Isolated colonic aspergillosis in an immunocompetent individual diagnosed by metagenomic next-generation sequencing: A case report

Abstract

BACKGROUND

Invasive aspergillosis (IA) is typically considered an opportunistic pulmonary infection in immunocompromised hosts. Its occurrence in immunocompetent individuals, particularly as an isolated infection of the lower gastrointestinal tract, is exceedingly rare. Such cases are frequently misdiagnosed as inflammatory bowel disease or other infectious enteritides, leading to delays in appropriate treatment. To the best of our knowledge, only 2 cases of primary (or isolated) intestinal aspergillosis (PA) have been reported in the English literature.

CASE SUMMARY

We report a case of a 48-year-old male, who previously underwent thyroidectomy for thyroid cancer but lacked the typical risk factors for IA. He presented to our hospital with refractory diarrhea accompanied by a 6 kg weight loss. Initial colonoscopy revealed erosions in the transverse colon. Routine blood tests and standard microbiological investigations (including bacterial cultures, parasite screening, and tuberculosis testing) were negative. Empirical antibiotic therapy and conventional symptomatic management proved ineffective. Ultimately, metagenomic next-generation sequencing (mNGS) of colonic biopsy tissue detected a relatively high abundance of Aspergillus fumigatus. Diarrhea ceased completely within 48 hours of initiating oral voriconazole therapy. A total treatment course of 12 days was administered, and the patient remained symptom-free during a 2-month follow-up period without recurrence.

CONCLUSION

For immunocompetent patients with refractory diarrhea, PA should be considered and mNGS-guided antifungals should be initiated.

Key Words: Invasive aspergillosis; Primary intestinal aspergillosis; Immunocompetent individual; Voriconazole; Metagenomic next-generation sequencing; Case report

Core Tip: This case report describes an unusual presentation of refractory diarrhea in a patient who was immunocompetent and had none of the usual risk factors. Despite comprehensive evaluations including endoscopy and histopathology, the etiology remained undetermined. Metagenomic next-generation sequencing (mNGS) identified Aspergillus fumigatus, guiding successful targeted treatment. This highlights the necessity of considering primary intestinal aspergillosis (PA) in certain patients and demonstrates the diagnostic value of mNGS for rare fungal enteritis. Although publication bias may exist, accumulating case reports support considering PA when diagnosing unexplained diarrhea. Furthermore, the use of mNGS is justified when conventional diagnostic methods are inconclusive.

INTRODUCTION

Invasive aspergillosis (IA) is a life-threatening fungal infection caused by environmental fungi, predominantly Aspergillus fumigatus (A. fumigatus), which are ubiquitous in soil and dust. The incidence of IA has increased with the rise of organ transplantation, chemotherapy, and use of high-dose corticosteroids or immunosuppressants. Infections with other species, such as Aspergillus niger and Aspergillus flavus, are also becoming more common[1,2]. In immunocompromised individuals, airborne Aspergillus species can colonize the sinuses or lungs, leading to invasive sinonasal or pulmonary disease. Intestinal aspergillosis usually results from hematogenous dissemination from a primary pulmonary or alternative fungal focus, specifically affecting a compromised intestinal mucosal barrier. Direct colonization of the compromised intestinal mucosa via ingestion of contaminated food or environmental spores is a rare occurrence[3]. Primary intestinal aspergillosis (PA) in immunocompetent individuals without traditional risk factors is exceptionally rare. Its infrequent occurrence means that is rarely considered in the differential diagnosis of abdominal pain, distension, and diarrhea, rendering clinical diagnosis extremely challenging[4].

The current case study illustrates that PA should be considered in immunocompetent individuals with persistent diarrhea, even without classic risk factors. It also suggests that metagenomic next-generation sequencing (mNGS) is a useful diagnostic tool for cases of unexplained chronic diarrhea. These findings offer new insights for clinical diagnosis and treatment.

