A retrospective series of gut aspergillosis in haematology patients

Surgical treatment of invasive fungal infection in pediatric oncology

BACKGROUND

Invasive fungal disease (IFD) is typically aggressive and related with high mortality in children with a hematological malignancy. The association of medical and surgical treatment may ameliorate the outcome. The aim of this study was to analyze the surgical treatment of fungal infections in pediatric oncological populations.

METHODS

Retrospective study (2000-2022) of a single-center experience. We reviewed the medical record of all patients with hematologic malignancies and IFD, analyzing the outcome.

RESULTS

From the 70 pediatric cases of hematologic malignancies with the diagnosis IFD over 22 years, we included in the present study 44 cases who required surgical approaches for either diagnosis or treatment. Twenty-one patients were males and the mean age was 11 (range 1-23) years. The main indications for surgery were lack of improvement following medical treatment and/or progression of fungal infection (80%) and diagnosis confirmation (20%). Only five patients needed an emergency operation for rapid worsening of symptoms. The most common site of infection was the lung (80%) and the most frequently identified pathogen was Aspergillus (75%). The most common surgical procedures were lobectomy (performed in 17 patients) and atypical lung resection (10). Complications of surgery were mostly treated by medical approach. The mean time of resumption of oncological treatment was 40 (range 0-150) days.

CONCLUSIONS

Surgery is an important step in the multimodal treatment of invasive fungal infection with excellent resolution rate. Overall mortality depends on the underlying malignancy.

Clinical characteristics, diagnosis, treatment, and outcome of patients with liver abscess due to Aspergillus spp: a systematic review of published cases

BACKGROUND

Aspergillus spp liver abscess is a relatively rare entity and thus far no systematic review has been performed examining patients' demographics, clinical manifestations, diagnosis, management, and outcome.

METHODS

We performed a systematic review of the literature using MEDLINE and LILACS databases. We searched for articles published in the period from January 1990 to December 24, 2022, to identify patients who developed liver abscesses due to Aspergillus spp.

RESULTS

Our search yielded 21 patients all of whom had invasive aspergillosis confirmed on liver biopsy. Of these patients 81% were adults, and 60% were males. The majority (86%) of patients were immunocompromised and 95% had symptomatic disease at the time of diagnosis. The most common symptoms were fever (79%), abdominal pain (47%), and constitutional symptoms (weight loss, chills, night sweats, fatigue) (38%). Liver enzymes were elevated in 50%, serum galactomannan was positive in 57%, and fungal blood cultures were positive in only 11%. Co-infection with other pathogens preceded development of apsergillosis in one-third of patients, and the majority of the abscesses (43%) were cryptogenic. In the remaining patients with known source, 28% of patients developed liver abscess through dissemination from the lungs, 19% through the portal vein system, and in 10% liver abscess developed through contiguous spread. The most common imaging modality was abdominal computerized tomography done in 86% of patients. Solitary abscess was present in 52% of patients while 48% had multiple abscesses. Inadequate initial empiric therapy was prescribed in 60% of patients and in 44% of patients definite treatment included combination therapy with two or more antifungal agents. Percutaneous drainage of the abscesses was done in 40% of patients, while 20% required liver resection for the treatment of the abscess. Overall mortality was very high at 38%.

CONCLUSION

Further studies are urgently needed for a better understanding of pathophysiology of liver aspergillosis and for developement of newer blood markers in order to expedite diagnosis and decrease mortality.

Role of biomarkers in the diagnosis of invasive aspergillosis in immunocompromised patients

BACKGROUND

Invasive aspergillosis is one of the important causes of infection in immunocompromised patients. This study aimed to evaluate the roles of biomarkers in the diagnosis of invasive aspergillosis and their relationship with antifungal stewardship programs.

METHODS

190 sera from 52 immunocompromised patients and volunteer individuals were included in this study. 18 immunocompromised volunteers without IA and 34 patients with probable and proven aspergillosis according to the European Organization for Research and Treatment of Cancer and the Mycoses Study Group consensus definitions were entered in this study. The respective sera were evaluated for procalcitonin, soluble triggering receptor expressed on myeloid cells-1 (sTREM-1) levels; white blood cells count (WBC) count, C reactive protein (CRP), lactate dehydrogenase (LDH), and erythrocyte sedimentation rate (ESR) values. Demographic data and clinical characteristics of patients were extracted from their files.

RESULTS

The male-to-female ratio and mean age of patients were 22/12 and 38.9 years, respectively. The hematologic disorder was the most predisposing factor (29/34, 85.3%). Sensitivity of biomarkers for diagnosis of invasive aspergillosis was 70.6% (cut off value > 190 pg/mL for sTREM-1, 71% (cut off value > 260 pg/mL) for PCT, 85.3% (cut off value > 193 U/L) for LDH, 94.1% (cut off value > 8 mg/l) for CRP, 64.7% (cut off value < 5200 cells/ml) for WBC, and 85.3% (cut off value > 23 mm/h) for ESR. Twelve patients died, with significantly increased sTREM-1 levels and decreased WBC count in them.

