lack of robust phenotypic markers. Thus, developing new molecular markers that are informative and cost-effective is key to providing quality information to explore genetic diversity within Paracoccidioides. We report using new amplified fragment length polymorphism (AFLP) markers and mating-type analysis for genotyping Paracoccidioides species. The bioinformatic analysis generated 144 in silico AFLP profiles, highlighting two discriminatory primer pairs combinations (#1 EcoRI-AC/MseI-CT and #2 EcoRI-AT/MseI-CT). The combinations #1 and #2 were used in vitro to genotype 165 Paracoccidioides isolates recovered from across a vast area of South America. Considering the overall scored AFLP markers in vitro (67-87 fragments), the values of polymorphism information content (PIC = 0.3345-0.3456), marker index (MI = 0.0018), effective multiplex ratio (E = 44.6788-60.3818), resolving power (Rp = 22.3152-34.3152), discriminating power (D = 0.5183-0.5553), expected heterozygosity (H = 0.4247-0.4443), and mean heterozygosity (H avp  = 0.00002-0.00004), demonstrated the utility of AFLP markers to speciate Paracoccidioides and to dissect both deep and fine-scale genetic structures. Analysis of molecular variance (AMOVA) revealed that the total genetic variance (65-66 %) was due to variability among P. brasiliensis complex and P. lutzii (PhiPT = 0.651-0.658, P < 0.0001), supporting a highly structured population. Heterothallism was the exclusive mating strategy, and the distributions of MAT1-1 or MAT1-2 idiomorphs were not significantly skewed (1:1 ratio) for P. brasiliensis s. str. (χ2 = 1.025; P = 0.3113), P. venezuelensis (χ2 = 0.692; P = 0.4054), and P. lutzii (χ2 = 0.027; P = 0.8694), supporting random mating within each species. In contrast, skewed distributions were found for P. americana (χ2 = 8.909; P = 0.0028) and P. restrepiensis (χ2 = 4.571; P = 0.0325) with a preponderance of MAT1-1. Geographical distributions confirmed that P. americana, P. restrepiensis, and P. lutzii are more widespread than previously thought. P. brasiliensis s. str. is by far the most widely occurring lineage in Latin America countries, occurring in all regions of Brazil. Our new DNA fingerprint assay proved to be rapid, reproducible, and highly discriminatory, to give insights into the taxonomy, ecology, and epidemiology of Paracoccidioides species, guiding disease-control strategies to mitigate PCM.

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.

Genome-Wide Association Analysis for Triazole Resistance in Aspergillus fumigatus

Aspergillus fumigatus is a ubiquitous fungus and the main agent of aspergillosis, a common fungal infection in the immunocompromised population. Triazoles such as itraconazole and voriconazole are the common first-line drugs for treating aspergillosis. However, triazole resistance in A. fumigatus has been reported in an increasing number of countries. While most studies of triazole resistance have focused on mutations in the triazole target gene cyp51A, >70% of triazole-resistant strains in certain populations showed no mutations in cyp51A. To identify potential non-cyp51A mutations associated with triazole resistance in A. fumigatus, we analyzed the whole genome sequences and triazole susceptibilities of 195 strains from 12 countries. These strains belonged to three distinct clades. Our genome-wide association study (GWAS) identified a total of six missense mutations significantly associated with itraconazole resistance and 18 missense mutations with voriconazole resistance. In addition, to investigate itraconazole and pan-azole resistance, Fisher's exact tests revealed 26 additional missense variants tightly linked to the top 20 SNPs obtained by GWAS, of which two were consistently associated with triazole resistance. The large number of novel mutations related to triazole resistance should help further investigations into their molecular mechanisms, their clinical importance, and the development of a comprehensive molecular diagnosis toolbox for triazole resistance in A. fumigatus.

Molecular Epidemiology of Aspergillus fumigatus in Chronic Pulmonary Aspergillosis Patients

Molecular fungal genotyping techniques developed and employed for epidemiological studies have understandably concentrated on establishing the genetic diversity of Aspergillus fumigatus in invasive aspergillosis due to its severity, the urgency for treatment, and the need to demonstrate possible sources. Some early studies suggested that these strains were phenotypically, if not genotypically, different from others. However, with improved discrimination and evaluations, incorporating environmental as well as clinical isolates from other Aspergillus conditions (e.g., chronic pulmonary aspergillosis and cystic fibrosis), this premise is no longer upheld. Moreover, with the onset of increased global triazole resistance, there has been a concerted effort to incorporate resistance profiling into genotyping studies and the realisation that the wider population of non-immunocompromised aspergillosis patients are at risk. This review summarises the developments in molecular genotyping studies that incorporate resistance profiling with attention to chronic pulmonary aspergillosis and an example of our UK experience.

