COVID-19-Associated Candidiasis (CAC): An Underestimated Complication in the Absence of Immunological Predispositions?

SARS-CoV-2 infection predisposes patients to coinfection with Staphylococcus aureus

Severe COVID-19 has been associated with coinfections with bacterial and fungal pathogens. Notably, patients with COVID-19 who develop Staphylococcus aureus bacteremia exhibit higher rates of mortality than those infected with either pathogen alone. To understand this clinical scenario, we collected and examined S. aureus blood and respiratory isolates from a hospital in New York City during the early phase of the pandemic from both SARS-CoV-2+ and SARS-CoV-2- patients. Whole genome sequencing of these S. aureus isolates revealed broad phylogenetic diversity in both patient groups, suggesting that SARS-CoV-2 coinfection was not associated with a particular S. aureus lineage. Phenotypic characterization of the contemporary collection of S. aureus isolates from SARS-CoV-2+ and SARS-CoV-2- patients revealed no notable differences in several virulence traits examined. However, we noted a trend toward overrepresentation of S. aureus bloodstream strains with low cytotoxicity in the SARS-CoV-2+ group. We observed that patients coinfected with SARS-CoV-2 and S. aureus were more likely to die during the acute phase of infection when the coinfecting S. aureus strain exhibited high or low cytotoxicity. To further investigate the relationship between SARS-CoV-2 and S. aureus infections, we developed a murine coinfection model. These studies revealed that infection with SARS-CoV-2 renders mice susceptible to subsequent superinfection with low cytotoxicity S. aureus. Thus, SARS-CoV-2 infection sensitizes the host to coinfections, including S. aureus isolates with low intrinsic virulence.

IMPORTANCE

The COVID-19 pandemic has had an enormous impact on healthcare across the globe. Patients who were severely infected with SARS-CoV-2, the virus causing COVID-19, sometimes became infected with other pathogens, which is termed coinfection. If the coinfecting pathogen is the bacterium Staphylococcus aureus, there is an increased risk of patient death. We collected S. aureus strains that coinfected patients with SARS-CoV-2 to study the disease outcome caused by the interaction of these two important pathogens. We found that both in patients and in mice, coinfection with an S. aureus strain lacking toxicity resulted in more severe disease during the early phase of infection, compared with infection with either pathogen alone. Thus, SARS-CoV-2 infection can directly increase the severity of S. aureus infection.

Candida Isolation During COVID-19: Microbiological Findings of a Prospective Study in a Regional Hospital

BACKGROUND

Prolonged hospitalization due to the COVID-19 pandemic gathered risk factors for developing invasive candidiasis.

AIM

To describe Candida spp. isolated from patients with clinical suspicion of COVID treated in a public hospital specialized in COVID-19 during the pandemic, considering the susceptibility profiles and the risk factors related to the species detected in a positive yeast culture.

METHODS

From different samples of 33 patients with comorbidities, 42 clinical isolates were identified by VITEKⓇ MS Plus. Antifungal susceptibility testing was performed using VITEKⓇ 2 Compact with the AST-YS08 card.

RESULTS

The most frequently identified species were C. albicans and C. glabrata, which were also the most common co-infections, Saprochaete capitata, an uncommon yeast was isolated in one patient. 85% of the co-infections were COVID positive and 100% of patients with a co-infection required mechanical ventilation (MV) which has been described as one of the major predisposing factors to candidiasis. Candida species vary in their response to treatment. In this study, 44% of isolates identified as C. glabrata were fluconazole-resistant, which were also immediately susceptible to caspofungin; this profile limits therapeutic options and emphasizes the importance of evaluating the susceptibility profile.

CONCLUSIONS

This work highlights the increase in isolation of different Candida species during COVID-19 and the importance of establishing criteria to declare Candida colonization or infection and the correct etiological identification to establish an agent-based antifungal treatment, to reduce the spreading risk of Candida spp. in the hospital environment, mortality, time, and cost of hospitalization.

A prediction model for secondary invasive fungal infection among severe SARS-CoV-2 positive patients in ICU

Background

The global COVID-19 pandemic has resulted in over seven million deaths, and IFI can further complicate the clinical course of COVID-19. Coinfection of COVID-19 and IFI (secondary IFI) pose significant threats not only to healthcare systems but also to patient lives. After the control measures for COVID-19 were lifted in China, we observed a substantial number of ICU patients developing COVID-19-associated IFI. This creates an urgent need for predictive assessment of COVID-19 patients in the ICU environment for early detection of suspected fungal infection cases.

Methods

This study is a single-center, retrospective research endeavor. We conducted a case-control study on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) positive patients. The cases consisted of patients who developed any secondary IFI during their ICU stay at Jilin University China-Japan Union Hospital in Changchun, Jilin Province, China, from December 1st, 2022, to August 31st, 2023. The control group consisted of SARS-CoV-2 positive patients without secondary IFI. Descriptive and comparative analyses were performed, and a logistic regression prediction model for secondary IFI in COVID-19 patients was established. Additionally, we observed an increased incidence of COVID-19-associated pulmonary aspergillosis (CAPA) during this pandemic. Therefore, we conducted a univariate subgroup analysis on top of IFI, using non-CAPA patients as the control subgroup.

Results

From multivariate analysis, the prediction model identified 6 factors that are significantly associated with IFI, including the use of broad-spectrum antibiotics for more than 2 weeks (aOR=4.14, 95% CI 2.03-8.67), fever (aOR=2.3, 95%CI 1.16-4.55), elevated log IL-6 levels (aOR=1.22, 95% CI 1.04-1.43) and prone position ventilation (aOR=2.38, 95%CI 1.15-4.97) as independent risk factors for COVID-19 secondary IFI. High BMI (BMI ≥ 28 kg/m2) (aOR=0.85, 95% CI 0.75-0.94) and the use of COVID-19 immunoglobulin (aOR=0.45, 95% CI 0.2-0.97) were identified as independent protective factors against COVID-19 secondary IFI. The Receiver Operating Curve (ROC) area under the curve (AUC) of this model was 0.81, indicating good classification.

Conclusion

We recommend paying special attention for the occurrence of secondary IFI in COVID-19 patients with low BMI (BMI < 28 kg/m2), elevated log IL-6 levels and fever. Additionally, during the treatment of COVID-19 patients, we emphasize the importance of minimizing the duration of broad-spectrum antibiotic use and highlight the potential of immunoglobulin application in reducing the incidence of IFI.

The "COVID effect" in culture-based clinical microbiology: Changes induced by COVID-19 pandemic in a Hungarian tertiary care center

BACKGROUND

The presence of bacterial and fungal coinfections plays an important role in the mortality of patients with coronavirus 2019 (COVID-19). We compared data from the 3 years before and 3 years after the COVID-19 pandemic outbreak to evaluate its effect on the traits of bacterial and fungal diseases.

METHODS

We retrospectively collected and analyzed data on positive respiratory tract samples (n = 13,133 samples from 7717 patients) and blood cultures (n = 23,652 from 9653 patients) between 2017 and 2022 from the Clinical Center of the University of Szeged, Hungary. We also evaluated antimicrobial susceptibility test results derived from 169,020 respiratory samples and 549,729 blood cultures to gain insight into changes in antimicrobial resistance.

RESULTS

The most common respiratory pathogen in the pre-COVID era was Pseudomonas aeruginosa, whereas Candida albicans was the most frequent during the pandemic. The number of respiratory isolates of Acinetobacter baumannii was also markedly increased. In blood cultures, Staphylococcus epidermidis, Escherichia coli, and S. aureus were dominant during the study period, and A. baumannii was widespread in blood cultures during the pandemic years. Resistance to ofloxacin, penicillin, piperacillin-tazobactam, ceftazidime, cefepime, imipenem, ceftolozane-tazobactam, and itraconazole increased significantly in the COVID era.

CONCLUSIONS

During the COVID-19 pandemic, there were changes in the prevalence of respiratory and blood culture pathogens at the Clinical Center of the University of Szeged. C. albicans became the predominant respiratory pathogen, and the number of A. baumannii isolates increased dramatically. Additionally, antimicrobial resistance notably increased during this period.