CASE PRESENTATION

Chief complaints

A 48-year-old male was admitted to our department due to persistent diarrhea for more than 50 days accompanied by a weight loss of 6 kg.

History of present illness

He had been hospitalized in our unit earlier in the disease course for right upper abdominal pain and watery diarrhea (5-7 episodes per day) lasting 1 week. Routine laboratory tests at that time showed no abnormalities; however, colonoscopy revealed erosions and multiple polyps in the transverse colon. Endoscopic and histopathological findings of transverse colon biopsies are presented in the Endoscopy and Pathology section. Consequently, the patient was treated symptomatically and underwent endoscopic polypectomy. He was discharged after partial relief of diarrhea, and was prescribed loperamide, Bacillus licheniformis, and esomeprazole for ongoing abdominal pain and loose stools. Despite this regimen, his diarrhea not only persisted but worsened to over 10 episodes daily, with a total weight loss of 6 kg occurring over more than 2 months. Following unsuccessful management at a local hospital, he was readmitted to our department. Conventional therapy for diarrhea and abdominal pain was provided, and the patient was treated with empirical quinolone antibiotics for more than 3 days; however, his diarrheal symptoms showed no signs of improvement. Despite a repeat colonoscopy and biopsy for histopathological evaluation, the underlying reason for the diarrhea could not be identified. Furthermore, during hospitalization, comprehensive workup confirmed the absence of an underlying immunodeficiency.

History of past illness

The patient had undergone a right radical thyroidectomy 2 years prior to treat papillary thyroid carcinoma and required daily levothyroxine sodium to treat post-operative hypothyroidism. The patient did not have the classic risk factors for IA, including neutropenia, active cancer, high-dose chemotherapy, a history of IA, or a history of allogeneic transplantation, graft-vs-host disease, and cytomegalovirus infection. Similarly, he had no history of conditions that could damage the intestinal mucosal barrier, such as severe burns, abdominal surgery, or inflammatory bowel disease (IBD).

Personal and family history

The patient, a seafood market employee, had no history of unsanitary dietary exposure, no similar symptoms among close contacts, and no recent travel to endemic regions. Additionally, he had no history of smoking or alcohol consumption, and no significant family medical history.

Physical examination

Upon admission, the patient’s vital signs were within normal ranges, and his cardiopulmonary exam was unremarkable. The abdomen was soft, non-distended, and mildly tender to deep palpation of the middle and lower quadrants without rebound tenderness.

Laboratory examinations

Routine laboratory findings were largely unremarkable (Table 1), including complete blood count, procalcitonin, C-reactive protein, liver and renal function markers, tumor markers, immune-related antibodies, and negative human immunodeficiency virus (HIV). A single electrolyte panel showed hypokalemia (potassium 3.47 mmol/L; normal range: 3.5-5.2 mmol/L). The routine stool test showed positivity for white blood cells, suggestive of an inflammatory component; however, routine bacterial cultures, parasite screening, and fungal cultures all yielded negative results. Crucially, specific fungal biomarkers, including serum (1,3)-β-D-glucan and galactomannan antigen, tested negative. Comprehensive immunological profiling, including quantitative assessment of immunoglobulins [IgG, IgM, IgA, IgE and specific IgE (commonly known as sIgE) to A. fumigatus] and lymphocyte subset analysis, was not performed as the patient's clinical presentation and initial laboratory workup did not suggest an underlying immunodeficiency.

Table 1 Laboratory findings on admission.

