Pan-Echinocandin-Resistant Candida glabrata Bloodstream Infection Complicating COVID-19: A Fatal Case Report. J Fungi (Basel). 2020;6. [PMID: 32899996 PMCID: PMC7559523 DOI: 10.3390/jof6030163]

Structures of trehalose-6-phosphate synthase, Tps1, from the fungal pathogen Cryptococcus neoformans: A target for antifungals

Invasive fungal diseases are a major threat to human health, resulting in more than 1.5 million annual deaths worldwide. The arsenal of antifungal therapeutics remains limited and is in dire need of drugs that target additional biosynthetic pathways that are absent from humans. One such pathway involves the biosynthesis of trehalose. Trehalose is a disaccharide that is required for pathogenic fungi to survive in their human hosts. In the first step of trehalose biosynthesis, trehalose-6-phosphate synthase (Tps1) converts UDP-glucose and glucose-6-phosphate to trehalose-6-phosphate. Here, we report the structures of full-length Cryptococcus neoformans Tps1 (CnTps1) in unliganded form and in complex with uridine diphosphate and glucose-6-phosphate. Comparison of these two structures reveals significant movement toward the catalytic pocket by the N terminus upon ligand binding and identifies residues required for substrate binding, as well as residues that stabilize the tetramer. Intriguingly, an intrinsically disordered domain (IDD), which is conserved among Cryptococcal species and closely related basidiomycetes, extends from each subunit of the tetramer into the "solvent" but is not visible in density maps. We determined that the IDD is not required for C. neoformans Tps1-dependent thermotolerance and osmotic stress survival. Studies with UDP-galactose highlight the exquisite substrate specificity of CnTps1. In toto, these studies expand our knowledge of trehalose biosynthesis in Cryptococcus and highlight the potential of developing antifungal therapeutics that disrupt the synthesis of this disaccharide or the formation of a functional tetramer and the use of cryo-EM in the structural characterization of CnTps1-ligand/drug complexes.

Structures of trehalose-6-phosphate synthase, Tps1, from the fungal pathogen Cryptococcus neoformans : a target for novel antifungals

Invasive fungal diseases are a major threat to human health, resulting in more than 1.5 million annual deaths worldwide. The arsenal of antifungal therapeutics remains limited and is in dire need of novel drugs that target additional biosynthetic pathways that are absent from humans. One such pathway involves the biosynthesis of trehalose. Trehalose is a disaccharide that is required for pathogenic fungi to survive in their human hosts. In the first step of trehalose biosynthesis, trehalose-6-phosphate synthase (Tps1) converts UDP-glucose and glucose-6-phosphate to trehalose-6-phosphate. Here, we report the structures of full-length Cryptococcus neoformans Tps1 (CnTps1) in unliganded form and in complex with uridine diphosphate and glucose-6-phosphate. Comparison of these two structures reveals significant movement towards the catalytic pocket by the N-terminus upon ligand binding and identifies residues required for substrate-binding, as well as residues that stabilize the tetramer. Intriguingly, an intrinsically disordered domain (IDD), which is conserved amongst Cryptococcal species and closely related Basidiomycetes, extends from each subunit of the tetramer into the "solvent" but is not visible in density maps. We determined that the IDD is not required for C. neoformans Tps1-dependent thermotolerance and osmotic stress survival. Studies with UDP-galactose highlight the exquisite substrate specificity of CnTps1. In toto , these studies expand our knowledge of trehalose biosynthesis in Cryptococcus and highlight the potential of developing antifungal therapeutics that disrupt the synthesis of this disaccharide or the formation of a functional tetramer and the use of cryo-EM in the structural characterization of CnTps1-ligand/drug complexes.

Significance Statement

Fungal infections are responsible for over a million deaths worldwide each year. Biosynthesis of a disaccharide, trehalose, is required for multiple pathogenic fungi to transition from the environment to the human host. Enzymes in the trehalose biosynthesis pathway are absent in humans and, therefore, are potentially significant targets for novel antifungal therapeutics. One enzyme in the trehalose biosynthesis is trehalose-6-phosphate synthase (Tps1). Here, we describe the cryo-electron microscopy structures of the CnTps1 homo-tetramer in the unliganded form and in complex with a substrate and a product. These structures and subsequent biochemical analysis reveal key details of substrate-binding residues and substrate specificity. These structures should facilitate structure-guided design of inhibitors against CnTps1.

Amphotericin B in the Era of New Antifungals: Where Will It Stand?

Amphotericin B (AmB) has long stood as a cornerstone in the treatment of invasive fungal infections (IFIs), especially among immunocompromised patients. However, the landscape of antifungal therapy is evolving. New antifungal agents, boasting novel mechanisms of action and better safety profiles, are entering the scene, presenting alternatives to AmB's traditional dominance. This shift, prompted by an increase in the incidence of IFIs, the growing demographic of immunocompromised individuals, and changing patterns of fungal resistance, underscores the continuous need for effective treatments. Despite these challenges, AmB's broad efficacy and low resistance rates maintain its essential status in antifungal therapy. Innovations in AmB formulations, such as lipid complexes and liposomal delivery systems, have significantly mitigated its notorious nephrotoxicity and infusion-related reactions, thereby enhancing its clinical utility. Moreover, AmB's efficacy in treating severe and rare fungal infections and its pivotal role as prophylaxis in high-risk settings highlight its value and ongoing relevance. This review examines AmB's standing amidst the ever-changing antifungal landscape, focusing on its enduring significance in current clinical practice and exploring its potential future therapeutic adaptations.

Prevalence of pharmaceuticals and personal care products, microplastics and co-infecting microbes in the post-COVID-19 era and its implications on antimicrobial resistance and potential endocrine disruptive effects

The COVID-19 (coronavirus disease 2019) pandemic's steady condition coupled with predominance of emerging contaminants in the environment and its synergistic implications in recent times has stoked interest in combating medical emergencies in this dynamic environment. In this context, high concentrations of pharmaceutical and personal care products (PPCPs), microplastics (MPs), antimicrobial resistance (AMR), and soaring coinfecting microbes, tied with potential endocrine disruptive (ED) are critical environmental concerns that requires a detailed documentation and analysis. During the pandemic, the identification, enumeration, and assessment of potential hazards of PPCPs and MPs and (used as anti-COVID-19 agents/applications) in aquatic habitats have been attempted globally. Albeit receding threats in the magnitude of COVID-19 infections, both these pollutants have still posed serious consequences to aquatic ecosystems and the very health and hygiene of the population in the vicinity. The surge in the contaminants post-COVID also renders them to be potent vectors to harbor and amplify AMR. Pertinently, the present work attempts to critically review such instances to understand the underlying mechanism, interactions swaying the current health of our environment during this post-COVID-19 era. During this juncture, although prevention of diseases, patient care, and self-hygiene have taken precedence, nevertheless antimicrobial stewardship (AMS) efforts have been overlooked. Unnecessary usage of PPCPs and plastics during the pandemic has resulted in increased emerging contaminants (i.e., active pharmaceutical ingredients and MPs) in various environmental matrices. It was also noticed that among COVID-19 patients, while the bacterial co-infection prevalence was 0.2-51%, the fungi, viral, protozoan and helminth were 0.3-49, 1-22, 2-15, 0.4-15% respectively, rendering them resistant to residual PPCPs. There are inevitable chances of ED effects from PPCPs and MPs applied previously, that could pose far-reaching health concerns. Furthermore, clinical and other experimental evidence for many newer compounds is very scarce and demands further research. Pro-active measures targeting effective waste management, evolved environmental policies aiding strict regulatory measures, and scientific research would be crucial in minimizing the impact and creating better preparedness towards such events among the masses fostering sustainability.

Microbiological profile of multidrug resistant bacteria before and during COVID-19 in CHU Mohammed VI

Background and Objectives

A new type of corona virus has caused Corona virus disease-19 and, subsequently, a global pandemic. All individuals are prone to the disease, so drastic measures were taken to prevent its spread. This study aimed to evaluate the impact of COVID-19 on the progression of the antimicrobial resistance rate by comparing two periods: before and during COVID-19.

Materials and Methods

We used a cross-sectional design to investigate the Antimicrobial Resistance (AMR) rate before (03/2019 to 03/2020) and during COVID-19 (03/2020 to 03/2021) in a University Hospital in Marrakech. The data were analyzed using SPSS Version 25.0.

Results

Among the 7106 specimens, there was a significant increase in the multidrug-resistant bacterial from 27.38% to 35.87% during COVID-19 (p<0.001), particularly in blood culture, cerebrospinal fluid, catheter, and pus. However, there was a non-significant change in puncture fluid, expectoration, protected distal sampling, joint fluid, stool culture, and genital sampling. A decrease in Multidrug-resistant bacteria (MDRB) was observed only in cytobacteriological urine tests (p<0.05). According to species, there was an increase in extended-spectrum beta-lactamase-producing Enterobacteriaceae, carbapenem-resistant Enterobacteriaceae, and methicillin-resistant Staphylococcus aureus.

Conclusion

In our study, it is particularly noticeable that the MDRB has increased. These results highlight the importance that the pandemic has not been able to slow the progression.

