Fungal infections in patients with inflammatory bowel disease: A systematic review

Oral Microbiota and Inflammatory Bowel Diseases: Detection of Emerging Fungal Pathogens and Herpesvirus

Background/Objectives: Ulcerative colitis (UC) and Crohn's disease (CD) are the usual clinical forms of inflammatory bowel disease (IBD). Changes in the oral microbiota, especially the presence of emerging fungi and herpesviruses, have been shown to worsen the clinical aspects of IBD. The aim of this study was to screen for emerging pathogens in the oral yeast microbiota and the presence of herpesvirus in IBD patients. Methods: Oral swabs of seven UC or CD patients were collected. The samples were plated on Sabouraud Dextrose Agar and subcultured on CHROMagar Candida and CHROMagar Candida Plus. Polyphasic taxonomy was applied and identified using molecular tools, such as MALDI-TOF MS and ITS partial sequencing. Multiplex qPCR was used to identify the herpesvirus. Results: The mean age was 38.67 ± 14.06 years, 57.14% were female, and two had diabetes. The CD patients presented with Rhodotorula mucilaginosa, Candida orthopsilosis and Kodamaea jinghongensis, while the UC patients presented with Cutaneotrichosporon dermatis, Candida glabrata, Candida lusitanea and Candida tropicalis. Two UC individuals had at least one herpesvirus. In the first individual, a co-detection of Herpes Simplex Virus 1 (HSV-1) and C. lusitaniae was observed. The second presented with co-infections of Epstein-Barr virus (EBV), Human Herpesvirus 7 (HHV-7) and C. tropicalis. Conclusions: We identified rarely described yeasts and co-infections in IBD patients, highlighting the need to identify emerging pathogens in the oral microbiota, as they may contribute to opportunistic infections.

Novel Curvularia species causing disseminated phaeohyphomycosis in a dog

Phaeohyphomycosis is an uncommon disease caused by dematiaceous fungi that is almost exclusively found in immunocompromised dogs. Here we describe the case of a dog treated with prednisone (1.1 mg/kg/day) and cyclosporine (11.2 mg/kg/day) for immune thrombocytopenia that developed cutaneous/subcutaneous lesions affecting both forelimbs 29 days after initiation of immunosuppression. The owner elected conservative outpatient treatment that consisted of wound care, antibiotics, mirtazapine, maropitant, and a dose reduction of prednisone (0.3 mg/kg/day) in lieu of biopsies or cultures. The dog was subsequently euthanized 13 days later because of an acute onset of increased respiratory rate and effort, obtunded mentation, and an inability to ambulate. Postmortem examination revealed widespread fungal dissemination in the heart, pericardium, intercostal muscles, lymph nodes, skin, subcutis, kidneys, lungs, pleura, and nasal cavity. Histopathology of the widespread plaques and nodules revealed fungal hyphae that were 4-8 µm in diameter, pigmented, variably septate, non-parallel, and toruloid with acute branching and occasional terminal bulbous dilations up to 20 µm in diameter, resembling chlamydoconidia. Yeast-like cells had a thick, variably pigmented wall and internal, foamy to granular, pale amphophilic contents. Fungal culture of swabs from the right elbow subcutaneous granulomas and from the left lateral pleural nodules yielded pure growth of Curvularia sp. Genomic DNA was extracted from harvested mycelia and molecular sequencing confirmed the presence of a novel Curvularia sp., C. arizonensis.

Raising the bar in ulcerative colitis management

Ulcerative colitis (UC) is a chronic inflammatory bowel disease characterized by growing incidence and prevalence around the world in the last few decades. The range of available existing treatment and strategies for its management is being implemented. Given the introduction of newly developed molecules and the lack of specific guidelines, drug positioning may represent a tough clinical challenge. UC management is mostly medical, and it has been shifting toward a more personalized approach with the aim to create a tailored strategy depending on the patient's profile. A treat-to target strategy seems to be the best approach to reach disease control as it allows to carry out therapeutic choices based on objective and specific parameters: histological, ultrasonographic, and molecular targets may add to the already used clinical, endoscopic, and biochemical targets. In addition, dual-targeted therapy has emerged as an attractive therapeutic strategy for patients not achieving remission. This review aims to provide an overview of the available strategies to raise the bar in UC.

Advances in the research of intestinal fungi in Crohn's disease

This article reviews of the original research published by Wu et al in the World Journal of Gastroenterology, delving into the pivotal role of the gut microbiota in the pathogenesis of Crohn's disease (CD). Insights were gained from fecal microbiota transplantation (FMT) in mouse models, revealing the intricate interplay between the gut microbiota, mesenteric adipose tissue (MAT), and creeping fat. The study uncovered the characteristics of inflammation and fibrosis in the MAT and intestinal tissues of patients with CD; moreover, through the FMT mouse model, it observed the impact of samples from healthy patients and those with CD on symptoms. The pathogenesis of CD is complex, and its etiology remains unclear; however, it is widely believed that gut microbiota dysbiosis plays a significant role. Recently, with the development and application of next-generation sequencing technology, research on the role of fungi in the pathogenesis and chronicity of CD has deepened. This editorial serves as a supplement to the research by Wu et al who discussed advances related to the study of fungi in CD.

The emerging role of the gut microbiota and its application in inflammatory bowel disease

Inflammatory bowel disease (IBD), including Crohn's disease and ulcerative colitis, is a complex disorder with an unknown cause. However, the dysbiosis of the gut microbiome has been found to play a role in IBD etiology, including exacerbated immune responses and defective intestinal barrier integrity. The gut microbiome can also be a potential biomarker for several diseases, including IBD. Currently, conventional treatments targeting pro-inflammatory cytokines and pathways in IBD-associated dysbiosis do not yield effective results. Other therapies that directly target the dysbiotic microbiome for effective outcomes are emerging. We review the role of the gut microbiome in health and IBD and its potential as a diagnostic, prognostic, and therapeutic target for IBD. This review also explores emerging therapeutic advancements that target gut microbiome-associated alterations in IBD, such as nanoparticle or encapsulation delivery, fecal microbiota transplantation, nutritional therapies, microbiome/probiotic engineering, phage therapy, mesenchymal stem cells (MSCs), gut proteins, and herbal formulas.

