The current state of clinical mycology in Africa: a European Confederation of Medical Mycology and International Society for Human and Animal Mycology survey

Comparative Analysis of the Clarus Aspergillus Galactomannan Enzyme Immunoassay Prototype for the Diagnosis of Invasive Pulmonary Aspergillosis in Bronchoalveolar Lavage Fluid

BACKGROUND

Galactomannan (GM) testing using Platelia Aspergillus enzyme immunoassay (Platelia AGM) from bronchoalveolar lavage fluid (BALF) aids in early diagnosis of invasive pulmonary aspergillosis (IPA). Globally, only a minority of laboratories have the capability to perform on-site GM testing, necessitating accessible and affordable alternatives. Hence, we conducted a comparative evaluation of the new clarus Aspergillus GM enzyme immunoassay prototype (clarus AGM prototype) with Platelia AGM using BALF samples.

METHODS

This is a single-center, prospective, cross-sectional study, where Platelia AGM testing was routinely performed followed by clarus AGM prototype testing in those with true positive or true negative AGM test results according to the 2020 EORTC/MSG and the 2024 FUNDICU consensus definitions. Descriptive statistics, ROC curve analysis, and Spearman's correlation analysis were used to evaluate analytical performance of the clarus AGM prototype assay.

RESULTS

This study enrolled 259 adult patients, of which 53 (20%) were classified as probable IPA, while 206 did not fulfill IPA-criteria. Spearman's correlation analysis revealed a strong correlation between the two assays (rho = 0.727, p < 0.001). The clarus AGM prototype had a sensitivity of 96% (51/53) and a specificity of 74% (153/206) for differentiating probable versus no IPA when using the manufacturer recommended cut-off. ROC curve analysis showed an AUC of 0.936 (95% CI 0.901-0.971) for the clarus AGM prototype, while the Platelia AGM yielded an AUC of 0.918 (95% CI 0.876-0.959).

CONCLUSIONS

Clarus AGM prototype demonstrated a strong correlation and promising test performance, comparable to Platelia AGM, rendering it a viable alternative in patients at risk of IPA.

Comparison of galactomannan lateral flow assay and enzyme immunoassay to identify Aspergillus spp. in bronchoalveolar lavage fluid

Aspergillus species can colonize and infect immunocompetent and immunocompromised hosts. Conventional fungal identification depends on microscopic analysis and microorganism medium growth. Other diagnostic methods, non-growth dependent, to invasive fungal infections, are the biomarkers that detect circulating polysaccharides, for example, 1-3-β-d-Glucan and galactomannan. Both are polysaccharides present on the external layer of fungi cell wall and can be detected in clinical samples during the growth of the fungus in the patient. This study aimed to compare the galactomannan detection of Lateral Flow Assay and Enzyme Immunoassay methods in Bronchoalveolar Lavage Fluid. The galactomannan antigen in Bronchoalveolar Lavage Fluid was measured using Enzyme Immunoassay according to the manufacturer's instructions (PLATELIA ASPERGILLUS™ BioRad) and, using a Lateral Flow Assay according to the manufacturer's instructions (Galactomannan LFA IMMY©). The 71 samples were Bronchoalveolar Lavage Fluid of patients hospitalized at Unicamp Clinical Hospital between 2019 and 2021; of these samples 12/71 (16.9 %) resulted in positive Galactomannan-Lateral Flow Assay. In contrast, Galactomannan-Enzyme Immunoassay resulted as positive in 9/71 (12.6 %) samples, a difference that showed not significant statistically (p-value = 0.36) Comparing both assays' results identified 8 divergences between them, about 11 % of the total sample. The Sensitivity (73.3 %), Specificity (92.35 %), Positive Predictive Value (62.85 %) and Negative Predictive Value (95.15 %) of Lateral Flow Assay were calculated using the Galactomannan Enzyme Immunoassay as standard. The Lateral Flow Assay demonstrated good results when compared with the Enzyme Immunoassay.

Systematic Review of Candidemia in Brazil: Unlocking Historical Trends and Challenges in Conducting Surveys in Middle-Income Countries

INTRODUCTION

Candidemia, a bloodstream infection predominantly affecting critically ill patients, poses a significant global health threat especially with the emergence of non-albicans Candida species, including drug-resistant strains. In Brazil, limited access to advanced diagnostic tools and trained microbiologists hampers accurate identification of Candida species and susceptibility to antifungals testing hindering surveillance efforts.

METHODS

We conducted a systematic review spanning publications from 2017 to 2023 addressing Candida species distribution and antifungal susceptibility among Brazilian patients with candidemia.

RESULTS

Despite initially identifying 7075 records, only 16 met inclusion criteria providing accurate information of 2305 episodes of candidemia. The predominant species were C. albicans, C. parapsilosis, and C. tropicalis, followed by notable proportions of Nakaseomyces glabratus. Limited access to diagnostic tests was evident as only 5 out of 16 studies on candidemia were able to report antifungal susceptibility testing results. In vitro resistance to echinocandins was rare (only 6/396 isolates, 1,5%). In counterpart, fluconazole exhibited resistance rates ranging from 0 to 43%, with great heterogeneity among different studies and species of Candida considered.

CONCLUSION

Our review underscores the critical need for enhanced surveillance and research efforts to address the evolving landscape of candidemia and antifungal resistance in Brazil. Despite some limitations, available data suggest that while resistance to echinocandins and amphotericin B remains rare, there is a growing concern regarding resistance to fluconazole among Candida species.

Infectious complications in the paediatric immunocompromised host: a narrative review

BACKGROUND

Infections are a major cause of morbidity in children with primary or secondary immunodeficiency, and have a negative impact on overall outcome.

OBJECTIVES

This narrative review presents select paediatric-specific aspects regarding the clinical impact, diagnosis, management, and follow-up of infectious complications in patients with primary and secondary immunodeficiencies.

SOURCES

PubMed until January 2024 and searched references in identified articles including the search terms: infection, immunodeficiency or cancer, diagnostics, antimicrobial agents, bacteria or fungus or virus, and follow-up.