Laboratory testing	Results	Reference values	Units
Inflammatory markers
CRP	< 10.0	0-10	mg/mL
PCT	< 0.05	< 0.5	ng/mL
Complete blood count
WBC	4.76	3.5-9.5	× 109/L
HB	150	130-175	g/L
PLT	206	125-350	× 109/L
NEUT	2.31	1.8-6.3	× 109/L
LYMPH	1.94	1.1-3.2	× 109/L
EO	0.06	0.02-0.52	× 109/L
BASO	0.03	0-0.06	× 109/L
Biochemistry
ALT	10.5	7-50	U/L
AST	12.1↓	13-40	U/L
Albumin	48.1	40-55	g/L
Creatinine	62.4	53-115	μmol/L
Sodium	140	137-147	mmol/L
Potassium	3.47↓	3.5-5.3	mmol/L
Stool examination
Parasite	Negative	Negative	-
WBC	Positive	0-1	-
Fungal culture	Negative	Negative	-
FOBT	Negative	Negative	-
Fungal serology
(1,3)-β-D-glucan	< 37.55	< 70	pg/mL
Galactomannan antigen	0.12	≤ 0.5	S/CO
Tumor markers
CEA	3.37	< 5.0	ng/mL
AFP	1	< 7	ng/mL
Tuberculosis
T-SPOT.TB	Positive	Negative	-
γ-IFN	378.0 ↑	< 14	pg/mL
HIV Ag-Ab	Negative	< 1.00	AU/mL
Auto-antibodies
ANA	Negative	Negative	-
dsDNA	Negative	Negative	-
ANAs	Negative	Negative	-
Voriconazole trough level	2.8	1-5.5	μg/mL

γ-IFN: Interferon-gamma; AFP: Alpha-fetoprotein; ALT: Alanine aminotransferase; ANA: Antinuclear antibody; ANAs: Antinuclear antibody profile; AST: Aspartate aminotransferase; BASO: Basophil count; CEA: Carcinoembryonic antigen; CRP: C-reactive protein; dsDNA: Double-stranded DNA; EO: Eosinophil count; FOBT: Fecal occult blood test; HB: Hemoglobin; HIV Ag-Ab: Human immunodeficiency virus antigen-antibody; LYMPH: Lymphocyte count; NEUT: Neutrophil count; PCT: Procalcitonin; PLT: Platelet count; T-SPOT.TB: T-cell spot test for tuberculosis; WBC: White blood cell.

Imaging examinations

Chest and upper abdominal computed tomography scans were unremarkable. Two sequential colonoscopies demonstrated progressive worsening of colonic erosions (Figure 1), with corresponding histopathological analyses of transverse colon biopsies confirming advancing inflammation on both occasions (Figure 2). However, the biopsy tissues from both pathological examinations were not subjected to periodic acid-Schiff (commonly referred to as PAS) or Grocott's methenamine silver (commonly referred to as GMS) staining.

Figure 1 Electronic colonoscopy images on two occasions. A: On day 8 of diarrhea, electronic colonoscopy (arrows) revealed a patchy erosion measuring approximately 4 mm × 3 mm in the transverse colon (hepatic flexure) (obtained by an experienced endoscopist). Image resolution is limited solely due to suboptimal bowel preparation; however, the colonic erosion remains discernible. The location of the erosion corresponded to the presentation of right upper quadrant pain; B and C: On day 64 of diarrhea, multiple erosions were observed in the ascending colon (arrows in B) and the transverse colon (arrows in C). Compared to panel A, the area of colonic mucosal erosion shown in panels B and C had significantly enlarged, which was consistent with the worsening diarrhea symptoms.

Figure 2 Pathological images. A: The biopsy specimen from the transverse colon mucosa on day 8 of diarrhea shows chronic inflammation, characterized by a diffuse infiltrate of lymphocytes and plasma cells in the lamina propria, accompanied by lymphoid hyperplasia and stromal edema (arrows). This suggests that the patient may have had a persistent, long-term asymptomatic inflammatory reaction in the transverse colon even before the onset of diarrhea; B: The biopsy specimen from the transverse colon mucosa on day 64 of diarrhea reveals moderate chronic inflammation, with an increased density of lymphocytes and plasma cells in the lamina propria, accompanied by mild active inflammation as evidenced by the presence of scattered neutrophils in the colonic mucosa (arrows). No caseous necrosis or granulomatous lesions are observed. Compared with panel A, the mucosal inflammation in panel B shows a tendency of progression; however, neither panel A nor panel B supports diagnoses such as intestinal tuberculosis or inflammatory bowel disease.