Extensive Genetic Diversity and Widespread Azole Resistance in Greenhouse Populations of Aspergillus fumigatus in Yunnan, China

Aspergillus fumigatus is the main cause of invasive aspergillosis (IA) with a high annual global incidence and mortality rate. Recent studies have indicated an increasing prevalence of azole-resistant A. fumigatus (ARAF) strains, with agricultural use of azole fungicides as a potential contributor. China has an extensive agricultural production system and uses a wide array of fungicides for crop production, including in modern growth facilities such as greenhouses. Soils in greenhouses are among the most intensively cultivated. However, little is known about the occurrence and distribution of ARAF in greenhouse soils. Here, we investigated genetic variation and triazole drug susceptibility in A. fumigatus from greenhouses around metropolitan Kunming in Yunnan, southwest China. Abundant allelic and genotypic variations were found among 233 A. fumigatus strains isolated from nine greenhouses in this region. Significantly, ∼80% of the strains were resistant to at least one medical triazole drug, with >30% showing cross-resistance to both itraconazole and voriconazole. Several previously reported mutations associated with triazole resistance in the triazole target gene cyp51A were also found in our strains, with a strong positive correlation between the frequency of mutations at the cyp51A promoter and that of voriconazole resistance. Phylogenetic analyses of cyp51A gene sequences showed evidence for multiple independent origins of azole-resistant genotypes of A. fumigatus in these greenhouses. Evidence for multiple origins of azole resistance and the widespread distributions of genetically very diverse triazole-resistant strains of A. fumigatus in greenhouses calls for significant attention from public health agencies.

IMPORTANCE The origin and prevalence of azole-resistant Aspergillus fumigatus have been attracting increasing attention from biologists, clinicians, and public health agencies. Current evidence suggests agricultural fungicide use as a major cause. In southwest China, greenhouses are used to produce large amounts of fruits, flowers, and vegetables for consumers throughout China as well as those in other countries, primarily in southeast Asia. Here, we found a very high frequency (∼80%) of triazole-resistant A. fumigatus in our sample, the highest reported so far, with a significant proportion of these strains resistant to both tested agricultural fungicides and medical triazole drugs. In addition, we found novel allelic and genotypic diversities and evidence for multiple independent origins of azole-resistant genotypes of A. fumigatus in greenhouse populations in this region. Our study calls for a systematic evaluation of the effects of azole fungicide usage in greenhouses on human health.

Genome-wide mapping using new AFLP markers to explore intraspecific variation among pathogenic Sporothrix species

Sporotrichosis is a chronic subcutaneous mycosis caused by Sporothrix species, of which the main aetiological agents are S. brasiliensis, S. schenckii, and S. globosa. Infection occurs after a traumatic inoculation of Sporothrix propagules in mammals' skin and can follow either a classic route through traumatic inoculation by plant debris (e.g., S. schenckii and S. globosa) or an alternative route through zoonotic transmission from animals (e.g., S. brasiliensis). Epizootics followed by a zoonotic route occur in Brazil, with Rio de Janeiro as the epicenter of a recent cat-transmitted epidemic. DNA-based markers are needed to explore the epidemiology of these Sporothrix expansions using molecular methods. This paper reports the use of amplified-fragment-length polymorphisms (AFLP) to assess the degree of intraspecific variability among Sporothrix species. We used whole-genome sequences from Sporothrix species to generate 2,304 virtual AFLP fingerprints. In silico screening highlighted 6 primer pair combinations to be tested in vitro. The protocol was used to genotype 27 medically relevant Sporothrix. Based on the overall scored AFLP markers (97-137 fragments), the values of polymorphism information content (PIC = 0.2552-0.3113), marker index (MI = 0.002-0.0039), effective multiplex ratio (E = 17.8519-35.2222), resolving power (Rp = 33.6296-63.1852), discriminating power (D = 0.9291-0.9662), expected heterozygosity (H = 0.3003-0.3857), and mean heterozygosity (Havp = 0.0001) demonstrated the utility of these primer combinations for discriminating Sporothrix. AFLP markers revealed cryptic diversity in species previously thought to be the most prevalent clonal type, such as S. brasiliensis, responsible for cat-transmitted sporotrichosis, and S. globosa responsible for large sapronosis outbreaks in Asia. Three combinations (#3 EcoRI-FAM-GA/MseI-TT, #5 EcoRI-FAM-GA/MseI-AG, and #6 EcoRI-FAM-TA/MseI-AA) provide the best diversity indices and lowest error rates. These methods make it easier to track routes of disease transmission during epizooties and zoonosis, and our DNA fingerprint assay can be further transferred between laboratories to give insights into the ecology and evolution of pathogenic Sporothrix species and to inform management and mitigation strategies to tackle the advance of sporotrichosis.

Gliotoxin Induces Cofilin Phosphorylation to Promote Actin Cytoskeleton Dynamics and Internalization of Aspergillus fumigatus Into Type II Human Pneumocyte Cells

Aspergillus fumigatus is able to internalize into lung epithelial cells to escape from immune attack for further dissemination. We previously reported that gliotoxin, a major mycotoxin of A. fumigatus, promotes this internalization; however, the mechanism remained unclear. Here, we report that gliotoxin is able to induce cofilin phosphorylation in A549 type II human pneumocytes. Either too high or too low a level of cofilin phosphorylation blocked the gliotoxin-induced actin cytoskeleton rearrangement and A. fumigatus internalization. LIM domain kinase 1 (LIMK1) and its upstream small GTPases (Cdc42 and RhoA, but not Rac1) predominantly mediated the gliotoxin-induced cofilin phosphorylation and A. fumigatus internalization. Simultaneously, gliotoxin significantly stimulated an increase in cAMP; however, adding an antagonist of PKA did not block gliotoxin-induced A. fumigatus internalization. In vivo, exogenous gliotoxin helped gliotoxin synthesis deficient strain gliPΔ invade into the lung tissue and the lung fungal burden increased markedly in immunosuppressed mice. In conclusion, these data revealed a novel role of gliotoxin in inducing cofilin phosphorylation mostly through the Cdc42/RhoA-LIMK1 signaling pathway to promote actin cytoskeleton rearrangement and internalization of A. fumigatus into type II human pneumocytes.