CONTENT

Major advances have been made in the early detection and management of patients with primary immunodeficiency, and multiple analyses report in children with cancer on risk groups and periods of risk for infectious complications. Although many diagnostic tools are comparable between children and adults, specific considerations have to be applied, such as minimizing the use of radiation. Antimicrobial drug development remains a major challenge in the paediatric setting, which includes the establishment of appropriate dosing and paediatric approval. Last, long-term follow-up and the impact of late effects are extremely important to be considered in the management of immunocompromised paediatric patients.

IMPLICATIONS

Although infectious disease supportive care of immunocompromised children and adolescents has considerably improved over the last three decades, close international collaboration is needed to target the specific challenges in this special population.

Candida auris: A Systematic Review of a Globally Emerging Fungal Pathogen in Africa

Candida auris is a World Health Organization critical priority fungal pathogen. We conducted a systematic review to describe its epidemiology in Africa. PubMed and Google scholar databases were searched between January 2009 and September 2023 for clinical studies on C. auris cases and/or isolates from Africa. Reviews were excluded. We included 19 studies, involving at least 2529 cases from 6 African countries with the most, 2372 (93.8%), reported from South Africa. Whole-genome sequencing of 127 isolates identified 100 (78.7%) as clade III. Among 527 isolates, 481 (91.3%) were resistant to fluconazole, 108 (20.5%) to amphotericin B, and 9 (1.7%) to micafungin. Ninety of 211 (42.7%) patients with clinical outcomes died. C. auris is associated with high mortality and antifungal resistance, yet this critical pathogen remains underreported in Africa. Collaborative surveillance, fungal diagnostics, antifungals, and sustainable infection control practices are urgently needed for containment.

The laboratory investigation, management, and infection prevention and control of Candida auris: a narrative review to inform the 2024 national guidance update in England

The emergent fungal pathogen Candida auris is increasingly recognised as an important cause of healthcare-associated infections globally. It is highly transmissible, adaptable, and persistent, resulting in an organism with significant outbreak potential that risks devastating consequences. Progress in the ability to identify C. auris in clinical specimens is encouraging, but laboratory diagnostic capacity and surveillance systems are lacking in many countries. Intrinsic resistance to commonly used antifungals, combined with the ability to rapidly acquire resistance to therapy, substantially restricts treatment options and novel agents are desperately needed. Despite this, outbreaks can be interrupted, and mortality avoided or minimised, through the application of rigorous infection prevention and control measures with an increasing evidence base. This review provides an update on epidemiology, the impact of the COVID-19 pandemic, risk factors, identification and typing, resistance profiles, treatment, detection of colonisation, and infection prevention and control measures for C. auris. This review has informed a planned 2024 update to the United Kingdom Health Security Agency (UKHSA) guidance on the laboratory investigation, management, and infection prevention and control of Candida auris. A multidisciplinary response is needed to control C. auris transmission in a healthcare setting and should emphasise outbreak preparedness and response, rapid contact tracing and isolation or cohorting of patients and staff, strict hand hygiene and other infection prevention and control measures, dedicated or single-use equipment, appropriate disinfection, and effective communication concerning patient transfers and discharge.

A diverse spectrum of mycoses histologically diagnosed in Ghana: Insights from a 10-year retrospective study

In Ghana, most laboratory diagnoses of severe mycoses are based on histopathology findings due to inadequate availability of serology, culture, and molecular tests. The aim of this study was to evaluate the spectrum of mycoses diagnosed in Ghana. We retrospectively reviewed reports from 2012 to 2021 from three major pathology laboratories in Ghana to identify reports indicating the presence of fungal elements and diagnosis of a mycosis, then extracted demographic, clinical history, site of infection, stain(s), used and diagnosed mycosis details. Over the 10-year period, 107 cases were found. No apparent increasing and decreasing trend in the number of cases per year or in a period was observed. The age range of affected patients was from 4 to 86 years. Special stains for fungi were only used in 22 of 107 (20.6%) of cases. The most frequently affected site was the sino-nasal area (34%). Mycosis type was determined for 58 (54.2%) cases, comprising aspergillosis (21), candidiasis (14), dermatophytosis (6), mucormycosis (3), two cases each of chromoblastomycosis, histoplasmosis, eumycetoma, entomophthoromycosis, sporotrichosis, and Malassezia infection and a single case each of cryptococcosis and deep onychomycosis. Of the 53 (49.5%) cases with presumptive diagnosis data, only seven (13.2%) had a pre-biopsy suspicion of mycosis. There is a wide spectrum of mycoses in Ghana, including endemic mycoses not previously reported. Improving the use of special fungal stains could increase yield and mycoses identification. Laboratory diagnostic capacity needs enhancement to complement histopathology investigations with serology, culture, and molecular methods.

Laboratory and clinical management capacity for invasive fungal infections: the Italian landscape

BACKGROUND

We assessed the laboratory diagnosis and treatment of invasive fungal disease (IFD) in Italy to detect limitations and potential for improvement.

METHODS

The survey was available online at www.clinicalsurveys.net/uc/IFI management capacity/, and collected variables such as (a) institution profile, (b) perceptions of IFD in the respective institution, (c) microscopy, (d) culture and fungal identification, (e) serology, (f) antigen detection, (g) molecular tests, (h) susceptibility testing and (i) therapeutic drug monitoring (TDM).

RESULTS

The laboratory capacity study received responses from 49 Italian centres, with an equitable geographical distribution of locations. The majority of respondents (n = 36, 73%) assessed the occurrence of IFD as moderate-high, with Aspergillus spp. being the pathogen of highest concern, followed by Candida spp. and Mucorales. Although 46 (94%) of the institutions had access to microscopy, less than half of them performed direct microscopy on clinical specimens always when IFD was suspected. Cultures were available in all assessed laboratories, while molecular testing and serology were available in 41 (83%), each. Antigen detection tests and antifungal drugs were also generally accessible (> 90%) among the participating institutions. Nevertheless, access to TDM was limited (n = 31, 63%), with a significant association established between therapeutic drug monitoring availability and higher gross domestic product per capita.

CONCLUSIONS

Apart from TDM, Italy is adequately prepared for the diagnosis and treatment of IFD, with no significant disparities depending on gross domestic product. Future efforts may need to focus on enhancing the availability and application of direct microscopic methods, as well as TDM, to promote optimal treatment and better patient outcomes.