Colonic Mucormycosis in Fistulizing Crohn's Disease

Gastrointestinal mucormycosis, a rare fatal fungal infection in an immunocompromised host, affects mainly the stomach. Colonic mucormycosis is infrequent and is associated with high mortality. Perianal involvement is seen in almost one-third of patients with Crohn's disease. Perianal Crohn's disease is a particularly debilitating form of the disease, which requires multidisciplinary care. It may also require profound immunosuppression with biological agents to control disease activity. Opportunistic infections can complicate the disease course in these patients. We present a case of a middle-aged female with perianal Crohn's disease on adalimumab who developed colonic mucormycosis causing a flare in her disease activity. This patient highlights the need to increase awareness about fungal infections as a cause of disease flare in inflammatory bowel disease.

Fungemia by Wickerhamomyces anomalus-A Narrative Review

Wickerhamomyces anomalus has been previously classified as Hansenula anomala, Pichia anomala, and Candida pelliculosa and was recently reclassified in the genus Wickerhamomyces after phylogenetic analysis of its genetic sequence. An increasing number of reports of human infections by W. anomalus have emerged, suggesting that this microorganism is an emerging pathogen. The present review aimed to provide data on the epidemiology, antifungal resistance, clinical characteristics, treatment, and outcomes of fungemia by W. anomalus by extracting all the available information from published original reports in the literature. PubMed/Medline, Cochrane Library, and Scopus databases were searched for eligible articles reporting data on patients with this disease. In total, 36 studies involving 170 patients were included. The age of patients with fungemia by W. anomalus ranged from 0 to 89 years; the mean age was 22.8 years, the median age was 2.2 years, with more than 37 patients being less than one month old, and 54% (88 out of 163 patients) were male. Regarding patients' history, 70.4% had a central venous catheter use (CVC), 28.7% were on total parenteral nutrition (TPN), 97% of neonates were hospitalized in the neonatal ICU (NICU), and 39.4% of the rest of the patients were hospitalized in the intensive care unit (ICU). Previous antimicrobial use was noted in 65.9% of patients. The most common identification method was the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) in 34.1%, VITEK and VITEK 2 in 20.6%, and ID32 C in 15.3%. W. anomalus had minimal antifungal resistance to fluconazole, echinocandins, and amphotericin B, the most commonly used antifungals for treatment. Fever and sepsis were the most common clinical presentation noted in 95.8% and 86%, respectively. Overall mortality was 20% and was slightly higher in patients older than one year. Due to the rarity of this disease, future multicenter studies should be performed to adequately characterize patients' characteristics, treatment, and outcomes, which will increase our understanding and allow drawing safer conclusions regarding optimal management.

Incidence of invasive fungal diseases in inflammatory bowel disease patients: A nationwide study in South Korea

BACKGROUND

Limited reports exist regarding invasive fungal diseases (IFDs) in inflammatory bowel disease (IBD) patients.

OBJECTIVES

This study aims to investigate the incidence and risk factors of IFDs, specifically invasive candidiasis, aspergillosis and pneumocystosis, in IBD patients in South Korea using nationwide data.

PATIENTS/METHODS

A population-based retrospective cohort of 42,913 IBD patients between January 2010 and December 2018 was evaluated using the Health Insurance Review and Assessment database. The primary outcome was the incidence of IFDs, including invasive candidiasis, aspergillosis and pneumocystosis, while the secondary outcome involved analysing the risk factors associated with each specific infection.

RESULTS

The study included a total of 42,913 IBD patients, with 29,909 (69.7%) diagnosed with ulcerative colitis (UC) and 13,004 (30.3%) diagnosed with Crohn's disease (CD). IFDs occurred in 166 IBD patients (0.4%), with 93 cases in UC patients and 73 cases in CD patients. The incidence rates of invasive candidiasis, aspergillosis and pneumocystosis in IBD patients were 0.71 per 1000 person-years (PYs), 0.15 per 1000 PYs and 0.12 per 1000 PYs, respectively. The cumulative incidence of invasive candidiasis (adjusted p-value <.001) and Pneumocystosis (adjusted p-value = .012) was found to be higher in CD patients than in UC patients. Each IFD had different risk factors, including IBD subtypes, age at diagnosis, anti-tumour necrotic factor agents or the Charlson comorbidity index.

CONCLUSION

Based on nationwide data in South Korea, this study shows that IFDs occur consistently in patients with IBD, albeit with a low frequency.

Invasive fungal diseases in patients with autoimmune diseases: a case series from the French RESSIF network

OBJECTIVES

We aimed to describe patients with autoimmune diseases (AID) developing invasive fungal disease (IFD) and identify factors associated with short-term mortality.

METHODS

We analysed cases of IFD associated with AID from the surveillance network of invasive fungal diseases (Réseau de surveillance des infections fongiques invasives, RESSIF) registry of the French national reference centre for invasive mycoses. We studied association of AID-specific treatments with 30-day mortality. We analysed total lymphocyte and CD4-T cell counts in patients with Pneumocystis jirovecii pneumonia (PCP).

RESULTS

From 2012 to 2018, 549 individuals with IFD and AID were included, mainly with PCP (n=227, 41.3%), fungemia (n=167, 30.4%) and invasive aspergillosis (n=84, 15.5%). Rheumatoid arthritis (RA) and anti-neutrophil cytoplasmic antibodies (ANCA)-associated vasculitides (AAV) were the most frequent AID in PCP (n=55 and 25, respectively) and invasive aspergillosis (n=15 and 10, respectively), inflammatory bowel diseases (IBDs) were predominant in fungemia (n=36). At IFD diagnosis, 365 (66.5%) patients received glucocorticoids (GCs), 285 (51.9%) immunosuppressants, 42 (7.7%) tumor necrosis factor (TNF)-α blockers, 75 (13.7%) other biologics. Mortality at 30 days was 28.1% (143/508). Fungemia and high-dose GCs were independently associated with higher 30-day mortality. In PCP patients, lymphopenia <1500/mm3 was frequent (132/179, 73.7%) even if CD4+T cell count exceeded 200/mm3 in 56/78 patients (71.8%) (median 472.5/mm3, IQR 160-858).