Nonrandom Distribution of Azole Resistance across the Global Population of Aspergillus fumigatus

The emergence of azole resistance in the pathogenic fungus Aspergillus fumigatus has continued to increase, with the dominant resistance mechanisms, consisting of a 34-nucleotide tandem repeat (TR34)/L98H and TR46/Y121F/T289A, now showing a structured global distribution. Using hierarchical clustering and multivariate analysis of 4,049 A. fumigatus isolates collected worldwide and genotyped at nine microsatellite loci using analysis of short tandem repeats of A. fumigatus (STRAf), we show that A. fumigatus can be subdivided into two broad clades and that cyp51A alleles TR34/L98H and TR46/Y121F/T289A are unevenly distributed across these two populations. Diversity indices show that azole-resistant isolates are genetically depauperate compared to their wild-type counterparts, compatible with selective sweeps accompanying the selection of beneficial mutations. Strikingly, we found that azole-resistant clones with identical microsatellite profiles were globally distributed and sourced from both clinical and environmental locations, confirming that azole resistance is an international public health concern. Our work provides a framework for the analysis of A. fumigatus isolates based on their microsatellite profile, which we have incorporated into a freely available, user-friendly R Shiny application (AfumID) that provides clinicians and researchers with a method for the fast, automated characterization of A. fumigatus genetic relatedness. Our study highlights the effect that azole drug resistance is having on the genetic diversity of A. fumigatus and emphasizes its global importance upon this medically important pathogenic fungus.IMPORTANCE Azole drug resistance in the human-pathogenic fungus Aspergillus fumigatus continues to emerge, potentially leading to untreatable aspergillosis in immunosuppressed hosts. Two dominant, environmentally associated resistance mechanisms, which are thought to have evolved through selection by the agricultural application of azole fungicides, are now distributed globally. Understanding the effect that azole resistance is having on the genetic diversity and global population of A. fumigatus will help mitigate drug-resistant aspergillosis and maintain the azole class of fungicides for future use in both medicine and crop protection.

Invasive Aspergillosis in Pediatric Leukemia Patients: Prevention and Treatment

The purpose of this article is to review and update the strategies for prevention and treatment of invasive aspergillosis (IA) in pediatric patients with leukemia and in patients with hematopoietic stem cell transplantation. The major risk factors associated with IA will be described since their recognition constitutes the first step of prevention. The latter is further analyzed into chemoprophylaxis and non-pharmacologic approaches. Triazoles are the mainstay of anti-fungal prophylaxis while the other measures revolve around reducing exposure to mold spores. Three levels of treatment have been identified: (a) empiric, (b) pre-emptive, and (c) targeted treatment. Empiric is initiated in febrile neutropenic patients and uses mainly caspofungin and liposomal amphotericin B (LAMB). Pre-emptive is a diagnostic driven approach attempting to reduce unnecessary use of anti-fungals. Treatment targeted at proven or probable IA is age-dependent, with voriconazole and LAMB being the cornerstones in >2yrs and <2yrs age groups, respectively.

Global Molecular Diversity of the Halotolerant Fungus Hortaea werneckii

A global set of clinical and environmental strains of the halotolerant black yeast-like fungus Hortaea werneckii are analyzed by multilocus sequencing and AFLP, and physiological parameters are determined. Partial translation elongation factor 1-α proves to be suitable for typing because of the presence/absence of introns and also the presence of several SNPs. Local clonal expansion could be established by a combination of molecular methods, while the population from the Mediterranean Sea water also responds differently to combined temperature and salt stress. The species comprises molecular populations, which in part also differ physiologically allowing further diversification, but clinical strains did not deviate significantly from their environmental counterparts.

Comparison of Two Highly Discriminatory Typing Methods to Analyze Aspergillus fumigatus Azole Resistance

Aspergillus fumigatus molecular typing has become increasingly more important for detecting outbreaks as well as for local and global epidemiological investigations and surveillance. Over the years, many different molecular methods have been described for genotyping this species. Some outstanding approaches are based on microsatellite markers (STRAf assay, which is the current gold standard), or based on sequencing data (TRESP typing improved in this work with a new marker and was renamed TRESPERG). Both methodologies were used to type a collection of 212 A. fumigatus isolates that included 70 azole resistant strains with diverse resistance mechanisms from different geographic locations. Our results showed that both methods are totally reliable for epidemiological investigations showing similar stratification of the A. fumigatus population. STRAf assay offered higher discriminatory power (D = 0.9993) than the TRESPERG typing method (D = 0.9972), but the latter does not require specific equipment or skilled personnel, allowing for a prompt integration into any clinical microbiology laboratory. Among azole resistant isolates, two groups were differentiated considering their resistance mechanisms: cyp51A single point mutations (G54, M220, or G448), and promoter tandem repeat integrations with or without cyp51A modifications (TR₃₄/L98H, TR₄₆/Y121F/A289T, or TR₅₃). The genotypic differences were assessed to explore the population structure as well as the genetic relationship between strains and their azole resistance profile. Genetic cluster analyses suggested that our A. fumigatus population was formed by 6–7 clusters, depending on the methodology. Also, the azole susceptible and resistance population showed different structure and organization. The combination of both methodologies resolved the population structure in a similar way to what has been described in whole-genome sequencing works.