An enhanced IL17 and muted type I interferon nasal epithelial cell state characterizes severe COVID-19 with fungal coinfection

Recent case reports and epidemiological data suggest that fungal infections represent an underappreciated complication among people with severe COVID-19. However, the frequency of fungal colonization in patients with COVID-19 and associations with specific immune responses in the airways remain incompletely defined. We previously generated a single-cell RNA-sequencing data set characterizing the upper respiratory microenvironment during COVID-19 and mapped the relationship between disease severity and the local behavior of nasal epithelial cells and infiltrating immune cells. Our previous study, in agreement with findings from related human cohorts, demonstrated that a profound deficiency in host immunity, particularly in type I and type III interferon signaling in the upper respiratory tract, is associated with rapid progression to severe disease and worse clinical outcomes. We have now performed further analysis of this cohort and identified a subset of participants with severe COVID-19 and concurrent detection of Candida species-derived transcripts within samples collected from the nasopharynx and trachea. Here, we present the clinical characteristics of these individuals. Using matched single-cell transcriptomic profiles of these individuals' respiratory mucosa, we identify epithelial immune signatures suggestive of IL17 stimulation and anti-fungal immunity. Further, we observe a significant expression of anti-fungal inflammatory cascades in the nasal and tracheal epithelium of all participants who went on to develop severe COVID-19, even among participants without detectable genetic material from fungal pathogens. Together, our data suggest that IL17 stimulation-in part driven by Candida colonization-and blunted interferon signaling represent a common feature of severe COVID-19 infection.

IMPORTANCE

In this paper, we present an analysis suggesting that symptomatic and asymptomatic fungal coinfections can impact patient disease progression during COVID-19 hospitalization. By looking into the presence of other pathogens and their effect on the host immune response during COVID-19 hospitalizations, we aim to offer insight into an underestimated scenario, furthering our current knowledge of determinants of severity that could be considered for future diagnostic and intervention strategies.

In Silico and In Vitro Evaluation of the Antifungal Activity of a New Chromone Derivative against Candida spp

Candida species are frequently implicated in the development of both superficial and invasive fungal infections, which can impact vital organs. In the quest for novel strategies to combat fungal infections, there has been growing interest in exploring synthetic and semi-synthetic products, particularly chromone derivatives, renowned for their antimicrobial properties. In the analysis of the antifungal activity of the compound (E)-benzylidene-chroman-4-one against Candida, in silico and laboratory tests were performed to predict possible mechanisms of action pathways, and in vitro tests were performed to determine antifungal activity (MIC and MFC), to verify potential modes of action on the fungal cell membrane and wall, and to assess cytotoxicity in human keratinocytes. The tested compound exhibited predicted affinity for all fungal targets, with the highest predicted affinity observed for thymidylate synthase (-102.589 kJ/mol). MIC and CFM values ranged from 264.52 μM (62.5 μg/mL) to 4232.44 μM (1000 μg/mL). The antifungal effect likely occurs due to the action of the compound on the plasma membrane. Therefore, (E)-benzylidene-chroman-4-one showed fungicidal-like activity against Candida spp., possibly targeting the plasma membrane.

Assessing Diagnosis of Candida Infections: A Study on Species Prevalence and Antifungal Resistance in Northern Morocco

The incidence of Candida infections has increased in the last decade, posing a serious threat to public health. Appropriately facing this challenge requires precise epidemiological data on species and antimicrobial resistance incidence, but many countries lack appropriate surveillance programs. This study aims to bridge this gap for Morocco by identifying and phenotyping a year-long collection of clinical isolates (n = 93) from four clinics in Tetouan. We compared the current standard in species identification with molecular methods and assessed susceptibility to fluconazole and anidulafungin. Our results identified limitations in currently used diagnostics approaches, and revealed that C. albicans ranks as the most prevalent species with 60 strains (64.52%), followed by C. glabrata with 14 (15.05%), C. parapsilosis with 6 (6.45%), and C. tropicalis with 4 (4.30%). In addition, we report the first identification of C. metapsilosis in Morocco. Susceptibility results for fluconazole revealed that some isolates were approaching MICs resistance breakpoints in C. albicans (2), and C. glabrata (1). Our study also identified anidulafungin resistant strains in C. albicans (1), C. tropicalis (1), and C. krusei (2), rendering the two strains from the latter species multidrug-resistant due to their innate resistance to fluconazole. These results raise concerns about species identification and antifungal resistance in Morocco and highlight the urgent need for more accurate methods and preventive strategies to combat fungal infections in the country.

Comparison of Candida colonization in intensive care unit patients with and without COVID-19: First prospective cohort study from Turkey

Candida species are the primary cause of fungal infections in intensive care units (ICUs). Despite the increasing prevalence of Candida-related infections, monitoring the progression of these infections from colonization in COVID-19 ICU patients lacks sufficient information. This study aims prospectively to compare 62 COVID-19 and 60 non-COVID-19 ICU patients from admission to discharge in terms of colonization development, rates, isolated Candida species, risk factors, and Candida infections during hospitalization. A total of 1464 samples were collected at specific time intervals from various body sites [mouth, skin (axilla), rectal, and urine]. All samples were inoculated onto CHROMagar Candida and CHROMagar Candida Plus media, and isolates identified using MALDI-TOF MS. COVID-19 patients exhibited significantly higher colonization rates in oral, rectal, and urine samples compared to non-COVID-19 patients, (p < 0.05). Among the Candida species, non-albicans Candida was more frequently detected in COVID-19 patients, particularly in oral (75.8%-25%; p < 0.001) and rectal regions (74.19% - 46.66%; p < 0.05). Colonization with mixed Candida species was also more prevalent in the oropharyngeal region (p < 0.05). Mechanical ventilation and corticosteroid use emerged as elevated risk factors among COVID-19 patients (p < 0.05). Despite the colonization prevalence, both COVID-19-positive and negative patients exhibited low incidences of Candida infections, with rates of 9.67% (n = 6/62) and 6.67% (n = 3/60), respectively. Consequently, although Candida colonization rates were higher in COVID-19 ICU patients, there was no significant difference in Candida infection development compared to the non-COVID-19 group. However, the elevated rate of non-albicans Candida isolates highlights potential future infections, particularly given their intrinsic resistance in prophylactic or empirical treatments if needed. Additionally, the high rate of mixed colonization emphasizes the importance of using chromogenic media for routine evaluation.

Risk analysis of candidemia and its effect on mortality in COVID 19 and non COVID 19 patients

Background and Objectives

Candidemia is the most common serious fungal infection in critically ill patients in intensive care units (ICU). It series fourth among bloodstream infectious agents. In this study, candidemia risk analysis was examined in COVID 19 and non-COVID 19 patients during the pandemic period.

Materials and Methods

COVID 19 and non-COVID 19 cases who were followed up with candidemia in the ICU of our hospital were retrospectively screened. Demographic data, intubation, central venous catheter (CVC), medications, and total parenteral nutrition (TPN) status were evaluated in terms of risk between the two groups. Isolated Candida species and susceptibilty were evaluated.

Results

When age, gender, medication, intubation, TPN and CVC were evaluated, no difference was seen in terms of risk. Differences were detected in terms of comorbidities. While the most frequently identified Candida species was C. albicans, the most frequently detected species in the COVID19 patient group was C. parapsilosis.

Conclusion

There was no difference in candidemia incidence and risk factors between the two groups. Since candidemias were evaluated in terms of comorbidities, it was determined that Diabetes Mellitus (DM) and chronic obstructive pulmoner disease (COPD) were more common in patients with COVID 19 and less common in coronary artery disease (CAD) and malignancy.

COVID-19 associated candidemia: From a shift in fungal epidemiology to a rise in azole drug resistance

Our understanding of fungal epidemiology and the burden of antifungal drug resistance in COVID-19-associated candidemia (CAC) patients is limited. Therefore, we conducted a retrospective multicenter study in Iran to explore clinical and microbiological profiles of CAC patients. Yeast isolated from blood, were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and subjected to antifungal susceptibility testing (AFST) using the broth microdilution method M27-A3 protocol. A total of 0.6% of the COVID-19 patients acquired CAC (43/6174). Fluconazole was the most widely used antifungal, and 37% of patients were not treated. Contrary to historic candidemia patients, Candida albicans and C. tropicalis were the most common species. In vitro resistance was high and only noted for azoles; 50%, 20%, and 13.6% of patients were infected with azole-non-susceptible (ANS) C. tropicalis, C. parapsilosis, and C. albicans isolates, respectively. ERG11 mutations conferring azole resistance were detected for C. parapsilosis isolates (Y132F), recovered from an azole-naïve patient. Our study revealed an unprecedented rise in ANS Candida isolates, including the first C. parapsilosis isolate carrying Y132F, among CAC patients in Iran, which potentially threatens the efficacy of fluconazole, the most widely used drug in our centers. Considering the high mortality rate and 37% of untreated CAC cases, our study underscores the importance of infection control strategies and antifungal stewardship to minimize the emergence of ANS Candida isolates during COVID-19.