CONCLUSION

According to our data, evaluation of the biomarkers can help in the diagnosis, management, and prediction of the severity of Aspergillus infection, and the rational use of antifungal agents in immunocompromised patients.

Aspergillus appendicitis complicating chemotherapy of leukemia: A case report and review of the literature

Introduction

The diagnosis of primary Aspergillus appendicitis can be missed or delayed because of its rarity. We report our experience of a case of Aspergillus appendicitis complicating chemotherapy of leukemia.

Presentation of case

A 48-year-old man who was diagnosed with acute myeloid leukemia developed high fever and epigastric pain two weeks after administration of his fourth consolidation chemotherapy. Right lower quadrant tenderness and rebound tenderness were noticed on physical examination, and the abdomen and pelvis computed tomography suggested acute perforated appendicitis with localized peritonitis. Emergency laparoscopy showed an inflamed appendix, which was resected. Pathology reports revealed invasive aspergillosis in the appendix. The patient recovered after high-dose antifungal therapy, although he required prolonged hospitalization.

Discussion

Acute appendicitis is very rarely caused by fungi infection with an overall incidence of up to 1.15 %. Differential diagnosis of fungal appendicitis without pathology report is challenging due to low incidence.

Conclusion

Isolated Aspergillus appendicitis is a rare disease that can progress without appropriate antifungal therapy even after surgical resection of the appendix. Surgeons should pay attention to pathology reports after appendectomy to avoid missing unusual cases, especially in immunocompromised patients.

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Fungal infections principally occur in the immunocompromised.

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Misdiagnosis and incorrect treatment are frequent in this rare disease entity.

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Early diagnosis and prompt surgery with antifungal treatment is best

Oesophageal and pulmonary invasive aspergillosis in a patient with multiple myeloma

Invasive aspergillosis (IA) is a serious fungal infection that primarily affects patients with prolonged and profound neutropenia, and compromised cell-mediated immunity. Aspergillosis of the oesophagus and gastrointestinal tract is uncommon but seen in advanced cases of disseminated IA. However, it is difficult to diagnose antemortem due to the poor specificity of the symptoms and the absence of characteristic imaging findings. Therefore, the reported cases of gastrointestinal aspergillosis have been associated with high morbidity and mortality, and frequently diagnosed postmortem. Here we present a successful outcome in a patient with relapsed and refractory multiple myeloma who had presented with febrile neutropenia, cough and dysphagia, and was diagnosed with disseminated IA comprising of pulmonary and oesophageal involvement. This case highlights the need for a high index of suspicion and the importance of invasive procedures for histopathology and molecular diagnostics to ensure an early diagnosis and therapeutic intervention.

Invasive mold infection of the gastrointestinal tract - A case series of 22 immunocompromised patients from a single academic center

Invasive mold infection (IMI) of the gastrointestinal (GI) tract is a rare complication in immunocompromised patients that carries a high mortality rate. It is most often described in the setting of disseminated disease. Early diagnosis and treatment are critical in its management, but this is rarely obtained, leading to delayed therapy. To describe the clinical characteristics, treatment and outcomes of this infection, we reviewed all the cases of adult patients with histopathological findings from autopsy or surgical specimens that demonstrated fungal invasion into the GI tract at Stanford Hospital & Clinics from January 1997 to August 2020. Twenty-two patients that met criteria were identified and they were all immunocompromised, either due to their underlying medical conditions or the treatments that they received. The most common underlying disease was hematological malignancies (63.6%) and the most common symptoms were abdominal pain, GI bleeding and diarrhea. A majority of patients (72.7%) had disseminated invasive mold infection, while the rest had isolated GI tract involvement. In 2/3 of our cases, the fungal genus or species was confirmed based on culture or PCR results. Given the very high mortality associated with GI mold infection, this diagnosis should be considered when evaluating immunocompromised patients with concerning GI signs and symptoms. A timely recognition of the infection, prompt initiation of appropriate antifungal therapy as well as surgical intervention if feasible, are key to improve survival from this devastating infection.

Every breath you take: Impacts of environmental dust exposure on intestinal barrier function-from the gut-lung axis to COVID-19

As countries continue to industrialize, major cities experience diminished air quality, whereas rural populations also experience poor air quality from sources such as agricultural operations. These exposures to environmental pollution from both rural and populated/industrialized sources have adverse effects on human health. Although respiratory diseases (e.g., asthma and chronic obstructive pulmonary disease) are the most commonly reported following long-term exposure to particulate matter and hazardous chemicals, gastrointestinal complications have also been associated with the increased risk of lung disease from inhalation of polluted air. The interconnectedness of these organ systems has offered valuable insights into the roles of the immune system and the micro/mycobiota as mediators of communication between the lung and the gut during disease states. A topical example of this relationship is provided by reports of multiple gastrointestinal symptoms in patients with coronavirus disease 2019 (COVID-19), whereas the rapid transmission and increased risk of COVID-19 has been linked to poor air quality and high levels of particulate matter. In this review, we focus on the mechanistic effects of environmental pollution on disease progression with special emphasis on the gut-lung axis.