CONCLUSION

IFD associated with AID occurs primarily in RA, AAV and IBD, especially when treated with GCs and immunosuppressants. Mortality is high, especially for patients on high-dose GCs. Lymphopenia may help identify risk of PCP, but normal CD4+T cell count does not rule out the risk. Further studies are needed to assess the individual risk factors for IFD.

Crohn’s disease in human immunodeficiency virus-infected patient: A case report

BACKGROUND

Inflammatory bowel disease (IBD) is an autoimmune condition treated with immunosuppressive drugs. However, the need for immune system suppression becomes questionable when infection with the human immunodeficiency virus (HIV) occurs simultaneously and impacts the course of IBD. Our reported case represents the clinical course, prescribed treatment and its effect, as well as clinical challenges faced by physicians in a combination of such diseases. We also present a comprehensive literature review of similar cases.

CASE SUMMARY

A 49-year-old woman suffering from a newly diagnosed Crohn’s disease was hospitalized due to exacerbated symptoms (abdominal pain, fever, and weight loss). During her hospital stay, she tested positive for HIV. With conservative treatment, the patient improved and was discharged. In the outpatient clinic, her HIV infection was confirmed as stage C3, and antiretroviral treatment was initiated immediately. That notwithstanding, soon the patient was rehospitalized with pulmonary embolism and developed a series of complications because of the subsequent coexistence of IBD and HIV. After intensive and meticulous treatment, the patient’s condition has improved and she remains in remission.

CONCLUSION

The paucity of studies and data on the coexistence of HIV and IBD leaves clinicians doubting the optimal treatment options.

Acute heart failure as an adverse event of tumor necrosis factor inhibitor therapy in inflammatory bowel disease: A review of the literature

Tumor necrosis factor inhibitors (anti-TNFs) are widely used therapies for the treatment of inflammatory bowel diseases (IBD); however, their administration is not risk-free. Heart failure (HF), although rare, is a potential adverse event related to administration of these medications. However, the exact mechanism of development of HF remains obscure. TNFα is found in both healthy and damaged hearts. Its effects are concentration- and receptor-dependent, promoting either cardio-protection or cardiomyocyte apoptosis. Experimental rat models with TNFα receptor knockout showed increased survival rates, less reactive oxygen species formation, and improved diastolic left ventricle pressure. However, clinical trials employing anti-TNF therapy to treat HF had disappointing results, suggesting abolishment of the cardioprotective properties of TNFα, making cardiomyocytes susceptible to apoptosis and oxidation. Thus, patients with IBD who have risk factors should be screened for HF before initiating anti-TNF therapy. This review aims to discuss adverse events associated with the administration of anti-TNF therapy, with a focus on HF, and propose some approaches to avoid cardiac adverse events in patients with IBD.

Antibiotic use as a risk factor for inflammatory bowel disease across the ages: a population-based cohort study

BACKGROUND

There is an increasing incidence of inflammatory bowel disease (IBD) for which environmental factors are suspected. Antibiotics have been associated with development of IBD in earlier generations, but their influence on IBD risk in adults is uncertain.

OBJECTIVE

To assess the impact of antibiotic exposure, including dose-response, timing and antibiotic class, on the risk of IBD in all individuals aged ≥10 years.

DESIGN

Using Denmark nationwide registries, a population-based cohort of residents aged ≥10 years was established between 2000 and 2018. Incidence rate ratios (IRRs) for IBD following antibiotic exposure were calculated using Poisson regression.

RESULTS

There were a total of 6 104 245 individuals, resulting in 87 112 328 person-years of follow-up, and 52 898 new cases of IBD. Antibiotic exposure was associated with an increased risk of IBD as compared with no antibiotic exposure for all age groups, although was greatest among individuals aged 40-60 years and ≥60 years (age 10-40 years, IRR 1.28, 95% CI 1.25 to 1.32; age 40-60 years, IRR 1.48, 95% CI 1.43 to 1.54; age ≥60 years, IRR 1.47, 95% CI 1.42 to 1.53). For all age groups a positive dose-response was observed, with similar results seen for both ulcerative colitis and Crohn's disease. The highest risk of developing IBD was seen 1-2 years after antibiotic exposure, and after use of antibiotic classes often prescribed to treat gastrointestinal pathogens.

CONCLUSION

Antibiotic exposure is associated with an increased risk of IBD, and was highest among individuals aged 40 years and older. This risk increased with cumulative antibiotic exposure, with antibiotics targeting gastrointestinal pathogens and within 1-2 years after antibiotic exposure.

Expansion of Opportunistic Enteric Fungal Pathogens and Occurrence of Gut Inflammation in Human Liver Echinococcosis

Increasing evidence shows that the gut fungal mycobiota is implicated in human disease. However, its relationship with chronic helminth infections, which cause immunosuppression and affect over 1 billion people worldwide, remains unexplored. In this study, we investigated the gut mycobiome and its associations with gut homeostasis in a severe helminth disease worldwide: liver echinococcosis. Fecal samples from 63 patients and 42 healthy controls were collected to characterize the fungal signatures using ITS1 sequencing, QIIME pipeline, and machine learning analysis. The levels of fecal calprotectin and serological anti-Saccharomyces cerevisiae antibodies (ASCA) in these subjects were experimentally measured. We found that fungal microbiota was significantly skewed in disease, with an overrepresentation of Aspergillus, Candida, Geotrichum, Kazachstania, and Penicillium and a decrease of Fusarium. Machine learning analysis revealed that the altered fungal features could efficiently predict infection with high sensitivity and specificity (area under the curve [AUC] = 0.93). The dysbiosis was characterized by expansions of multiple opportunistic pathogens (Aspergillus spp. and Candida spp.). Clinical association analysis revealed that host immunity might link to the expansions of the invasive fungi. Accompanying the opportunistic pathogen expansion, the levels of fungi-associated fecal calprotectin and serological ASCA in the patients were elevated, suggesting that gut inflammation and microbiota translocation occurred in this generally assumed extraintestinal disease. This study highlights enteric fungal pathogen expansions and increased levels of markers for fungi-associated mucosal inflammation and intestinal permeability as hallmarks of liver echinococcosis. IMPORTANCE Helminth infection affects over 1 billion people worldwide. However, its relationship with the gut mycobiome remains unknown. Among the most prevalent helminth diseases, human hydatid disease (echinococcosis) is highlighted as one of the most important (second/third for alveolar/cystic echinococcosis) foodborne parasitic diseases at the global level. Herein, we investigated the mycobiome and gut homeostasis (i.e., inflammation and permeability) in human echinococcosis. Our results revealed that fungal dysbiosis with an expansion of opportunistic pathogens and increased levels of fecal calprotectin and serum ASCA are hallmarks of human liver echinococcosis. Host immunity is associated with enteric fungal expansions. These findings suggest that an extraintestinal helminth infection is able to alter gut fungal microbiota and impair gut homeostasis, which resembles concomitant gut symptoms in inflammatory gut-related diseases (e.g., AIDS). In clinical practice, physicians need to take cautious medical consideration of gut health for nonintestinal helminth diseases.