Antimicrobial Resistance in Qatar: Prevalence and Trends before and Amidst the COVID-19 Pandemic

Antimicrobial resistance (AMR) is a global healthcare challenge with substantial morbidity, mortality, and management costs. During the COVID-19 pandemic, there was a documented increase in antimicrobial consumption, particularly for severe and critical cases, as well as noticeable travel and social restriction measures that might influenced the spectrum of AMR. To evaluate the problem, retrospective data were collected on bacterial infections and antimicrobial susceptibility patterns in Qatar before and after the pandemic from 1 January 2019 to 31 December 2021, covering 53,183 pathogens isolated from reported infection episodes. The findings revealed a significant resistance pattern for extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-EBC), carbapenem-resistant Enterobacteriaceae (CR-EBC), and carbapenem-resistant Pseudomonas aeruginosa (CRPA), ciprofloxacin-resistant Salmonella and methicillin-resistant Staphylococcus aureus (MRSA). For correlation with social restrictions, ESBL-EBC and MRSA were positively correlated with changing patterns of international travel (ρ = 0.71 and 0.67, respectively; p < 0.05), while CRPA was moderately correlated with the number of COVID-19 hospitalized patients (ρ = 0.49; p < 0.05). CREBC and CRPA respiratory infections were associated with hospitalized patients (OR: 3.08 and 2.00, respectively; p < 0.05). The findings emphasize the challenges experienced during the COVID-19 pandemic and links to international travel, which probably will influence the local epidemiology of AMR that needs further surveillance and control strategies.

Utility of incorporation of beta-D-glucan and T2Candida testing for diagnosis and treatment of candidemia

The additive role of non-culture-based methods for the diagnosis of candidemia remains unknown. We evaluated 2 clinical practices followed in our hospitals for the diagnosis of candidemia, namely practice#1 including a combination of blood cultures and T2Candida, and practice#2 that also included Beta-D-glucan (BDG). Three out of 96 patients testing positive with practice#1 received a complete antifungal course. Of the 120 patients evaluated with practice#2, 29 were positive. Only 55.2% of those received a complete course. We observed significant differences in antifungal utilization, with 268.5 antifungal days/1000 patient-days for practice#1, as opposed to 371.9 days for practice#2, a nearly 40% difference. However, we found similar rates of antifungal discontinuation among negative patients at 3 days of testing (36.8% and 37.0% respectively). No differences were detected in death and/or subsequent diagnosis of candidemia. In summary, addition of BDG was interpreted variably by clinicians, was associated with an increase in antifungal utilization, and did not correlate with measurable clinical benefits for patients.

Nanotechnology-based fungal detection and treatment: current status and future perspective

Fungal infections impose a significant impact on global health and encompass major expenditures in medical treatments. Human mycoses, a fungal co-infection associated with SARS-CoV-2, is caused by opportunistic fungal pathogens and is often overlooked or misdiagnosed. Recently, there is increasing threat about spread of antimicrobial resistance in fungus, mostly in hospitals and other healthcare facilities. The diagnosis and treatment of fungal infections are associated with several issues, including tedious and non-selective detection methods, the growth of drug-resistant bacteria, severe side effects, and ineffective drug delivery. Thus, a rapid and sensitive diagnostic method and a high-efficacy and low-toxicity therapeutic approach are needed. Nanomedicine has emerged as a viable option for overcoming these limitations. Due to the unique physicochemical and optical properties of nanomaterials and newer biosensing techniques, nanodiagnostics play an important role in the accurate and prompt differentiation and detection of fungal diseases. Additionally, nano-based drug delivery techniques can increase drug permeability, reduce adverse effects, and extend systemic circulation time and drug half-life. This review paper is aimed at highlighting recent, promising, and unique trends in nanotechnology to design and develop diagnostics and treatment methods for fungal diseases.

The changing epidemiology of fungal infections

Invasive fungal diseases are common complications in critically ill patients and in those with significant underlying imbalanced immune systems. Fungal co-, and/or super-infections are emerging and have become a rising concern within the last few years. In Europe, cases of candidiasis and aspergillosis dominate, followed by mucormycosis in India. Epidemiological studies show an increasing trend in the incidence of all three entities. Parallel to this, a shift within the underlying fungal pathogens is observed. More non-albicans Candida infections and aspergillosis with cryptic species are on the rise; cryptic species may cover intrinsic resistance to azoles and other antifungal drugs. The recent COVID-19 pandemic led to a significantly increasing incidence of invasive fungal diseases among hospitalized patients.

Antimicrobial activity of Stachys rupestris Montbret et Aucher ex Benth. and inactivation of the pathogens inoculated on lab-made skin by the essential oil

The aim of this study was to investigate the antimicrobial activity of Stachys rupestris essential oil and inactivation of the pathogens on lab-made skin the oil in the fight against Escherichia coli, Acinetobacter baumannii, Staphylococcus aureus, Enterococcus faecalis, Candida albicans and Candida tropicalis. S. rupestris EO was extracted by hydrodistillation, and its contents were analyzed by GCMS. Logarithmic reduction of the pathogens inoculated on the artificial skin surface by S. rupestris EO was studied for the first time. The highest inhibition zone was 22.1 mm on C. tropicalis, while the lowest IZ was 0.1 mm on E. coli. The other zones were 20.01 mm for Acinetobacter baumannii, 20.02 mm for Enterococcus faecalis, 20.01 mm for Staphylococcus aureus, 22.03 for Candida albicans (p < 0.05). As a result, S. rupestris essential oil was effective on most of the microorganisms and might be increased to use in the treatment of skin infections in the future.

Severe Candida infections in critically ill patients with COVID-19

The frequency of co-infections with bacterial or fungal pathogens has constantly increased among critically ill patients with coronavirus disease 2019 (COVID-19) during the pandemic. Candidemia was the most frequently reported invasive fungal co-infection. The onset of candidemia in COVID-19 patients was often delayed compared to non-COVID-19 patients. Additionally, Candida invasive infections in COVID-19 patients were more often linked to invasive procedures (e.g., invasive mechanical ventilation or renal replacement therapy) during the intensive care stay and the severity of illness rather than more "classic" risk factors present in patients without COVID-19 (e.g., underlying diseases and prior hospitalization). Moreover, apart from the increased incidence of candidemia during the pandemic, a worrying rise in fluconazole-resistant strains was reported, including a rise in the multidrug-resistant Candida auris. Regarding outcomes, the development of invasive Candida co-infection had a negative impact, increasing morbidity and mortality compared to non-co-infected COVID-19 patients. In this narrative review, we present and critically discuss information on the diagnosis and management of invasive fungal infections caused by Candida spp. in critically ill COVID-19 patients.

[Candida albicans: risk factor in covid-19 patients]

The Candida Albicans fungus in our body can cause various conditions and will depend directly on the systemic condition of the host. Patients with COVID-19 who have previously presented this fungus can increase the likelihood of morbidity and mortality, since this microorganism can be located in areas that correspond to the respiratory system, generating a functional deficit. If not treated timely, it will proliferate into the blood and digestive system. Many patients with respiratory difficulties on account of this condition require mechanical ventilation to combat it.

Objective

To relate the presence of Candida Albicans as an aggravating factor in patients with COVID-19.

Materials and

methods: A literature review took place using the Redalyc, Scielo, PubMed, Research gate, Science direct, Google Scholar databases. The inclusion criteria used were: articles in English and Spanish, along with articles published from 2020 up to date. There were 65 scientific articles that met the search criteria and were analyzed. The analysis determined that oral candidiasis negatively affects patients with COVID-19 infection, increasing the risk of admission to the ICU with the use of artificial ventilators.