Infectious diseases of the upper gastrointestinal tract

A broad spectrum of pathogens produce gastrointestinal disease. The ongoing spread of human immunodeficiency virus/acquired immune deficiency syndrome, the increased use of immunosuppressive therapy and the persistence of overcrowding and suboptimal sanitation in underdeveloped areas facilitate both disease transmission from environmental and foodborne sources and person-to-person transmission. Clinicians increasingly rely on endoscopic biopsy sample interpretation to diagnose gastrointestinal infections. Thus, pathologists must be aware of diagnostic features of a variety of microbial pathogens. Detection with molecular techniques also allows for correlation between infectious agents and their histopathological features, which has expanded our knowledge of the inflammatory changes produced by infectious agents. This review covers infectious disorders of the upper gastrointestinal tract encountered in surgical pathology. Clinical, endoscopic and pathological features are presented. The review emphasises morphological features of viruses, bacteria, fungi and parasites that may be found in tissue samples, and the inflammatory patterns that they produce. Differential diagnoses and useful ancillary techniques are discussed.

Intestinal Aspergillosis: Systematic Review on Patterns of Clinical Presentation and Management

Background: Intestinal aspergillosis (IA) is a rare entity primarily discovered in immunocompromised patients. Because of its low incidence, IA is not considered routinely in the differential of abdominal pain, distension, and diarrhea. A systematic characterization of demographics, comorbidities, clinical presentations, and outcomes can help surgeons recognize and manage IA in critically ill patients. Methods: Two independent authors carried out the literature search using PubMed, MEDLINE, and Scopus databases. The Mesh terms utilized were: 'intestinal' and 'aspergillosis' combined with the Boolean operator 'AND' (synonyms were combined with the Boolean operator 'OR'). Intestinal aspergillosis was defined as inflammation of the gastrointestinal tract (duodenum to rectum) caused by Aspergillus spp. All articles reporting IA were included. Articles describing aspergillosis of the esophagus or stomach were excluded. Statistical analysis was performed using SPSS software (version 18; SPSS Inc., Chicago, IL). Results: Forty-two articles reporting 56 cases were included in the study. Mean age was 44.9 ± 20.5 years. Male to female ratio was 29:27. The most common condition in patients who developed IA was transplantation (19 patients; 34%). The most common clinical presentations of IA were abdominal pain (21 patients; 38%) and diarrhea 12 patients; 21%). Sixty-six percent of patients had primary IA whereas 34% developed IA secondarily to systemic infection. Diagnostic modalities included exploratory laparotomy (35 patients; 63%) and endoscopy (7 patients; 13%). Mean time to diagnosis was 8.6 ± 11.3 days. Intestinal aspergillosis was limited to the small bowel in 61% of patients. In 43 (77%) patients, bowel resection is the definitive treatment, whereas 13 (23%) patients underwent antifungal therapy alone. Mortality rate was 39%. Sixty-three percent of patients treated with surgery survived, compared with 46% treated with antifungal therapy alone (p = 0.34). Conclusion: Intestinal aspergillosis is a life-threatening condition with a mortality rate of 39%. Extrapulmonary IA is seen in patients with neutropenia, sepsis, inflammatory conditions, and immunosuppression. Patients who undergo surgery are more likely to survive this infection.

Occurrence and species diversity of human-pathogenic Mucorales in commercial food-stuffs purchased in Paris area

Mucormycoses are life-threatening fungal diseases that affect a variety of patients including those with diabetes mellitus or hematological malignancies. The responsible agents, the Mucorales, are opportunistic pathogens originating from the environment such as soil or decaying organic matter. The aim of the present study was to assess the prevalence and diversity of human-pathogenic species of Mucorales in commercially available foodstuffs in France. All food samples were purchased from January 2014 to May 2015 in France. A total of 159 dried food samples including spices and herbs (n = 68), herbal tea (n = 19), cereals (n = 19), vegetables (n = 14), and other foodstuffs (n = 39) were analyzed. Each strain of Mucorales was identified phenotypically, and molecular identification was performed by ITS sequencing. From the 28 (17.6%) samples that were culture-positive for Mucorales, 30 isolates were recovered. Among the isolates, 13 were identified as Rhizopus arrhizus var. arrhizus, 10 R. arrhizus var. delemar, two Rhizopus microsporus, one Lichtheimia corymbifera, three Lichtheimia ramosa, and one Syncephalastrum racemosum. Culture-positive samples originated from different countries (Europe, Asia) and brands. The samples most frequently contaminated by Mucorales were spices and herbs (19/68, 27.9%), followed by herbal tea (2/19, 10.5%), cereals (2/19, 10.5%), other food products (5/39, 12.8%). The present study showed that human-pathogenic Mucorales were frequently recovered from commercially available foodstuffs in France with a large diversity of species. The potential danger represented by Mucorales present in food for immunocompromised patients should be further analyzed.