Candida albicans and Antifungal Peptides

Candida albicans, a ubiquitous opportunistic fungal pathogen, plays a pivotal role in human health and disease. As a commensal organism, it normally resides harmlessly within the human microbiota. However, under certain conditions, C. albicans can transition into a pathogenic state, leading to various infections collectively known as candidiasis. With the increasing prevalence of immunocompromised individuals and the widespread use of invasive medical procedures, candidiasis has become a significant public health concern. The emergence of drug-resistant strains further complicates treatment options, highlighting the urgent need for alternative therapeutic strategies. Antifungal peptides (AFPs) have gained considerable attention as potential candidates for combating Candida spp. infections. These naturally occurring peptides possess broad-spectrum antimicrobial activity, including specific efficacy against C. albicans. AFPs exhibit several advantageous properties, such as rapid killing kinetics, low propensity for resistance development, and diverse mechanisms of action, making them promising alternatives to conventional antifungal agents. In recent years, extensive research has focused on discovering and developing novel AFPs with improved efficacy and selectivity against Candida species. Advances in biotechnology and synthetic peptide design have enabled the modification and optimization of natural peptides, enhancing their stability, bioavailability, and therapeutic potential. Nevertheless, several challenges must be addressed before AFPs can be widely implemented in clinical practice. These include optimizing peptide stability, enhancing delivery methods, overcoming potential toxicity concerns, and conducting comprehensive preclinical and clinical studies. This commentary presents a short overview of candidemia and AFP; articles and reviews published in the last 10 years were searched on The National Library of Medicine (National Center for Biotechnology Information-NIH-PubMed). The terms used were C. albicans infections, antimicrobial peptides, antifungal peptides, antifungal peptides mechanisms of action, candidemia treatments and guidelines, synthetic peptides and their challenges, and antimicrobial peptides in clinical trials as the main ones. Older publications were cited if they brought some relevant concept or helped to bring a perspective into our narrative. Articles older than 20 years and those that appeared in PubMed but did not match our goal to bring updated information about using antifungal peptides as an alternative to C. albicans infections were not considered.

Streptomyces: a natural source of anti-Candida agents

Introduction. There is an urgent need to source new compounds that can combat the current threat of serious infection caused by Candida spp. and contend with the problem of antimicrobial resistance.

Gap. A synthesis of the evidence available from the current literature is needed to identify promising antifungal chemotherapeutics.

Aim. To highlight anti-Candida compounds derived from Streptomyces spp. (a well-known source of antimicrobial compounds) that could translate to potential candidates for future clinical practice.

Methodology. A comprehensive review was conducted across three scientific literature databases spanning a 13-year period.

Results. We identified 151 compounds with anti-Candida activity. Amongst these, 40 were reported with very strong inhibitory activity, having minimum inhibitory concentrations (MICs) against Candida spp. of <3.5 µg ml−1, 66 compounds were considered strong inhibitors and 45 compounds exhibited moderate inhibitory potential. From an analysis of the MICs, we deduced that the actinomycin-like compounds RSP01 and RSP02 were probably the most promising anti-Candida compounds. Other antifungals of note included filipin-like compounds, which demonstrated superior inhibition to amphotericin B and activity against Candida glabrata and Candida krusei, and bafilomycin derivatives, which had substantial inhibition against Candida parapsilosis.

Conclusion. It is essential to recognize the limitations inherent in the quest for new antifungals, which encompass toxicity, in vivo effectiveness and constraints associated with limited data access. However, further investigation through in-depth study and emerging technologies is of paramount importance, given that there are still many more compounds to discover. This review highlights the importance of antifungal compounds derived from Streptomyces , which demonstrate robust inhibition, and, in many cases, low toxicity, making them promising candidates for the development of novel antifungal agents.

COVID-19-associated candidiasis and the emerging concern of Candida auris infections

The incidence of COVID-19-associated candidiasis (CAC) is increasing, resulting in a grave outcome among hospitalized patients with COVID-19. The most alarming condition is the increasing incidence of multi-drug resistant Candida auris infections among patients with COVID-19 worldwide. The therapeutic strategy towards CAC caused by common Candida species, such as Candida albicans, Candida tropicalis, and Candida glabrata, is similar to the pre-pandemic era. For non-critically ill patients or those with a low risk of azole resistance, fluconazole remains the drug of choice for candidemia. For critically ill patients, those with a history of recent azole exposure or with a high risk of fluconazole resistance, echinocandins are recommended as the first-line therapy. Several novel therapeutic agents alone or in combination with traditional antifungal agents for candidiasis are potential options in the future. However, for multidrug-resistant C. auris infection, only echinocandins are effective. Infection prevention and control policies, including strict isolation of the patients carrying C. auris and regular screening of non-affected patients, are suggested to prevent the spread of C. auris among patients with COVID-19. Whole-genome sequencing may be used to understand the epidemiology of healthcare-associated candidiasis and to better control and prevent these infections.

Secondary fungal infections in SARS-CoV-2 patients: pathological whereabouts, cautionary measures, and steadfast treatments

The earliest documented COVID-19 case caused by the SARS-CoV-2 coronavirus occurred in Wuhan, China, in December 2019. Since then, several SARS-CoV-2 mutants have rapidly disseminated as exemplified by the community spread of the recent omicron variant. The disease already attained a pandemic status with ever-dwindling mortality even after two and half years of identification and considerable vaccination. Aspergillosis, candidiasis, cryptococcosis and mucormycosis are the prominent fungal infections experienced by the majority of SARS-CoV-2 high-risk patients. In its entirety, COVID-19's nexus with these fungal infections may worsen the intricacies in the already beleaguered high-risk patients, making this a topic of substantial clinical concern. Thus, thorough knowledge of the subject is necessary. This article focuses on the concomitant fungal infection(s) in COVID-19 patients, taking into account their underlying causes, the screening methods, manifested drug resistance, and long-term effects. The information and knowledge shared herein could be crucial for the management of critically ill, aged, and immunocompromised SARS-CoV-2 patients who have had secondary fungal infections (SFIs).

Immunotherapies against human bacterial and fungal infectious diseases: A review

Nations' ongoing struggles with a number of novel and reemerging infectious diseases, including the ongoing global health issue, the SARS-Co-V2 (severe acute respiratory syndrome coronavirus 2) outbreak, serve as proof that infectious diseases constitute a serious threat to the global public health. Moreover, the fatality rate in humans is rising as a result of the development of severe infectious diseases brought about by multiple drug-tolerant pathogenic microorganisms. The widespread use of traditional antimicrobial drugs, immunosuppressive medications, and other related factors led to the establishment of such drug resistant pathogenic microbial species. To overcome the difficulties commonly encountered by current infectious disease management and control processes, like inadequate effectiveness, toxicities, and the evolution of drug tolerance, new treatment solutions are required. Fortunately, immunotherapies already hold great potential for reducing these restrictions while simultaneously expanding the boundaries of healthcare and medicine, as shown by the latest discoveries and the success of drugs including monoclonal antibodies (MAbs), vaccinations, etc. Immunotherapies comprise methods for treating diseases that specifically target or affect the body's immune system and such immunological procedures/therapies strengthen the host's defenses to fight those infections. The immunotherapy-based treatments control the host's innate and adaptive immune responses, which are effective in treating different pathogenic microbial infections. As a result, diverse immunotherapeutic strategies are being researched more and more as alternative treatments for infectious diseases, leading to substantial improvements in our comprehension of the associations between pathogens and host immune system. In this review we will explore different immunotherapies and their usage for the assistance of a broad spectrum of infectious ailments caused by various human bacterial and fungal pathogenic microbes. We will discuss about the recent developments in the therapeutics against the growing human pathogenic microbial diseases and focus on the present and future of using immunotherapies to overcome these diseases. Graphical AbstractThe graphical abstract shows the therapeutic potential of different types of immunotherapies like vaccines, monoclonal antibodies-based therapies, etc., against different kinds of human Bacterial and Fungal microbial infections.

A parallel and silent emerging pandemic: Antimicrobial resistance (AMR) amid COVID-19 pandemic

World is in the middle of the pandemic (COVID-19), caused by SARS-COV-2 virus, which is a significant global health crisis after Spanish influenza in the beginning of 20th century. Progressive drastic steps have been enforced to minimize the transmission of the disease. Likewise, in the current years, antimicrobial resistance (AMR) has been referred as one of the potential perils to the global economy and health; however, it is now veiled under the present pandemic. During the current pandemic, AMR to available frontline antibiotics may prove fatal and life threatening to bacterial and fungal infections during routine procedures like elective surgery, C-sections, etc. Currently, a swift elevation in multidrug-resistant organisms (MDROs), like carbapenem-resistant New Delhi metallo-β-lactamase (NDM)-producing Acinetobacter baumannii, Enterobacterales, extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae, methicillin-resistant Staphylococcus aureus (MRSA), multi-triazole-resistant Aspergillus fumigatus and pan-echinocandin-resistant Candida glabrata has been seen. Thereupon, the global outbreak of COVID-19 also offers some important ramification for developing antimicrobial drug resistance. This article aims to highlights episodes and aspects of AMR prevalence, impact of management and mismanagement of COVID-19 crisis, hospital settings, community, environment, and travel on the AMR during the current pandemic.