Tuberkulose und andere durch Luft übertragbare Infektionserkrankungen: Krankenhaushygiene zur Vermeidung und Eindämmung

Die Tuberkulose (TB) gehört weltweit zu den am häufigsten auftretenden Infektionskrankheiten und wird fast ausschließlich über die Luft (aerogen) übertragen. Nachdem in Deutschland die Lungentuberkulosefallzahlen über Jahre hinweg stagnierten, ist seit 2013 wieder ein Anstieg der Inzidenzen zu verzeichnen (RKI 2016). Als Ursache hierfür werden die aktuellen demographischen Entwicklungen (Migration und Mobilität) gesehen. Die Kenntnis der epidemiologischen Situation ist von zentraler Bedeutung, um bei Vorliegen der Verdachtsdiagnose Tuberkulose sowie der Einbeziehung einer möglichen Resistenzproblematik frühzeitig adäquate krankenhaushygienische Maßnahmen einzuleiten. Als aerogen übertragbar werden auch die Aspergillose sowie Masern, Windpocken und Herpes zoster eingestuft (CDC 2007). Die Aspergillose ist eine relativ seltene, aber häufig letal verlaufende Pilzinfektion, die überwiegend bei immunsupprimierten Patienten auftritt. Krankenhaushygienische Schutzmaßnahmen können die Risiken einer Exposition und somit das Erkrankungsrisiko minimieren. Die zentralen Maßnahmen zur Kontrolle und Prävention von aerogen übertragbaren Infektionen sind Gegenstand dieses Kapitels.

Ultraviolet germicidal irradiation in tap water contaminated by Aspergillus spp

We investigated the effect of ultraviolet germicidal irradiation (UVI) from a low-pressure mercury lamp on several pathogenic Aspergillus spp. including A. flavipes, A. flavus, A. fumigatus, A. glaucus, A. nidulans, A. niger, A. terreus, A. ustus and A. versicolor suspended in tap water under laboratory-scale conditions. It was shown that within 10 s of exposure, time species such as A. glaucus, A. niudulans and A. ustus were completely inactivated, while 40 s were needed for the elimination of all the species tested. A. flavus and A. niger were found to be less susceptible than other species. Based on these results we conclude that UV disinfection could effectively inactivate Aspergillus spp. in tap water. Such disinfection could be used to reduce potential exposure of high-risk patients to fungal aerosols, particularly in hospital settings, where point-of-use (POU) UV light devices could be installed to provide safe water at a very low cost.

Abundance, genetic diversity and sensitivity to demethylation inhibitor fungicides of Aspergillus fumigatus isolates from organic substrates with special emphasis on compost

BACKGROUND

Aspergillus fumigatus is a widespread fungus that colonizes dead organic substrates but it can also cause fatal human diseases. Aspergilloses are treated with demethylation inhibitor (DMI) fungicides; however, resistant isolates appeared recently in the medical and also environmental area. The present study aims at molecular characterizing and quantifying A. fumigatus in major environmental habitats and determining its sensitivity to medical and agricultural DMI fungicides.

RESULTS

A. fumigatus was isolated only rarely from soil and meadow/forest organic matter but high concentrations (10³ to 10⁷  cfu/g) were detected in substrates subjected to elevated temperatures, such as compost and silage. High genetic diversity of A. fumigatus from compost was found based on SSR markers, distinguishing among fungal isolates even when coming from the same substrate sample, while subclustering was observed based on mutations in cyp51A gene. Several cyp51A amino acid substitutions were found in 15 isolates, although all isolates were fully sensitive to the tested DMI fungicides, with exception of one isolate in combination with one fungicide.

CONCLUSION

This study suggests that the tested A. fumigatus isolates collected in Italy, Spain and Hungary from the fungus' major living habitats (compost) and commercial growing substrates are not potential carriers for DMI resistance in the environment. © 2017 Society of Chemical Industry.

Use of AFLP for the study of eukaryotic pathogens affecting humans

Amplified fragment length polymorphism (AFLP) is a genotyping technique based on PCR amplification of specific restriction fragments from a particular genome. The methodology has been extensively used in plant biology to solve a variety of scientific questions, including taxonomy, molecular epidemiology, systematics, population genetics, among many others. The AFLP share advantages and disadvantages with other types of molecular markers, being particularly useful in organisms with no previous DNA sequence knowledge. In eukaryotic pathogens, the technique has not been extensively used, although it has the potential to solve many important issues as it allows the simultaneous examination of hundreds or even thousands of polymorphic sites in the genome of the organism. Here we describe the main applications published on the use of AFLP in eukaryotic pathogens, with emphasis in species of the groups fungi, protozoa and helminths, and discuss the role of this methodology in the context of new techniques derived from the advances of the next generation sequencing.

Free chlorine and monochloramine inactivation kinetics of Aspergillus and Penicillium in drinking water

Fungi are near-ubiquitous in potable water distribution systems, but the disinfection kinetics of commonly identified fungi are poorly studied. In the present study, laboratory scale experiments were conducted to evaluate the inactivation kinetics of Aspergillus fumigatus, Aspergillus versicolor, and Penicillium purpurogenum by free chlorine and monochloramine. The observed inactivation data were then fit to a delayed Chick-Watson model. Based on the model parameter estimation, the Ct values (integrated product of disinfectant concentration C and contact time t over defined time intervals) for 99.9% inactivation of the tested fungal strains ranged from 48.99 mg min/L to 194.7 mg min/L for free chlorine and from 90.33 mg min/L to 531.3 mg min/L for monochloramine. Fungal isolates from a drinking water system (Aspergillus versicolor and Penicillium purpurogenum) were more disinfection resistant than Aspergillus fumigatus type and clinical isolates. The required 99.9% inactivation Ct values for the tested fungal strains are higher than E. coli, a commonly monitored indicator bacteria, and within a similar range for bacteria commonly identified within water distribution systems, such as Mycobacterium spp. and Legionella spp.