Delayed Diagnosis of a Diffuse Invasive Gastrointestinal Aspergillosis in an Immunocompetent Patient

Invasive aspergillosis represents a clinical picture frequently associated with host's immunosuppression which usually involves a high morbidity and mortality. In general, the most frequent fungal entry is the lungs with secondary hematogenous dissemination, but there are other hypotheses like a gastrointestinal portal of entry. There are some rare publications of cases with invasive aspergillosis in immunocompetent patients. We present the case of an immunocompetent patient without any risk factors except for age, ICU stay, and surgical intervention, who developed a septic shock by invasive gastrointestinal aspergillosis as primary infection. Due to the unusualness of the case, despite all the measures taken, the results were obtained postmortem. We want to emphasize the need not to underestimate the possibility for an invasive aspergillosis in an immunocompetent patient. Not only pulmonary but also gastrointestinal aspergillosis should be taken into account in the differential diagnosis to avoid a delay of treatment.

The Mycobiome in Health and Disease: Emerging Concepts, Methodologies and Challenges

Fungal disease is an increasingly recognised global clinical challenge associated with high mortality. Early diagnosis of fungal infection remains problematic due to the poor sensitivity and specificity of current diagnostic modalities. Advances in sequencing technologies hold promise in addressing these shortcomings and for improved fungal detection and identification. To translate such emerging approaches into mainstream clinical care will require refinement of current sequencing and analytical platforms, ensuring standardisation and consistency through robust clinical benchmarking and its validation across a range of patient populations. In this state-of-the-art review, we discuss current diagnostic and therapeutic challenges associated with fungal disease and provide key examples where the application of sequencing technologies has potential diagnostic application in assessing the human ‘mycobiome’. We assess how ready access to fungal sequencing may be exploited in broadening our insight into host–fungal interaction, providing scope for clinical diagnostics and the translation of emerging mycobiome research into clinical practice.

Educational Case: Ischemic Disorders of the Gut in Adult Patients

The following fictional case is intended as a learning tool within the Pathology Competencies for Medical Education (PCME), a set of national standards for teaching pathology. These are divided into three basic competencies: Disease Mechanisms and Processes, Organ System Pathology, and Diagnostic Medicine and Therapeutic Pathology. For additional information, and a full list of learning objectives for all three competencies, see http://journals.sagepub.com/doi/10.1177/2374289517715040. ¹.

Comparison of GeneXpert and line probe assay for detection of Mycobacterium tuberculosis and rifampicin-mono resistance at the National Tuberculosis Reference Laboratory, Kenya

BACKGROUND

The dual challenge of low diagnostic sensitivity of microscopy test and technical challenge of performing a TB culture test poses a problem for case detection and initiation of Tuberculosis (TB) second-line treatment. There is thus need for a rapid, reliable and easily accessible assay. This comparative analysis was performed to assess diagnostic performance characteristics of GeneXpert MTB/RIF and Line Probe Assay (LPA).

METHODS

Three hundred twenty nine sputum samples of patients across the 47 counties in Kenya suspected to have drug resistant TB were picked and subjected to GeneXpert, LPA and Culture MGIT at the National TB Reference Laboratory. Sensitivity, specificity and predictive values were then determined to assess the performance characteristics of the various assays.

RESULTS

Against culture MGIT as the gold standard for TB diagnosis, GeneXpert had a sensitivity, specificity, positive predictive value, and negative predictive value of 78.5, 64.9, 59.4 and 82.2% respectively while LPA had 98.4, 66.0, 65.4 and 98.4%. For diagnosis of rifampicin mono-resistance GeneXpert had a moderate agreement (Kappa 0.59, P < 0.01) (sensitivity 62.50%, specificity 96.50%) while LPA that had almost perfect agreement (Kappa = 0.89, p < 0.01) with a (sensitivity 90.0% and specificity 99.1%).

CONCLUSION

LPA has a better performance characteristic to GeneXpert and an alternative to culture with regards to detection of RIF's mono-resistance.

Primary intestinal aspergillosis resulting in acute intestinal volvulus after autologous stem cell transplantation in a patient with relapsed non-Hodgkin lymphoma: report on a rare infectious complication and a review of the literature

Objectives: Since primary intestinal aspergillosis is a severe infectious complication with a high morbidity and mortality in immunocompromised patients, we want to draw attention to this rare entity and the importance of early recognition. Methods: We report a case of documented primary intestinal aspergillosis in a patient receiving an autologous stem cell transplantation (SCT). Furthermore, this article gives a short reflection on the occurrence of invasive aspergillosis in autologous SCT and the value of serum galactomannan levels based on literature search and linked with the case. Results: In this case the patient presented on day +8 after autologous SCT for a relapsed diffuse large B-cell lymphoma with an acute abdomen with urgent need for surgical intervention. Biopsy revealed the presence of fungal colonies due to aspergillosis and voriconazole was started. Until that day the systematically taken serum galactomannan tests were all negative or pending. Initially there was some resistance to perform surgery in the presence of neutropenia and thrombocytopenia but in the end it provided the definitive diagnosis and should not be delayed. Until now this patient is in good health and retains a complete remission. Conclusion: With this case, we would like to emphasize that early recognition of primary intestinal aspergillosis is of the utmost importance as it is a rare but serious infectious complication. It should be included in the differential diagnosis of neutropenic patients with sudden onset abdominal pain and ongoing fever, even in the absence of a positive serum galactomannan.