Genetic testing

Because previous examinations failed to identify a cause of the patient's diarrhea, we subsequently analyzed mucosal biopsy tissue from the transverse colon using mNGS during the second colonoscopy. On day 69 of diarrhea, mNGS identified 2958 sequences of Aspergillus (a relatively high abundance), with 383 identified as A. fumigatus with 99% confidence, implicating this species as the causative pathogen. The sequencing results for the strain are available through the National Center for Biotechnology Information (NCBI) repository, registered under the accession number PRJNA1333823 (https://www.ncbi.nlm.nih.gov/sra/PRJNA1333823).

FINAL DIAGNOSIS

Based on the patient’s comprehensive profile (detailed above), we suspected that he had developed PA.

TREATMENT

A biopsy of the transverse colon mucosa revealed a high abundance of A. fumigatus by mNGS. In line with the patient’s clinical profile and the Australasian Antifungal Guidelines Steering Committee’s Consensus guidelines for the diagnosis and management of invasive aspergillosis, 2021[5], we initiated presumptive antifungal therapy with oral voriconazole. The dosing regimen consisted of a loading dose of 6 mg/kg every 12 hours on day 1, followed by a maintenance dose of 4 mg/kg every 12 hours. Trough voriconazole levels were monitored and remained within the recommended therapeutic range at 2.8 μg/mL[6]. The complete cessation of diarrhea within 48 hours strongly indicated A. fumigatus as the causative pathogen rather than a colonizer or contaminant. The patient was discharged on oral voriconazole (4 mg/kg every 12 hours) to ensure continued therapeutic efficacy.

OUTCOME AND FOLLOW-UP

Voriconazole was discontinued 1 week post-discharge during an outpatient visit, as the patient’s abdominal discomfort had resolved and blood tests were normal. Six weeks after cessation of medication, there was no recurrence of abdominal pain or diarrhea, and nutritional status had recovered. Trough voriconazole level at follow-up was 0.1 μg/mL.

DISCUSSION

The incidence of IA is increasing with the wider use of small molecule-targeted inhibitors and immunotherapies[7]; however, its early diagnosis remains challenging. Although current guidelines regard histopathological examination and culture as the diagnostic gold standard[5,8], histopathology is invasive and obtaining suitable specimens can be difficult. Blood and tissue cultures are time-consuming, lack sensitivity, and offer limited value for early diagnosis. Because intestinal infections have non-specific symptoms and lack distinct imaging findings, fungal stains like PAS or GMS are not routinely ordered during initial histopathological evaluation, which prioritize common conditions such as IBD, intestinal tuberculosis, and polyps. Thus, diagnosing PA in immunocompetent individuals who lack traditional risk factors is challenging. Of note, the diagnosis often relies on evidence from non-culture-based techniques, coupled with a positive response to diagnostic antifungal therapy and absence of relapse during follow-up.

mNGS has emerged as a powerful technology over the past decade, showing promise for closing diagnostic gaps in invasive fungal diseases (IFDs)[9], although it has yet to be incorporated into major IFD management guidelines. To date, only 1 case of intestinal aspergillosis diagnosed by mNGS has been reported[10]. The use of mNGS was a critical and beneficial tool for our case. The diagnostic process was complicated due to several confounding factors. First, the patient was immunocompetent, as evidenced by a normal peripheral lymphocyte count, negative HIV serology, absence of autoantibodies, and no relevant medical or pharmacological history. Although specific immunoglobulin and lymphocyte subset analyses were not tested, the collective clinical data showed no indication of an underlying immunodeficiency. Second, the case presented with atypical symptoms, a lack of relevant imaging findings, and negative results from both culture-based and non-culture-based assays for fungal growth and biomarkers (e.g., serum galactomannan testing). Ultimately, mNGS detected a high level of A. fumigatus, guiding the correct treatment. This supports the conclusion by Ye et al[10] that mNGS should be considered a diagnostic option for IA and other rare IFDs.