Evaluation of Blood Cultures from SARS-CoV-2-Positive and Negative Adult Patients

Bacteremia and fungemia are significant causes of morbidity and mortality that frequently occur as co-infections with viral respiratory infections, including SARS-CoV-2. The aim of this study was to evaluate the microorganisms that were isolated from the blood cultures of SARS-CoV-2-positive and negative patients and investigate their antimicrobial resistance patterns. A retrospective analysis was performed of 22,944 blood cultures sent to the laboratory between November 2020 and December 2021. Blood culture analyses were performed using the BD Bactec FX automated system. Identification was carried out using conventional methods, namely, VITEK-2 and MALDI-TOF MS. Antibacterial/antifungal susceptibility tests were performed according to EUCAST/CLSI recommendations. SARS-CoV-2 tests were performed with RT-PCR. Culture positivity was detected in 1630 samples from 652 patients. Of these 652 patients, 633 were tested for SARS-CoV-2; 118 (18.6%) were positive and 515 (81.3%) were negative. The bacteria and fungi that were isolated at the highest rate in SARS-CoV-2-positive patients were methicillin-resistant coagulase-negative staphylococci (MR-CoNS) (21.5%), Escherichia coli (12.4%), Klebsiella pneumoniae (12.4%), Candida albicans (1.65%), and Candida glabrata complex (1.65%), while in the negative patients, the highest rates were for E. coli (21.3%), MR-CoNS (13.5%), K. pneumoniae (12.05%), C. albicans (2.1%), Candida parapsilosis (1.1%), and Candida tropicalis (0.9%). No statistically significant difference was determined between COVID-19-positive and negative patients in terms of detection, such as with the Pseudomonas spp., Enterococcus spp., and methicillin-resistant Staphylococcus aureus isolated from the blood cultures (p > 0.05). The most common isolate was MR-CoNS in SARS-CoV-2-positive patients (p = 0.028). Acinetobacter baumannii was more frequent (p = 0.004) and carbapenem-resistant K. pneumoniae was isolated at a higher rate (60% vs. 43%) in SARS-CoV-2-positive patients compared to SARS-CoV-2-negative patients (p > 0.05). These findings highlight the fact that isolation procedures should not be disregarded and the distribution of bacterial/fungal agents of bloodstream infections and their antibiotic resistance should be followed up during a pandemic, such as in the case of COVID-19.

Invasive Candidiasis in Adult Patients with COVID-19: Results of a Multicenter Study in St. Petersburg, Russia

We studied the risk factors, etiology, clinical manifestations, and treatment outcomes of COVID-19-associated invasive candidiasis (COVID-IC) in adult patients admitted to six medical facilities in St. Petersburg. (November 2020-December 2022). In this retrospective study, we included 72 patients with COVID-IC with a median age of 61 years (range 29-96), 51% of whom were women. The predisposing factors for COVID-IC were a central venous catheter (CVC) for more than 10 days (the odds ratio (OR) = 70 [15-309]), abdominal surgical treatment performed in the previous 2 weeks (OR = 8.8 [1.9-40.3]), bacteremia (OR = 10.6 [4.8-23.3]), pulmonary ventilation (OR = 12.9 [5.9-28.4]), and hemodialysis (OR = 11.5 [2.5-50.8]). The signs and symptoms of COVID-IC were non-specific: fever (59%), renal failure (33%), liver failure (23%), and cardiovascular failure (10%). Candida albicans (41%) predominated among the pathogens of the candidemia. The multidrug-resistant Candida species C. auris (23%) and C. glabrata (5%) were also identified. Empirical therapy was used in 21% of COVID-IC patients: azole-93%, echinocandin-7%. The majority of COVID-IC patients (79%) received, after laboratory confirmation of the diagnosis of IC, fluconazole (47%), voriconazole (25%), echinocandin (26%), and amphotericin B (2)%. The 30 days overall survival rate was 45%. The prognosis worsened concomitant bacteremia, hemodialysis, and long-term therapy by systemic glucocorticosteroids (SGCs), bronchial colonization with Candida spp. The survival prognosis was improved by the early change/replacement of CVC (within 24 h), the initiation of empirical therapy, and the use of echinocandin. Conclusions: We highlighted the risk factors that predispose COVID-19 patients to candidiasis and worsen the survival prognosis. Their individual effects in patients with COVID-19 must be well understood to prevent the development of opportunistic co-infections that drastically lower chances of survival.

COVID-19 and candiduria: an investigation of the risk factors and immunological aspects

Secondary fungal infections are frequently observed in COVID-19 patients. However, the occurrence of candiduria in these patients and its risk factors are underexplored. We evaluated the risk factors of candiduria in COVID-19 patients, including inflammatory mediators that could be used as prognostic markers. Clinical information, laboratory test results, and outcomes were collected from severely ill COVID-19 patients with and without candiduria. Candida species identification, antifungal susceptibility, and plasma inflammatory mediators' measurements were performed. Regression logistic and Cox regression model were used to evaluate the risk factors. A higher risk of longer hospitalization and mortality were observed in patients with candiduria compared to those with COVID-19 only. Candiduria was caused by Candida albicans, C. glabrata, and C. tropicalis. Isolates with intermediate susceptibility to voriconazole and resistant to caspofungin were identified. Classic factors such as the use of corticosteroids and antibacterials, the worsening of renal function, and hematological parameters (hemoglobin and platelets) were found to predispose to candiduria. The mediators IL-1β, IL-1ra, IL-2, CXCL-8, IL-17, IFN-γ, basic FGF, and MIP-1β were significantly increased in patients with COVID-19 and candiduria. Furthermore, IFN-γ, IL-1ra, and CXCL-8 were associated with the occurrence of candiduria in COVID-19 patients, whereas basic FGF, IL-1β, and CXCL-8 were associated with the risk of death in these patients. Classical and immunological factors were associated with worse prognosis among patients with COVID-19 and candiduria. Some mediators, especially CXCL-8, can be a reliable biomarker of fungal coinfection and may guide the diagnostic and the treatment of these patients.

Microbial Landscape and Antibiotic-Susceptibility Profiles of Microorganisms in Patients with Bacterial Pneumonia: A Comparative Cross-Sectional Study of COVID-19 and Non-COVID-19 Cases in Aktobe, Kazakhstan

This cross-sectional study investigated the microbial landscape and antibiotic-resistance patterns in patients with bacterial pneumonia, with a focus on the impact of COVID-19. Sputum samples from individuals with bacterial pneumonia, including coronavirus disease 2019-positive polymerase chain reaction (COVID-19-PCR+), COVID-19-PCR- and non-COVID-19 patients, were analyzed. Surprisingly, the classic etiological factor of bacterial pneumonia, Streptococcus pneumoniae, was rarely isolated from the sputum samples. Furthermore, the frequency of multidrug-resistant pathogens was found to be higher in non-COVID-19 patients, highlighting the potential impact of the pandemic on antimicrobial resistance. Strains obtained from COVID-19-PCR+ patients exhibited significant resistance to commonly used antibiotics, including fluoroquinolones and cephalosporins. Notably, the ESKAPE pathogens, Staphylococcus aureus, Klebsiella pneumoniae, Pseudomonas aeruginosa, Enterobacter cloacae, and Enterobacter aerogenes, were identified among the isolated microorganisms. Our findings underscore the urgent need for infection control measures and responsible antibiotic use in healthcare settings, as well as the importance of enhancing pneumonia diagnostics and implementing standardized laboratory protocols.

COVID-19 Is an Independent Risk Factor for Detrimental Invasive Fungal Disease in Patients on Veno-Venous Extracorporeal Membrane Oxygenation: A Retrospective Study

Invasive fungal disease (IFD) is associated with the mortality of patients on extracorporeal membrane oxygenation (ECMO). Several risk factors for IFD have been identified in patients with or without ECMO. Here, we assessed the relevance of coronavirus disease (COVID-19) for the occurrence of IFD in patients on veno-venous (V-V) ECMO for respiratory failure. In a retrospective analysis of all ECMO cases between January 2013 and December 2022 (2020-2022 for COVID-19 patients), active COVID-19 and the type, timing and duration of IFD were investigated. Demographics, hospital, ICU length of stay (LoS), duration of ECMO, days on invasive mechanical ventilation, prognostic scores (Respiratory ECMO Survival Prediction (RESP) score, Charlson Comorbidity Index (CCI), Therapeutic Intervention Scoring System (TISS)-10, Sequential Organ Failure Assessment (SOFA) score and Simplified Acute Physiology Score (SAPS)-II) and length of survival were assessed. The association of COVID-19 with IFD was investigated using propensity score matching and uni- and multivariable logistic regression analyses. We identified 814 patients supported with ECMO, and 452 patients were included in further analyses. The incidence of IFD was 4.8% and 11.0% in patients without and with COVID-19, respectively. COVID-19 status represented an independent risk factor for IFD (OR 4.30; CI 1.72-10.85; p: 0.002; multivariable regression analysis). In patients with COVID-19, 84.6% of IFD was candidemia and 15.4% represented invasive aspergillosis (IA). All of these patients died. In patients on V-V ECMO, we report that COVID-19 is an independent risk factor for IFD, which is associated with a detrimental prognosis. Further studies are needed to investigate strategies of antifungal therapy or prophylaxis in these patients.