Microbiological Safety of Dried Spices

Spices in the desiccated state provide an environment that allows the survival of many foodborne pathogens. Currently, the incidence of pathogen-positive spices imported into the United States is 1.9 times higher than for any other imported food. Correspondingly, imported spices have been associated with numerous foodborne outbreaks and multiple product recalls. Despite the association with recalls and outbreaks, the actual pathogen populations in spices, when found, are frequently extremely small. In addition to pathogenic bacterial species, toxigenic molds have been frequently recovered from spices, and aflatoxins have been found in as many as 58% of the spices sampled. The presence of toxigenic molds is especially problematic to the immunocompromised or those on immunosuppressive therapy and has been linked to gut aspergillosis. Numerous detection methods, including both traditional and advanced DNA regimes, are being tested to optimize recovery of pathogens from spices. Further, a number of new inactivation intervention methods to decontaminate spices are examined and discussed.

Invasive aspergillosis causing gastric necrosis and perforation: A case report

Aspergillosis is an opportunistic infection commonly seen in immunocompromised patients. Patients with hematological malignancies, postorgan transplantation, or those with comorbid conditions are susceptible to the development of invasive aspergillosis. Lungs are the main portal of entry and are thus most commonly involved. Aspergillosis can involve the gut, causing vascular thrombosis leading to ischemia and necrosis of the gut wall, resulting in perforation. Primary gastric involvement has been rarely seen, with few case reports in the literature. We report a rare case of primary invasive gastric aspergillosis in a 60‐year‐old diabetic and cirrhotic woman, who presented with clinical features of perforation peritonitis. Exploratory laparotomy was performed, and a 6 cm × 6 cm perforation with necrotizing inflammation was found in the distal stomach, pylorus, and duodenum. Distal gastrectomy with Billroth II reconstruction was performed. Pathology demonstrated septate fungal hyphae invading the gastric wall transmurally. The morphology was compatible with those of Aspergillus spp. Liposomal amphotericin B was started immediately after surgery based on the presence of unusually large areas of necrosis and perforation with blackish exudate covering the ulcer base. Unfortunately, the patient succumbed to rapidly progressive fungal septicemia despite early surgical intervention and critical care management. We recommend that any large confluent areas of gastric ulceration and necrosis with blackish exudates in an appropriate setting should evoke suspicion of invasive fungal infection. These patients should be started on prophylactic broadspectrum antifungal therapy immediately, which may be switched over to specific therapy once the diagnosis is confirmed.

Pathologic Features of Infectious Gastritis

This manuscript presents a review of infectious causes of gastritis aimed at the practicing anatomic pathologist. We shall highlight unique histologic findings and clinical attributes that will assist those analyzing endoscopically obtained mucosal biopsies of the stomach or resection specimens.

Inflammatory and infectious manifestations of immunodeficiency in the gastrointestinal tract

Immune compromise may result from genetic abnormalities, HIV/AIDS, or consequences of therapy for neoplastic and autoimmune diseases. Many immunocompromised patients develop severe gastrointestinal symptoms, particularly diarrhea, accompanied by non-specific or mild endoscopic abnormalities; mucosal biopsy with pathologic interpretation has a major role in the diagnosis and management of these patients. Immunocompromised individuals are at risk for all the diseases that affect those with a healthy immune system, but they are also prone to other illnesses that rarely affect immunocompetent patients. This review discusses the gastrointestinal manifestations of primary and acquired immunodeficiency, chemotherapy-related injury, and infections that show a predilection for immunocompromised patients. Key histologic features and relevant differential diagnoses are emphasized.

Multiple small bowel perforations due to invasive aspergillosis in a patient with acute myeloid leukemia: case report and a systematic review of the literature

PURPOSE

Invasive aspergillosis (IA) represents a major cause of morbidity and mortality in immunocompromised patients. Involvement of the gastrointestinal tract by Aspergillus is mostly reported as part of a disseminated infection from a primary pulmonary site and only rarely as an isolated organ infection.

METHODS

We report a case of small bowel perforation due to IA in a patient with acute leukemia under chemotherapy and pulmonary aspergillosis. We performed a systematic review of the literature as well.

RESULTS

A 43-year-old man with acute myeloid leukemia under chemotherapy developed severe neutropenia and pulmonary aspergillosis due to Aspergillus flavus. He developed melena and hemodynamic failure and a contrast-enhanced ultrasound scan suggested active intestinal bleeding. During emergency laparotomy we found multiple intestinal abscesses, several perforations of intestinal loop and Aspergillus flavus was isolated from the abscesses. Resection of the jejunum was performed. The patient received voriconazole and finally recovered. The patient is now alive and in complete disease remission. From literature review we found 35 intestinal IA previously published in single case reports or small case series as well.

