Diagnosis and Treatment of Chronic Skin Infection Caused by Scedosporium apiospermum

Summary

This case report presents a rare skin infection caused by Scedosporium apiospermum in an immunosuppressed patient that was successfully diagnosed using next-generation sequencing and treated with surgical debridement and voriconazole.

Abstract

This case report presents a 77-year-old male with purplish-red, blister-like lesions on the right forearm. A background of long-term corticosteroid therapy for pemphigus led to significant immunosuppression. Initial laboratory investigations, including bacterial and fungal cultures as well as histopathological analysis, yielded inconclusive results. To identify the causative pathogen, next-generation sequencing (NGS) was performed on tissue samples, which confirmed the presence of Scedosporium apiospermum, a rare opportunistic fungus. Based on this result, a targeted treatment strategy was implemented, involving multiple surgical debridements and systemic antifungal therapy with voriconazole. The therapeutic response was favorable, with complete resolution of the infection and no signs of recurrence during an 8-month follow-up period. This case highlights the clinical value of NGS in diagnosing rare and atypical infections, particularly in immunocompromised settings where conventional methods may fail. It also underscores the importance of a multidisciplinary treatment approach that integrates timely surgical intervention with appropriate antifungal therapy to achieve optimal patient outcomes.

Introduction

Skin and soft tissue infections (SSTIs) are among the most frequently encountered conditions in clinical practice, leading to repeated outpatient visits, prolonged hospitalizations, long-term disability, and even mortality. The incidence of SSTIs continues to rise annually, with severe cases often requiring a combination of aggressive surgical intervention and broad-spectrum antimicrobial therapy¹.

Although dozens of pathogens may be involved in SSTIs, bacterial infections remain the most common. However, in recent years, the increasing prevalence of geriatric comorbidities and widespread use of immunosuppressive therapies have contributed to a notable rise in opportunistic fungal infections². These infections are frequently challenging to diagnose and manage, particularly because their clinical manifestations often overlap with those of bacterial or viral etiologies. While some fungal pathogens exhibit distinctive features, most cutaneous infections present with non-specific symptoms, underscoring the need for early and accurate pathogen identification.

Traditional diagnostic techniques, including culture and histopathology, often lack sensitivity or require prolonged turnaround times. In contrast, NGS offers an unbiased and rapid method of pathogen detection. NGS can detect low-abundance organisms with a sequencing depth typically ranging from 10⁶-10⁷ reads per sample and can identify rare or unexpected pathogens, even when conventional methods fail³. Nevertheless, NGS also has limitations, including high cost, potential for detecting non-pathogenic colonizers, and the need for specialized data interpretation.

Here, this report presents a rare case of cutaneous infection caused by Scedosporium apiospermum (S. apiospermum), initially manifesting as non-specific purplish-red macules and ultimately diagnosed through NGS technology. A review of the diagnostic and therapeutic process provides insights into the clinical management of similar infections.

CASE PRESENTATION:
A 77-year-old male presented to our hospital with progressively enlarging skin lesions on his right hand for more than 20 days, which broke down for 10 days. The patient unintentionally noticed two black skin lesions of rice-size on the dorsal surface of the right forearm, located at the proximal and distal ends of the forearm about 5 cm from the wrist, without local erythema, swelling, pain, or ulceration. About 2 weeks ago, before the patient visited the hospital, the lesions gradually increased to the size of a bean, and a clear fluid appeared inside. About 10 days before the visit, the lesions broke down, with yellow watery fluid flowing out, turning into blood-like exudates, without local inflammation. The patient repeatedly went to the local hospital to receive symptomatic treatment, such as antiseptic dressing, lighting, vitamin supplementation, and cephalosporin anti-infection, but obtained no improvement. Conversely, the patient developed moderate pitting edema in both lower extremities, and subsequently, the right forearm became swollen. The precise operation of the hand was affected, and the skin temperature around the lesions increased. Eventually, the patient was referred to the hospital.

The patient, a farmer with long-term residence in rural areas, had a 1-year history of pemphigus and was receiving oral methylprednisolone at a dose of three tablets per day. Three months prior, disease recurrence occurred during dose tapering, leading to a 1-week hospitalization. Following discharge, oral methylprednisolone was resumed at ten tablets per day, with a tapering schedule of one tablet per week, reaching a dose of 5.5 tablets 4 days before presentation.