Multicentric Study on the Clinical Mycology Capacity and Access to Antifungal Treatment in Portugal

The success of the clinical management of invasive fungal diseases (IFD) is highly dependent on suitable tools for timely and accurate diagnosis for effective treatment. An in-depth analysis of the ability of European institutions to promptly and accurately diagnose IFD was previously conducted to identify limitations and aspects to improve. Here, we evaluated and discussed the specific case of Portugal, for which, to our knowledge, there are no reports describing the national mycological diagnostic capacity and access to antifungal treatment. Data from 16 Portuguese medical institutions were collected via an online electronic case report form covering different parameters, including institution profile, self-perceived IFD incidence, target patients, diagnostic methods and reagents, and available antifungals. The majority of participating institutions (69%) reported a low-very low incidence of IFD, with Candida spp. indicated as the most relevant fungal pathogen, followed by Aspergillus spp. and Cryptococcus spp. All institutions had access to culture and microscopy, whereas 94 and 88% were able to run antigen-detection assays and molecular tests, respectively. All of the institutions capable of providing antifungal therapy declared to have access to at least one antifungal. However, echinocandins were only available at 85% of the sites. Therapeutic drug monitoring (TDM) was reported to remain a very restricted practice in Portugal, being available in 19% of the institutions, with the TDM of itraconazole and posaconazole performed in only 6% of them. Importantly, several of these resources are outsourced to external entities. Except for TDM, Portugal appears to be well-prepared concerning the overall capacity to diagnose and treat IFD. Future efforts should focus on promoting the widespread availability of TDM and improved access to multiple classes of antifungals, to further improve patient outcomes.

The Nairobi Declaration 2023: A commitment to address deadly yet neglected fungal diseases in Africa

On May 30th and 31st, 2023, delegates representing various African subregions, together with global representatives from the International Society of Human and Animal Mycology (ISHAM), the European Confederation of Medical Mycology (ECMM), the United States Centre for Disease Control and Prevention (CDC), and Global Action for Fungal Infections (GAFFI), convened in Nairobi, Kenya under the aegis of the Pan African Mycology Working Group, a working group of ISHAM. The meeting objectives were, amongst others, to deliberate on a continental response to the World Health Organisation Fungal Priority Pathogen List and facilitate interaction between global and regional leaders. Country delegates and international speakers addressed Africa's fungal disease burden; capacity for diagnosis and management; ongoing surveillance; knowledge gaps and trends in invasive fungal diseases such as Candida auris, mucormycosis, aspergillosis, and Acquired Immune Deficiency Syndrome (AIDS)-related mycoses; and current laboratory practice. During the technical sessions, expert panels deliberated on establishing and financing of national/regional surveillance networks for mycoses; establishing and sustaining African-led collaborations; expanding on existing laboratory and point-of-care diagnostic capacity as well as planning a mycology reference laboratory service and network in Africa. The meeting also highlighted successful African-led collaborations, capacity building, and clinical trial initiatives. The meeting conclusions informed the resolutions of the Nairobi Declaration calling for improved awareness; strong collaborations between clinical and laboratory teams across Africa; improved fungal disease surveillance within the continent; access to antifungals and diagnostics; and leveraging qualified human resources for mycology present within and outside Africa to facilitate trainings, collaborations, and exchanges.

Re-estimation of the burden of serious fungal diseases in Uganda

Background

It is of utmost importance to monitor any change in the epidemiology of fungal diseases that may arise from a change in the number of the at-risk population or the availability of local data.

Objective

We sought to update the 2015 publication on the incidence and prevalence of serious fungal diseases in Uganda.

Methods

Using the Leading International Fungal Education methodology, we reviewed published data on fungal diseases and drivers of fungal diseases in Uganda. Regional or global data were used where there were no Ugandan data.

Results

With a population of ~45 million, we estimate the annual burden of serious fungal diseases at 4,099,357 cases (about 9%). We estimated the burden of candidiasis as follows: recurrent Candida vaginitis (656,340 cases), oral candidiasis (29,057 cases), and esophageal candidiasis (74,686 cases) in HIV-infected people. Cryptococcal meningitis annual incidence is estimated at 5553 cases, Pneumocystis pneumonia at 4604 cases in adults and 2100 cases in children. For aspergillosis syndromes, invasive aspergillosis annual incidence (3607 cases), chronic pulmonary aspergillosis (26,765 annual cases and 63,574 5-year-period prevalent cases), and prevalence of allergic bronchopulmonary aspergillosis at 75,931 cases, and severe asthma with fungal sensitization at 100,228 cases. Tinea capitis is common with 3,047,989 prevalent cases. For other mycoses, we estimate the annual incidence of histoplasmosis to be 646 cases and mucormycosis at 9 cases.

Conclusion

Serious fungal diseases affect nearly 9% of Ugandans every year. Tuberculosis and HIV remain the most important predisposition to acute fungal infection necessitating accelerated preventive, diagnostic, and therapeutic interventions for the management of these diseases.

Fungal diseases in Africa: Closing the gaps in diagnosis and treatment through implementation research and advocacy