CONCLUSION

Clinical manifestations of gastrointestinal aspergillosis are nonspecific, such as abdominal pain, and only occasionally it presents as an acute abdomen. Antemortem detection of bowel involvement is rarely achieved and, only in cases of complicated gastrointestinal aspergillosis, the diagnosis is achieved thanks to the findings during surgery. Gastrointestinal aspergillosis should be suspected in patients with severe and prolonged neutropenia with or without pulmonary involvement in order to consider the right therapy and prompt surgery.

High Throughput Sequencing for Detection of Foodborne Pathogens

High-throughput sequencing (HTS) is becoming the state-of-the-art technology for typing of microbial isolates, especially in clinical samples. Yet, its application is still in its infancy for monitoring and outbreak investigations of foods. Here we review the published literature, covering not only bacterial but also viral and Eukaryote food pathogens, to assess the status and potential of HTS implementation to inform stakeholders, improve food safety and reduce outbreak impacts. The developments in sequencing technology and bioinformatics have outpaced the capacity to analyze and interpret the sequence data. The influence of sample processing, nucleic acid extraction and purification, harmonized protocols for generation and interpretation of data, and properly annotated and curated reference databases including non-pathogenic "natural" strains are other major obstacles to the realization of the full potential of HTS in analytical food surveillance, epidemiological and outbreak investigations, and in complementing preventive approaches for the control and management of foodborne pathogens. Despite significant obstacles, the achieved progress in capacity and broadening of the application range over the last decade is impressive and unprecedented, as illustrated with the chosen examples from the literature. Large consortia, often with broad international participation, are making coordinated efforts to cope with many of the mentioned obstacles. Further rapid progress can therefore be prospected for the next decade.

Challenges in microbiological diagnosis of invasive Aspergillus infections

Invasive aspergillosis (IA) has been increasingly reported in populations other than the historical hematology patients and there are new questions about the performance of microbiological tools. Microscopy and culture have been completed by biomarkers, either antigens or DNA, and in blood or respiratory specimens or both. First studied in hematology, the antigen galactomannan performance in serum is low in other patient populations where the pathophysiology of the infection can be different and the prevalence of IA is much lower. DNA detection with polymerase chain reaction (PCR) in blood or serum (or both) has reached a certain level of acceptance thanks to consensus methods based on real-time quantitative PCR (qPCR). When used on respiratory specimens, galactomannan and qPCR depend on standardization of the sampling and the diverse mycological procedures. Thus, culture remains the main diagnostic criterion in critically ill patients. The current trend toward more effective anti-mold prophylaxis in hematology hampers the yield of a screening strategy, as is usually performed in hematology. Therefore, circulating biomarkers as confirmatory tests should be considered and their performance should be reappraised in each new setting. The use of azole prophylaxis also raises the issue of selecting azole-resistance Aspergillus fumigatus isolates. Ideally, the biomarkers will be more efficient when individual genetic risks of IA are defined. Culture, though not standardized, remains a key element for the diagnosis of IA and has the advantage to easily detect molds other than A. fumigatus. It is still unclear whether next-generation sequencing will replace culture in the future.

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

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

Analysis of peritoneal galactomannan for the diagnosis of Aspergillus peritonitis

Here, we report a patient developing a postoperative peritoneal infection by Aspergillus fumigatus. While galactomannan serum levels were negative throughout the time course, galactomannan levels in peritoneal fluids yielded high results. Serological testing of peritoneal fluids for fungal antigens might be a useful and easily applicable tool to support diagnosis of intraabdominal aspergillosis, which represents a rare type of invasive fungal infection.

Invasive Fungal Infections Acquired from Contaminated Food or Nutritional Supplements: A Review of the Literature

Fungi are an integral part of the natural environment and, therefore, play many roles in relation to food: some fungi are used in food production, some are food sources themselves, and some are agents of food spoilage. Some fungi that contaminate food can also be harmful to human health. The harmful but noninfectious health consequences of mycotoxins have been well-characterized, but the extent to which fungi in food pose a risk for invasive infections is unknown. We conducted a literature review to identify cases of invasive fungal infections (IFIs) believed to have resulted from ingestion or inhalation of food, beverages, or dietary supplements (excluding Saccharomyces infections). We identified 11 publications describing cases or small outbreaks of IFIs related to foods or beverages and three describing IFIs related to dietary supplements. These food-associated IFIs were predominantly mold infections, and the few yeast infections were associated with dairy products. Suspected foodborne IFIs appear to be rare, but are increasingly described in the electronically searchable literature. They are associated with a variety of foods, are due to a variety of fungal pathogens, and primarily occur in persons with immunosuppressive conditions or other predisposing factors. Various guidelines for high-risk patients recommend avoidance of certain food products that may contain high levels of fungi, but further work is needed to evaluate the effectiveness of these restrictive diets in preventing fungal infections. The relationships between food spoilage, food insecurity, and IFI risk are another area that may warrant further exploration.