Assessing and Reassessing the Association of Comorbidities and Coinfections in COVID-19 Patients

Coronavirus disease 2019 (COVID-19) has posed an enormous global health and economic burden. To date, 324 million confirmed cases and over 5.5 million deaths have been reported. Several studies have reported comorbidities and coinfections associated with complicated and serious COVID-19 infections. Data from retrospective, prospective, case series, and case reports from various geographical locations were assessed, which included ~ 2300 COVID-19 patients with varying comorbidities and coinfection. We report that Enterobacterales with Staphylococcus aureus was the most while Mycoplasma pneumoniae was the least prevalent coinfection in COVID-19 patients with a comorbidity. In this order, hypertension, diabetes, cardiovascular disease, and pulmonary disease were the prevalent comorbidities observed in COVID-19 patients. There was a statistically significant difference in the prevalent comorbidities observed in patients coinfected with Staphylococcus aureus and COVID-19 and a statistically non-significant difference in the prevalent comorbidities in patients coinfected with Mycoplasma pneumoniae and COVID-19 as compared to similar infections in non-COVID-19 coinfection. We report a significant difference in the prevalent comorbidities recorded in COVID-19 patients with varying coinfections and varying geographic study regions. Our study provides informative data on the prevalence of comorbidities and coinfections in COVID-19 patients to aid in evidence-based patient management and care.

Macrophage internalization creates a multidrug-tolerant fungal persister reservoir and facilitates the emergence of drug resistance

Candida glabrata is a major fungal pathogen notable for causing recalcitrant infections, rapid emergence of drug-resistant strains, and its ability to survive and proliferate within macrophages. Resembling bacterial persisters, a subset of genetically drug-susceptible C. glabrata cells can survive lethal exposure to the fungicidal echinocandin drugs. Herein, we show that macrophage internalization induces cidal drug tolerance in C. glabrata, expanding the persister reservoir from which echinocandin-resistant mutants emerge. We show that this drug tolerance is associated with non-proliferation and is triggered by macrophage-induced oxidative stress, and that deletion of genes involved in reactive oxygen species detoxification significantly increases the emergence of echinocandin-resistant mutants. Finally, we show that the fungicidal drug amphotericin B can kill intracellular C. glabrata echinocandin persisters, reducing emergence of resistance. Our study supports the hypothesis that intra-macrophage C. glabrata is a reservoir of recalcitrant/drug-resistant infections, and that drug alternating strategies can be developed to eliminate this reservoir.

Bacterial Epidemiology and Antimicrobial Resistance Profiles of Respiratory Specimens of Children with Pneumonia in Hainan, China

Purpose

To investigate the bacterial species and antimicrobial susceptibility of respiratory specimens of children with pneumonia in Hainan, China.

Methods

A total of 5017 specimens, including 4986 sputum samples, 19 bronchoalveolar lavage fluid samples and 12 tracheal tube tip samples from hospitalized children with pneumonia from April 1, 2021 to March 31, 2022 were studied. All the bacterial isolates were identified and confirmed with the VITEK 2 system. Antimicrobial susceptibility of all isolates was determined using the Kirby-Bauer method or the VITEK 2 Compact automatic system, following the breakpoints recommended by the Clinical and Laboratory Standards Institute.

Results

A total of 996 bacterial isolates were collected and classified into 24 species. The top 10 most frequent species were Haemophilus influenzae (356 isolates, 35.7%), Streptococcus pneumoniae (128, 12.9%), Moraxella catarrhalis (114, 11.5%), Escherichia coli (89, 8.9%), Staphylococcus aureus (89, 8.9%), Klebsiella pneumoniae (82, 8.2%), Acinetobacter baumannii (31, 3.1%), Pseudomonas aeruginosa (28, 2.8%), Enterobacter cloacae (18, 1.8%), and Streptococcus agalactiae (13, 1.3%). 70.5% strains had the resistant (R) and/or intermediate (I) phenotypes to at least one of the tested drugs, with a large proportion (54.6%) showing resistance to two or more commonly used antibiotics. In addition, 60.5% (69/114) of M. catarrhalis strains and 42.9% (153/356) of H. influenzae strains produced β-lactamases while 19.1% (17/89) E. coli and 6.1% (5/82) K. pneumoniae strains produced extended-spectrum β-lactamases.

Conclusion

A diversity of pathogenic bacteria were isolated from the respiratory tract of children with pneumonia in Hainan, China. High-frequency resistance to first-line antimicrobial drugs was observed in Gram-negative and Gram-positive bacteria, including 544 isolates resistant to at least two antibiotics. Rapid identification and susceptibility testing should be implemented for children with bacterial pneumonia in Hainan before drug treatment is recommended.

Robust cross-cohort gut microbiome associations with COVID-19 severity

Although many recent studies have examined associations between the gut microbiome and COVID-19 disease severity in individual patient cohorts, questions remain on the robustness across international cohorts of the biomarkers they reported. Here, we performed a meta-analysis of eight shotgun metagenomic studies of COVID-19 patients (comprising 1,023 stool samples) and 23 > 16S rRNA gene amplicon sequencing (16S) cohorts (2,415 total stool samples). We found that disease severity (as defined by the WHO clinical progression scale) was associated with taxonomic and functional microbiome differences. This alteration in gut microbiome configuration peaks at days 7-30 post diagnosis, after which the gut microbiome returns to a configuration that becomes more similar to that of healthy controls over time. Furthermore, we identified a core set of species that were consistently associated with disease severity across shotgun metagenomic and 16S cohorts, and whose abundance can accurately predict disease severity category of SARS-CoV-2 infected subjects, with Actinomyces oris abundance predicting population-level mortality rate of COVID-19. Additionally, we used relational diet-microbiome databases constructed from cohort studies to predict microbiota-targeted diet patterns that would modulate gut microbiota composition toward that of healthy controls. Finally, we demonstrated the association of disease severity with the composition of intestinal archaeal, fungal, viral, and parasitic communities. Collectively, this study has identified robust COVID-19 microbiome biomarkers, established accurate predictive models as a basis for clinical prognostic tests for disease severity, and proposed biomarker-targeted diets for managing COVID-19 infection.

Assessment of Risk Factors and Clinical Outcomes in Hospitalized COVID-19 Patients with Candida spp. Co-infections: Species Distribution and Antifungal Susceptibility Patterns of Isolates

INTRODUCTION

Fungal co-infections are considered an important complication in hospitalized patients with SARS-CoV-2 that can be attributed to disease aggravation, increased mortality, and poor outcomes. This study was conducted to determine the species distribution and antifungal susceptibility patterns of Candida isolates from hospitalized COVID-19 patients in Shiraz, Iran, in addition to associated risk factors and outcomes of co-infections with Candida species.

MATERIALS AND METHODS

In this single-center study, a total of 106 hospitalized COVID-19 patients were evaluated for clinical characteristics and outcomes. Species identification was performed by ITS1-5.8S-ITS2 gene sequencing. Antifungal susceptibility testing to fluconazole, itraconazole, voriconazole, posaconazole, caspofungin, amphotericin B, and nystatin was determined according to the M27-A3/S4 CLSI protocol.

RESULTS

Candida species were recovered from 48% (51/106) of hospitalized COVID-19 patients. Statistical analysis showed that patients who had heart failure, bacterial co-infection, and were receiving empirical antifungal therapy had a higher risk of developing Candida co-infection. In total, 71 Candida isolates were recovered, of which C. albicans (69%) was the most prevalent isolate. The majority of the Candida isolates were susceptible to all classes of tested antifungal drugs.

DISCUSSION

Our results elucidate a high rate of Candida co-infections among hospitalized COVID-19 patients. Comorbidities such as heart failure, HTN, COPD, bacterial infections as well as therapeutic interventions including catheterization, mechanical ventilation, and ICU admission increased the risk of Candida spp. isolation from the bloodstream, respiratory tract and urine samples, which led to a higher in-hospital mortality rate. Additionally, obtained data clarified that empirical antifungal therapy was not as successful as anticipated.

When to Initiate Antifungal Treatment in COVID-19 Patients with Secondary Fungal Co-infection

Purpose of Review

Severe-acute respiratory coronavirus 2 (SARS-CoV-2) has been driving the health care delivery system for over 2 years. With time, many issues related to co-infections in COVID-19 patients are constantly surfacing. There have been numerous reports about various fungal co-infections in patients with COVID-19. The extent of severity of fungal pathogens has been recognized as a substantial cause of morbidity and mortality in this population. Awareness, understanding, and a systematic approach to managing fungal co-infections in COVID-19 patients are important. No guidelines have enumerated the stepwise approach to managing the fungal infections co-occurring with COVID-19. This review is intended to present an overview of the fungal co-infections in COVID-19 patients and their stepwise screening and management.

Recent Findings

The most common fungal infections that have been reported to co-exist with COVID-19 are Candidemia, Aspergillosis, and Mucormycosis. Prevalence of co-infections in COVID-19 patients has been reported to be much higher in hospitalized COVID-19 patients, especially those in intensive care units. While clear pathogenetic mechanisms have not been delineated, COVID-19 patients are at a high risk of invasive fungal infections.

Summary

As secondary fungal infections have been challenging to treat in COVID-19 patients, as they tend to affect the critically ill or immunocompromised patients, a delay in diagnosis and treatment may be fatal. Antifungal drugs should be initiated with caution after carefully assessing the immune status of the patients, drug interactions, and adverse effects. The crucial factors in successfully treating fungal infections in COVID-19 patients are optimal diagnostic approach, routine screening, and timely initiation of antifungal therapy.

Natural products and their semi-synthetic derivatives against antimicrobial-resistant human pathogenic bacteria and fungi

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COVID-19 pandemic has traumatized the entire world. During this outbreak, an upsurge in MDR-associated pathogenic microbial organisms has been recorded.

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The increasing human microbial diseases pose a severe danger to global human safety.