Candida tropicalis Infection Modulates the Gut Microbiome and Confers Enhanced Susceptibility to Colitis in Mice

BACKGROUND & AIMS

We previously showed that abundance of Candida tropicalis is significantly greater in Crohn's disease patients compared with first-degree relatives without Crohn's disease. The aim of this study was to determine the effects and mechanisms of action of C tropicalis infection on intestinal inflammation and injury in mice.

METHODS

C57BL/6 mice were inoculated with C tropicalis, and colitis was induced by administration of dextran sodium sulfate in drinking water. Disease severity and intestinal permeability subsequently were evaluated by endoscopy, histology, quantitative reverse-transcription polymerase chain reaction, as well as 16S ribosomal RNA and NanoString analyses (NanoString Technologies, Seattle, WA).

RESULTS

Infected mice showed more severe colitis, with alterations in gut mucosal helper T cells (Th)1 and Th17 cytokine expression, and an increased frequency of mesenteric lymph node-derived group 2 innate lymphoid cells compared with uninfected controls. Gut microbiome composition, including changes in the mucin-degrading bacteria, Akkermansia muciniphila and Ruminococcus gnavus, was altered significantly, as was expression of several genes affecting intestinal epithelial homeostasis in isolated colonoids, after C tropicalis infection compared with uninfected controls. In line with these findings, fecal microbiome transplantation of germ-free recipient mice using infected vs uninfected donors showed altered expression of several tight-junction proteins and increased susceptibility to dextran sodium sulfate-induced colitis.

CONCLUSIONS

C tropicalis induces dysbiosis that involves changes in the presence of mucin-degrading bacteria, leading to altered tight junction protein expression with increased intestinal permeability and followed by induction of robust Th1/Th17 responses, which ultimately lead to an accelerated proinflammatory phenotype in experimental colitic mice.

Bile Acid Regulates the Colonization and Dissemination of Candida albicans from the Gastrointestinal Tract by Controlling Host Defense System and Microbiota

Candida albicans (CA), a commensal and opportunistic eukaryotic organism, frequently inhabits the gastrointestinal (GI) tract and causes life-threatening infections. Antibiotic-induced gut dysbiosis is a major risk factor for increased CA colonization and dissemination from the GI tract. We identified a significant increase of taurocholic acid (TCA), a major bile acid in antibiotic-treated mice susceptible to CA infection. In vivo findings indicate that administration of TCA through drinking water is sufficient to induce colonization and dissemination of CA in wild-type and immunosuppressed mice. Treatment with TCA significantly reduced mRNA expression of immune genes ang4 and Cxcr3 in the colon. In addition, TCA significantly decreased the relative abundance of three culturable species of commensal bacteria, Turicibacter sanguinis, Lactobacillus johnsonii, and Clostridium celatum, in both cecal contents and mucosal scrapings from the colon. Taken together, our results indicate that TCA promotes fungal colonization and dissemination of CA from the GI tract by controlling the host defense system and intestinal microbiota that play a critical role in regulating CA in the intestine.

Disseminated Coccidioidomycosis in an Adolescent With Crohn's Disease

Coccidioidomycosis is a systemic mycosis caused by Coccidioides immitis/posadasii. This dimorphic fungus is endemic to the Southwestern United States, particularly in California and Arizona. Most infections are asymptomatic or mild, but around 5% of patients develop complicated pulmonary infection, and approximately 1% may progress to disseminated disease. We present the case of an adolescent male with Crohn's disease who received the integrin inhibitor, vedolizumab, and developed disseminated coccidioidomycosis. This case underscores the importance of considering severe and/or disseminated coccidioidomycosis in immunosuppressed children. In our case, clinical suspicion and bronchoscopy helped confirm the diagnosis and facilitate appropriate evaluation and treatment.

The important role of fungi in inflammatory bowel diseases

Inflammatory bowel disease (IBD) is a life-threatening and chronic inflammatory disease of gastrointestinal tissue, with complex pathogenesis. Current research on IBD has mainly focused on bacteria; however, the role of fungi in IBD is largely unknown due to the incomplete annotation of fungi in current genomic databases. With the development of molecular techniques, the gut mycobiome has been found to have great diversity. In addition, increasing evidence has shown intestinal mycobiome plays an important role in the physiological and pathological processes of IBD. In this review, we will systemically introduce the recent knowledge about multi-dimensional fungal dysbiosis associated with IBD, the interactions between fungus and bacteria, the role of fungi in inflammation in IBD, and highlight recent advances in the potential therapeutic role of fungus in IBD, which may hold the keys to develop new predictive, therapeutic or prognostic approaches in IBD.