Fungal Infections Identified with Multiplex PCR in Severe COVID-19 Patients during Six Pandemic Waves

Background and Objectives: With an increasing number of severe COVID-19 cases presenting with secondary fungal infections, this study aimed to determine the prevalence of fungal co-infections in severe COVID-19 patients across the six waves, identify the most common fungal pathogens associated with severe COVID-19, and explore any potential links between patient characteristics, therapeutic strategies, and the prevalence and type of fungal infection. Materials and Methods: A retrospective analysis was conducted on severe COVID-19 patients admitted to the Infectious Diseases and Pulmonology Hospital, "Victor Babes", Romania, between March 2020 and August 2022. Samples were collected from respiratory specimens, blood, and urine, after which a standard nucleic acid extraction protocol was employed. Patients were divided into groups with and without fungal infections, identified using multiplex PCR. The groups were compared based on demographic data, comorbidities, pandemic wave number, and clinical outcomes. Results: Out of 288 patients, 96 (33.3%) had fungal infections, with Candida spp. being the most common. Patients with fungal infections had higher rates of obesity (35.4% vs. 21.4%, p = 0.010) and a higher Charlson comorbidity index (CCI > 2) (37.5% vs 25.0%, p = 0.027). Ventilator use was significantly higher in the fungal infection group (45.8% vs. 18.8%; p < 0.001), as was ICU admission (39.6% vs. 26.6%; p = 0.024) and mortality (32.3% vs 12.0%; p < 0.001). The distribution of different fungal species varied across the pandemic waves, with no statistical significance (p = 0.209). The mortality risk notably increased with the degree of drug resistance (OR for three or more drug resistances = 6.71, p < 0.001). The second, fourth, and fifth pandemic waves were significantly associated with higher mortality risk (OR = 3.72, 3.61, and 4.08, respectively, all p < 0.001). Aspergillus spp. and Mucor spp. infections were significantly associated with increased mortality risk (OR = 4.61 and 6.08, respectively, both p < 0.001). Conclusions: Our study indicates a significant presence of fungal co-infections among severe COVID-19 patients that is associated with increased morbidity and mortality, particularly in patients with drug-resistant infections. These findings underline the necessity for comprehensive diagnostic approaches and tailored treatment strategies in managing COVID-19 patients, especially during specific pandemic waves and in patients with particular fungal infections. Further research is required to understand the implications of these co-infections and their management.

Opportunistic Fungal Invasion in COVID-19 Pandemic: A Critical Review in Diagnosis and Management

Severe acute respiratory syndrome corona virus-2 (SARS-CoV-2) is the culprit behind the pandemic across the globe in recent decades. Variants of SARS-CoV especially coronavirus disease 2019 (COVID-19)-related fungus might not be identified or might be misdiagnosed on a worldwide scale. Patients of COVID-19 acquired invasive mycoses, especially if they are very ill or immunosuppressed. Clinical intervention based on various standard guidelines would be necessary to guarantee that Aspergillus and Candida -infected COVID-19 patients are adequately treated. To facilitate clinical professionals, doctors, paramedics, and laboratory staff in the treatment of various variants of COVID-19 patients with concurrent aspergillosis, candidiasis, mucormycosis, or cryptococcosis, a tabulation format is drafted in this study. We believe it is prudent to take into account the general nature, and variety of the mycosis that is arriving, the strength and limits of the diagnostic tools, clinical conditions, and the need for standardized or customized therapy in various coronavirus-infected patients.

The triangle relationship between human genome, gut microbiome, and COVID-19: opening of a Pandora's box

Since the pandemic started, the coronavirus disease 2019 (COVID-19) has spread worldwide. In patients with COVID-19, the gut microbiome (GM) has been supposed to be closely related to the progress of the disease. The gut microbiota composition and human genetic variation are also connected in COVID-19 patients, assuming a triangular relationship between the genome, GM, and COVID-19. Here, we reviewed the recent developments in the study of the relationship between gut microbiota and COVID-19. The keywords "COVID-19," "microbiome," and "genome" were used to search the literature in the PubMed database. We first found that the composition of the GM in COVID-19 patients varies according to the severity of the illness. Most obviously, Candida albicans abnormally increased while the probiotic Bifidobacterium decreased in severe cases of COVID-19. Interestingly, clinical studies have consistently emphasized that the family Lachnospiraceae plays a critical role in patients with COVID-19. Additionally, we have demonstrated the impact of microbiome-related genes on COVID-19. Specially, we focused on angiotensin-converting enzyme 2's dual functions in SARS-CoV-2 infection and gut microbiota alternation. In summary, these studies showed that the diversity of GMs is closely connected to COVID-19. A triangular relationship exists between COVID-19, the human genome, and the gut flora, suggesting that human genetic variations may offer a chance for a precise diagnosis of COVID-19, and the important relationships between genetic makeup and microbiome regulation may affect the therapy of COVID-19.

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).

Invasive Fungal Infections Associated with COVID-19

The COVID-19 pandemic caused >6 million deaths worldwide, often from respiratory failure. Complications frequently occurred in hospitalized patients, particularly in the intensive care unit. Among these, fungal infections were a cause of high morbidity and mortality. Invasive aspergillosis, candidiasis and mucormycosis were the most serious of these infections. Risk factors included alterations in immune defense mechanisms by COVID-19 itself, as well as immunosuppression due to various therapies utilized in severely ill patients. Diagnosis was often challenging due to lack of sensitivity of current testing. Outcomes were generally poor, due to significant co-morbidities and delayed diagnosis, with mortality rates >50% in some studies. High index of clinical suspicion is needed to facilitate early diagnosis and initiation of appropriate antifungal therapy.

Oral Myco- and Bacteriobiota and Yeast Infections in Mechanically Ventilated COVID-19 Patients

Critically ill COVID-19 patients requiring mechanical ventilation in the intensive care unit are at risk of developing invasive candidiasis. In this study we aimed to (1) characterize oral cultivable mycobiota of mechanically ventilated adult COVID-19 patients in an ICU setting by sampling four distinct oral niches in two fixed time points with regards to oral health status, (2) investigate Candida spp. infections in this population, and (3) compare oral mycobiota with selected bacteriobiota strains during the observation in the ICU. We recruited 56 adult COVID-19 patients who qualified for mechanical ventilation. Patients received either standard or extended oral care procedures with tooth brushing. Oral samples were taken first within 36 h and after 7 days of intubation. Yeast-like fungi were identified by MALDI/TOF mass spectrometry. Yeast infection cases were retrospectively analyzed. Candida spp. in oral sampling was identified in 80.4% and 75.7%, C. albicans in 57.1% and 61.1%, and non-albicans Candida species in 48.2% and 47.2% patients at baseline and follow-up, respectively. There were no differences in the overall CFU counts of Candida spp. species and individual Candida species in oral samples, both at baseline and follow-up. At baseline, a higher prevalence of Candida spp. was associated with a higher identification rate of Lactobacillus spp. (64.4% vs. 27.3%, p = 0.041). At follow-up, there was a borderline lower prevalence of Candida spp. in patients with Lactobacillus spp. identified (57.1% vs. 87.0%, p = 0.057). The incidence rate of candidiasis was 5.4% and the incidence density was 3.1/1000 pds. In conclusion, non-albicans Candida species in oral samples were identified in nearly half of patients. Oral health was moderately impaired. A high incidence of yeast infections, including invasive cases, in patients hospitalized in the ICU due to COVID-19 and requiring mechanical ventilation was noted. Severe COVID-19 and disease-specific interventions within the ICU possibly played a major role promoting Candida spp. infections.

Skin Manifestations Among Patients Admitted with COVID-19: A Cross-Sectional Study at a University-Based Tertiary Hospital in Jordan

Background

COVID-19 pandemic hit the entire world with severe health and economic consequences. Although the infection primarily affected the respiratory system, it was soon recognized that COVID-19 has a multi-systemic component with various manifestations including cutaneous involvement.

Objective

The main objective of this study is to assess the incidence and patterns of cutaneous manifestations among moderate-to-severe COVID-19 patients who required hospitalization and whether there was a prognostic indication for cutaneous involvement and the outcome in terms of recovery or death.

Methods

This is a cross-sectional observational study that included inpatients who were diagnosed with a moderate or severe COVID-19 infection. The demographic and clinical data of patients were assessed including age, sex, smoking, and comorbidities. All patients were examined clinically for the presence of skin manifestations. Patients were followed for the outcome of COVID-19 infection.