Beyond the diagnostic challenge, the pathogenesis occurring in this immunocompetent individual (host) was intriguing. We hypothesize that chronic occupational exposure to A. fumigatus conidia, combined with pre-existing mucosal damage, triggered a localized immunopathological response. Carbohydrates in the fungal cell wall are known to act as intrinsic adjuvants that drive a Th2-biased response[11]. Furthermore, repeated exposure has been shown to induce a complex co-evolution of Th1, Th2, and Th17 responses[12-14]. Thus, the progressive colonic inflammation in our patient had likely resulted from such a dysregulated local immune reaction: An "immune misdirection", whereby the host's response, rather than a fungal invasion, became the primary driver of tissue injury. Nonetheless, the lack of specific immunologic profiling for our case remains a limitation that will need to be included in future investigations of other similar cases, if possible.

To systematically contextualize the rarity and distinctive features of our case, we conducted a structured literature review. We searched PubMed for English-language case reports and series published up to August 2025 using the following query: ("intestinal aspergillosis" OR "colonic aspergillosis" OR "gastrointestinal aspergillosis") AND ("immunocompetent" OR "non-immunocompromised"). We excluded cases with classic immunosuppression (e.g., hematologic malignancy, solid organ transplantation, advanced HIV/acquired immune deficiency syndrome, or prolonged high-dose corticosteroids). This targeted search and screening process identified only two prior cases that met these criteria fully[3,15], unequivocally confirming the exceptional rarity of PA in immunocompetent hosts.

Cha et al[3] reported the first case of lower gastrointestinal aspergillosis in an immunocompetent individual lacking typical risk factors. The authors theorized that the patient’s immune system may have been compromised by their stay in the intensive care unit, use of piperacillin-sulbactam, and mechanical ventilation. They compared these factors to the previously reported non-classic risk factors identified for invasive pulmonary aspergillosis found in critically ill patients prior to 2015. They proposed that these factors, along with hyperglycemia in diabetes, can impair immune responses and contribute to invasive gastrointestinal aspergillosis.

Díaz Alcázar et al[15] also reported the case of a 72-year-old immunocompetent patient who rapidly developed systemic aspergillosis affecting the nervous system, responded poorly to antifungal therapy, and ultimately died. The patient in our case was middle-aged. Despite refractory diarrhea lasting more than 60 days and endoscopic evidence of progressive intestinal involvement, his disease remained confined to the lower gastrointestinal tract. He also lacked any of the non-classic risk factors identified by Díaz Alcázar et al[15] or a history of diabetes. We hypothesize that younger age explains his milder symptoms and localized disease compared to the case reported by Díaz Alcázar et al[15]. We speculate that long-term occupational exposure in a seafood market, an environment conducive to fungal proliferation, represents a non-traditional risk factor for this case. However, this hypothesis requires further validation through more reports or experimental investigations.

A comprehensive 2021 literature review by Yelika et al[4] established that this condition almost invariably occurs as part of a disseminated infection in severely immunocompromised hosts. Furthermore, cases reported since 2021 have continued to adhere to this pattern[10,16-20]. In contrast, our case represents a definitive exception to this established clinical paradigm, being characterized by the absence of any underlying immunodeficiency or evidence of extraintestinal dissemination - underscoring its unique status as a localized primary gastrointestinal infection in an immunocompetent individual.