Association of Infliximab and Vedolizumab Trough Levels with Reported Rates of Adverse Events: A Cross-Sectional Study

Infliximab and vedolizumab are effective treatments for inflammatory bowel disease (IBD), although associated with adverse events (AE). While low or non-existent drug levels and positive antidrug antibodies have been associated with therapeutic failure, there is no clear association between higher drug levels and AE. A cross-sectional study consisting of Crohn’s disease (CD) and ulcerative colitis (UC) patients receiving infliximab or vedolizumab at the Sheba Medical Center was performed. Patients completed a questionnaire regarding AEs related to biological therapy. Serum trough levels obtained on the same day were analyzed. Objective measures of outcomes were retrieved from medical records. Questionnaires were completed by infliximab (n = 169) and vedolizumab (n = 88)-treated therapy patients. Higher infliximab levels were only numerically associated with the occurrence of at least one AE (p = 0.08). When excluding fatigue and abdominal pain, higher infliximab levels were statistically associated with the occurrence of at least one AE (p = 0.03). Vedolizumab drug levels > 18 μg/mL were also linked with the occurrence of more AEs. No specific association was observed between the increased levels of either infliximab or vedolizumab and specific AEs (neurological symptoms, upper GI symptoms, infectious complications, and musculoskeletal symptoms). As significant AEs are very rare, additional multi-center studies are required.

Association of Fungi and Archaea of the Gut Microbiota with Crohn's Disease in Pediatric Patients-Pilot Study

The composition of bacteria is often altered in Crohn’s disease (CD), but its connection to the disease is not fully understood. Gut archaea and fungi have recently been suggested to play a role as well. In our study, the presence and number of selected species of fungi and archaea in pediatric patients with CD and healthy controls were evaluated. Stool samples were collected from children with active CD (n = 54), non-active CD (n = 37) and control subjects (n = 33). The prevalence and the number of selected microorganisms were assessed by real-time PCR. The prevalence of Candida tropicalis was significantly increased in active CD compared to non-active CD and the control group (p = 0.011 and p = 0.036, respectively). The number of Malassezia spp. cells was significantly lower in patients with active CD compared to the control group, but in non-active CD, a significant increase was observed (p = 0.005 and p = 0.020, respectively). There were no statistically significant differences in the colonization by archaea. The obtained results indicate possible correlations with the course of the CD; however, further studies of the entire archeobiome and the mycobiome are necessary in order to receive a complete picture.

Fingolimod Potentiates the Antifungal Activity of Amphotericin B

Candida albicans (C. albicans) is an opportunistic human fungal pathogen that can cause severe infection in clinic. Its incidence and mortality rate has been increasing rapidly. Amphotericin B (AMB), the clinical golden standard antifungal agent, has severe side effects that limit its clinical application. Thus, lowering the concentration and increasing the efficacy of AMB in a combinatorial antifungal therapy have been pursued by both industry and academia. Here we identify that fingolimod (FTY720), an immunomodulatory drug used for oral treatment of relapsing-remitting multiple sclerosis, can potentiate the efficacy of AMB against C. albicans growth synergistically. Furthermore, we observe an antifungal efficacy of FTY720 in combination with AMB against diverse fungal pathogens. Intriguingly, cells treated with both drugs are hypersensitive to endothelial endocytosis and macrophage killing. This is later found to be due to the hyperaccumulation of reactive oxygen species and the corresponding increase in activities of superoxide dismutase and catalase in the cells that received combinatorial treatment. Therefore, the combination of AMB and FTY720 provides a promising antifungal strategy.

Candida albicans-The Virulence Factors and Clinical Manifestations of Infection

Candida albicans is a common commensal fungus that colonizes the oropharyngeal cavity, gastrointestinal and vaginal tract, and healthy individuals' skin. In 50% of the population, C. albicans is part of the normal flora of the microbiota. The various clinical manifestations of Candida species range from localized, superficial mucocutaneous disorders to invasive diseases that involve multiple organ systems and are life-threatening. From systemic and local to hereditary and environmental, diverse factors lead to disturbances in Candida's normal homeostasis, resulting in a transition from normal flora to pathogenic and opportunistic infections. The transition in the pathophysiology of the onset and progression of infection is also influenced by Candida's virulence traits that lead to the development of candidiasis. Oral candidiasis has a wide range of clinical manifestations, divided into primary and secondary candidiasis. The main supply of C. albicans in the body is located in the gastrointestinal tract, and the development of infections occurs due to dysbiosis of the residential microbiota, immune dysfunction, and damage to the muco-intestinal barrier. The presence of C. albicans in the blood is associated with candidemia-invasive Candida infections. The commensal relationship exists as long as there is a balance between the host immune system and the virulence factors of C. albicans. This paper presents the virulence traits of Candida albicans and clinical manifestations of specific candidiasis.

Antibiotic-induced gut metabolome and microbiome alterations increase the susceptibility to Candida albicans colonization in the gastrointestinal tract

Antibiotic-induced alterations in the gut ecosystem increases the susceptibility to Candida albicans, yet the mechanisms involved remains poorly understood. Here we show that mice treated with the broad-spectrum antibiotic cefoperazone promoted the growth, morphogenesis and gastrointestinal (GI) colonization of C. albicans. Using metabolomics, we revealed that the cecal metabolic environment of the mice treated with cefoperazone showed a significant alteration in intestinal metabolites. Levels of carbohydrates, sugar alcohols and primary bile acids increased, whereas carboxylic acids and secondary bile acids decreased in antibiotic treated mice susceptible to C. albicans. Furthermore, using in-vitro assays, we confirmed that carbohydrates, sugar alcohols and primary bile acids promote, whereas carboxylic acids and secondary bile acids inhibit the growth and morphogenesis of C. albicans. In addition, in this study we report changes in the levels of gut metabolites correlated with shifts in the gut microbiota. Taken together, our in-vivo and in-vitro results indicate that cefoperazone-induced metabolome and microbiome alterations favor the growth and morphogenesis of C. albicans, and potentially play an important role in the GI colonization of C. albicans.

Long-term outcome of patients with Crohn's disease on home parenteral nutrition

OBJECTIVES

In patients with Crohn's disease (CD) and intestinal failure, home parenteral nutrition (HPN) is a necessary lifesaving treatment. The aim of this study was to investigate the long-term outcomes of patients with CD after initiation of HPN.

METHODS

This study included patients with CD receiving HPN for intestinal failure. The patients were treated at Osaka University Hospital between January 2000 and December 2019. Patients' demographic characteristics, HPN dependence and complications, and mortality were analyzed. HPN dependence was estimated using the Kaplan-Meier method. Cox regression analysis was used for between-group comparisons.