Spatial Patterns and Impacts of Environmental and Climatic Factors on Canine Sinonasal Aspergillosis in Northern California

Sinonasal aspergillosis (SNA) causes chronic nasal discharge in dogs and has a worldwide distribution, although most reports of SNA in North America originate from the western USA. SNA is mainly caused by Aspergillus fumigatus, a ubiquitous saprophytic filamentous fungus. Infection is thought to follow inhalation of spores. SNA is a disease of the nasal cavity and/or sinuses with variable degrees of local invasion and destruction. While some host factors appear to predispose to SNA (such as belonging to a dolichocephalic breed), environmental risk factors have been scarcely studied. Because A. fumigatus is also the main cause of invasive aspergillosis in humans, unraveling the distribution and the environmental and climatic risk factors for this agent in dogs would be of great benefit for public health studies, advancing understanding of both distribution and risk factors in humans. In this study, we reviewed electronic medical records of 250 dogs diagnosed with SNA between 1990 and 2014 at the University of California Davis Veterinary Medical Teaching Hospital (VMTH). A 145-mile radius catchment area around the VMTH was selected. Data were aggregated by zip code and incorporated into a multivariate logistic regression model. The logistic regression model was compared to an autologistic regression model to evaluate the effect of spatial autocorrelation. Traffic density, active composting sites, and environmental and climatic factors related with wind and temperature were significantly associated with increase in disease occurrence in dogs. Results provide valuable information about the risk factors and spatial distribution of SNA in dogs in Northern California. Our ultimate goal is to utilize the results to investigate risk-based interventions, promote awareness, and serve as a model for further studies of aspergillosis in humans.

Fungal Contaminants in Drinking Water Regulation? A Tale of Ecology, Exposure, Purification and Clinical Relevance

Microbiological drinking water safety is traditionally monitored mainly by bacterial parameters that indicate faecal contamination. These parameters correlate with gastro-intestinal illness, despite the fact that viral agents, resulting from faecal contamination, are usually the cause. This leaves behind microbes that can cause illness other than gastro-intestinal and several emerging pathogens, disregarding non-endemic microbial contaminants and those with recent pathogenic activity reported. This white paper focuses on one group of contaminants known to cause allergies, opportunistic infections and intoxications: Fungi. It presents a review on their occurrence, ecology and physiology. Additionally, factors contributing to their presence in water distribution systems, as well as their effect on water quality are discussed. Presence of opportunistic and pathogenic fungi in drinking water can pose a health risk to consumers due to daily contact with water, via several exposure points, such as drinking and showering. The clinical relevance and influence on human health of the most common fungal contaminants in drinking water is discussed. Our goal with this paper is to place fungal contaminants on the roadmap of evidence based and emerging threats for drinking water quality safety regulations.

A New Aspergillus fumigatus Typing Method Based on Hypervariable Tandem Repeats Located within Exons of Surface Protein Coding Genes (TRESP)

Aspergillus fumigatus is a saprotrophic mold fungus ubiquitously found in the environment and is the most common species causing invasive aspergillosis in immunocompromised individuals. For A. fumigatus genotyping, the short tandem repeat method (STRAf) is widely accepted as the first choice. However, difficulties associated with PCR product size and required technology have encouraged the development of novel typing techniques. In this study, a new genotyping method based on hypervariable tandem repeats within exons of surface protein coding genes (TRESP) was designed. A. fumigatus isolates were characterized by PCR amplification and sequencing with a panel of three TRESP encoding genes: cell surface protein A; MP-2 antigenic galactomannan protein; and hypothetical protein with a CFEM domain. The allele sequence repeats of each of the three targets were combined to assign a specific genotype. For the evaluation of this method, 126 unrelated A. fumigatus strains were analyzed and 96 different genotypes were identified, showing a high level of discrimination [Simpson’s index of diversity (D) 0.994]. In addition, 49 azole resistant strains were analyzed identifying 26 genotypes and showing a lower D value (0.890) among them. This value could indicate that these resistant strains are closely related and share a common origin, although more studies are needed to confirm this hypothesis. In summary, a novel genotyping method for A. fumigatus has been developed which is reproducible, easy to perform, highly discriminatory and could be especially useful for studying outbreaks.

Risk stratification for invasive fungal infections in patients with hematological malignancies: SEIFEM recommendations

Invasive fungal infections (IFIs) are an important cause of morbidity and mortality in immunocompromised patients. Patients with hematological malignancies undergoing conventional chemotherapy, autologous or allogeneic hematopoietic stem cell transplantation are considered at high risk, and Aspergillus spp. represents the most frequently isolated micro-organisms. In the last years, attention has also been focused on other rare molds (e.g., Zygomycetes, Fusarium spp.) responsible for devastating clinical manifestations. The extensive use of antifungal prophylaxis has reduced the infections from yeasts (e.g., candidemia) even though they are still associated with high mortality rates. This paper analyzes concurrent multiple predisposing factors that could favor the onset of fungal infections. Although neutropenia is common to almost all hematologic patients, other factors play a key role in specific patients, in particular in patients with AML or allogeneic HSCT recipients. Defining those patients at higher risk of IFIs may help to design the most appropriate diagnostic work-up and antifungal strategy.