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The infectious microbes have developed multiple tolerance strategies to overcome the negative drug impacts.

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Several naturally occurring chemicals produced from bacteria, plants, animals, marine species, and other sources with antimicrobial characteristics have been reviewed.

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These compounds show promise in minimizing the globally increasing microbial diseases.

Human infectious diseases caused by various microbial pathogens, in general, impact a large population of individuals every year. These microbial diseases that spread quickly remain to be a big issue in various health-related domains and to withstand the negative drug impacts, the antimicrobial-resistant pathogenic microbial organisms (pathogenic bacteria and pathogenic fungi) have developed a variety of resistance processes against many antimicrobial drug classes. During the COVID-19 outbreak, there seems to be an upsurge in drug and multidrug resistant-associated pathogenic microbial species. The preponderance of existing antimicrobials isn’t completely effective, which limits their application in clinical settings. Several naturally occurring chemicals produced from bacteria, plants, animals, marine species, and other sources are now being studied for antimicrobial characteristics. These natural antimicrobial compounds extracted from different sources have been demonstrated to be effective against a variety of diseases, although plants remain the most abundant source. These compounds have shown promise in reducing the microbial diseases linked to the development of drug tolerance and resistance. This paper offers a detailed review of some of the most vital and promising natural compounds and their derivatives against various human infectious microbial organisms. The inhibitory action of different natural antimicrobial compounds, and their possible mechanism of antimicrobial action against a range of pathogenic fungal and bacterial organisms, is provided. The review will be useful in refining current antimicrobial (antifungal and antibacterial) medicines as well as establishing new treatment strategies to tackle the rising number of human bacterial and fungal-associated infections.

COVID-19 associated rhinomaxillary mucormycosis

During COVID-19 pandemic, fulminant deep fungal infection started emerging in India, known as Mucormycosis. This type of mucormycosis was termed as COVID-19 associated mucormycosis (CAM). These patients had previous history of COVID-19 infection. Such cases were mainly reported in immunocompromised patients such as patients with poorly controlled diabetes and chronic renal diseases etc. Rhinomaxillary mucormycosis is an aggressive, fulminant, fatal deep fungal infection of head and neck region. Early diagnosis and prompt treatment can reduce the mortality and morbidity associated with the disease; hence we present case series of rhinomaxillary mucormycosis to create awareness amongst dental surgeons.

Fungal Infection in Co-infected Patients With COVID-19: An Overview of Case Reports/Case Series and Systematic Review

Fungal co-infections are frequent in patients with coronavirus disease 2019 (COVID-19) and can affect patient outcomes and hamper therapeutic efforts. Nonetheless, few studies have investigated fungal co-infections in this population. This study was performed to assess the rate of fungal co-infection in patients with COVID-19 as a systematic review. EMBASE, MEDLINE, and Web of Science were searched considering broad-based search criteria associated with COVID-19 and fungal co-infection. We included case reports and case series studies, published in the English language from January 1, 2020 to November 30, 2021, that reported clinical features, diagnosis, and outcomes of fungal co-infection in patients with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Totally, 54 case reports and 17 case series were identified, and 181 patients (132 men, 47 women, and 2 not mentioned) co-infected with COVID-19 and fungal infection enrolled. The frequency of fungal co-infection among patients with COVID-19 was 49.7, 23.2, 19.8, 6.6, and 0.5% in Asia, America, Europe, Africa, and Australia, respectively. Diabetes (59.6%) and hypertension (35.9%) were found as the most considered comorbidities in COVID-19 patients with fungal infections. These patients mainly suffered from fever (40.8%), cough (30.3%), and dyspnea (23.7%). The most frequent findings in the laboratory results of patients and increase in C-reactive protein (CRP) (33.1%) and ferritin (18.2%), and lymphopenia (16%) were reported. The most common etiological agents of fungal infections were Aspergillus spp., Mucor spp., Rhizopus spp., and Candida spp. reported in study patients. The mortality rate was 54.6%, and the rate of discharged patients was 45.3%. Remdesivir and voriconazole were the most commonly used antiviral and antifungal agents for the treatment of patients. The global prevalence of COVID-19-related deaths is 6.6%. Our results showed that 54.6% of COVID-19 patients with fungal co-infections died. Thus, this study indicated that fungal co-infection and COVID-19 could increase mortality. Targeted policies should be considered to address this raised risk in the current pandemic. In addition, fungal infections are sometimes diagnosed late in patients with COVID-19, and the severity of the disease worsens, especially in patients with underlying conditions. Therefore, patients with fungal infections should be screened regularly during the COVID-19 pandemic to prevent the spread of the COVID-19 patients with fungal co-infection.

Repurposing benzbromarone as antifolate to develop novel antifungal therapy for Candida albicans

Fungal infections in humans are responsible for mild to severe infections resulting in systemic effects that cause a large amount of mortality. Invasive fungal infections are having similar symptomatic effects to those of COVID-19. The COVID-19 patients are immunocompromised in nature and have a high probability of developing severe fungal infections, resulting in the development of further complications. The existing antifungal therapy has associated problems related to the development of drug resistance, being sub-potent in nature, and the presence of undesirable toxic effects. The fungal dihydrofolate reductase is an essential enzyme involved in the absorption of dietary folic acid and its conversion into tetrahydrofolate, which is a coenzyme required for the biosynthesis of the fungal nucleotides. Thus, in the current study, an attempt has been made to identify potential folate inhibitors of Candida albicans by a computational drug repurposing approach. Based upon the molecular docking simulation-based virtual screening followed by the molecular dynamic simulation of the macromolecular complex, benzbromarone has been identified as a potential anti-folate agent for the development of a novel therapy for the treatment of candidiasis.

An overview of COVID-19 related to fungal infections: what do we know after the first year of pandemic?

In 2019, severe acute respiratory syndrome caused by CoV-2 virus became a pandemic worldwide, being the fast spread of the disease due to the movement of infected people from one country to another, from one continent to another, or within the same country. Associated comorbidities are important factors that predispose to any fungal coinfections. Because of the importance of fungal infections in COVID-19 patients, the aim of this work was to collect data of the more encountered mycoses related to patients undergoing this disease. Aspergillosis was the first COVID-19-related fungal infection reported, being A. fumigatus the most frequent species for CAPA. Other fungal infections related include mainly candidiasis and mucormycosis, being Rhizopus spp. the more prevalent species found. Influenza-associated pulmonary aspergillosis is well documented; thus, similar complications are expected in severe forms of COVID-19 pneumonia. Therefore, in patients with COVID-19, it is important to take special attention to the surveillance and suspicion of fungal coinfections that might worsen the patient's prognosis.

Delineating the impact of COVID-19 on antimicrobial resistance: An Indian perspective

The COVID-19 pandemic has shattered millions of lives globally and continues to be a challenge to public health due to the emergence of variants of concern. Fear of secondary infections following COVID-19 has led to an escalation in antimicrobial use during the pandemic, while some antimicrobials have been repurposed as treatments for SARS-CoV-2, further driving antimicrobial resistance. India is one of the largest producers and consumers of antimicrobials globally, hence the task of curbing antimicrobial resistance is a huge challenge. Practices like empirical antimicrobial prescription and repurposing of drugs in clinical settings, self-medication and excessive use of antimicrobial hygiene products may have negatively impacted the prevalence of antimicrobial resistance in India. However, the expanded production of antimicrobials and disinfectants during the pandemic in response to increased demand may have had an even greater impact on the threat of antimicrobial resistance through major impacts on the environment. The review provides an outline of the impact COVID-19 can have on antimicrobial resistance in clinical settings and the possible outcomes on the environment. This review calls for the upgrading of existing antimicrobial policies and emphasizes the need for research studies to understand the impact of the pandemic on antimicrobial resistance in India.

Clinical impact of Candida respiratory tract colonization and acute lung infections in critically ill patients with COVID-19 pneumonia

Coronavirus disease 2019 (COVID-19), which is attributable to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been causing a worldwide health issue. Airways colonization by Candida spp. is prevalent among patients on automatic ventilation in intensive care units (ICUs). This research aimed to ascertain the risk factors and roles of Candida spp. respiratory tract colonization, and Candida lung infection during the progression of COVID-19 pneumonia in critically ill patients. In total, Candida spp. were recovered in 69 from 100 immunosuppressed patients with COVID-19. Bronchoscopy was used to collect the Bronchoalveolar lavage (BAL) specimens. For the identification of Candida spp. PCR sequencing was done using the ITS1 and ITS4 primers. The amplification of the HWP1 gene was conducted to identify the Candida albicans complex. The antifungal activities of fluconazole, itraconazole, voriconazole, amphotericin B and caspofungin against Candida spp. were evaluated using the Clinical and Laboratory Standards Institute M60. In 63.77% of the patients, Candida respiratory colonization at D0 and D14 had no impact on the severity of COVID-19. In comparison to C. albicans strains, Candida respiratory disorder with C. glabrata had influenced the severity of COVID-19 for critically ill patients following adjustment for the risk factors of COVID-19 (P < 0.05). Amphotericin B and caspofungin showed superior activity against all Candida spp. All antifungal agents showed 100% sensitivity against the two C. africana strains. Our observation on patients who used automatic ventilation, respiratory colonization by Candida spp. was not seen to influence the infection or death caused by COVID-19. Amphotericin B and caspofungin showed superior activity against all Candida spp. and were recommended for the treatment regime of pulmonary candidiasis associated with COVID-19 infection. Although “Candida pneumonia” is rarely being reported in critically ill patients, Candida airway colonization mainly by Candida albicans is common especially among patients with diabetes, malignancies, and kidney disorders.