RESULTS

Twenty-one patients with CD received HPN. HPN dependence rates were 85%, 75%, 75%, and 64%, respectively, at 2, 5, 10, and 15 y after HPN initiation. Patients who weaned off HPN exhibited lower rates of immunomodulator therapy and additional intensive CD treatment (P < 0.05). Multivariate analysis revealed that not requiring additional intensive CD treatment was a significant factor in weaning off HPN. Two patients (9%) died, at a median of 14.9 y after HPN initiation, due to HPN-related liver disease and CD-associated carcinoma. Among all patients, 61% experienced catheter-related bloodstream infections (CRBSIs), with an incidence of 0.32/1000 catheter-days. Methicillin-resistant bacteria and Candida spp. each accounted for 27% of all pathogens detected in CRBSI.

CONCLUSIONS

Patients with CD receiving HPN had a good prognosis, despite frequent CRBSIs in which methicillin-resistant bacteria and fungi were common pathogens. Some patients with CD can wean off HPN, even after a long period of HPN treatment. A stable disease condition during HPN might be an important factor for weaning off HPN.

Trends and outcomes of fungal infections in hospitalized patients of inflammatory bowel disease: a nationwide analysis

BACKGROUND

Immunosuppressive therapy is being increasingly used in the management of inflammatory bowel disease (IBD) which comprises of ulcerative colitis (UC) and Crohn's disease (CD). Patients on immunosuppressive therapy are at increased risk of developing opportunistic fungal infections. We conducted this analysis to describe the epidemiology of opportunistic fungal infections in this cohort.

METHODS

We analyzed the National Inpatient Sample (NIS) database for all subjects with discharge diagnosis of IBD (UC and Crohn's disease) & Fungal infections (Histoplasmosis, Pneumocystosis, Cryptococcosis, Aspergillosis, Blastomycosis, candidiasis, Coccidioidomycosis) as primary or secondary diagnosis via ICD 9 codes during the period from 2002-2014.

RESULTS

In UC, the incidence of all fungal infections was more in age above 50 (except for pneumoconiosis) male gender (except Candidiasis) and in Caucasians. In CD, the incidence was more in age above 50 (except Pneumocystosis, Blastomycosis & Coccidioidomycosis), female gender (except Histoplasmosis, Pneumocystosis & Cryptococcosis) and in Caucasians. Histoplasmosis and Blastomycosis were more prevalent in Midwest, Cryptococcosis and Candidiasis in South, Coccidioidomycosis in west in both UC and CD. Age above 50, south region, HIV, Congestive heart failure, underlying malignancies, diabetes mellitus with complications, chronic pulmonary disease, anemia, rheumatoid arthritis, collagen vascular disease, pulmonary circulation disorders, weight loss were significant predictors of fungal infections in IBD. The yearly trend showed a consistent small rise in incidence, and the mortality dropped till 2006 to peak again in 2008 with a subsequent decline.

CONCLUSIONS

Our study is the first one to describe the basic demographics features and characteristics of opportunistic fungal infections in hospitalized patients with IBD. The yearly incidence of fungal infections did not show a significant rise. The mortality increased between 2006-2008 and a significant difference remains between IBD patients with and without fungal infections. One explanation of rise in mortality but a consistent incidence could be due to the use of biologics that did not increase but compromised the ability of IBD patients to fight opportunistic fungal infections.

Inflammatory Bowel Diseases: Host-Microbial-Environmental Interactions in Dysbiosis

Crohn's Disease (CD) and Ulcerative Colitis (UC) are world-wide health problems in which intestinal dysbiosis or adverse functional changes in the microbiome are causative or exacerbating factors. The reduced abundance and diversity of the microbiome may be a result of a lack of exposure to vital commensal microbes or overexposure to competitive pathobionts during early life. Alternatively, many commensal bacteria may not find a suitable intestinal niche or fail to proliferate or function in a protective/competitive manner if they do colonize. Bacteria express a range of factors, such as fimbriae, flagella, and secretory compounds that enable them to attach to the gut, modulate metabolism, and outcompete other species. However, the host also releases factors, such as secretory IgA, antimicrobial factors, hormones, and mucins, which can prevent or regulate bacterial interactions with the gut or disable the bacterium. The delicate balance between these competing host and bacteria factors dictates whether a bacterium can colonize, proliferate or function in the intestine. Impaired functioning of NOD2 in Paneth cells and disrupted colonic mucus production are exacerbating features of CD and UC, respectively, that contribute to dysbiosis. This review evaluates the roles of these and other the host, bacterial and environmental factors in inflammatory bowel diseases.

Kodamaea ohmeri infections in humans: A systematic review

BACKGROUND

Kodamaea ohmeri, previously known as Pichia ohmeri or Yamadazyma ohmeri, belongs to the Saccharomycetaceae family and the Ascomycetae class, is the telomorphic form of C guilliermondii var. membranaefaciens and is frequently mistaken for Candida, as they belong to the same family. It has been isolated from environmental sources, such as sand, pools, seawater and fruits, while the last decades it is recognised as a rare pathogen that causes life-threatening infections in humans. The purpose of this study was to systemically review all published cases of K ohmeri infections in the literature and describe the epidemiology, microbiology, antimicrobial susceptibility, treatment and outcomes of these infections in humans.

METHODS

Systematic review of PubMed (through 27th December 2019) for studies providing epidemiological, clinical, microbiological as well as treatment data and outcomes of K ohmeri infections.

RESULTS

A total of 35 studies, containing data of 44 patients, were included in the analysis. The most common K ohmeri infections were those of the bloodstream, infective endocarditis and onychomycosis. Previous antibiotic use, presence of a central venous catheter, parenteral nutrition and cancer were very common among patients. Mortality was high in the case of fungemias but low for other types of infections. Amphotericin B and fluconazole are the most common agents used for treatment, even though alarming MICs for fluconazole were noted.

CONCLUSIONS

This systematic review thoroughly describes infections by K ohmeri and provides information on their epidemiology, clinical presentation, microbiology, antibiotic resistance patterns, treatment and outcomes.