Microbial pathogens in source and treated waters from drinking water treatment plants in the United States and implications for human health

An occurrence survey was conducted on selected pathogens in source and treated drinking water collected from 25 drinking water treatment plants (DWTPs) in the United States. Water samples were analyzed for the protozoa Giardia and Cryptosporidium (EPA Method 1623); the fungi Aspergillus fumigatus, Aspergillus niger and Aspergillus terreus (quantitative PCR [qPCR]); and the bacteria Legionella pneumophila (qPCR), Mycobacterium avium, M. avium subspecies paratuberculosis, and Mycobacterium intracellulare (qPCR and culture). Cryptosporidium and Giardia were detected in 25% and in 46% of the source water samples, respectively (treated waters were not tested). Aspergillus fumigatus was the most commonly detected fungus in source waters (48%) but none of the three fungi were detected in treated water. Legionella pneumophila was detected in 25% of the source water samples but in only 4% of treated water samples. M. avium and M. intracellulare were both detected in 25% of source water, while all three mycobacteria were detected in 36% of treated water samples. Five species of mycobacteria, Mycobacterium mucogenicum, Mycobacterium phocaicum, Mycobacterium triplex, Mycobacterium fortuitum, and Mycobacterium lentiflavum were cultured from treated water samples. Although these DWTPs represent a fraction of those in the U.S., the results suggest that many of these pathogens are widespread in source waters but that treatment is generally effective in reducing them to below detection limits. The one exception is the mycobacteria, which were commonly detected in treated water, even when not detected in source waters.

Practice Guidelines for the Diagnosis and Management of Aspergillosis: 2016 Update by the Infectious Diseases Society of America

It is important to realize that guidelines cannot always account for individual variation among patients. They are not intended to supplant physician judgment with respect to particular patients or special clinical situations. IDSA considers adherence to these guidelines to be voluntary, with the ultimate determination regarding their application to be made by the physician in the light of each patient's individual circumstances.

Azole-resistant Aspergillus fumigatus in Denmark: a laboratory-based study on resistance mechanisms and genotypes

Azole-resistant Aspergillus fumigatus originating from the environment as well as induced during therapy are continuously emerging in Danish clinical settings. We performed a laboratory-based retrospective study (2010-2014) of azole resistance and genetic relationship of A. fumigatus at the national mycology reference laboratory of Denmark. A total of 1162 clinical and 133 environmental A. fumigatus isolates were identified by morphology, thermotolerance and/or β-tubulin sequencing. Screening for azole resistance was carried out using azole agar, and resistant isolates were susceptibility tested by the EUCAST (European Committee on Antimicrobial Susceptibility Testing) E.Def 9.2 reference method and CYP51A sequenced. Genotyping was performed for outbreak investigation and, when appropriate, short tandem repeat Aspergillus fumigatus microsatellite assay. All 133 environmental A. fumigatus isolates were azole susceptible. However, from 2010 to 2014, there was an increasing prevalence of azole resistance (from 1.4 to 6% isolates (p <0.001) and 1.8 to 4% patients (p <0.05)) among the clinical isolates, with the well-known environmental CYP51A variant TR34/L98H responsible for >50% of the azole resistance mechanisms. Among 184 Danish A. fumigatus isolates, 120 unique genotypes were identified and compared to a collection of 1822 international genotypes. Seven (5.8%) Danish genotypes were shared between isolates within Denmark but with different origin, 19 (15.8%) were shared with foreign genotypes, and two (11.8%) of 17 genotypes of isolates carrying the TR34/L98H resistance mechanisms were identical to two Dutch TR34/L98H isolates. Our findings underlines the demand for correct identification and susceptibility testing of clinical mould isolates. Furthermore, although complex, genotyping supported the hypotheses regarding clonal expansion and the potential of a single origin for the TR34/L98H clone.

PCR-Internal Transcribed Spacer (ITS) genes sequencing and phylogenetic analysis of clinical and environmental Aspergillus species associated with HIV-TB co infected patients in a hospital in Abeokuta, southwestern Nigeria

BACKGROUND

Aspergillosis has been identified as one of the hospital acquired infections but the contribution of water and inhouse air as possible sources of Aspergillus infection in immunocompromised individuals like HIV-TB patients have not been studied in any hospital setting in Nigeria.

OBJECTIVE

To identify and investigate genetic relationship between clinical and environmental Aspergillus sp. associated with HIV-TB co infected patients.

METHODS

DNA extraction, purification, amplification and sequencing of Internal Transcribed Spacer (ITS) genes were performed using standard protocols. Similarity search using BLAST on NCBI was used for species identification and MEGA 5.0 was used for phylogenetic analysis.

RESULTS

Analyses of sequenced ITS genes of selected fourteen (14) Aspergillus isolates identified in the GenBank database revealed Aspergillus niger (28.57%), A. tubingensis (7.14%), A. flavus (7.14%) and A. fumigatus (57.14%). Aspergillus in sputum of HIV patients were Aspergillus niger, A. fumigatus, A. tubingensis and A. flavus. Also, A. niger and A. fumigatus were identified from water and open-air. Phylogenetic analysis of sequences yielded genetic relatedness between clinical and environmental isolates.

CONCLUSION

Water and air in health care settings in Nigeria are important sources of Aspergillus sp. for HIV-TB patients.