Fungal diseases impose an escalating burden on public health in Africa, exacerbated by issues such as delayed diagnosis, inadequate therapy, and limited access to healthcare resources, resulting in significant morbidity and mortality. Effectively tackling these challenges demands a comprehensive approach encompassing research, training, and advocacy initiatives. Recent clinical mycology surveys conducted by Global Action for Fungal Infection (GAFFI) and the European Confederation of Medical Mycology/International Society for Human and Animal Mycology (ECMM/ISHAM) have underscored gaps in fungal diagnostics and the availability and accessibility of antifungal therapy in Africa. The World Health Organization (WHO) Fungal Priority Pathogens List (FPPL) identifies fungi of critical or high importance to human health, providing a roadmap for action and highlighting the urgent need for prioritizing fungal diseases and developing targeted interventions within the African context. To enhance diagnosis and treatment, it is imperative to invest in comprehensive training programs for healthcare workers across all levels and disciplines. Equipping them with the necessary knowledge and skills will facilitate early detection, accurate diagnosis, and appropriate management of fungal infections. Moreover, implementation science research in medical mycology assumes a pivotal role in bridging the gap between knowledge and practice. By identifying the barriers and facilitators that influence the adoption of diagnostic techniques and public health interventions, tailored strategies can be formulated to improve their implementation within healthcare settings. Advocacy plays a critical role in raising awareness regarding the profound impact of fungal diseases on public health in Africa. Engaging policymakers, healthcare providers, researchers, industry experts and communities underscore the importance of addressing these diseases and galvanize efforts for change. Substantial investment in surveillance, research and development specifically focused on fungal diseases is indispensable for advancing our understanding of local epidemiology, developing effective interventions, and ultimately improving patient outcomes. In conclusion, closing the gaps in diagnosing and treating fungal diseases in Africa demands concerted research and advocacy initiatives to ensure better healthcare delivery, reduced mortality rates, and improved public health outcomes.

Access to the World Health Organization-recommended essential diagnostics for invasive fungal infections in critical care and cancer patients in Africa: A diagnostic survey

BACKGROUND

Invasive fungal infections (IFIs) contribute to significant morbidity and mortality among patients with haemato-oncological conditions, seriously ill hospitalised patients and those in intensive care (ICU). We surveyed for the World Health Organization-recommended essential diagnostic tests for IFIs in these risk groups in Africa.

METHODS

The Global Action For Fungal Infections (GAFFI) evaluated the different levels of access to both diagnostics for IFIs for populations in Africa, with the aim of building a comparative dataset and a publicly available interactive map. Data was collected through a validated questionnaire administered to a country leader in relevant topics (i.e., HIV, laboratory coordination) and/or Ministry of Health representatives and followed up with 2 rounds of validation by video calls, and later confirmation by email of findings.

RESULTS

Initial data was collected from 48 African countries covering 99.65 % of the population. Conventional diagnostics such as blood cultures, direct microscopy and histopathology were often used for diagnosis of IFIs in more than half of the facilities. Bronchoscopy was rarely done or not done in 20 countries (population 649 million). In over 40 African countries (population >850 million), Aspergillus antigen testing was never performed in either the public or private sectors. Computed tomography (CT) imaging is routinely used in 27 (56 %) of countries in the public sector and 21 44 %) in the private sector. However, magnetic resonance imaging remains relatively uncommon in most African countries.

CONCLUSIONS

There are critical gaps in the availability of essential diagnostics for IFIs in Africa, particularly Aspergillus antigen testing and modern medical imaging modalities. Early diagnosis and commencement of targeted therapy of IFIs are critical for optimal outcomes from complex cancer therapies.

Social Mycology: Using Social Media Networks in the Management of Aspergillosis and Other Mycoses

Online social media networks are an integral part of modern life. Microblogging sites such as Twitter have hundreds of millions of active users globally and have been enthusiastically adopted by many in the medical profession. For advancing a relatively neglected field such as fungal infection, this can be especially advantageous. Education, research networking, case discussions and public and patient engagement can all be greatly enhanced through the use of social media networks. This review highlights the ways in which this can work successfully in the case of aspergillosis and fungal infection in general, as well as highlighting the dangers and pitfalls of social media medicine.

The Current and Future States of Diagnostic Tests for Histoplasmosis with a Focus on People with HIV and Disseminated Histoplasmosis

Histoplasmosis is caused by Histoplasma capsulatum and, although endemic in large parts of the world, is often underrecognized in many locations. In addition to underrecognition, inadequate availability of diagnostic tests is a major contributor to poor outcomes in disseminated disease in people with HIV. For those with advanced HIV and disseminated disease, antibody testing is less useful. Culture and histopathology can be useful in this situation, but each has limitations, including variable sensitivity by site and, in the case of culture, the need for a biosafety level three laboratory and a long period of growth. Antigen testing has proven useful for disseminated histoplasmosis due to the excellent sensitivity of urine. Yet, turnaround is slower than ideal due to use in a limited number of centers. The development of lateral flow assays has the potential to make for true rapid point-of-care assays for histoplasmosis, but in order to meet that promise, the tests must be widely available and affordable.

Overcoming clinical challenges in the management of invasive fungal infections in low- and middle-income countries (LMIC)

INTRODUCTION

The management of invasive fungal infections (IFIs) in low- and middle-income countries (LMIC) is a serious challenge due to limited epidemiology studies, sub-optimal laboratory facilities, gap in antifungal management training and resources. Limited studies highlighted distinctive epidemiology of IFIs in those countries, and difficulty in distinguishing from closely related infections. To overcome the gaps for appropriate management of IFIs, innovative approaches are required.

AREAS COVERED

Extensive literature search and discussion with experts have helped us to summarize the epidemiology, diagnostic and management difficulties in managing IFIs in LMIC, and recommend certain solutions to overcome the challenges.

EXPERT OPINION

The strategies to overcome the challenges in diagnosis may include local epidemiology study, training of healthcare workers, association of fungal infections with already existing budgeted national programs, development and incorporation of point-of-care test (POCT) for prompt diagnosis, simplifying clinical diagnostic criteria suitable for LMIC, judicious use of available expertise, and diagnostic stewardship. For management strategies judicious use of antifungal, partnering with industry for inexpensive antifungal agents, development of LMIC specific guidelines for cost-effective management of IFIs and fungal outbreaks, improvement of infection control practices, advocacy for implementation of WHO recommended antifungal use, and integration of IFIs with public health.

Cross-sectional investigation of mycological diagnosis challenges in Saudi Arabia

Background

The global incidence of fungal infection has increased dramatically over the last two decades. Fungal diseases threaten both immunocompetent, and immunocompromised patients. The current fungal diagnostics status in Saudi Arabia needs to be evaluated, especially with the increase of the immunosuppressed population. This cross-sectional study investigated the gaps in mycological diagnosis on a national level.

Materials and methods

The call interview questionnaire responses were collected to evaluate the demand for fungal assays, diagnostic methods' quality, and mycological expertise of laboratory technologists in both public and private medical intuitions. The data were analyzed using (IBM SPSS ^® software version 22.0).