Opportunistic Infections Are More Prevalent in Crohn's Disease and Ulcerative Colitis: A Large Population-Based Study

BACKGROUND

Opportunistic infections (OIs) are more common in patients with inflammatory bowel disease (IBD); however, there have been limited large-scale studies of OIs in IBD. We investigated the epidemiological characteristics of OI in Crohn's disease (CD) and ulcerative colitis (UC) using a large population-based database.

METHODS

Data were collected from a commercial database (Explorys Inc., Cleveland, OH, USA) that provided electronic health records from 26 major integrated US health care systems from 1999 to March 2018. In this data set, we identified all CD and UC patients, based on Systemized Nomenclature of Medicine-Clinical Terms. Within these cohorts, we identified a variety of OIs and compared the prevalence rate of OI in individuals with IBD with that of controls (patients in the database between March 2013 and March 2018 without the diagnosis of IBD).

RESULTS

Explorys included 153,290 patients with CD and 128,540 patients with UC between March 2013 and March 2018. The prevalence of OIs was 17.8% in CD, 19.2% in UC, and 7% in non-IBD controls. When compared with non-IBD controls, all OIs were more common in CD (prevalence ratio [PR], 2.54; 95% confidence interval [CI], 2.51-2.57) and UC (PR, 2.74; 95% CI, 2.71-2.77). Overall, viral infections were numerically more common, whereas bacterial infections had the highest PRs in CD and UC when compared with controls without IBD.

CONCLUSIONS

We found significantly higher rates of OI in IBD. Our study suggests the need for close follow-up of IBD patients to diagnose and provide vaccinations where applicable for prevention of infections.

Review article: fungal alterations in inflammatory bowel diseases

BACKGROUND

Emerging data suggest that alterations in gut fungi may be associated with the pathogenesis of inflammatory bowel disease (IBD). In healthy individuals, gut commensal fungi act synergistically with other members of the microbiota to maintain homeostasis but their role in IBD is less clear.

AIM

To review the role of gut fungi and their trans-kingdom interactions with bacteria in IBD METHODS: A literature search was conducted on Ovid and Pubmed to select relevant animal and human studies that have reported fungi and IBD.

RESULTS

There is an increased total fungal load particularly of Candida and Malassezia species in the faeces and mucosa of Crohn's disease patients, and a lower fungal diversity in the faeces of ulcerative colitis patients. Caspase recruitment domain-containing protein (CARD)-9 polymorphism in Crohn's disease patients favours Malassezia colonisation that worsens gut inflammation. Diet high in carbohydrates increased the total abundance of Candida species, whereas protein-rich diet had the opposite effect. Anti-fungal therapies are mostly used to treat Candida albicans or Histoplasma capsulatum infections in IBD, whereas pilot studies of supplementing fungal probiotics Saccharomycopsis fibuligera, Saccharomyces boulardii and Saccharomyces cerevisiae CNCM I-3856 strain showed therapeutic effects in IBD.

CONCLUSIONS

Gut fungi are altered in patients with Crohn's disease and ulcerative colitis. Modulation of the fungal microbiota can be considered as a therapeutic approach for IBD. Future research should focus on understanding how the fungal microbiota interacts with other components of the gut microbiota in association with the pathogenesis and development of IBD.

Perianal Histoplasmosis Presenting as a Mass Suspicious for Malignancy: A Case Report with Review of Gastrointestinal Manifestations of Histoplasmosis

Patient: Male, 66

Final Diagnosis: Perianal histoplasmosis

Symptoms: Perianal pain

Medication: —

Clinical Procedure: Surgical biopsy of the lesion

Specialty: Pathology

Serious and Opportunistic Infections in Elderly Patients With Inflammatory Bowel Disease

Inflammatory bowel disease (IBD) is often treated with biologics and immunomodulators, which can place elderly IBD patients at risk for serious and opportunistic infections. This article provides an updated account of research on therapies in IBD that are associated with an increased infection risk. Relevant serious and opportunistic infections in the elderly population are discussed along with methods for prevention and treatment. The incidence of infection increases with age and the degree of immunosuppression. Emphasis should be placed on performing vaccinations at the time of IBD diagnosis. Additionally, patients receiving immunosuppressive therapy should avoid live vaccines. Physicians should have a greater awareness of the increased risk of infection in elderly adults and the need for screening for infection prior to initiation of immunosuppressive IBD therapies.

The gut virome in inflammatory bowel disease pathogenesis: From metagenomics to novel therapeutic approaches

The association of intestinal dysbiosis with the pathogenesis of inflammatory bowel disease has been well established. Besides bacteria, microbiota comprises yeasts, archaea, protists and viruses, neglected actors in inflammatory bowel disease-associated microbiota. In the past, a great limitation in studying microbiota composition was the low sensitivity of sequencing technologies and that few computational approaches were sufficient to thoroughly analyse the whole microbiome. However, new cutting-edge technologies in nucleic acid sequencing, -omics analysis and the innovative statistics and bioinformatics pipelines made possible more sensitive and accurate metagenomics, ultimately identifying novel players in intestinal inflammation, including prokaryotic and eukaryotic viruses, that together form the gut virome. The discovery of peculiar inflammatory bowel disease-associated microbial strains will not only shed new light on inflammatory bowel disease aetiogenesis, they may also support the development of novel therapeutic strategies not merely treating symptoms, but precisely counteracting the primary cause of chronic intestinal inflammation.

Armillifer Infections in Humans: A Systematic Review

Armillifer is a genus of obligate parasites belonging to the Pentastomida subclass that was first described as a cause of human disease in 1847. Human infection by Armillifer is rare and not widely known. These parasites are transmitted to humans by handling or eating undercooked meat from infected snakes, which are the definitive hosts, or oral uptake of environmental ova. The aim of this systematic review was to record all available evidence regarding infections by Armillifer in humans. A systematic review of PubMed (through 21 December 2018) for studies providing epidemiological, clinical, microbiological, as well as treatment data and outcomes of Armillifer infections was conducted. A total of 26 studies, containing data of 40 patients, were eventually included in the analysis. The most common sites of infection were the peritoneal cavity, the liver, the lower respiratory and the abdominal tract. The commonest infecting species was A. armillatus and most patients were asymptomatic; however, when symptoms occurred, the commonest was abdominal pain, even though unusual presentations occurred, such as hepatic encephalopathy or neurologic symptoms. Most cases were diagnosed at surgery or by imaging, and most patients were not treated. Mortality was low, but the majority of the cases with ocular infection lead to permanent loss of vision.