Physical examination revealed two large ruptured lesions on the right forearm, accompanied by localized erythema, swelling, elevated skin temperature, tissue necrosis, and clear fluid exudation, along with impaired fine motor function of the fingers (Figure 1). Pitting edema was observed in both lower extremities, while other findings were unremarkable. Laboratory tests indicated mildly elevated leukocyte levels at 10.8 × 10⁹/L (normal: 4-10 × 10⁹/L), with neutrophil predominance (78%), and a normal high-sensitivity C-reactive protein (hs-CRP) level of 3.5 mg/L (normal <10 mg/L). Exudate from the lesion was collected for bacterial culture, which indicated a small amount of Scedosporium apiospermum. However, due to the environmental ubiquity of this fungus⁴, the result was initially considered contamination, particularly as no bacteria were detected in a separate culture of exudate from the same lesion. Magnetic resonance imaging (MRI) of the right forearm revealed diffuse high signal intensity on T2-weighted images, suggesting the presence of infection (Figure 2).

Then, empirical cephalosporin antibiotic treatment was given, and the hormone use was adjusted to methylprednisolone injection 20 mg per day, and a debridement procedure was performed. The specimen obtained during the surgery was cultured for bacteria and subjected to pathology. Out of three separate surgical tissue samples cultured, none yielded bacterial growth, and histopathology indicated granulomatous inflammation with central granulocytic microabscesses. After a dermatology consultation, further pathogen identification was recommended.

A second debridement procedure was performed, and tissue culture identified Pseudomonas aeruginosa. The antibiotic regimen was subsequently adjusted to etimicin (150 mg) in combination with cefminox (2 g twice daily) for anti-infective therapy. Following this intervention and further debridement, localized necrosis and infection of the wound gradually improved. Skin grafting was eventually performed successfully, and the patient was discharged with ongoing medication.

However, shortly after discharge, a pustular rash resembling the initial presentation reappeared on the right forearm, progressively enlarged, and ulcerated (Figure 3), necessitating a second hospitalization. Laboratory tests at readmission showed leukocytes at 11.0 × 10⁹/L (77% neutrophils) and hs-CRP of 4.0 mg/L. MRI revealed progression of the infectious lesion compared to earlier imaging. To identify the causative pathogen, multiple diagnostic tests were conducted on surgically obtained tissue samples, including bacterial culture, tuberculosis testing, fungal culture, next-generation sequencing (NGS) (Table 1), and histopathological examination (Figure 4). The bacterial culture again identified Scedosporium apiospermum, while the fungal culture yielded negative results. Histopathology and immunohistochemistry indicated a suspected fungal infection. NGS confirmed a definitive S. apiospermum infection.

Based on these findings, consultation with the infectious disease department was undertaken, and combined therapy with voriconazole and surgical debridement was initiated. Drug levels were monitored regularly throughout the course of treatment. Following the seventh debridement, the patient was successfully discharged. At 8-month follow-up, no recurrence was observed, and the sensory and motor function of the right upper limb had fully recovered (Figure 5 and Figure 6).

Diagnosis, Assessment, and Plan:
The initial assessment included physical examination, laboratory tests, and imaging (MRI). Bacterial culture of exudate identified S. apiospermum, but the results were treated as contaminants. Repeated debridements and cultures yielded mixed or negative results. Histopathology was non-specific. Ultimately, NGS confirmed the diagnosis. The treatment plan included multiple debridements, adjusted antibiotics, and voriconazole. Regular monitoring of drug levels was conducted.

Protocol

The surgical procedure was approved and conducted per the hospital's ethical committee guidelines.Informed consent was obtained from all individual participants included in the study.

1. Initial evaluation and sample collection

1. Perform a comprehensive inspection of the affected skin, focusing on signs of erythema, swelling, ulceration, necrosis, and purulent discharge.
   NOTE: Record baseline visual assessment (photos, dimensions) and document initial clinical signs (erythema, edema).
2. Record a complete medical history, including the use of immunosuppressive agents (e.g., corticosteroids, chemotherapy, biologics), and document comorbidities such as diabetes, peripheral vascular disease, or recent trauma.
3. Collect wound exudate using a sterile swab. Swab the base and margins of the ulcer by rotating the swab gently for at least 5 s. Immediately place the swab into Amies transport medium and store at 4 °C. Confirm sample quality visually (adequate exudate on swab); if inadequate, repeat sampling immediately.
   NOTE: Ensure transport to the microbiology lab within 2 h. If delayed, process within 24 h under refrigerated conditions.