Results

A total of 57 hospitals from all Saudi regions participated in the questionnaire; however, only 32% received or processed mycological samples. Most participants were from the Mecca region (25%), Riyadh region (19%), and Eastern region (14%). The top fungal isolates identified were Candida spp., Aspergillus spp., and dermatophyte. Fungal investigation is highly requested by intensive care, dermatology, and obstetrics and gynecology units. Most laboratories rely on fungal culture and microscopic examination, which mostly identify Candida to the genus level, and use 37°C incubators for culture (67%). Antifungal susceptibility testing (AST) and serological and molecular methods are rarely performed and mostly outsourced. Using accurate identification and AST are the primary factors to improve fungal diagnosis in respect to turnaround time and cost. The three major obstacles identified were availability of facility (47%), reagents and kits (32%), and good training (21%).

Conclusions

The results indicated that fungal diagnosis demand was relatively higher in high-population regions. This study highlighted the gaps in fungal diagnostics reference laboratories to encourage their improvement in Saudi hospitals.

Emergomycosis in Africa: Time to Pay Attention to This Emerging Deadly Fungal Infection

Emergomycosis is an emerging deadly infectious disease caused primarily by a little-known airborne pathogen Emergomyces africanus, which can cause clinical management challenge especially in patients with advanced HIV disease. This minireview describes Es. africanus as the main cause of emergomycosis in Africa as well as considers contributing factors to the difficulties encountered in managing this infection. Emergomycosis is common in HIV-positive persons with low CD4 lymphocyte count and has an estimated fatality of 50%. The infection exhibits airborne transmission with pulmonary and extrapulmonary manifestations leading to skin lesions. However, the pathogenesis of Es. africanus is still poorly understood. The management of the infection is complicated due to lack of defined diagnostic and therapeutic guidelines. Limited expertise, poor research funding, and lack of awareness and national surveillance are thought to impact the recognition and prioritisation of the infection. These factors may ultimately assign emergomycosis a 'neglected infection status' even as it is suspected to be prevalent in more African countries than previously recognised. Increased awareness and integrated and targeted strategies such as mobilising manpower in clinical mycology are of paramount importance in managing emergomycosis in Africa and beyond.

Diagnosis and Treatment of Invasive Aspergillosis Caused by Non-fumigatus Aspergillus spp

With increasing frequency, clinical and laboratory-based mycologists are consulted on invasive fungal diseases caused by rare fungal species. This review aims to give an overview of the management of invasive aspergillosis (IA) caused by non-fumigatus Aspergillus spp.-namely A. flavus, A. terreus, A. niger and A. nidulans-including diagnostic and therapeutic differences and similarities to A. fumigatus. A. flavus is the second most common Aspergillus spp. isolated in patients with IA and the predominant species in subtropical regions. Treatment is complicated by its intrinsic resistance against amphotericin B (AmB) and high minimum inhibitory concentrations (MIC) for voriconazole. A. nidulans has been frequently isolated in patients with long-term immunosuppression, mostly in patients with primary immunodeficiencies such as chronic granulomatous disease. It has been reported to disseminate more often than other Aspergillus spp. Innate resistance against AmB has been suggested but not yet proven, while MICs seem to be elevated. A. niger is more frequently reported in less severe infections such as otomycosis. Triazoles exhibit varying MICs and are therefore not strictly recommended as first-line treatment for IA caused by A. niger, while patient outcome seems to be more favorable when compared to IA due to other Aspergillus species. A. terreus-related infections have been reported increasingly as the cause of acute and chronic aspergillosis. A recent prospective international multicenter surveillance study showed Spain, Austria, and Israel to be the countries with the highest density of A. terreus species complex isolates collected. This species complex seems to cause dissemination more often and is intrinsically resistant to AmB. Non-fumigatus aspergillosis is difficult to manage due to complex patient histories, varying infection sites and potential intrinsic resistances to antifungals. Future investigational efforts should aim at amplifying the knowledge on specific diagnostic measures and their on-site availability, as well as defining optimal treatment strategies and outcomes of non-fumigatus aspergillosis.

The current state of laboratory mycology in Asia/Pacific: A survey from the European Confederation of Medical Mycology (ECMM) and International Society for Human and Animal Mycology (ISHAM)

INTRODUCTION

Invasive fungal infections (IFIs) in Asia/Pacific are a particular threat to patients with malignancies, uncontrolled diabetes mellitus or undiagnosed/untreated human immunodeficiency virus infection and acquired immunodeficiency syndrome (HIV/AIDS). Adequate and early access to diagnostic tools and antifungals is essential for IFI clinical management and patient survival.

METHODS

Details on institution profile, self-perception on IFI, and access to microscopy, culture, serology, antigen detection, molecular testing, and therapeutic drug monitoring for IFI were collected in a survey.

RESULTS

As of June 2022, 235 centres from 40 countries/territories in Asia/Pacific answered the questionnaire. More than half the centres were from six countries: India (25%), China (17%), Thailand (5%), Indonesia, Iran, and Japan (4% each). Candida spp. (93%) and Aspergillus spp. (75%) were considered the most relevant pathogens. Most institutions had access to microscopy (98%) or culture-based approaches (97%). Furthermore, 79% of centres had access to antigen detection, 66% to molecular assays, and 63% to antibody tests. Access to antifungals varied between countries/territories. At least one triazole was available in 93% of the reporting sites (voriconazole [89%] was the most common mould-active azole), whereas 80% had at least one amphotericin B formulation, and 72% had at least one echinocandin.

CONCLUSION

According to the replies provided, the resources available for IFI diagnosis and management vary among Asia/Pacific countries/territories. Economical or geographical factors may play a key role in the incidence and clinical handling of this disease burden. Regional cooperation may be a good strategy to overcome shortcomings.