Fungi, Water Supply and Biofilms

Even though it has been studied for many years, water-related infectious risk still exists in both care and community environments due to the possible presence of numerous microorganisms such as bacteria, fungi and protists. People can be exposed directly to these microorganisms either through aerosols and water, after ingestion, inhalation, skin contact and entry through mucosal membranes, or indirectly usually due to pre-treatment of some medical devices. Species belonging to genera such as Aspergillus, Penicillium, Pseudallesheria, Fusarium, Cuninghamella, Mucor and in some particular cases Candida have been isolated in water from health facilities and their presence is particularly related to the unavoidable formation of a polymicrobial biofilm in waterlines. Fungi isolation methods are based on water filtration combined with conventional microbiology cultures and/or molecular approaches; unfortunately, these are still poorly standardized. Moreover, due to inappropriate culture media and inadequate sampling volumes, the current standardized methods used for bacterial research are not suitable for fungal search. In order to prevent water-related fungal risk, health facilities have implemented measures such as ultraviolet radiation to treat the input network, continuous chemical treatment, chemical or thermal shock treatments, or microfiltration at points of use. This article aims to provide an overview of fungal colonization of water (especially in hospitals), involvement of biofilms that develop in waterlines and application of preventive strategies.

Transcriptome Profiles of Human Lung Epithelial Cells A549 Interacting with Aspergillus fumigatus by RNA-Seq

Lung epithelial cells constitute the first defense line of host against the inhaled Aspergillus fumigatus; however, the transcriptional response of human alveolar type II epithelial cells was still unclear. Here we used RNA-Seq technology to assess the transcriptome profiles of A549 cells following direct interaction with conidia of A. fumigatus. The total number of identified genes was 19118. Compared with uninfected A549 cells, 459 genes were differentially expressed in cells co-incubated with conidia for 8 h, including 302 up-regulated genes and 157 down-regulated genes. GO and KEGG pathway enrichment analysis showed that most of the up-regulated genes were related to immune response, chemotaxis and inflammatory response and enriched in cytokine-cytokine receptor interaction, JAK-STAT and MAPK signaling pathways. The down-regulated genes were mainly enriched for terms associated with development, hemopoiesis and ion transport. Among them, EGR4 and HIST1H4J gene had the maximum of fold change in up-regulated and down-regulated genes, respectively. Fourteen up-regulated genes and three down-regulated genes were further validated and significant increase on expression of IL-6, IL-8 and TNF-α in A549 cells were confirmed by qRT-PCR during the interaction of A549 cells with A. fumigatus. Besides, western blot showed that expression of two proteins (ARC, EGR1) significantly increased in A549 cells during interaction with A. fumigatus conidia for 8h. Interference of endogenous expression of ARC or EGR1 protein in A549 cells reduced the internalization of A. fumigatus. These results provided important insights into dynamic changes of gene expression in lung epithelial cells, especially its strong immunological response against A. fumigatus infection.

En-suite bathrooms in protected haematology wards: a source of filamentous fungal contamination?

BACKGROUND

In spite of 25 recently built high-risk haematology rooms with a protected environment and fitted with en-suite bathrooms in our university hospital centre in 2008, sporadic cases of hospital-acquired invasive aspergillosis remained in these wards.

AIM

This study aimed to identify unsuspected environmental sources of filamentous fungal contamination in these rooms.

METHODS

Over two months, environmental fungal flora in the air (150 samples) as well as air particle counting and physical environmental parameters (airspeed, temperature, humidity, pressure) were prospectively monitored twice on the sampling day in all 25 protected rooms and en-suite bathrooms in use, and on bathroom surfaces (150 samples).

FINDINGS

In rooms under laminar airflow, in the presence of patients during sampling sessions, fungi were isolated in two samples (4%, 2/50) with a maximum value of 2cfu/500L (none was Aspergillus sp.). However, 88% of the air samples (44/50) in the bathroom were contaminated with a median range and maximum value of 2 and 16cfu/500L. Aspergillus spp. were involved in 24% of contaminated samples (12/44) and A. fumigatus in 6% (3/44). Bathroom surfaces were contaminated by filamentous fungi in 5% of samples (8/150).

CONCLUSION

This study highlighted that en-suite bathrooms in protected wards are likely to be a source of fungi. Before considering specific treatment of air in bathrooms, technicians have first corrected the identified deficiencies: replacement of high-efficiency particulate air filters, improvement of air control automation, and restoration of initial technical specifications. Assessment of measure effectiveness is planned.

Phylogenetic analyses on the diversity of Aspergillus fumigatus sensu lato based on five orthologous loci

One hundred isolates of Aspergillus fumigatus sensu lato mainly from China, as well as from Australia, France, India, Indonesia, Ireland, UK, and USA were analyzed to infer their sequence types (STs) and population diversity based on partial calmodulin, calcineurin regulatory subunit B, beta-tubulin, cytochrome C and calcineurin catalytic subunit A genes as well as their mating types, using ClonalFrame, Structure and MEGA software. Our results inferred 48 STs and showed that most of the STs or lineages evolved independently and without clear population structure among them. Whereas one lineage was recognized that could be a true population and in which one clade might diverge into another distinct lineage, namely, a cryptic species, A. neoellipticus. In addition, we found that mutation, parasexual, and sexual recombination could, respectively, play specific roles in the evolution of these fungi. Our results also showed that MAT1-1/MAT1-2 mating type ratios of A. fumigatus sensu lato was biased to nearly 1:1.4 (20/28) when clone-corrected, but when not clone-corrected, the ratio of MAT1-1/MAT1-2 was so biased as near 1:2 (35/65), which might mean that isolates with MAT1-2 are in the process of losing sexual ability preceding those with MAT1-1.