Characteristic clinical features of Aspergillus appendicitis: Case report and literature review

This work aims to facilitate diagnosing Aspergillus appendicitis, which can be missed clinically due to its rarity, by proposing a clinical pentad for Aspergillus appendicitis based on literature review and one new case. The currently reported case of pathologically-proven Aspergillus appendicitis was identified by computerized search of pathology database at William Beaumont Hospital, 1999-2014. Prior cases were identified by computerized literature search. Among 10980 pathology reports of pathologically-proven appendicitis, one case of Aspergillus appendicitis was identified (rate = 0.01%). A young boy with profound neutropenia, recent chemotherapy, and acute myelogenous leukemia presented with right lower quadrant pain, pyrexia, and generalized malaise. Abdominal computed tomography scan showed a thickened appendiceal wall and periappendiceal inflammation, suggesting appendicitis. Emergent laparotomy showed an inflamed, thickened appendix, which was resected. The patient did poorly postoperatively with low-grade-fevers while receiving antibacterial therapy, but rapidly improved after initiating amphotericin therapy. Microscopic examination of a silver stain of the appendectomy specimen revealed fungi with characteristic Aspergillus morphology, findings confirmed by immunohistochemistry. Primary Aspergillus appendicitis is exceptionally rare, with only 3 previously reported cases. All three cases presented with (1)-neutropenia, (2)-recent chemotherapy, (3)-acute leukemia, and (4)-suspected appendicitis; (5)-the two prior cases initially treated with antibacterial therapy, fared poorly before instituting anti-Aspergillus therapy. The current patient satisfied all these five criteria. Based on these four cases, a clinical pentad is proposed for Aspergillus appendicitis: clinically-suspected appendicitis, neutropenia, recent chemotherapy, acute leukemia, and poor clinical response if treated solely by antibacterial/anti-candidial therapy. Patients presenting with this proposed pentad may benefit from testing for Aspergillus infection by silver-stains/immunohistochemistry and considering empirical anti-Aspergillus therapy pending a tissue diagnosis.

Invasive Primary Colonic Aspergillosis in the Immunocompetent Host without Classical Risk Factors

Invasive aspergillosis (IA), generally considered an opportunistic infection in immunocompromised hosts, is associated with high morbidity and mortality. IA commonly occurs in the respiratory tract with isolated reports of aspergillosis infection in the nasal sinuses, central nervous system, skin, liver, and urinary tract. Extra-pulmonary aspergillosis is usually observed in disseminated disease. To date, there are a few studies regarding primary and disseminated gastrointestinal (GI) aspergillosis in immunocompromised hosts. Only a few cases of primary GI aspergillosis in non-immunocompromised hosts have been reported; of these, almost all of them involved the upper GI tract. We describe a very rare case of IA involving the lower GI tract in the patient without classical risk factors that presented as multiple colon perforations and was successfully treated by surgery and antifungal treatment. We also review related literature and discuss the characteristics and risk factors of IA in the immunocompetent hosts without classical risk factors. This case that shows IA should be considered in critically ill patients, and that primary lower GI aspergillosis may also occur in the immunocompetent hosts without classical risk factors.

Chronic infections of the small intestine

PURPOSE OF REVIEW

Chronic infections of the small intestine cause significant morbidity and mortality globally. This review focuses on the recent advances in the field of our understanding of selected intestinal infections.

RECENT FINDINGS

Primary and secondary immunodeficiency increase the susceptibility to many chronic intestinal infections. Endoscopy and intestinal biopsies are central to establishing a diagnosis of these conditions. Tuberculosis (TB) remains a major global health challenge. Emerging therapeutic agents to counteract multidrug-resistant strains have shown clinical efficacy, but concerns regarding mortality remain. PCR-based diagnostic TB tests have the potential to reduce diagnostic delays, but remain to be validated for intestinal infections. Adjunctive diagnostic imaging modalities can differentiate infections from Crohn's disease with increasing accuracy. Whipple's disease remains rare, but there have been substantial advances in our understanding of the causative organism Tropheryma whipplei. Extended treatment with broad-spectrum antibiotics is effective in most cases. The narrow therapeutic window and limited armamentarium for treating invasive filamentous fungal infections contribute to their significant morbidity and high rates of mortality.

SUMMARY

The speed and accuracy of diagnosing chronic intestinal infections have improved with recent imaging and laboratory methodologies. Significant research opportunities remain for clinicians and scientists to improve the diagnostic accuracy and clinical outcomes of chronic intestinal infections.

The role of surgical debridement in different clinical manifestations of invasive aspergillosis

Invasive aspergillosis (IA) has a wide spectrum of clinical presentations and is associated with high mortality rates. Early initiation of systemic antimould therapy remains the most important measure to reduce mortality. Surgical debridement is an important additional therapeutic option mainly in cases of extrapulmonary IA. The main intention for surgical intervention in IA is to obtain material for diagnosis and antifungal susceptibility testing. There are, however, also therapeutic implications for surgical interventions in rare manifestation of IA such as endocarditis or mycotic aneurysm. Here, we will review the role of surgical interventions in the treatment of different clinical manifestations of IA.