Antimicrobial resistance (AMR) in COVID-19 patients: a systematic review and meta-analysis (November 2019-June 2021)

BACKGROUND

Pneumonia from SARS-CoV-2 is difficult to distinguish from other viral and bacterial etiologies. Broad-spectrum antimicrobials are frequently prescribed to patients hospitalized with COVID-19 which potentially acts as a catalyst for the development of antimicrobial resistance (AMR).

OBJECTIVES

We conducted a systematic review and meta-analysis during the first 18 months of the pandemic to quantify the prevalence and types of resistant co-infecting organisms in patients with COVID-19 and explore differences across hospital and geographic settings.

METHODS

We searched MEDLINE, Embase, Web of Science (BioSIS), and Scopus from November 1, 2019 to May 28, 2021 to identify relevant articles pertaining to resistant co-infections in patients with laboratory confirmed SARS-CoV-2. Patient- and study-level analyses were conducted. We calculated pooled prevalence estimates of co-infection with resistant bacterial or fungal organisms using random effects models. Stratified meta-analysis by hospital and geographic setting was also performed to elucidate any differences.

RESULTS

Of 1331 articles identified, 38 met inclusion criteria. A total of 1959 unique isolates were identified with 29% (569) resistant organisms identified. Co-infection with resistant bacterial or fungal organisms ranged from 0.2 to 100% among included studies. Pooled prevalence of co-infection with resistant bacterial and fungal organisms was 24% (95% CI 8-40%; n = 25 studies: I2 = 99%) and 0.3% (95% CI 0.1-0.6%; n = 8 studies: I2 = 78%), respectively. Among multi-drug resistant organisms, methicillin-resistant Staphylococcus aureus, carbapenem-resistant Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa and multi-drug resistant Candida auris were most commonly reported. Stratified analyses found higher proportions of AMR outside of Europe and in ICU settings, though these results were not statistically significant. Patient-level analysis demonstrated > 50% (n = 58) mortality, whereby all but 6 patients were infected with a resistant organism.

CONCLUSIONS

During the first 18 months of the pandemic, AMR prevalence was high in COVID-19 patients and varied by hospital and geography although there was substantial heterogeneity. Given the variation in patient populations within these studies, clinical settings, practice patterns, and definitions of AMR, further research is warranted to quantify AMR in COVID-19 patients to improve surveillance programs, infection prevention and control practices and antimicrobial stewardship programs globally.

Critically ill patients with COVID-19 show lung fungal dysbiosis with reduced microbial diversity in Candida spp colonized patients

Background

The COVID-19 pandemic has intensified interest in how the infection affects the lung microbiome of critically ill patients and how it contributes to acute respiratory distress syndrome (ARDS). We aimed to characterize the lower respiratory tract mycobiome of critically ill patients with COVID-19 in comparison to patients without COVID-19.

Methods

We performed an internal transcribed spacer 2 (ITS2) profiling with the Illumina MiSeq platform on 26 respiratory specimens from patients with COVID-19 as well as from 26 patients with non–COVID-19 pneumonia.

Results

Patients with COVID-19 were more likely to be colonized with Candida spp. ARDS was associated with lung dysbiosis characterized by a shift to Candida species colonization and a decrease of fungal diversity. We also observed higher bacterial phylogenetic distance among taxa in colonized patients with COVID-19. In patients with COVID-19 not colonized with Candida spp., ITS2 amplicon sequencing revealed an increase of Ascomycota unassigned spp. and 1 Aspergillus spp.–positive specimen. In addition, we found that corticosteroid therapy was frequently associated with positive Galactomannan cell wall component of Aspergillus spp. among patients with COVID-19.

Conclusion

Our study underpins that ARDS in patients with COVID-19 is associated with lung dysbiosis and that an increased density of Ascomycota unassigned spp. is present in patients not colonized with Candida spp.

Antimicrobial Use in Hospitalised Patients with COVID-19: An International Multicentre Point-Prevalence Study

Studies suggest that the incidence of coinfections in patients with the coronavirus disease 2019 (COVID-19) is low, but a large number of patients receive antimicrobials during hospitalisation. This may fuel a rise in antimicrobial resistance (AMR). We conducted a multicentre point-prevalence survey in seven tertiary university hospitals (in medical wards and intensive care units) in Croatia, Italy, Serbia and Slovenia. Of 988 COVID-19 patients, 521 were receiving antibiotics and/or antifungals (52.7%; range across hospitals: 32.9–85.6%) on the day of the study. Differences between hospitals were statistically significant (χ2 (6, N = 988) = 192.57, p < 0.001). The majority of patients received antibiotics and/or antifungals within 48 h of admission (323/521, 62%; range across hospitals: 17.4–100%), their most common use was empirical (79.4% of prescriptions), and pneumonia was the main indication for starting the treatment (three-quarters of prescriptions). The majority of antibiotics prescribed (69.9%) belonged to the “Watch” group of the World Health Organization AWaRe classification. The pattern of antimicrobial use differed across hospitals. The data show that early empiric use of broad-spectrum antibiotics is common in COVID-19 patients, and that the pattern of antimicrobial use varies across hospitals. Judicious use of antimicrobials is warranted to prevent an increase in AMR.

Plasma cell-free RNA characteristics in COVID-19 patients

The pathogenesis of COVID-19 is still elusive, which impedes disease progression prediction, differential diagnosis, and targeted therapy. Plasma cell-free RNAs (cfRNAs) carry unique information from human tissue and thus could point to resourceful solutions for pathogenesis and host-pathogen interactions. Here, we performed a comparative analysis of cfRNA profiles between COVID-19 patients and healthy donors using serial plasma. Analyses of the cfRNA landscape, potential gene regulatory mechanisms, dynamic changes in tRNA pools upon infection, and microbial communities were performed. A total of 380 cfRNA molecules were up-regulated in all COVID-19 patients, of which seven could serve as potential biomarkers (AUC > 0.85) with great sensitivity and specificity. Antiviral (NFKB1A, IFITM3, and IFI27) and neutrophil activation (S100A8, CD68, and CD63)–related genes exhibited decreased expression levels during treatment in COVID-19 patients, which is in accordance with the dynamically enhanced inflammatory response in COVID-19 patients. Noncoding RNAs, including some microRNAs (let 7 family) and long noncoding RNAs (GJA9-MYCBP) targeting interleukin (IL6/IL6R), were differentially expressed between COVID-19 patients and healthy donors, which accounts for the potential core mechanism of cytokine storm syndromes; the tRNA pools change significantly between the COVID-19 and healthy group, leading to the accumulation of SARS-CoV-2 biased codons, which facilitate SARS-CoV-2 replication. Finally, several pneumonia-related microorganisms were detected in the plasma of COVID-19 patients, raising the possibility of simultaneously monitoring immune response regulation and microbial communities using cfRNA analysis. This study fills the knowledge gap in the plasma cfRNA landscape of COVID-19 patients and offers insight into the potential mechanisms of cfRNAs to explain COVID-19 pathogenesis.

Analysis of Fungal and Bacterial Co-Infections in Mortality Cases among Hospitalized Patients with COVID-19 in Taipei, Taiwan

Fungal or bacterial co-infections in patients with H1N1 influenza have already been reported in many studies. However, information on the risk factors, complications, and prognosis of mortality cases with coronavirus disease 2019 (COVID-19) are limited. We aimed to assess 36 mortality cases of 178 hospitalized patients among 339 patients confirmed to have had SARS-CoV-2 infections in a medical center in the Wenshan District of Taipei, Taiwan, between January 2020 and September 2021. Of these 36 mortality cases, 20 (60%) were men, 28 (77.7%) were aged >65 years, and the median age was 76 (54–99) years. Comorbidities such as hypertension, coronary artery disease, and chronic kidney disease were more likely to be found in the group with length of stay (LOS) > 7 d. In addition, the laboratory data indicating elevated creatinine-phosphate-kinase (CPK) (p < 0.001) and lactic acid dehydrogenase (LDH) (p = 0.05), and low albumin (p < 0.01) levels were significantly related to poor prognosis and mortality. The respiratory pathogens of early co-infections (LOS < 7 d) in the rapid progression to death group (n = 7 patients) were two bacteria (22.2%) and seven Candida species (77.8.7%). In contrast, pathogens of late co-infections (LOS > 7 d) (n = 27 patients) were 20 bacterial (54.1%), 16 Candida (43.2%), and only 1 Aspergillus (2.7%) species. In conclusion, the risk factors related to COVID-19 mortality in the Wenshan District of Taipei, Taiwan, were old age, comorbidities, and abnormal biomarkers such as low albumin level and elevated CPK and LDH levels. Bacterial co-infections are more common with Gram-negative pathogens. However, fungal co-infections are relatively more common with Candida spp. than Aspergillus in mortality cases of COVID-19.