Invasive Pulmonary Aspergillosis

Invasive pulmonary aspergillosis is growing in incidence, as patients at risk are growing in diversity. Outside the classical context of neutropenia, new risk factors are emerging or newly identified, such as new anticancer drugs, viral pneumonias and hepatic dysfunctions. Clinical signs remain unspecific in these populations and the diagnostic work-up has considerably expanded. Computed tomography is key to assess the pulmonary lesions of aspergillosis, whose various features must be acknowledged. Positron-emission tomography can bring additional information for diagnosis and follow-up. The mycological argument for diagnosis is rarely fully conclusive, as biopsy from a sterile site is challenging in most clinical contexts. In patients with a risk and suggestive radiological findings, probable invasive aspergillosis is diagnosed through blood and bronchoalveolar lavage fluid samples by detecting galactomannan or DNA, or by direct microscopy and culture for the latter. Diagnosis is considered possible with mold infection in lack of mycological criterion. Nevertheless, the therapeutic decision should not be hindered by these research-oriented categories, that have been completed by better adapted ones in specific settings. Survival has been improved over the past decades with the development of relevant antifungals, including lipid formulations of amphotericin B and new azoles. New antifungals, including first-in-class molecules, are awaited.

Salvage Treatment for Invasive Aspergillosis and Mucormycosis: Challenges, Recommendations and Future Considerations

Invasive mold diseases are devastating systemic infections which demand meticulous care in selection, dosing, and therapy monitoring of antifungal drugs. Various circumstances regarding PK/PD properties of the applied drug, resistance/tolerance of the causative pathogen or host intolerability can lead to failure of the initial antifungal therapy. This necessitates treatment adaption in the sense of switching antifungal drug class or potentially adding another drug for a combination therapy approach. In the current state of drastically limited options of antifungal drug classes adaption of therapy remains challenging. Current guidelines provide restricted recommendations only and emphasize individual approaches. However, novel antifungals, incorporating innovative mechanisms of action, show promising results in late stage clinical development. These will expand options for salvage therapy in the future potentially as monotherapy or in combination with conventional or other novel antifungals. We outline current recommendations for salvage therapy including PK/PD considerations as well as elucidate possible future treatment options for invasive aspergillosis and mucormycosis.

Unveiling the Hungarian landscape of laboratory and clinical management capacities for invasive fungal infections: navigating the frontlines against fungal menaces

Background

Antifungal diagnostic capacity has been documented in various countries, there is a lack of comprehensive research on clinical mycology diagnostics and treatment in Hungary.

Methods

We conducted an online survey encompassing questions that explored various aspects of the mycology diagnostic and antifungal therapy-related information. The survey aimed to gather details about institutional profiles, perceptions of invasive fungal infections (IFIs), and access to microscopy, culture, serology, antigen detection, molecular testing, and therapeutic drug monitoring.

Results

As of May 2023, a total of 17 institutions responded to the questionnaire. Seven participants categorized the institutional incidence of IFI as 'very low', four as 'low', and six as 'mild'. The majority of centers identified Candida spp. (94%) and Aspergillus spp. (82%) as the most prevalent fungal pathogens. Nearly half of the laboratories (47%) reported using matrix-assisted laser desorption/ionization-time of flight mass spectrometry for identification. All institutions had access to microscopy and culture-based diagnostic approaches. A significant number of centers had access to antigen detection (71%) and various molecular assays (59%). Regarding antifungal agents, all reporting sites used at least one triazole, with voriconazole (77%) being the most common mold-active azole. Furthermore, 71% of the centers applied at least one formulation of amphotericin B, and 65% to one echinocandin. However, only 18% of the centers used 5-flucytosine.

Conclusion

Resource availability for diagnosing and treating IFI in Hungary varies across hospitals based on location. Surveys help identify gaps and limitations in this area. To address these challenges, interregional cooperation within Hungary could be a facilitating strategy.

The current state of laboratory mycology and access to antifungal treatment in Europe: a European Confederation of Medical Mycology survey

Access to the appropriate tools is crucial for early diagnosis and clinical management of invasive fungal infections. This Review aims to describe the invasive fungal infection diagnostic capacity of Europe to better understand the status and the most pressing aspects that need improvement. To our knowledge, this is the first time that the mycological diagnostic capability and access to antifungal treatments of institutions has been evaluated at a pan-European level. Between Nov 1, 2021, and Jan 31, 2022, 388 institutions in Europe self-assessed their invasive fungal infection management capability. Of the 388 participating institutions from 45 countries, 383 (99%) had access to cultures, 375 (97%) to microscopy, 363 (94%) to antigen-detection assays, 329 (85%) to molecular tests (mostly PCR), and 324 (84%) to antibody tests for diagnosis and management. With the exception of microscopy, there were considerable differences in access to techniques among countries according to their gross domestic product. At least one triazole was available in 363 (94%) of the institutions, one echinocandin in 346 (89%), and liposomal amphotericin B in 301 (78%), with country gross domestic product-based differences. Differences were also observed in the access to therapeutic drug monitoring. Although Europe is well prepared to manage invasive fungal infections, some institutions do not have access to certain diagnostic tools and antifungal drugs, despite most being considered essential by WHO. These limitations need to be overcome to ensure that all patients receive the best diagnostic and therapeutic management.

Diagnostic capacity for invasive fungal infections in advanced HIV disease in Africa: a continent-wide survey

BACKGROUND

Fungal infections are common causes of death and morbidity in those with advanced HIV infection. Data on access to diagnostic tests in Africa are scarce. We aimed to evaluate the diagnostic capacity for invasive fungal infections in advanced HIV disease in Africa.

METHODS

We did a continent-wide survey by collecting data from 48 of 49 target countries across Africa with a population of more than 1 million; for Lesotho, only information on the provision of cryptococcal antigen testing was obtained. This survey covered 99·65% of the African population. We did the survey in six stages: first, questionnaire development, adaptation, and improvement; second, questionnaire completion by in-country respondents; third, questionnaire review and data analysis followed by video conference calls with respondents; fourth, external validation from public or private sources; fifth, country validation by video conference with senior figures in the Ministry of Health; and sixth, through five regional webinars led by the Africa Centres for Disease Control and Prevention with individual country profiles exchanged by email. Data was compiled and visualised using the Quantum Geographic Information System software and Natural Earth vectors to design maps showing access.