Results

A total of 821 patients (356 females and 465 males) aged 4-95 years were included. More than half of patients (54.6%) aged >60 years. A total of 678 patients (82.6%) had at least one comorbid condition, mostly hypertension and diabetes mellitus. Sixty-two patients (7.55%) developed rashes; 5.24% cutaneous and 2.31% oral. The rashes were then grouped into five major types: group A, Exanthema: morbilliform, papulovesicular, varicella-like. Group B, Vascular: Chilblain-like lesions, purpuric/petechial, livedoid lesions. Group C, Reactive erythemas: Urticaria, Erythema multiforme. Group D, other skin rashes including flare-up of pre-existing disease, and O for oral involvement. Most patients (70%) developed rash after admission. The most frequent skin rashes were reactive erythema (23.3%), followed by vascular (20.9%), exanthema (16.3%), and other rashes with flare-ups of pre-existing diseases (39.5%). Smoking and loss of taste were associated with the appearance of various skin rashes. However, no prognostic implications were found between cutaneous manifestations and outcome.

Conclusion

COVID-19 infection may present with various skin manifestations including worsening of pre-existing skin diseases.

Invasive candidiasis: current clinical challenges and unmet needs in adult populations

Invasive candidiasis (IC) is a serious infection caused by several Candida species, and the most common fungal disease in hospitals in high-income countries. Despite overall improvements in health systems and ICU care in the last few decades, as well as the development of different antifungals and microbiological techniques, mortality rates in IC have not substantially improved. The aim of this review is to summarize the main issues underlying the management of adults affected by IC, focusing on specific forms of the infection: IC developed by ICU patients, IC observed in haematological patients, breakthrough candidaemia, sanctuary site candidiasis, intra-abdominal infections and other challenging infections. Several key challenges need to be tackled to improve the clinical management and outcomes of IC patients. These include the lack of global epidemiological data for IC, the limitations of the diagnostic tests and risk scoring tools currently available, the absence of standardized effectiveness outcomes and long-term data for IC, the timing for the initiation of antifungal therapy and the limited recommendations on the optimal step-down therapy from echinocandins to azoles or the total duration of therapy. The availability of new compounds may overcome some of the challenges identified and increase the existing options for management of chronic Candida infections and ambulant patient treatments. However, early identification of patients that require antifungal therapy and treatment of sanctuary site infections remain a challenge and will require further innovations.

Fungal Drug Response and Antimicrobial Resistance

Antifungal resistance is a growing concern as it poses a significant threat to public health. Fungal infections are a significant cause of morbidity and mortality, especially in immunocompromised individuals. The limited number of antifungal agents and the emergence of resistance have led to a critical need to understand the mechanisms of antifungal drug resistance. This review provides an overview of the importance of antifungal resistance, the classes of antifungal agents, and their mode of action. It highlights the molecular mechanisms of antifungal drug resistance, including alterations in drug modification, activation, and availability. In addition, the review discusses the response to drugs via the regulation of multidrug efflux systems and antifungal drug-target interactions. We emphasize the importance of understanding the molecular mechanisms of antifungal drug resistance to develop effective strategies to combat the emergence of resistance and highlight the need for continued research to identify new targets for antifungal drug development and explore alternative therapeutic options to overcome resistance. Overall, an understanding of antifungal drug resistance and its mechanisms will be indispensable for the field of antifungal drug development and clinical management of fungal infections.

Gut microbiota in COVID-19: key microbial changes, potential mechanisms and clinical applications

The gastrointestinal tract is involved in coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The gut microbiota has important roles in viral entry receptor angiotensin-converting enzyme 2 (ACE2) expression, immune homeostasis, and crosstalk between the gut and lungs, the 'gut-lung axis'. Emerging preclinical and clinical studies indicate that the gut microbiota might contribute to COVID-19 pathogenesis and disease outcomes; SARS-CoV-2 infection was associated with altered intestinal microbiota and correlated with inflammatory and immune responses. Here, we discuss the cutting-edge evidence on the interactions between SARS-CoV-2 infection and the gut microbiota, key microbial changes in relation to COVID-19 severity and host immune dysregulations with the possible underlying mechanisms, and the conceivable consequences of the pandemic on the human microbiome and post-pandemic health. Finally, potential modulatory strategies of the gut microbiota are discussed. These insights could shed light on the development of microbiota-based interventions for COVID-19.

A Retrospective Assessment of Sputum Samples and Antimicrobial Resistance in COVID-19 Patients

Data on bacterial or fungal pathogens and their impact on the mortality rates of Western Romanian COVID-19 patients are scarce. As a result, the purpose of this research was to determine the prevalence of bacterial and fungal co- and superinfections in Western Romanian adults with COVID-19, hospitalized in in-ward settings during the second half of the pandemic, and its distribution according to sociodemographic and clinical conditions. The unicentric retrospective observational study was conducted on 407 eligible patients. Expectorate sputum was selected as the sampling technique followed by routine microbiological investigations. A total of 31.5% of samples tested positive for Pseudomonas aeruginosa, followed by 26.2% having co-infections with Klebsiella pneumoniae among patients admitted with COVID-19. The third most common Pathogenic bacteria identified in the sputum samples was Escherichia coli, followed by Acinetobacter baumannii in 9.3% of samples. Commensal human pathogens caused respiratory infections in 67 patients, the most prevalent being Streptococcus penumoniae, followed by methicillin-sensitive and methicillin-resistant Staphylococcus aureus. A total of 53.4% of sputum samples tested positive for Candida spp., followed by 41.1% of samples with Aspergillus spp. growth. The three groups with positive microbial growth on sputum cultures had an equally proportional distribution of patients admitted to the ICU, with an average of 30%, compared with only 17.3% among hospitalized COVID-19 patients with negative sputum cultures (p = 0.003). More than 80% of all positive samples showed multidrug resistance. The high prevalence of bacterial and fungal co-infections and superinfections in COVID-19 patients mandates for strict and effective antimicrobial stewardship and infection control policies.

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.

Coincidence of Candida Endophthalmitis, and Aspergillus and Pneumocystis jirovecii Pneumonia in a COVID-19 Patient: Case Report

INTRODUCTION

Coronavirus disease 2019 (COVID-19) is associated with immune system dysfunction and makes patients vulnerable to opportunistic infections. This report presents a patient with a history of COVID-19, suffering from opportunistic infections.

CASE DESCRIPTION

We reported a 64-year-old man complaining of progressive visual loss in his left eye, who had previously been hospitalized for three weeks due to COVID-19. In the ophthalmologic assessment, large foci of dense subretinal and intraretinal infiltrations involving the macula were observed (compatible with endogenous fungal endophthalmitis). Real-time PCR result of intraocular fluid was positive for Candida spp. During subsequent hospitalization, the patient also suffered from fever and productive coughs (manifestations of pneumonia caused by Aspergillus fumigatus and Pneumocystis jirovecii). In response to antibiotic therapy, the fever and coughs subsided, and the ocular examination revealed a dramatic decrease in the size of retinal infiltrations.

CONCLUSIONS

In patients with severe COVID-19, long-term ICU admission and immunosuppressive drugs lead to immune system dysfunction and make the patient more susceptible to opportunistic infections. Consequently, fungal pathogens such as Aspergillus, Pneumocystis jirovecii, and Candida spp. may cause infection in different body organs. Thus, clinicians should be alert and have clinical suspicion to diagnose accurately and manage patients accordingly.

COVID-19 Is a Confounder of Increased Candida Airway Colonisation

An increased incidence of invasive fungal infection was reported in SARS-CoV-2-infected patients hospitalised in the intensive care unit. However, the impact of COVID-19 on Candida airway colonisation has not yet been assessed. This study aimed to test the impact of several factors on Candida airway colonisation, including SARS-CoV-2 infection. We conducted a two-pronged monocentric retrospective study. First, we analysed the prevalence of positive yeast culture in respiratory samples obtained from 23 departments of the University Hospital of Marseille between 1 January 2018 and 31 March 2022. We then conducted a case-control study, comparing patients with documented Candida airway colonisation to two control groups. We observed an increase in the prevalence of yeast isolation over the study period. The case-control study included 300 patients. In the multivariate logistic regression, diabetes, mechanical ventilation, length of stay in the hospital, invasive fungal disease, and the use of antibacterials were independently associated with Candida airway colonisation. The association of SARS-CoV-2 infection with an increased risk of Candida airway colonisation is likely to be a consequence of confounding factors. Nevertheless, we found the length of stay in the hospital, mechanical ventilation, diabetes, and the use of antibacterials to be statistically significant independent risk factors of Candida airway colonisation.