Fungal Infections Other Than Invasive Aspergillosis in COVID-19 Patients

Invasive fungal disease (IFD) associated with Coronavirus Disease 2019 (COVID-19) has focussed predominantly on invasive pulmonary aspergillosis. However, increasingly emergent are non-Aspergillus fungal infections including candidiasis, mucormycosis, pneumocystosis, cryptococcosis, and endemic mycoses. These infections are associated with poor outcomes, and their management is challenged by delayed diagnosis due to similarities of presentation to aspergillosis or to non-specific features in already critically ill patients. There has been a variability in the incidence of different IFDs often related to heterogeneity in patient populations, diagnostic protocols, and definitions used to classify IFD. Here, we summarise and address knowledge gaps related to the epidemiology, risks, diagnosis, and management of COVID-19-associated fungal infections other than aspergillosis.

The role of SARS-CoV-2 immunosuppression and the therapy used to manage COVID-19 disease in the emergence of opportunistic fungal infections: A review

Since December 2019 SARS-CoV-2 infections have affected millions of people worldwide. Along with the increasing number of COVID-19 patients, the number of cases of opportunistic fungal infections among the COVID-19 patients is also increasing. There have been reports of the cases of aspergillosis and candidiasis in the COVID-19 patients. The COVID-19 patients have also been affected by rare fungal infections such as histoplasmosis, pneumocystosis, mucormycosis and cryptococcosis. These fungal infections are prolonging the stay of COVID-19 patients in hospital. In this study several published case reports, case series, prospective and retrospective studies were investigated to explore and report the updated information regarding candidiasis, crytptococcosis, aspergillosis, mucormycosis, histoplasmosis, and pneumocystosis infections in COVID-19 patients. In this review, the risk factors of these co-infections in COVID-19 patients have been reported. There have been reports that the comorbidities and the treatment with corticoids, monoclonal antibodies, use of mechanical ventilation, and use of antibiotics during COVID-19 management are associated with the emergence of fungal infections in the COVID-19 patients. Hence, this review analyses the role of these therapies and comorbidities in the emergence of these fungal infections among COVID-19 patients. This review will help to comprehend if these fungal infections are the result of the co-morbidities, and treatment protocol followed to manage COVID-19 patients or directly due to the SARS-CoV-2 infection. The analysis of all these factors will help to understand their role in fungal infections among COVID-19 patients which can be valuable to the scientific community.

OUP accepted manuscript

Studies demonstrated the impact of the COVID-19 pandemic in the prevalence and susceptibility profiles of bacterial and fungal organisms. We analyzed 4821 invasive fungal isolates collected during 2018, 2019, and 2020 in 48 hospitals worldwide to evaluate the impact of this event in the occurrence and susceptibility rates of common fungal species. Isolates were tested using the CLSI broth microdilution method. While the percentage of total isolates that were C. glabrata (n = 710 isolates) or C. krusei (n = 112) slightly increased in 2020, the percentage for C. parapsilosis (n = 542), A. fumigatus (n = 416), and C. lusitaniae (n = 84) significantly decreased (P < .05). Fluconazole resistance in C. glabrata decreased from 5.8% in 2018–2019 to 2.0% in 2020, mainly due to fewer hospitals in the US having these isolates (5 vs. 1 hospital). Conversely, higher fluconazole-resistance rates were noted for C. parapsilosis (13.9 vs. 9.8%) and C. tropicalis (3.5 vs. 0.7%; P < .05) during 2020. Voriconazole resistance also increased for these species. Echinocandin resistance was unchanged among Candida spp. Voriconazole susceptibility rates in A. fumigatus were similar in these two periods (91.7% in 2018 and 2019 vs. 93.0% in 2020). Changes were also noticed in the organisms with smaller numbers of collected isolates. We observed variations in the occurrence of organisms submitted to a global surveillance and the susceptibility patterns for some organism-antifungal combinations. As the COVID-19 pandemic is still ongoing, the impact of this event must continue to be monitored to guide treatment of patients affected by bacterial and fungal infections.

A High Frequency of Candida auris Blood Stream Infections in Coronavirus Disease 2019 Patients Admitted to Intensive Care Units, Northwestern India: A Case Control Study

Background

The ongoing pandemic of coronavirus disease 2019 (COVID-19) has overwhelmed healthcare facilities and raises an important novel concern of nosocomial transmission of Candida species in the intensive care units (ICUs).

Methods

We evaluated the incidence and risk factors for development of candidemia in 2384 COVID-19 patients admitted during August 2020–January 2021 in ICUs of 2 hospitals (Delhi and Jaipur) in India. A 1:2 case-control matching was used to identify COVID-19 patients who did not develop candidemia as controls.

Results

A total of 33 patients developed candidemia and accounted for an overall incidence of 1.4% over a median ICU stay of 24 days. A 2-fold increase in the incidence of candidemia in COVID-19 versus non-COVID-19 patients was observed with an incidence rate of 14 and 15/1000 admissions in 2 ICUs. Candida auris was the predominant species (42%) followed by Candida tropicalis. Multivariable regression analysis revealed the use of tocilizumab, duration of ICU stay (24 vs 14 days), and raised ferritin level as an independent predictor for the development of candidemia. Azole resistance was observed in C auris and C tropicalis harboring mutations in the azole target ERG11 gene. Multilocus sequence typing (MLST) identified identical genotypes of C tropicalis in COVID-19 patients, raising concern for nosocomial transmission of resistant strains.

Conclusions

Secondary bacterial infections have been a concern with the use of tocilizumab. In this cohort of critically ill COVID-19 patients, tocilizumab was associated with the development of candidemia. Surveillance of antifungal resistance is warranted to prevent transmission of multidrug-resistant strains of nosocomial yeasts in COVID-19 hospitalized patients.

Invasive Fungal Infections Complicating COVID-19: A Narrative Review

Invasive fungal infections (IFIs) can complicate the clinical course of COVID-19 and are associated with a significant increase in mortality, especially in critically ill patients admitted to an intensive care unit (ICU). This narrative review concerns 4099 cases of IFIs in 58,784 COVID-19 patients involved in 168 studies. COVID-19-associated invasive pulmonary aspergillosis (CAPA) is a diagnostic challenge because its non-specific clinical/imaging features and the fact that the proposed clinically diagnostic algorithms do not really apply to COVID-19 patients. Forty-seven observational studies and 41 case reports have described a total of 478 CAPA cases that were mainly diagnosed on the basis of cultured respiratory specimens and/or biomarkers/molecular biology, usually without histopathological confirmation. Candidemia is a widely described secondary infection in critically ill patients undergoing prolonged hospitalisation, and the case reports and observational studies of 401 cases indicate high crude mortality rates of 56.1% and 74.8%, respectively. COVID-19 patients are often characterised by the presence of known risk factors for candidemia such as in-dwelling vascular catheters, mechanical ventilation, and broad-spectrum antibiotics. We also describe 3185 cases of mucormycosis (including 1549 cases of rhino-orbital mucormycosis (48.6%)), for which the main risk factor is a history of poorly controlled diabetes mellitus (>76%). Its diagnosis involves a histopathological examination of tissue biopsies, and its treatment requires anti-fungal therapy combined with aggressive surgical resection/debridement, but crude mortality rates are again high: 50.8% in case reports and 16% in observational studies. The presence of other secondary IFIs usually diagnosed in severely immunocompromised patients show that SARS-CoV-2 is capable of stunning the host immune system: 20 cases of Pneumocystis jirovecii pneumonia, 5 cases of cryptococcosis, 4 cases of histoplasmosis, 1 case of coccidioides infection, 1 case of pulmonary infection due to Fusarium spp., and 1 case of pulmonary infection due to Scedosporium.

Clinical outcomes in patients co-infected with COVID-19 and Staphylococcus aureus: a scoping review

BACKGROUND

Endemic to the hospital environment, Staphylococcus aureus (S. aureus) is a leading bacterial pathogen that causes deadly infections such as bacteremia and endocarditis. In past viral pandemics, it has been the principal cause of secondary bacterial infections, significantly increasing patient mortality rates. Our world now combats the rapid spread of COVID-19, leading to a pandemic with a death toll greatly surpassing those of many past pandemics. However, the impact of co-infection with S. aureus remains unclear. Therefore, we aimed to perform a high-quality scoping review of the literature to synthesize the existing evidence on the clinical outcomes of COVID-19 and S. aureus co-infection.

METHODS

A scoping review of the literature was conducted in PubMed, Scopus, Ovid MEDLINE, CINAHL, ScienceDirect, medRxiv, and the WHO COVID-19 database using a combination of terms. Articles that were in English, included patients infected with both COVID-19 and S. aureus, and provided a description of clinical outcomes for patients were eligible. From these articles, the following data were extracted: type of staphylococcal species, onset of co-infection, patient sex, age, symptoms, hospital interventions, and clinical outcomes. Quality assessments of final studies were also conducted using the Joanna Briggs Institute's critical appraisal tools.

RESULTS

Searches generated a total of 1922 publications, and 28 articles were eligible for the final analysis. Of the 115 co-infected patients, there were a total of 71 deaths (61.7%) and 41 discharges (35.7%), with 62 patients (53.9%) requiring ICU admission. Patients were infected with methicillin-sensitive and methicillin-resistant strains of S. aureus, with the majority (76.5%) acquiring co-infection with S. aureus following hospital admission for COVID-19. Aside from antibiotics, the most commonly reported hospital interventions were intubation with mechanical ventilation (74.8 %), central venous catheter (19.1 %), and corticosteroids (13.0 %).

CONCLUSIONS

Given the mortality rates reported thus far for patients co-infected with S. aureus and COVID-19, COVID-19 vaccination and outpatient treatment may be key initiatives for reducing hospital admission and S. aureus co-infection risk. Physician vigilance is recommended during COVID-19 interventions that may increase the risk of bacterial co-infection with pathogens, such as S. aureus, as the medical community's understanding of these infection processes continues to evolve.