New insights concerning the occurrence of fungi in water sources and their potential pathogenicity

Fungi are known to occur ubiquitously in the environment. In the past years, the occurrence of filamentous fungi in the aquatic environment has been a subject of growing interest. This study describes the occurrence of various fungal genera in different drinking water sources being Penicillium and Trichoderma the most representative ones (30% and 17%, respectively). Also, 24 fungal species that have not been previously described in the aquatic environment are reported in this study, being once again the major species from the Penicillium genera. This study therefore contributes to the knowledge on the richness of fungi diversity in water. 68% of the described species were found to be able to grow at 30 °C but only Aspergillus fumigatus, Aspergillus viridinutans and Cunninghamella bertholletiae were able to grow at the higher temperature tested (42 °C). 66% of the species that were able to grow at 30 °C have spore sizes below 5 μm which enables them to cause breathing infections. These were therefore identified as potential pathogenic species.

[Aspergillus species in hospital environments with pediatric patients in critical condition]

BACKGROUND

Aspergillus is a group of opportunistic fungi that cause infections, with high morbimortality in immunosuppressed patients. Aspergillus fumigatus is the most frequent species in these infections, although the incidence of other species has increased in the last few years.

AIMS

To evaluate the air fungal load and the diversity of Aspergillus species in hospitals with pediatric patients in critical condition.

METHODS

The Intensive Care Unit and Burns Unit of a pediatric hospital were sampled every 15 days during the autumn and spring seasons. The air samples were collected with SAS Super 100(®) and the surface samples were collected by swab method.

RESULTS

The UFC/m(3) counts found exceeded the acceptable levels. The UFC/m(3) and the diversity of Aspergillus species found in the Intensive Care Unit were higher than those found in the Burns Unit. The fungal load and the diversity of species within the units were higher than those in control environments. The use of both methods -SAS and swab- allowed the detection of a higher diversity of species, with 96 strains of Aspergillus being isolated and 12 species identified. The outstanding findings were Aspergillus sydowii, Aspergillus niger, Aspergillus flavus, Aspergillus terreus and Aspergillus parasiticus, due to their high frequency. Aspergillus fumigatus, considered unacceptable in indoor environments, was isolated in both units.

CONCLUSIONS

Aspergillus was present with high frequency in these units. Several species are of interest in public health for being potential pathogenic agents. Air control and monitoring are essential in the prevention of these infections.

Is azole resistance in Aspergillus fumigatus a problem in Spain?

Aspergillus fumigatus complex comprises A. fumigatus and other morphologically indistinguishable cryptic species. We retrospectively studied 362 A. fumigatus complex isolates (353 samples) from 150 patients with proven or probable invasive aspergillosis or aspergilloma (2, 121, and 6 samples, respectively) admitted to the hospital from 1999 to 2011. Isolates were identified using the β-tubulin gene, and only 1 isolate per species found in each sample was selected. Antifungal susceptibility to azoles was determined using the CLSI M38-A2 procedure. Isolates were considered resistant if they showed an MIC above the breakpoints for itraconazole, voriconazole, or posaconazole (>2, >2, or >0.5 μg/ml). Most of the samples yielded only 1 species (A. fumigatus [n = 335], A. novofumigatus [n = 4], A. lentulus [n = 3], A. viridinutans [n = 1], and Neosartorya udagawae [n = 1]). The remaining samples yielded a combination of 2 species. Most of the patients were infected by a single species (A. fumigatus [n = 143] or A. lentulus [n = 2]). The remaining 5 patients were coinfected with multiple A. fumigatus complex species, although A. fumigatus was always involved; 4 of the 5 patients were diagnosed in 2009 or later. Cryptic species were less susceptible than A. fumigatus. The frequency of resistance among A. fumigatus complex and A. fumigatus to itraconazole, voriconazole, and posaconazole was 2.5 and 0.3%, 3.1 and 0.3%, and 4.2 and 1.8%, respectively, in the per-isolate analysis and 1.3 and 0.7%, 2.6 and 0.7%, and 6 and 4% in the per-patient analysis. Only 1 of the 6 A. fumigatus isolates in which the cyp51A gene was sequenced had a mutation at position G448. The proportion of patients infected by azole-resistant A. fumigatus isolates was low.

Identification and typing of isolates of Cyphellophora and relatives by use of amplified fragment length polymorphism and rolling circle amplification

The species diversity and identification of black fungi belonging to Cyphellophora and Phialophora, which colonize and infect human skin and nails, were studied using amplified fragment length polymorphism (AFLP). A total of 76 Cyphellophora and Phialophora isolates were evaluated, and their delimitation was compared to earlier studies using multilocus sequencing. The results of the AFLP analysis and sequencing were in complete agreement with each other. Seven species-specific padlock probes for the most prevalent species were designed on the basis of the ribosomal DNA internal transcribed spacer region, and identification of the respective species could easily be achieved with the aid of rolling circle amplification.

Plumbing of hospital premises is a reservoir for opportunistically pathogenic microorganisms: a review

Several bacterial species that are natural inhabitants of potable water distribution system biofilms are opportunistic pathogens important to sensitive patients in healthcare facilities. Waterborne healthcare-associated infections (HAI) may occur during the many uses of potable water in the healthcare environment. Prevention of infection is made more challenging by lack of data on infection rate and gaps in understanding of the ecology, virulence, and infectious dose of these opportunistic pathogens. Some healthcare facilities have been successful in reducing infections by following current water safety guidelines. This review describes several infections, and remediation steps that have been implemented to reduce waterborne HAIs.