The Hidden Cost of Modern Medical Interventions: How Medical Advances Have Shaped the Prevalence of Human Fungal Disease

Life expectancy in the West is the highest it has ever been, due to the introduction of better hygiene practices and sophisticated medical interventions for cancer, autoimmunity and infectious disease. With these modern advances, a rise in the prevalence of opportunistic infections has also been observed. These include several fungal infections, which present a particular clinical challenge due to the lack of fungal vaccines, limited diagnostics and increasing antifungal drug resistance. This mini-review outlines how modern-day clinical practices have shaped the recent increase in fungal diseases observed in the last few decades. We discuss new research that has implicated the use of immune-modulating drugs in the enhanced susceptibility of vulnerable patients to life-threatening fungal infections.

Review article: managing the adverse events caused by anti-TNF therapy in inflammatory bowel disease

BACKGROUND

Biological therapy is currently widely used to treat IBD. Infliximab, adalimumab and golimumab are currently licensed anti-TNF therapies. Biosimilar anti-TNF monoclonal antibodies are increasingly used. Anti-TNF therapies are widely used and their adverse effects are well characterised, and may cause significant morbidity and mortality in a small proportion of exposed patients. Gastroenterologists need to understand the mechanisms for these effects, recognise these swiftly and manage such events appropriately.

AIM

To cover the range of potential adverse reactions as a result of biologic therapy and specifically management of these events.

METHODS

A Medline and Pubmed search was undertaken. Search terms included were "anti-TNF," "infliximab" or "adalimumab" or "golimumab" combined with the keywords "ulcerative colitis" or "Crohn's disease" or "inflammatory bowel disease" and then narrowed to articles containing the keywords "complications," "side effects" or "adverse events" or "safety profile." International guidelines were also reviewed where relevant.

RESULTS

Adverse events discussed in this review include infusion reactions, blood disorders and infections (including bacterial, viral, fungal and opportunistic infections) as well as autoimmune, dermatological disorders, cardiac and neurological conditions. Malignancies including solid organ, haematological and those linked to viral disease are discussed.

CONCLUSIONS

Anti-TNF therapy has wide-ranging effects on the immune system resulting in a spectrum of potential adverse events in a small proportion of patients. Research advances are improving the understanding, recognition and management of these adverse events.

Escherichia hermannii Infections in Humans: A Systematic Review

Eshcerichia hermannii is a member of the Enterobacteriaceae, first described in 1982 and reclassified as a distinct species in the Escherichia genus after identifying biochemical and genomic differences from E. coli. It is a rare cause of human infections and is supposed to be a co-infector rather than an autonomous cause of infection. The aim of this systematic review was to record and evaluate all available evidence regarding human infections by E. hermannii. A systematic review of PubMed (through 21 December 2018) for studies providing epidemiological, clinical, and microbiological information, as well as treatment data and outcomes of E. hermannii infections was performed. A total of 16 studies, containing data of 17 patients, were eventually included in the analysis. The most common E. hermannii infections were bacteremias, urinary tract, and central nervous system infections. The complication rate, like the occurrence of sepsis, was high. Cephalosporins and aminoglycosides were the most common agents used for treatment. This systematic review describes bacterial infections by E. hermannii and provides information on the epidemiology, clinical presentation, antibiotic resistance, treatment, and outcomes associated with these infections.

Disseminated cryptococcosis in Crohn's disease: a case report

BACKGROUND

Gastrointestinal (GI) cryptococcosis is rarely reported. Most cases were diagnosed during evaluation of comorbid conditions, incidental findings, or postmortem. Here, we present a case of Crohn's disease with gastrointestinal cryptococcosis that resembled exacerbation of Crohn's disease.

CASE PRESENTATION

A 64-year-old woman with Crohn's disease (CD) was referred to Siriraj Hospital due to worsening of abdominal pain and watery diarrhea for 2 weeks. The dose of immunosuppressive agents was increased for presumed exacerbation of CD. Pathologic examination of tissue obtained from polypoid mass at ileocecal valve and multiple clean-based ulcers at cecum revealed active ileitis and colitis with multiple round shape organisms with capsule, which was compatible with Cryptococcus species. Disseminated cryptococcosis was diagnosed due to gastrointestinal involvement and presumed pulmonary involvement regarding the presence of an oval-shaped cavitary lesion on chest X-ray and computed tomography of the lung. Patient was successfully treated with amphotericin B followed by fluconazole with satisfactory result.

CONCLUSION

Early diagnosis of gastrointestinal cryptococcosis in Crohn's disease is difficult due to the lack of specific symptoms and sign or mimicking an exacerbation of Crohn's disease. Seeking for other site of involvement in disseminated cryptococcosis including lung or central nervous system as well as detection of serum cryptococcal antigen would be helpful for early diagnosis and management.

Granulomatous response to invasive pulmonary aspergillosis in an immunotherapy-naive host, a maladaptive response?

Pulmonary aspergillosis causes a wide spectrum of disease, ranging from asymptomatic airway colonization to severe invasive disease, contingent on the host's immune status and underlying pulmonary anatomy. The invasive form of aspergillosis is a rare occurrence in the immunocompetent population. Nevertheless, patients with a compromised innate immune response are at greatest risk. We present a case of a patient with known Crohn's disease who developed invasive pulmonary aspergillosis. His clinical picture was further complicated by an uncommon immune response characterized by the development of granulomas encasing the Aspergillus forms found on his lung biopsy, likely representing a maladaptive response, possibly related to the effects of his granulomatous disease in the lungs. He was successfully treated with antifungal therapy and video assisted thoracoscopic surgery with placement of thoracostomy tube drainage for a parapneumonic effusion. We will discuss the factors leading to his atypical presentation and clinical outcome.