Oral Candidiasis in Adult and Pediatric Patients with COVID-19

Oral Candidiasis (OC) is an opportunistic fungal infection of the oral cavity, frequently reported under local and systemic predisposing circumstances. While the recurrence of OC HIV-infected subjects has been well described and reported, the association between oral candidiasis and the SARS-CoV-2 infection is a recent finding that still is worthy of further study. The present paper focuses on this novel association, reporting the incidence and prevalence of OC occurring during and after COVID-19 and the possible etiopathogenic mechanisms underlying the onset of OC in COVID-19 subjects. The work found that the immune inflammatory hypo reactions and immunosuppression found in children and adults with COVID-19 could favor the proliferation colonization of Candida species and the following infection. At the same time, poor oral hygiene and iatrogenic causes seem to be the main risk factors.

The Impact of COVID-19 Infection on Miscellaneous Inflammatory Disorders of the Gastrointestinal Tract

The novel coronavirus pandemic of COVID-19 has emerged as a highly significant recent threat to global health with about 600,000,000 known infections and more than 6,450,000 deaths worldwide since its emergence in late 2019. COVID-19 symptoms are predominantly respiratory, with mortality largely related to pulmonary manifestations, but the virus also potentially infects all parts of the gastrointestinal tract with related symptoms and manifestations that affect patient treatment and outcome. COVID-19 can directly infect the gastrointestinal tract because of the presence of widespread angiotensin-converting enzyme 2 receptors in the stomach and small intestine that can cause local COVID-19 infection and associated inflammation. This work reviews the pathopysiology, clinical manifestations, workup, and treatment of miscellaneous inflammatory disorders of the gastrointestinal tract other than inflammatory bowel disease.

Protective Efficacy of Anti-Hyr1p Monoclonal Antibody against Systemic Candidiasis Due to Multi-Drug-Resistant Candida auris

Candida auris is a multi-drug-resistant fungal pathogen that can survive outside the host and can easily spread and colonize the healthcare environment, medical devices, and human skin. C. auris causes serious life-threatening infections (up to 60% mortality) in immunosuppressed patients staying in such contaminated healthcare facilities. Some isolates of C. auris are resistant to virtually all clinically available antifungal drugs. Therefore, alternative therapeutic approaches are urgently needed. Using in silico protein modeling and analysis, we identified a highly immunogenic and surface-exposed epitope that is conserved between C. albicans hyphal-regulated protein (Cal-Hyr1p) and Hyr1p/Iff-like proteins in C. auris (Cau-HILp). We generated monoclonal antibodies (MAb) against this Cal-Hyr1p epitope, which recognized several clinical isolates of C. auris representing all four clades. An anti-Hyr1p MAb prevented biofilm formation and enhanced opsonophagocytic killing of C. auris by macrophages. When tested for in vivo efficacy, anti-Hyr1p MAb protected 55% of mice against lethal systemic C. auris infection and showed significantly less fungal burden. Our study is highly clinically relevant and provides an effective alternative therapeutic option to treat infections due to MDR C. auris.

Multiple Candida strains causing oral infection in COVID-19 patients under corticosteroids and antibiotic therapy: An observational study

Introduction

The occurrence of oral candidiasis (OC) is expected in patients with COVID-19, especially those with moderate to severe forms of infection who are hospitalized and may be on long-term use of broad-spectrum antibiotics or prolonged corticosteroid therapy. We aimed to characterize clinical conditions, the prevalence profile of Candida species, and outcomes of COVID-19 patients with OC.

Methods

In this observational study, oral samples were obtained from COVID-19 patients suspected of OC admitted to Razi teaching hospital. Patients with OC were monitored daily until discharge from the hospital. Species identification was performed by a two-step multiplex assay named YEAST PLEX, which identifies 17 clinically important uncommon to common yeast strains.

Results

Among the 4133 patients admitted with COVID-19, 120 (2.90%) suffered from OC. The onset of signs and symptoms of OC in patients was, on average (2.92 ± 3.596 days) with a range (of 1-29 days). The most common OC presentation was white or yellow macules on the buccal surface or the tongue. In (39.16%) of patients suffering from OC multiple Candida strains (with two or more Candida spp.) were identified. The most common Candida species were C. albicans (60.57%), followed by C. glabrata (17.14%), C. tropicalis (11.42%), C. kefyr (10.83%) and C. krusei (3.42%). Notably, OC caused by multiple Candida strains was more predominant in patients under corticosteroid therapy (P <0.0001), broad-spectrum antibiotics therapy (P = 0.028), and those who used nasal corticosteroid spray (P <0.0001). The majority of patients who recovered from OC at the time of discharge were patients with OC by single Candida species (P = 0.049).

Discussion

Use of corticosteroids and antimicrobial therapy in COVID-19 patients increases risk of OC by multiple Candida strains.

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.

Candida Species Isolation from Hospitalized Patients with COVID-19-A Retrospective Study

Coronavirus disease 2019 (COVID-19), a disease characterized by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has so far led to hundreds of millions of infections and millions of deaths. Fungal infections are known to complicate COVID-19 patients and are associated with significant morbidity and mortality. The aim of this study was to assess the incidence of positive cultures for Candida spp. among patients hospitalized with COVID-19, describe their characteristics and identify factors associated with overall mortality in this patient population. Hospitalized COVID-19 patients with Candida spp. isolation were retrospectively assessed and their clinical, laboratory and microbiological characteristics were assessed and evaluated. In total, 69 patients with COVID-19 had a positive culture for Candida spp., representing a rate of 4.5% among all hospitalized COVID-19 patients. Their median age was 78 years (IQR 67-85 years) and 44.9% were male. Hospitalized patients with COVID-19 and Candida spp. isolation who died were older, were more likely to have a diagnosis of dementia, and had higher Charlson comorbidity index, higher Candida score and higher 4C score. Candida score was identified with a multivariate logistic regression analysis model to be independently associated with mortality. The most commonly identified Candida species was C. albicans, followed by C. tropicalis and C. glabrata and the most common source was the urine, even though in most cases the positive culture was not associated with a true infection. Thus, Candida score may be used in COVID-19 patients with isolation of Candida spp. from different body specimens for mortality risk stratification.

Revised Guidelines for Coronavirus Disease 19 Management in Hematopoietic Cell Transplantation and Cellular Therapy Recipients (August 2022)

This document is intended as a guide for diagnosis and management of Coronavirus Disease 2019 (COVID-19), caused by the virus SARS-CoV-2, in adult and pediatric HCT and cellular therapy patients. This document was prepared using available data and with expert opinion provided by members of the (ASTCT) Infectious Diseases Special Interest Group (ID-SIG) and is an update of pervious publication. Since our original publication in 2020, the NIH and IDSA have published extensive guidelines for management of COVID-19 which are readily accessible ( NIH Guidelines , IDSA Guidelines ). This update focuses primarily on issues pertaining specifically to HCT/cellular therapy recipients. Information provided in this manuscript may change as new information becomes available.

Defective antifungal immunity in patients with COVID-19

The COVID-19 pandemic has placed a huge strain on global healthcare and been a significant cause of increased morbidity and mortality, particularly in at-risk populations. This disease attacks the respiratory systems and causes significant immune dysregulation in affected patients creating a perfect opportunity for the development of invasive fungal disease (IFD). COVID-19 infection can instill a significant, poorly regulated pro-inflammatory response. Clinically induced immunosuppression or pro-inflammatory damage to mucosa facilitate the development of IFD and Aspergillus, Mucorales, and Candida infections have been regularly reported throughout the COVID-19 pandemic. Corticosteroids and immune modulators are used in the treatment of COVID-19. Corticosteroid use is also a risk factor for IFD, but not the only reason for IFD in COVID -19 patients. Specific dysregulation of the immune system through functional exhaustion of Natural killer (NK) cells and T cells has been observed in COVID-19 through the expression of the exhaustion markers NK-G2A and PD-1. Reduced fungicidal activity of neutrophils from COVID-19 patients indicates that immune dysfunction/imbalance are important risk factors for IFD. The COVID-19 pandemic has significantly increased the at-risk population for IFD. Even if the incidence of IFD is relatively low, the size of this new at-risk population will result in a substantial increase in the overall, annual number of IFD cases. It is important to understand how and why certain patients with COVID-19 developed increased susceptibility to IFD, as this will improve our understanding of risk of IFD in the face of future pandemics but also in a clinical era of increased clinical immuno-suppression/modulation.