FINDINGS

Data were collected between Oct 1, 2020, and Oct 31, 2022 in the 48 target countries. We found that cryptococcal antigen testing is frequently accessible to 358·39 million (25·5%) people in 14 African countries. Over 1031·49 million (73·3%) of 1·4 billion African people have access to a lumbar puncture. India ink microscopy is frequently accessible to 471·03 million (33·5%) people in 23 African countries. About 1041·62 million (74·0%) and 1105·11 million (78·5%) people in Africa do not have access to histoplasmosis and Pneumocystis pneumonia diagnostics in either private or public facilities, respectively. Fungal culture is available in 41 countries covering a population of 1·289 billion (94%) people in Africa. MRI is routinely accessible to 453·59 million (32·2%) people in Africa and occasionally to 390·58 million (27·8%) people. There was a moderate correlation between antiretroviral therapy usage and external expenditure on HIV care (R²=0·42) but almost none between external expenditure and AIDS death rate (R²=0·18), when analysed for 40 African countries.

INTERPRETATION

This survey highlights the enormous challenges in the diagnosis of HIV-associated Pneumocystis pneumonia, cryptococcal disease, histoplasmosis, and other fungal infections in Africa. Urgent political and global health leadership could improve the diagnosis of fungal infections in Africa, reducing avoidable deaths.

FUNDING

Global Action For Fungal Infections.

Invasive Fungal Diseases in Africa: A Critical Literature Review

Invasive fungal diseases (IFDs) are of huge concern in resource-limited settings, particularly in Africa, due to the unavailability of diagnostic armamentarium for IFDs, thus making definitive diagnosis challenging. IFDs have non-specific systemic manifestations overlapping with more frequent illnesses, such as tuberculosis, HIV, and HIV-related opportunistic infections and malignancies. Consequently, IFDs are often undiagnosed or misdiagnosed. We critically reviewed the available literature on IFDs in Africa to provide a better understanding of their epidemiology, disease burden to guide future research and interventions. Cryptococcosis is the most encountered IFD in Africa, accounting for most of the HIV-related deaths in sub-Saharan Africa. Invasive aspergillosis, though somewhat underdiagnosed and/or misdiagnosed as tuberculosis, is increasingly being reported with a similar predilection towards people living with HIV. More cases of histoplasmosis are also being reported with recent epidemiological studies, particularly from Western Africa, showing high prevalence rates amongst presumptive tuberculosis patients and patients living with HIV. The burden of pneumocystis pneumonia has reduced significantly probably due to increased uptake of anti-retroviral therapy among people living with HIV both in Africa, and globally. Mucormycosis, talaromycosis, emergomycosis, blastomycosis, and coccidiomycosis have also been reported but with very few studies from the literature. The emergence of resistance to most of the available antifungal drugs in Africa is yet of huge concern as reported in other regions. IFDs in Africa is much more common than it appears and contributes significantly to morbidity and mortality. Huge investment is needed to drive awareness and fungi related research especially in diagnostics and antifungal therapy.

Comparative analysis of Galactomannan Lateral Flow Assay, Galactomannan Enzyme Immunoassay and BAL culture for Diagnosis of COVID-19 associated pulmonary aspergillosis

BACKGROUND

Galactomannan Enzyme Immunoassay (GM-EIA) is proved to be a cornerstone in the diagnosis of COVID-19-associated pulmonary aspergillosis (CAPA), its use is limited in middle and low-income countries, where the application of simple and rapid test, including Galactomannan Lateral Flow Assay (GM-LFA), is highly appreciated. Despite such merits, limited studies directly compared GM-LFA to GM-EIA. Herein we compared the diagnostic features of GM-LFA, GM-EIA, and BAL culture for CAPA diagnosis in Iran, a developing country.

MATERIALS/METHODS

Diagnostic performance of GM-LFA and GM-EIA in BAL (GM indexes ≥ 1) and serum (GM indexes > 0.5), i.e., sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) and areas under the curve (AUC), were evaluated using BAL (n=105) and serum (n=101) samples from mechanically ventilated COVID-19 patients in intensive care units. Patients were classified based on the presence of host factors, radiological findings, and mycological evidences according to 2020 ECMM/ISHAM consensus criteria for CAPA diagnosis.

RESULTS

The Aspergillus GM-LFA for serum and BAL samples showed a sensitivity of 56.3% and 60.6%, specificity of 94.2% and 88.9%, PPV of 81.8% and 71.4%, NPV of 82.3% and 83.1%, when compared to BAL culture, respectively. GM-EIA showed sensitivities of 46.9% and 54.5%, specificities of 100% and 91.7%, PPVs of 100% and 75%, NPVs of 80.2% and 81.5% for serum and BAL samples, respectively.

CONCLUSION

Our study found GM-LFA as a reliable simple and rapid diagnostic tool, which could circumvent the shortcomings of culture and GM-EIA and be pivotal in timely initiation of antifungal treatment.

COVID-19 associated multisystemic mucormycosis from India: a multicentric retrospective study on clinical profile, predisposing factors, cumulative mortality and factors affecting outcome

PURPOSE

The clinical course of COVID-19 has been complicated by secondary infections, including bacterial and fungal infections. The rapid rise in the incidence of invasive mucormycosis in these patients is very much concerning. COVID-19-associated mucormycosis was detected in huge numbers during the second wave of the COVID-19 pandemic in India, with several predisposing factors indicated in its pathogenesis. This study aimed to evaluate the epidemiology, predisposing factor, cumulative mortality and factors affecting outcomes among the coronavirus disease COVID-19-associated mucormycosis (CAM).

METHODS

A multicenter retrospective study across three tertiary health care centers in Southern part of India was conducted during April-June 2021.

RESULTS

Among the 217 cases of CAM, mucormycosis affecting the nasal sinuses was the commonest, affecting 95 (44%) of the patients, orbital extension seen in 84 (38%), pulmonary (n = 25, 12%), gastrointestinal (n = 6, 3%), isolated cerebral (n = 2) and disseminated mucormycosis (n = 2). Diabetes mellitus, high-dose systemic steroids were the most common underlying disease among CAM patients. The mucormycosis-associated case-fatality at 6 weeks was 14%, cerebral or GI or disseminated mucormycosis had 9 times higher risk of death compared to other locations. Extensive surgical debridement along with sequential antifungal drug treatment improved the survival in mucormycosis patients.