2. Imaging and empirical treatment

1. Perform MRI using T1-weighted, T2-weighted, and contrast-enhanced fat-suppressed sequences to evaluate soft tissue integrity and rule out osteomyelitis.
   NOTE: Absence of deep-tissue fluid collections, abscess formation, or osteomyelitis confirmed radiologically.
2. Administer intravenous ceftriaxone at 2 g in 100 mL of normal saline over 30 min once daily as empirical antibiotic therapy.
   NOTE: Adjust antibiotics based on local antibiogram and culture results.
3. Taper corticosteroids by 25-50% under the supervision of an attending physician. Monitor for signs of adrenal insufficiency and infection rebound.
   NOTE: Regular evaluation of clinical symptoms (fatigue, nausea, hypotension) and cortisol levels is required, if clinically indicated.

3. Surgical debridement procedures

1. In the operating room under sterile conditions, excise visibly necrotic or infected tissue using a scalpel and bipolar electrocautery set at 30-40 W for soft tissue cutting. Visually confirm removal of all visibly necrotic tissue until healthy bleeding margins are achieved.
2. Collect at least three tissue specimens from distinct regions (central ulcer base, ulcer margin, and deep tissue). Place each in sterile, labeled containers for microbiological and histopathological analysis.
   NOTE: Tissue samples must be visually confirmed to represent distinct tissue regions (healthy margin, necrotic center, deep subcutaneous).
3. Schedule repeat debridements every 48-72 h based on the clinical appearance of the wound, presence of necrosis, granulation tissue formation, CRP levels (>10 mg/L), and leukocyte count (>10 × 10⁹/L).
   NOTE: Observe and document progressive granulation tissue formation (>50% of wound bed), reduced edema, declining CRP (<10 mg/L), and leukocyte counts (<10 × 10⁹/L).

4. Pathogen identification and NGS testing

1. Stain tissue sections using Gram and Grocott's methenamine silver (GMS) stains. Incubate for 30 min at room temperature. Stain tissue sections using Gram stain (crystal violet, 0.5% w/v, followed by Gram's iodine, 1% w/v, and counterstain with safranin, 0.25% w/v) and Grocott's methenamine silver (GMS) stain according to standard protocols. Incubate the sections with the staining reagents for 30 min at room temperature.
2. Extract total DNA using a commercial kit following the standard protocol: lyse tissue in 180 µL of tissue lysis buffer (ATL buffer) and 20 µL of Proteinase K, incubate at 56 °C for 1-3 h. Measure DNA concentration (>10 ng/µL) and purity (A260/A280 ratio between 1.7-2.0) spectrophotometrically.
3. Perform next-generation sequencing (NGS) on an appropriate platform using validated microbial panels.
   1. Extract DNA from tissue samples using a DNA Mini Kit following the manufacturer's protocol. Quantify DNA using a dsDNA HS Assay Kit and normalize input to 1 ng/µL. Prepare sequencing libraries using a DNA Library Prep Kit.
   2. Load libraries on an Illumina MiSeq platform (2 × 150 bp paired-end mode) using a Reagent Kit. Select Generate FASTQ from the control software run setup screen, and set the cluster density target to 800-1,200 K/mm².
   3. After sequencing, perform base calling and demultiplexing using bcl2fastq software with default parameters. Filter reads with Q30 > 85%.
   4. Import FASTQ files into a data analysis and visualization software. Use the Map Reads to Reference function with the following parameters:
      Reference: Scedosporium apiospermum genome
      Mismatch cost = 2, Insertion cost = 3, Deletion cost = 3
      Length fraction = 0.9, Similarity fraction = 0.95
      Enable Map paired reads and select Global alignment.
   5. Use Create Sequencing QC Report to check depth and uniformity of coverage. Confirm diagnosis only when >95% sequence identity is achieved with ≥10× read coverage across the mapped genome.
   6. Include a positive control (Candida albicans genomic DNA) and a negative control (blank extraction) in each sequencing run to exclude contamination or false positives.
      NOTE: Successful sequencing run with adequate coverage (>10×) and pathogen identification meeting diagnostic criteria.