Epidemiology and outcomes of culture-positive bloodstream pathogens prior to and during the SARS-CoV-2 pandemic: a multicenter evaluation

Background

Bloodstream infections (BSIs) are an important cause of morbidity and mortality in hospitalized patients. We evaluate incidence of community- and hospital-onset BSI rates and outcomes before and during the SARS-CoV-2 pandemic.

Methods

We conducted a retrospective cohort study evaluating patients who were hospitalized for ≥ 1 day with discharge or death between June 1, 2019, and September 4, 2021, across 271 US health care facilities. Community- and hospital-onset BSI and related outcomes before and during the SARS-CoV-2 pandemic, including intensive care admission rates, and overall and ICU-specific length of stay (LOS) was evaluated. Bivariate correlations were calculated between the pre-pandemic and pandemic periods overall and by SARS-CoV-2 testing status.

Results

Of 5,239,692 patient admissions, there were 20,113 community-onset BSIs before the pandemic (11.2/1000 admissions) and 39,740 (11.5/1000 admissions) during the pandemic (P ≤ 0.0062). Corresponding rates of hospital-onset BSI were 2,771 (1.6/1000 admissions) and 6,864 (2.0/1000 admissions; P < 0.0062). Compared to the pre-pandemic period, rates of community-onset BSI were higher in patients who tested negative for SARS-CoV-2 (15.8/1000 admissions), compared with 9.6/1000 BSI admissions among SARS-CoV-2-positive patients. Compared with patients in the pre-pandemic period, SARS-CoV-2-positive patients with community-onset BSI experienced greater ICU admission rates (36.6% vs 32.8%; P < 0.01), greater ventilator use (10.7% vs 4.7%; P < 0.001), and longer LOS (12.2 d vs 9.1 d; P < 0.001). Rates of hospital-onset BSI were higher in the pandemic vs the pre-pandemic period (2.0 vs 1.5/1000; P < 0.001), with rates as high a 7.3/1000 admissions among SARS-CoV-2-positive patients. Compared to the pre-pandemic period, SARS-CoV-2-positive patients with hospital-onset BSI had higher rates of ICU admission (72.9% vs 55.4%; P < 0.001), LOS (34.8 d vs 25.5 d; P < 0.001), and ventilator use (52.9% vs 21.5%; P < 0.001). Enterococcus species, Staphylococcus aureus, Klebsiella pneumoniae, and Candida albicans were more frequently detected in the pandemic period.

Conclusions and relevance

This nationally representative study found an increased risk of both community-onset and hospital-onset BSI during the SARS-CoV-2 pandemic period, with the largest increased risk in hospital-onset BSI among SARS-CoV-2-positive patients. SARS-CoV-2 positivity was associated with worse outcomes.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-022-07810-8.

Clinical Challenges of Emerging and Re-Emerging Yeast Infections in the Context of the COVID-19 Pandemic

During the geological eras, some fungi, through adaptation and/or environmental/ecological pressure, interacted directly and indirectly with humans, through occasionally harmful interaction interdependent on the individual’s immunological condition. Infections caused by yeasts are underreported, subjugated, and underdiagnosed, and treatment is restricted to a few drugs, even after the significant progress of medicine and pharmacology. In the last centuries, antagonistically, there has been an exponential increase of immunocompromised individuals due to the use of immunosuppressive drugs such as corticosteroids, increased cases of transplants, chemotherapeutics, autoimmune diseases, neoplasms, and, more recently, coronavirus disease 2019 (COVID-19). This review aims to survey emerging and re-emerging yeast infections in the current clinical context. Currently, there is an immense clinical challenge for the rapid and correct diagnosis and treatment of systemic mycoses caused by yeasts due to the terrible increase in cases in the current context of COVID-19.

Global Emergence of Resistance to Fluconazole and Voriconazole in Candida parapsilosis in Tertiary Hospitals in Spain During the COVID-19 Pandemic

BACKGROUND

Candida parapsilosis is a frequent cause of candidemia worldwide. Its incidence is associated with the use of medical implants, such as central venous catheters or parenteral nutrition. This species has reduced susceptibility to echinocandins, and it is susceptible to polyenes and azoles. Multiple outbreaks caused by fluconazole-nonsusceptible strains have been reported recently. A similar trend has been observed among the C. parapsilosis isolates received in the last 2 years at the Spanish Mycology Reference Laboratory.

METHODS

Yeast were identified by molecular biology, and antifungal susceptibility testing was performed using the European Committee on Antimicrobial Susceptibility Testing protocol. The ERG11 gene was sequenced to identify resistance mechanisms, and strain typing was carried out by microsatellite analysis.

RESULTS

We examined the susceptibility profile of 1315 C. parapsilosis isolates available at our reference laboratory between 2000 and 2021, noticing an increase in the number of isolates with acquired resistance to fluconazole, and voriconazole has increased in at least 8 different Spanish hospitals in 2020-2021. From 121 recorded clones, 3 were identified as the most prevalent in Spain (clone 10 in Catalonia and clone 96 in Castilla-Leon and Madrid, whereas clone 67 was found in 2 geographically unrelated regions, Cantabria and the Balearic Islands).

CONCLUSIONS

Our data suggest that concurrently with the coronavirus disease 2019 pandemic, a selection of fluconazole-resistant C. parapsilosis isolates has occurred in Spain, and the expansion of specific clones has been noted across centers. Further research is needed to determine the factors that underlie the successful expansion of these clones and their potential genetic relatedness.

Profile of Co-Infection Prevalence and Antibiotics Use among COVID-19 Patients

Bacterial co-infection in COVID-19 patients significantly contributes to the worsening of the prognosis based on morbidity and mortality. Information on the co-infection profile in such patients could help to optimize treatment. The purpose of this study was to describe bacterial co-infections associated with microbiological, clinical, and laboratory data to reduce or avoid a secondary infection. A retrospective cohort study was conducted at Sant'Anna and San Sebastiano Hospital from January 2020 to December 2021. Bacterial co-infection was detected in 14.3% of the COVID-19-positive patients. The laboratory findings on admission showed significant alterations in the median D-dimer, C-reactive protein, interleukin-6, and lactate dehydrogenase values compared to normal values. All inflammatory markers were significantly elevated. The most common pathogens isolated from blood cultures were E. faecalis and S. aureus. Instead, the high prevalence of respiratory tract infections in the COVID-19 patients was caused by P. aeruginosa (41%). In our study, 220 (82.4%) of the COVID-19 patients received antimicrobial treatment. Aminoglycosides and β-lactams/β-lactamase inhibitors showed the highest resistance rates. Our results showed that older age, underlying conditions, and abnormal laboratory parameters can be risk factors for co-infection in COVID-19 patients. The antibiotic susceptibility profile of bacterial pathogen infection provides evidence on the importance, for the clinicians, to rationalize and individualize antibiotic usage.

Severe COVID-19 is associated with fungal colonization of the nasopharynx and potent induction of IL-17 responses in the nasal epithelium

Recent case reports and epidemiological data suggest fungal infections represent an under-appreciated complication among people with severe COVID-19. However, the frequency of fungal colonization in patients with COVID-19 and associations with specific immune responses in the airways remain incompletely defined. We previously generated a single-cell RNA-sequencing (scRNA-seq) dataset characterizing the upper respiratory microenvironment during COVID-19, and mapped the relationship between disease severity and the local behavior of nasal epithelial cells and infiltrating immune cells. Our study, in agreement with findings from related human cohorts, demonstrated that a profound deficiency in host immunity, particularly in type I and type III interferon signaling in the upper respiratory tract, is associated with rapid progression to severe disease and worse clinical outcomes. We have now performed further analysis of this cohort and identified a subset of participants with severe COVID-19 and concurrent detection of Candida species-derived transcripts within samples collected from the nasopharynx and trachea. Here, we present the clinical characteristics of these individuals, including confirmatory diagnostic testing demonstrating elevated serum (1, 3)-β-D-glucan and/or confirmed fungal culture of the predicted pathogen. Using matched single-cell transcriptomic profiles of these individuals' respiratory mucosa, we identify epithelial immune signatures suggestive of IL-17 stimulation and anti-fungal immunity. Further, we observe significant expression of anti-fungal inflammatory cascades in the nasal and tracheal epithelium of all participants who went on to develop severe COVID-19, even among participants without detectable genetic material from fungal pathogens. Together, our data suggests that IL-17 stimulation - in part driven by Candida colonization - and blunted type I/III interferon signaling represents a common feature of severe COVID-19 infection.