Predisposing factors of important invasive fungal coinfections in COVID-19 patients: a review article

Severe acute respiratory syndrome coronavirus-2 has caused a devastating pandemic lasting for more than a year. To date, 47 million individuals have been infected and 1.2 million individuals have died worldwide. Some of the most important coinfections in patients with coronavirus disease 2019 (COVID-19) are opportunistic invasive fungal infections (OIFIs), which are sometimes not rapidly diagnosed and are often diagnosed after death. Aspergillosis and candidiasis are the most prevalent OIFIs in patients with COVID-19. Mycormycosis, cryptococcosis, and other fungal diseases have also been documented more rarely. This review aimed to summarize factors affecting COVID-19 transmission, prevalence, morbidity, and mortality in Iran as well as to review common OIFIs in patients with COVID-19. Immunological factors, underlying diseases, and social, cultural, and environmental factors can affect COVID-19 transmission. There is a need to improve diagnostic and therapeutic criteria for OIFIs and to optimize management procedures so that patients with OIFIs can receive treatment as rapidly as possible. Screening of patients with confirmed COVID-19 for OIFIs at the treating physician’s discretion could enable early OIFI diagnosis, treatment, and mortality reduction.

Overview on the Prevalence of Fungal Infections, Immune Response, and Microbiome Role in COVID-19 Patients

Patients with severe COVID-19, such as individuals in intensive care units (ICU), are exceptionally susceptible to bacterial and fungal infections. The most prevalent fungal infections are aspergillosis and candidemia. Nonetheless, other fungal species (for instance, Histoplasma spp., Rhizopus spp., Mucor spp., Cryptococcus spp.) have recently been increasingly linked to opportunistic fungal diseases in COVID-19 patients. These fungal co-infections are described with rising incidence, severe illness, and death that is associated with host immune response. Awareness of the high risks of the occurrence of fungal co-infections is crucial to downgrade any arrear in diagnosis and treatment to support the prevention of severe illness and death directly related to these infections. This review analyses the fungal infections, treatments, outcome, and immune response, considering the possible role of the microbiome in these patients. The search was performed in Medline (PubMed), using the words "fungal infections COVID-19", between 2020-2021.

Bacterial co-infection in patients with SARS-CoV-2 in the Kingdom of Bahrain

BACKGROUND

The coronavirus disease 2019 (COVID-19) pandemic presents a significant challenge to the medical profession, increasing in the presence of microbial co-infection. Bacterial and Fungal co-infections increase the risk of morbidity and mortality in patients with COVID-19.

AIM

To study the bacterial profile in patients with COVID-19 who needed admission to receive treatment in the main centres concerned with managing COVID-19 disease in the Kingdom of Bahrain.

METHODS

The study was a retrospective observational analysis of the bacterial profile and the bacterial resistance in patients with confirmed COVID-19 disease who needed admission to receive treatment in the main centres assigned to manage patients with COVID-19 disease in the Kingdom of Bahrain from February to October 2020. We used the electronic patients' records and the microbiology laboratory data to identify patients' demographics, clinical data, microbial profile, hospital or community-acquired, and the outcomes.

RESULTS

The study included 1380 patients admitted with confirmed COVID-19 disease during the study period. 51% were admitted from February to June, and 49% were admitted from July to October 2020, with a recurrence rate was 0.36%. There was a significant increase in bacterial and fungal co-infection in the second period compared to the first period. The most common isolated organisms were the gram-negative bacteria (mainly Klebsiella pneumoniae, Pseudomonas aeruginosa, multi-drug resistant Acinetobacter baumannii, and Escherichia coli), the gram-positive bacteria (mainly coagulase negative Staphylococci, Enterococcus faecium, Enterococcus faecalis, Staphylococcus aureus) and fungaemia (Candida galabrata, Candida tropicalis, Candida albicans, Aspergillus fumigatus, Candida parapsilosis, Aspergillus niger). The hospital-acquired infection formed 73.8%, 61.6%, 100% gram-negative, gram-positive and fungaemia. Most of the hospital-acquired infection occurred in the second period with a higher death rate than community-acquired infections.

CONCLUSION

Bacterial and fungal co-infections in patients admitted with confirmed COVID-19 disease pose higher morbidity and mortality risks than those without co-infections. We should perform every effort to minimize these risks.

Bacterial co-infection in patients with SARS-CoV-2 in the Kingdom of Bahrain

BACKGROUND

The coronavirus disease 2019 (COVID-19) pandemic presents a significant challenge to the medical profession, increasing in the presence of microbial co-infection. Bacterial and Fungal co-infections increase the risk of morbidity and mortality in patients with COVID-19.

AIM

To study the bacterial profile in patients with COVID-19 who needed admission to receive treatment in the main centres concerned with managing COVID-19 disease in the Kingdom of Bahrain.

METHODS

The study was a retrospective observational analysis of the bacterial profile and the bacterial resistance in patients with confirmed COVID-19 disease who needed admission to receive treatment in the main centres assigned to manage patients with COVID-19 disease in the Kingdom of Bahrain from February to October 2020. We used the electronic patients’ records and the microbiology laboratory data to identify patients’ demographics, clinical data, microbial profile, hospital or community-acquired, and the outcomes.

RESULTS

The study included 1380 patients admitted with confirmed COVID-19 disease during the study period. 51% were admitted from February to June, and 49% were admitted from July to October 2020, with a recurrence rate was 0.36%. There was a significant increase in bacterial and fungal co-infection in the second period compared to the first period. The most common isolated organisms were the gram-negative bacteria (mainly Klebsiella pneumoniae, Pseudomonas aeruginosa, multi-drug resistant Acinetobacter baumannii, and Escherichia coli), the gram-positive bacteria (mainly coagulase negative Staphylococci, Enterococcus faecium, Enterococcus faecalis, Staphylococcus aureus) and fungaemia (Candida galabrata, Candida tropicalis, Candida albicans, Aspergillus fumigatus, Candida parapsilosis, Aspergillus niger). The hospital-acquired infection formed 73.8%, 61.6%, 100% gram-negative, gram-positive and fungaemia. Most of the hospital-acquired infection occurred in the second period with a higher death rate than community-acquired infections.

CONCLUSION

Bacterial and fungal co-infections in patients admitted with confirmed COVID-19 disease pose higher morbidity and mortality risks than those without co-infections. We should perform every effort to minimize these risks.

Epidemiology of Systemic Mycoses in the COVID-19 Pandemic

The physiopathologic characteristics of COVID-19 (high levels of inflammatory cytokines and T-cell reduction) promote fungal colonization and infection, which can go unnoticed because the symptoms in both diseases are very similar. The objective of this work was to study the current epidemiology of systemic mycosis in COVID-19 times. A literature search on the subject (January 2020–February 2021) was performed in PubMed, Embase, Cochrane Library, and LILACS without language restrictions. Demographic data, etiological agent, risk factors, diagnostic methods, antifungal treatment, and fatality rate were considered. Eighty nine publications were found on co-infection by COVID-19 and pneumocystosis, candidiasis, aspergillosis, mucormycosis, coccidioidomycosis, or histoplasmosis. In general, the co-infections occurred in males over the age of 40 with immunosuppression caused by various conditions. Several species were identified in candidiasis and aspergillosis co-infections. For diagnosis, diverse methods were used, from microbiological to molecular. Most patients received antifungals; however, the fatality rates were 11–100%. The latter may result because the clinical picture is usually attributed exclusively to SARS-CoV-2, preventing a clinical suspicion for mycosis. Diagnostic tests also have limitations beginning with sampling. Therefore, in the remainder of the pandemic, these diagnostic limitations must be overcome to achieve a better patient prognosis.

Antifungal Drug Susceptibility and Genetic Characterization of Fungi Recovered from COVID-19 Patients

Fungal infections are common complications of respiratory viral infections and are associated with the increased need for intensive care and elevated mortality. Data regarding microbiological and molecular characteristics of such infections in COVID-19 patients are scarce. Here, we performed a comprehensive analysis, including species identification, antifungal susceptibility testing, molecular resistance determinants analysis, typing, and retrospective clinical data review, of fungal isolates recovered from 19 COVID-19 patients, who were hospitalized at the Hackensack University Medical Center (HUMC) in Hackensack, New Jersey, USA, in the initial phase of the pandemic from April–May 2020. In total, 17 Candida albicans, two C. parapsilosis, and two Aspergillus fumigatus were analyzed. All Candida spp. isolates were susceptible to micafungin and azole drugs (fluconazole, voriconazole, posaconazole, itraconazole, isavuconazole). A. fumigatus isolates were susceptible to micafungin and all triazole drugs except fluconazole (intrinsic resistance). Multilocus sequence typing (MLST) of C. albicans isolates revealed 15 different sequence types (STs), which clustered below the clade-defining limit of p-distance < 0.04. Pulsed-field gel electrophoresis (PFGE) karyotyping revealed no chromosomal rearrangements in these isolates. A. fumigatus isolates were of different, non-related genotypes. We speculate that virus- and drug-induced immunosuppression (94.7% of the patients received corticosteroids), together with prolonged hospital stay (median duration of 29 days) and mechanical ventilation (median duration of 24 days) likely increased the susceptibility to secondary respiratory and bloodstream infections in the studied patient population. The presence of fungi in blood or respiratory tract fluid was a prognosticator for poor clinical outcome, which presented as an 89.5% 30-day mortality in our patient cohort.