5. Antifungal therapy

1. Reconstitute voriconazole in 100 mL of 0.9% saline. Infuse 6 mg/kg intravenously over 1-2 h every 12 h for 2 doses, then 4 mg/kg every 12 h as maintenance.
2. Collect blood 30 min prior to the 5^th maintenance dose. Measure voriconazole trough concentration using LC-MS/MS standard protocols (Figure 7).
   NOTE: Adjust dose to maintain therapeutic trough levels of 1.0-5.5 µg/mL.
3. Continue antifungal therapy for the duration of hospitalization. Monitor treatment efficacy via CRP, procalcitonin, radiological improvement, and clinical status (e.g., fever, edema resolution).
   NOTE: Achieve radiological improvement (MRI: reduction in inflammatory edema), normalization of CRP/procalcitonin (<0.5 ng/mL), and clinical resolution of fever and local infection symptoms.

6. Recovery and follow-up

1. Proceed with split-thickness skin grafting (0.015-0.020 inch) using an air dermatome once the wound bed is sterile and granulation tissue is visibly healthy.
   NOTE: Wound bed confirmed sterile (negative repeat culture), granulation tissue covers >90% of wound area, and no visible infection signs prior to grafting.
2. Schedule outpatient follow-up at 1, 2, and 4 weeks post-discharge, then monthly for 6 months. Assess for recurrence, healing progression, pain (using VAS), and functional outcomes (e.g., joint mobility).
   NOTE: Document wound size reduction (weekly), complete re-epithelialization within the expected timeline (<8 weeks), improved functional status (joint mobility ≥ 80% baseline), and pain reduction (VAS ≤ 3).
3. Record all clinical parameters, including wound size reduction, infection markers, MRI findings, and treatment duration. Store anonymized patient data in a secure case report form for analysis and publication.
   NOTE:Final outcomes recorded and reviewed monthly, confirming maintained wound closure, absence of infection recurrence at 6-month follow-up, and documented patient satisfaction and functional restoration.

Results

A 77-year-old male with a history of pemphigus under long-term methylprednisolone therapy presented with progressive skin lesions on his right forearm. Initial evaluation, including physical examination (Figure 1) and MRI (Figure 2), revealed two ulcerated lesions with surrounding tissue edema and suspected deep soft tissue infection. Routine exudate culture detected Scedosporium apiospermum, but this was initially regarded as environmental contaminatio...

Discussion

Skin is frequently exposed to pathogens, including bacteria, fungi, viruses, rickettsia, and parasites, with Staphylococcus aureus and β-haemolytic streptococci remaining the predominant causes of infection⁵. In recent decades, fungal skin infections have increased significantly, with mortality rates exceeding 50% among susceptible populations⁶. Scedosporium apiospermum, in particular, is recognized as a significant human fungal pathogen

Materials

List of materials used in this article

Name	Company	Catalog Number	Comments
Bipolar electrocautery	BAISHENG	20173251560
Ceftriaxone	Roche	H10983036
CLC Genomics Workbench	Qiagen	v23.0	Data analysis and visualizaion software
Corticosteroids	Pfizer	Hj20170197
DNeasy Blood & Tissue Kit	Qiagen	https://www.qiagen.com/us/products/discovery -and-translational-research/dna -rna-purification/dna-purification /genomic-dna/dneasy-blood-and -tissue-kit
Labeled containers	3L	N/A
MiSeq	Illumina	https://www.illumina.com/systems/ sequencing-platforms/miseq.html	NGS
MiSeq Control Software	Illumina	https://www.illumina.com/systems/ sequencing-platforms/miseq.html
MiSeq Reagent Kit v3	Illumina	https://www.illumina.com/products/ by-type/sequencing-kits/cluster-gen -sequencing-reagents/miseq- reagent-kit-v3.html
MRI	SIEMENS	3146466
Nextera XT DNA Library Prep Kit	Illumina	https://www.illumina.com/products /by-type/sequencing-kits/library- prep-kits/nextera-xt-dna.html	DNA Library Prep Kit
QIAamp DNA Mini Kit	Qiagen	51304	DNA extraction kit
Qubit dsDNA HS Assay Kit	Thermo Fisher Scientific	https://www.thermofisher.com/in/en /home/industrial/spectroscopy- elemental-isotope-analysis/ molecular-spectroscopy/fluorometers /qubit/qubit-assays.html?ef_id=: G:s&s_kwcid=AL!3652!10!775157 26968096!!!!77515743318006!!3 80468453!1240249321530142& cid=bid_pca_aqb_r01_co_cp1359_pj t0000_bid00000_0se_bng_bt_pur_con
Scalpel	JZ	20140019
Sterile swab	Meidike Gene	MWS001
Voriconazole	Pfizer	H20150168