CONCLUSION

Judicious and appropriate management of the predisposing factor and factors affecting mortality associated with CAM with multi-disciplinary approach and timely surgical and medical management can be much helpful in achieving a successful outcome.

Emergence and Genomic Characterization of Multidrug Resistant Candida auris in Nigeria, West Africa

Candida auris is an emerging multidrug-resistant fungal pathogen that has become a worldwide public health threat due to the limitations of treatment options, difficulty in diagnosis, and its potential for clonal transmission. Four ICU patients from three different healthcare facilities in Southern Nigeria presented features suggestive of severe sepsis and the blood cultures yielded the growth of Candida spp., which was identified using VITEK 2 as C. auris. Further confirmation was performed using whole genome sequencing (WGS). From the genomic analysis, two had mutations that conferred resistance to the antifungal azole group and other non-synonymous mutations in hotspot genes, such as ERG2, ERG11, and FKS1. From the phylogenetic analysis, cases 2 and 4 had a confirmed mutation (ERG11:Y132F) that conferred drug resistance to azoles clustered with clade 1, whilst cases 1 and 3 clustered with clade 4. Three of the patients died, and the fourth was most likely a case of colonization since he received no antifungals and was discharged home. These first cases of C. auris reported from Nigeria were most likely introduced from different sources. It is of public health importance as it highlights diagnostic gaps in our setting and the need for active disease surveillance in the region.

Pulmonary and Extrapulmonary Manifestations of Fungal Infections Misdiagnosed as Tuberculosis: The Need for Prompt Diagnosis and Management

Fungal infections commonly present with myriad symptoms that mimic other clinical entities, notable amongst which is tuberculosis. Besides histoplasmosis and chronic pulmonary aspergillosis, which can mimic TB, this review has identified several other fungal infections which also do. A total of 80 individual cases misdiagnosed as TB are highlighted: aspergillosis (n = 18, 22.5%), histoplasmosis (n = 16, 20%), blastomycosis (n = 14, 17.5%), cryptococcosis (n = 11, 13.8%), talaromycosis (n = 7, 8.8%), coccidioidomycosis (n = 5, 6.3%), mucormycosis (n = 4, 5%), sporotrichosis (n = 3, 3.8%), phaeohyphomycosis (n = 1, 1.3%) and chromoblastomycosis (n = 1, 1.3%). Case series from India and Pakistan reported over 100 cases of chronic and allergic bronchopulmonary aspergillosis had received anti-TB therapy before the correct diagnosis was made. Forty-five cases (56.3%) had favorable outcomes, and 25 (33.8%) died, outcome was unclear in the remainder. Seventeen (21.3%) cases were infected with human immunodeficiency virus (HIV). Diagnostic modalities were histopathology (n = 46, 57.5%), culture (n = 42, 52.5%), serology (n = 18, 22.5%), cytology (n = 2, 2.5%), gene sequencing (n = 5, 6.3%) and microscopy (n = 10, 12.5%) including Gram stain, India ink preparation, bone marrow smear and KOH mount. We conclude that the above fungal infections should always be considered or ruled out whenever a patient presents with symptoms suggestive of tuberculosis which is unconfirmed thereby reducing prolonged hospital stay and mortalities associated with a delayed or incorrect diagnosis of fungal infections.

Prevalence of COVID-19-Associated Pulmonary Aspergillosis: Critical Review and Conclusions

First reports of cases and case series of COVID-19-associated pulmonary aspergillosis (CAPA) emerged during the first months of the pandemic. Prevalence rates varied widely due to the fact that CAPA was, and still remains, challenging to diagnose in patients with COVID-19-associated acute respiratory failure (ARF). The clinical picture and radiological findings of CAPA are unspecific and can resemble those of severe COVID-19. Hence, mycological evidence became a key component in establishing a diagnosis. However, blood tests lack sensitivity in early treatable phases of CAPA and once positive, mortality has been shown to exceed 80% despite systemic antifungal therapy. The primarily airway invasive growth in non-neutropenic patients and the late occurrence of angioinvasion in the course of disease may mainly account for these diagnostic obstacles. Testing of bronchoalveolar lavage (BAL) is therefore crucial in the diagnostic process, but was rarely performed during the early phase of the pandemic, which potentially interfered with the accuracy of reported prevalence. Current guidelines recommend treatment of CAPA during its early airway invasive phase, which may result in some overtreatment (i.e., treatment in patients that may not develop angioinvasive infection) and adverse drug events, yet there is no viable alternative approach. Timely treatment of cases needs to be ensured for patients with mycological evidence of CAPA in the lower respiratory tract given the independent contribution of CAPA to devastating mortality rates of around 50% that have been shown in multiple studies. Here, we review the evolution of reported CAPA prevalence and the role of CAPA as an important opportunistic infection affecting COVID-19 patients in intensive care units (ICUs).

Gut microbiota associated with cryptococcal meningitis and dysbiosis caused by anti-fungal treatment

The gut microbiota is a dynamic and highly diverse microbial ecosystem that affects many aspects of the host's physiology. An improved understanding of the gut microbiota could lead to better strategies for the diagnosis and therapy of cryptococcal meningitis (CM), but the impact of Cryptococcus infection and anti-fungal treatment on the gut microbiota has rarely been studied. We characterized the diversity and composition of the gut microbiota in CM patients at diagnosis and healthy controls (HCs) using metagenomic sequencing and determined the effects of anti-fungal drugs. We found that CM patients had distinct bacterial and fungal compositions compared with HCs, with eight differentially abundant fungal and 72 differentially abundant bacterial species identified between the two groups. CM patients showed an increased abundance of Enterococcus avium, Leuconostoc mesenteroides, and Weissella cibaria, and a decreased abundance of Prevotella spp. compared with HCs. However, anti-fungal treatment only led to minor changes in the intestinal microbiota. Moreover, both positive and negative correlations existed in fungal, bacterial, and clinical indicators. Our study suggests that the Cryptococcus neoformans infection caused a distinct dysbiosis of the gut microbiota and contributes valuable information implying potential links between the CM and gut microbiota.