Risk Factors for Fungal Co-Infections in Critically Ill COVID-19 Patients, with a Focus on Immunosuppressants

Severe cases of coronavirus disease 2019 (COVID-19) managed in the intensive care unit are prone to complications, including secondary infections with opportunistic fungal pathogens. Systemic fungal co-infections in hospitalized COVID-19 patients may exacerbate COVID-19 disease severity, hamper treatment effectiveness and increase mortality. Here, we reiterate the role of fungal co-infections in exacerbating COVID-19 disease severity as well as highlight emerging trends related to fungal disease burden in COVID-19 patients. Furthermore, we provide perspectives on the risk factors for fungal co-infections in hospitalized COVID-19 patients and highlight the potential role of prolonged immunomodulatory treatments in driving fungal co-infections, including COVID-19-associated pulmonary aspergillosis (CAPA), COVID-19-associated candidiasis (CAC) and mucormycosis. We reiterate the need for early diagnosis of suspected COVID-19-associated systemic mycoses in the hospital setting.

Resistance to Echinocandins Complicates a Case of Candida albicans Bloodstream Infection: A Case Report

Invasive candidiasis is known to be one of the most common healthcare-associated complications and is caused by several Candida species. First-line drugs, particularly echinocandins, are effective, but there are increasing reports of resistance to these molecules, though rarely related to C. albicans. Even though the rate of echinocandins resistance remains low (<3%), sporadic cases are emerging. Here, we present a case of bloodstream infection by a pan-echinocandin-resistant Candida albicans affecting a critically ill patient, who died in an intensive care unit following therapeutic failure and multiple organ dysfunction syndrome. This case highlights the need to suspect pan-echinocandin resistance in patients with prolonged echinocandin exposure, particularly in the presence of urinary tract colonization. Our study shows the importance of sequencing to predict therapeutic failure in patients treated with echinocandins and persistent candidemia.

Risk Factors for Mortality in Adult COVID-19 Patients Who Develop Bloodstream Infections Mostly Caused by Antimicrobial-Resistant Organisms: Analysis at a Large Teaching Hospital in Italy

The aim of this study was to characterize COVID-19 (SARS-CoV-2-infected) patients who develop bloodstream infection (BSI) and to assess risk factors associated with in-hospital mortality. We conducted a retrospective observational study of adult patients admitted for ≥48 h to a large Central Italy hospital for COVID-19 (1 March to 31 May 2020) who had or had not survived at discharge. We included only patients having blood cultures drawn or other inclusion criteria satisfied. Kaplan–Meier survival or Cox regression analyses were performed of 293 COVID-19 patients studied, 46 patients (15.7%) had a hospital-acquired clinically relevant BSI secondary to SARS-CoV-2 infection, accounting for 58 episodes (49 monomicrobial and 9 polymicrobial) in total. Twelve episodes (20.7%) occurred at day 3 of hospital admission. Sixty-nine species were isolated, including Staphylococcus aureus (32.8%), Enterobacterales (20.7%), Enterococcus faecalis (17.2%), Candida (13.8%) and Pseudomonas aeruginosa (10.3%). Of 69 isolates, 27 (39.1%) were multidrug-resistant organisms. Twelve (54.5%) of 22 patients for whom empirical antimicrobial therapy was inappropriate were infected by a multidrug-resistant organism. Of 46 patients, 26 (56.5%) survived and 20 (43.5%) died. Exploring variables for association with in-hospital mortality identified > 75-year age (HR 2.97, 95% CI 1.15–7.68, p = 0.02), septic shock (HR 6.55, 95% CI 2.36–18.23, p < 0.001) and BSI onset ≤ 3 days (HR 4.68, 95% CI 1.40–15.63, p = 0.01) as risk factors independently associated with death. In our hospital, mortality among COVID-19 patients with BSI was high. While continued vigilance against these infections is essential, identification of risk factors for mortality may help to reduce fatal outcomes in patients with COVID-19.

Candidemia among Iranian Patients with Severe COVID-19 Admitted to ICUs

As a novel risk factor, COVID-19 has led to an increase in the incidence of candidemia and an elevated mortality rate. Despite being of clinical importance, there is a lack of data regarding COVID-19-associated candidemia (CAC) among Iranian patients. Therefore, in this retrospective study, we assessed CAC epidemiology in the intensive care units (ICUs) of two COVID-19 centers in Mashhad, Iran, from early November 2020 to late January 2021. Yeast isolates from patients’ blood were identified by 21-plex polymerase chain reaction (PCR) and sequencing, then subjected to antifungal susceptibility testing according to the CLSI M27-A3 protocol. Among 1988 patients with COVID-19 admitted to ICUs, seven had fungemia (7/1988; 0.03%), among whom six had CAC. The mortality of the limited CAC cases was high and greatly exceeded that of patients with COVID-19 but without candidemia (100% (6/6) vs. 22.7% (452/1988)). In total, nine yeast isolates were collected from patients with fungemia: five Candida albicans, three C. glabrata, and one Rhodotorula mucilaginosa. Half of the patients infected with C. albicans (2/4) were refractory to both azoles and echinocandins. The high mortality of patients with CAC, despite antifungal therapy, reflects the severity of the disease in these patients and underscores the importance of rapid diagnosis and timely initiation of antifungal treatment.

Increased antimicrobial resistance during the COVID-19 pandemic

In addition to SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) infection itself, an increase in the incidence of antimicrobial resistance poses collateral damage to the current status of the COVID-19 (coronavirus disease 2019) pandemic. There has been a rapid increase in multidrug-resistant organisms (MDROs), including extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae, carbapenem-resistant New Delhi metallo-β-lactamase (NDM)-producing Enterobacterales, Acinetobacter baumannii, methicillin-resistant Staphylococcus aureus (MRSA), pan-echinocandin-resistant Candida glabrata and multi-triazole-resistant Aspergillus fumigatus. The cause is multifactorial and is particularly related to high rates of antimicrobial agent utilisation in COVID-19 patients with a relatively low rate of co- or secondary infection. Appropriate prescription and optimised use of antimicrobials according to the principles of antimicrobial stewardship as well as quality diagnosis and aggressive infection control measures may help prevent the occurrence of MDROs during this pandemic.

Pulmonary Candidiasis Associated with COVID-19: Evaluation of Causative Agents and their Antifungal Susceptibility Patterns

BACKGROUND

The purpose of the present study was to isolate Candida species from individuals with the COVID-19 disease and evaluate the susceptibility pattern of Candida spp. to routine antifungal drugs.

MATERIALS AND METHODS

A total of 25 Candida spp. isolated from hospitalized patients with COVID-19, who were suspected to have pulmonary candidiasis, and 26 archived Candida spp. specimens were enrolled in this study. For the identification of Candida spp., PCR was performed to detect and amplify the ITS1 and ITS4 genes. Then the products were subjected to the Msp I restriction enzyme to precisely identify the species. The amplification of the WHP1 gene was conducted to identify Candida albicans species. The antifungal activities of routine drugs and the synthesize AuNPs against Candida spp. were assessed based on the protocols presented by the Clinical and Laboratory Standards Institute M60.

RESULTS

In the present study, C. albicans (24; 96%) and C. parapsilosis (1; 4%) were identified as the etiologic agents of the pulmonary candidiasis associated with the COVID-19 infection. Voriconazol and amphotericin B had superior activity against all the isolates in this study. Treatment with fluconazole and itraconazole did not significantly change the formation of colony-forming units (CFU). However, treatment with the AuNPs significantly decreased (within the range of 92-99.1%; P<0.05) the number of CFUs.

CONCLUSION

The azole prophylaxis has likely been associated with the development of resistant isolates; the results of the present study suggested the promising role of novel antifungal agents such as AuNPs in overcoming drug resistant fungi.

Increased incidence of candidemia in a tertiary care hospital with the COVID-19 pandemic

Background

The incidence of candidemia in our hospital has been stable over an 18‐year period (1.3 episodes per 1000 admissions). Since March 2020, we have observed an increase in cases of candidemia.

Methods

In March 2020, the hospital was prepared to receive patients with COVID‐19, with cancellation of elective procedures, discharge of less sick patients and the activation of beds for COVID‐19. We compared the incidence of candidemia in 2 periods: from January 2019 to February 2020 (period 1) and from March to September 2020 (period 2).

Results

We diagnosed 41 episodes of candidemia, 16 in period 1 and 25 in period 2 (9 COVID‐19 patients). Compared with non‐COVID‐19 patients, COVID‐19 patients with candidemia were more likely to be under mechanical ventilation (100% vs. 34.4%, P < .001). The median number of monthly admissions in period 1 and 2 was 723 (interquartile range 655‐836) and 523 (interquartile range 389‐574), respectively. The incidence of candidemia (per 1000 admissions) was 1.54 in period 1 and 7.44 in period 2 (P < .001). In period 2, the incidence of candidemia (per 1000 admissions) was 4.76 if we consider only cases of candidemia in non‐COVID‐19 patients, 2.68 if we consider only cases of candidemia in COVID‐19 patients and 14.80 considering only admissions of patients with COVID‐19.

Conclusions

The increase in the incidence of candidemia in our hospital may be attributed to 2 factors: a reduction in the number of admissions (denominator) and the occurrence of candidemia in COVID‐19 patients.