The management of IA rests on three pillars: Antifungal therapy (prophylactic, empirical, or targeted), surgical intervention (e.g., drainage), and reversal of predisposing conditions. For patients without immunosuppression, successful outcome largely depends on early diagnosis[5]. A significant proportion of reported cases progressed to systemic aspergillosis of varying severity due to delayed diagnosis and treatment. In all instances, central nervous system involvement proved fatal. Previous case reports[15,21,22] have demonstrated that IA has a high mortality rate and that early diagnosis and timely therapeutic intervention are of critical importance. Existing guidelines strongly recommend initiating empirical antifungal therapy as early as possible, based on the patient's clinical condition, when there is a high suspicion of fungal infection[5].

Although our patient did not develop disseminated disease or severe sequelae, it is important to note that prolonged diarrhea can lead to shock, electrolyte imbalances, acid-base disturbances, and even life-threatening complications. Therefore, we identified several periods for prescribing empirical antifungal therapy before making a definitive diagnosis. First, following the early initiation of symptom-based treatment and resolution of potentially confusing coexisting conditions (e.g., intestinal polyp removal), the patient’s diarrhea briefly improved, only to then undergo dramatic exacerbation. Second, another key consideration was the patient's long-term occupational exposure in a fungus-prone environment and endoscopic evidence of mucosal barrier damage. Third, there was a lack of improvement of diarrhea after more than 3 days of empirical antibiotic therapy. Even though such cases are exceedingly rare for physicians to encounter, these three clues should prompt consideration of empirical antifungal therapy. Otherwise, as speculated by scholars like Li et al[21], delayed IA diagnosis and treatment can cause secondary hematogenous dissemination at any time, potentially leading to severe complications or death.

For our case, the duration of antifungal therapy to treat IA was notably shorter than the courses reported for other cases in the existing literature[3,10], where treatment was continued until complete resolution of symptoms and normalization of laboratory parameters. Currently, no definitive guidelines are established for the optimal treatment duration and management is individualized based on the patient’s clinical response and immune status[5,10]. In our patient, who was immunocompetent, the abdominal symptoms resolved completely within 48 hours and did not recur, eliminating the need for a prolonged therapy aiming to support immune recovery or manage comorbidities. Thus, the shorter course was deemed sufficient. Regardless, future case studies are needed to establish more definitive evidence for treatment duration.

The preferred first-line treatment for the vast majority of patients with IA is voriconazole (intravenous or oral), being in accordance with guidelines[5,23-25]. Although oral voriconazole demonstrated remarkable efficacy in our case, alternative strategies may be considered for others in similar clinical scenarios. For example, patients with severe disease, oral intolerance, or concerns regarding drug absorption, should be provided the option of intravenous formulations for induction therapy; of note, intravenous voriconazole remains the primary recommended agent[5]. Alternative intravenous options include isavuconazole, amphotericin B, caspofungin, and micafungin. For long-term maintenance therapy in outpatient settings, such as for subacute invasive pulmonary aspergillosis, oral triazoles (e.g., voriconazole or itraconazole) are generally preferred over intravenous formulations. Regardless, drug selection must be guided by local availability, cost, patient comorbidities, and monitoring capacity. Oral voriconazole represents an optimal and guideline-recommended choice for oral-tolerant patients with localized disease. Clinicians need to remain familiar with alternative intravenous induction regimens and other oral azoles for maintenance therapy, however, to facilitate individualized treatment planning.

CONCLUSION

This case highlights that A. fumigatus can cause persistent diarrhea even in immunocompetent individuals without classic risk factors. Occupational exposure and mucosal injury are potential contributing factors. mNGS proved transformative in diagnosing this rare fungal enteritis. For unexplained diarrhea, tissue mNGS should be considered early when routine tests are negative and empirical antibiotic therapy fails. Empirical antifungal therapy should be started in a timely fashion when diarrhea remains refractory despite conventional diagnostic and therapeutic approaches.

ACKNOWLEDGEMENTS

We would like to extend our sincere gratitude and appreciation to all of the medical personnel of the 900^th Hospital of PLA Joint Logistic Support Force who contributed to the care of this patient. We would also thank the patient and his family for allowing us to share in his experience for the betterment of all those who come after him in facing a similar health crisis.