Primary gut aspergillosis in a patient with acute myeloid leukaemia: the importance of early suspicion and definitive treatment

Aspergillus infection is a known complication in immunocompromised patients, particularly in those with impaired neutrophil function. The pathophysiology of respiratory tract infection and disseminated disease are well understood, and guidelines exist for early detection and treatment. The gut has been speculated to be the potential portal of entry for Aspergillus, though previous case series outline that this is often discovered late and results in high morbidity and mortality. Early clinical suspicion, with definitive surgical intervention and antifungal treatment with voriconazole, can significantly increase the chances of survival. In this article, the authors discuss a case of primary gut aspergillosis with secondary dissemination in a patient with acute myeloid leukaemia who developed serious sequelae.

Microbiological food safety and a low-microbial diet to protect vulnerable people

Low-microbial diets are advised by many institutions for people with neutropenia resulting from treatment with immunosuppressive drugs or medical conditions that increase their susceptibility to foodborne disease. In this article, the main microbiological hazards associated with foods are outlined, and a low-microbial diet in which higher-risk foods are replaced by lower-risk foods is described.

Primary hepatic aspergillosis following induction chemotherapy for acute leukemia

Invasive aspergillosis (IA) contributes significantly to the burden of infectious complications in heavily immunosuppressed patients with acute leukemia. The infection is typically acquired via inhalation into the respiratory tract, and the lungs are most commonly involved. However, disseminated disease may occur and reports of isolated extrapulmonary infection suggest the gastrointestinal tract is likely an additional portal of entry for this organism. We describe a case of primary hepatic aspergillosis in a patient with acute myelogenous leukemia. The patient did not respond to medical therapy with antifungals and ultimately required surgical exploration and drainage. IA should be considered in an immunosuppressed patient with hepatic abscesses and may require a combined surgical and medical approach to therapy.

Retroperitoneal aspergilloma

We report a previously healthy 8-year-old boy who presented to the hospital with a palpable abdominal mass, fever and abdominal pain. CT and MRI scans confirmed a large mass that was centered in the retroperitoneum. The lesion was biopsied and the histology showed branching hyphae. Tissue cultures grew Aspergillus fumigatus and a diagnosis of aspergilloma was made. The immunological work-up did not reveal an immunodeficiency. This case is a unique presentation of aspergilloma presenting in an unusual location and in an immunocompetent patient.

Laboratory diagnosis of invasive aspergillosis: from diagnosis to prediction of outcome

Invasive aspergillosis (IA), an infection caused by fungi in the genus Aspergillus, is seen in patients with immunological deficits, particularly acute leukaemia and stem cell transplantation, and has been associated with high rates of mortality in previous years. Diagnosing IA has long been problematic owing to the inability to culture the main causal agent A. fumigatus from blood. Microscopic examination and culture of respiratory tract specimens have lacked sensitivity, and biopsy tissue for histopathological examination is rarely obtainable. Thus, for many years there has been a great interest in nonculture-based techniques such as the detection of galactomannan, β -D-glucan, and DNA by PCR-based methods. Recent meta-analyses suggest that these approaches have broadly similar performance parameters in terms of sensitivity and specificity to diagnose IA. Improvements have been made in our understanding of the limitations of antigen assays and the standardisation of PCR-based DNA detection. Thus, in more recent years, the debate has focussed on how these assays can be incorporated into diagnostic strategies to maximise improvements in outcome whilst limiting unnecessary use of antifungal therapy. Furthermore, there is a current interest in applying these tests to monitor the effectiveness of therapy after diagnosis and predict clinical outcomes. The search for improved markers for the early and sensitive diagnosis of IA continues to be a challenge.

Voriconazole hepatotoxicity in severe liver dysfunction

There are no studies regarding to these effects in patients with severe liver dysfunction.

OBJECTIVES

The aims of this study were to characterize voriconazole hepatotoxicity in patients with severe liver dysfunction and to compare it with a matched cohort treated with liposomal amphotericin B.

METHODS

This is an observational study, in which adults patients treated with at least 4 doses of voriconazole were included. Patients treated with liposomal amphotericin B were used as control group.

RESULTS

Sixty nine percent of patients treated with voriconazole showed changes in liver function tests (LFTs) during therapy. They showed elevated transaminases in 35%, cholestasis in 15% or a combination of both in 45%. According to the CTC classification, all patients with hepatotoxicity had a severe reaction. The Roussel Uclaf Causality Assessment Method score in all patients with hepatotoxicity was greater than 8. There was a correlation between initial loading dose greater than 300 mg (4.5 mg/kg) and the risk of hepatotoxicity (p < 0.001). The control group developed alterations in the LFTs in only 10.3% of patients.

CONCLUSION

Voriconazole should be used with caution in patients with severe liver dysfunction and following liver transplantation, with frequent monitoring of LFTs or using liposomal amphotericin B instead.

Infections in Leukemia and Hematopoietic Stem Cell Transplantation

Infections are one of the most common complications in patients diagnosed with leukemia and serve as a major obstacle to treatment. Through the early 1970s, infections were the most common cause of death in patients diagnosed with acute leukemia, but improvement in treatment and supportive care over the past few decades, coupled with expanded prophylaxis and prevention regimens, have led to reduction in both the frequency and severity of infections. Regardless, due in part to an aging cancer population and the diversity of cancer treatments and procedures, infectious diseases remain a major cause of morbidity and mortality in patients with leukemia.