Pulmonary parenchymal involvement caused by Tropheryma whipplei

Application of metagenomic next-generation sequencing in the diagnosis and treatment of acute pneumonia caused by Tropheryma whipplei

OBJECTIVE

The treatment plan and process for acute pneumonia caused by Tropheryma whipplei have not been clearly defined. The study aimed to conduct a retrospective analysis of the treatment for patients with acute pneumonia, caused by Tropheryma whipplei, diagnosed through metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF).

METHODS

All patients underwent routine blood examinations and chest CT scans. Electronic fiberoptic bronchoscopy was performed to collect BALF samples from the lesion subsegments. The BALF samples were subjected to mNGS analysis. During hospitalization, all patients were treated with imipenem-cilastatin combined with compound sulfamethoxazole (SMZ-TMP) tablets for anti-infection, and they took SMZ-TMP orally for 3 months after discharge and followed up.

RESULTS

We identified 7 cases where Tropheryma whipplei was the primary pathogen, with 3 of these cases having it as the sole detected pathogen. The clinical manifestations of acute Tropheryma whipplei pneumonia are atypical. Chest CT scans revealed that 3 cases had exudative lesions in both lungs, 4 cases had unilateral pulmonary exudative lesions, 3 cases had bilateral pulmonary nodules, 2 cases had interstitial changes, and 3 cases had pleural effusion. Following treatment, all follow-up cases showed no recurrence.

CONCLUSIONS

The mNGS examination of bronchoalveolar lavage fluid can significantly improve the early diagnosis of acute pneumonia caused by Tropheryma whipplei. The treatment involving imipenem-cilastatin combined with SMZ-TMP, followed by oral SMZ-TMP for three months, is effective.

Pulmonary infection caused by Tropheryma whipplei: a case report and review of the literature

BACKGROUND

Tropheryma whipplei pneumonia is an infrequent medical condition. The clinical symptoms associated with this disease are nonspecific, often resulting in misdiagnosis or missed diagnosis. Therefore, sharing and summarizing the experiences in the diagnosis and treatment of this disease can deepen global understanding and awareness of it.

CASE PRESENTATION

The patient is a 78-year-old married Han Chinese female who was admitted to the hospital after experiencing fever, dry cough, and fatigue for 4 days. A lung computed tomography scan revealed inflammatory exudation in the lower left lung, accompanied by pleural effusion. The bronchoalveolar lavage fluid was subjected to further analysis using metagenomic next-generation sequencing, which identified 41 genetic sequences associated with Tropheryma whipplei. Consequently, she was diagnosed with Tropheryma whipplei pneumonia. After initiating treatment with doxycycline and biapenem, the patient's symptoms showed significant improvement. Upon discharge, the patient continued treatment with a combination of doxycycline and hydroxychloroquine, which was discontinued after 4 days. At 12-month follow-up, the patient reported overall good health, with no symptoms of fever, cough, or any other discomfort.

CONCLUSION

Tropheryma whipplei pneumonia is a rare condition with nonspecific symptoms. The application of metagenomic next-generation sequencing technology in pulmonary infections helps to rapidly identify rare pathogens, providing a solid foundation for precise and effective antibacterial treatment for patients.

A case of pneumonia caused by infection with Tropheryma whipplei complicated by cryptococcus during treatment with a Janus kinase inhibitor: a case report

This report describes the case of a 41-year-old male patient complaining of a hacking cough. The patient was treated with a Janus kinase (JAK) inhibitor for psoriasis. Blood tests revealed mild lymphopenia and high levels of serum cryptococcal antigen. Chest computed tomography revealed infection in the lower lobe of the left lung. Metagenomic next-generation sequencing of bronchoalveolar lavage fluid revealed Tropheryma whipplei. Tropheryma whipplei and Cryptococcus antimicrobial therapies were sequentially administered. During follow-up, the patient showed clinical and radiographic improvement. Tropheryma whipplei is an opportunistic Gram-positive rod-shaped bacterium belonging to the family Actinomycetes. Lung involvement is an unusual but classic manifestation of Whipple's disease. This is the first report of pneumonia caused by infection with Tropheryma whipplei complicated by Cryptococcus. To our knowledge, this is the first case report of Tropheryma whipplei infection following the use of JAK inhibitors. Clinicians should be aware of opportunistic infections that can occur during treatment with JAK inhibitors.

Tropheryma whipplei detected by metagenomic next-generation sequencing in bronchoalveolar lavage fluid

Whipple's disease is a chronic systemic infectious disease that mainly affects the gastrointestinal tract. In some cases, Tropheryma whipplei can cause infection at the implant site or even throughout the body. In this study, we collected alveolar lavage fluid samples from patients with Tropheryma whipplei from 2020 to 2022, and retrospectively analyzed the clinical data of Tropheryma whipplei positive patients. Patient's past history, clinical manifestations, laboratory examinations, chest CT findings, treatment, and prognosis were recorded. 16 BALFs (70/1725, 4.0 %) from 16 patients were positive for Tropheryma whipplei. 8 patients were male with an average age of 50 years. The main clinical symptoms of patients included fever (9/16), cough (7/16), dyspnea (7/16), and expectoration (5/16), but neurological symptoms and arthralgia were rare. Cardiovascular and cerebrovascular diseases were the most common comorbidity (n=8). The main laboratory characteristics of the patient are red blood cell count, hemoglobin, total protein and albumin below normal levels (11/16), and/or creatinine above normal levels(14/16). Most chest computed tomography mainly show focal or patchy heterogeneous infection (n=5) and pleural effusion (n=8). Among the 6 samples, Tropheryma whipplei was the sole agent, and Klebsiella pneumoniae was the most common detected other pathogens. Metagenomic next-generation sequencing technology has improved the detection rate and attention of Tropheryma whipplei. Further research is needed to distinguish whether Tropheryma whipplei present in respiratory samples is a pathogen or an innocent bystander.

Clinical, Laboratory, and Imaging Characteristics of Tropheryma Whipplei Detection in Bronchoalveolar Lavage Fluid Using Next-Generation Sequencing: A Case-Control Study

Objective

The aim of this study was to assess the prevalence of Tropheryma whipplei (TW) infection in the population and to investigate the clinical symptoms, as well as the laboratory and imaging characteristics of patients testing positive for TW using next-generation sequencing (NGS).

Methods

A retrospective review was conducted on 1346 bronchoalveolar lavage fluid (BALF) samples collected between January 2021 and September 2023. The case group comprised patients with TW detected using NGS while the control group included 65 randomly chosen Gram-positive bacterial infection patients without TW. Comparative analyses were carried out on the basic demographics, laboratory parameters, and imaging findings between the two groups. Additionally, the case group underwent an in-depth examination of underlying diseases, pathogens, final diagnoses, treatment strategies.

Results

The case group comprised of 51 patients with TW, constituting 3.8% of the total. There was no significant difference in gender and age between the case and control groups (P = 0.84, P = 0.07). Symptoms such as coughing, expectoration, wheezing, fever, and hemoptysis are less commonly detected in the case group with a higher incidence of chest pain when compared to the control group (P >0.05). The case group exhibited decreased albumin levels and increased C-reactive protein and D-dimer levels compared to normal levels. Imaging findings in the case group commonly included nodules, patchy images, and interstitial changes, the most common underlying disease is cardiovascular disease, and the most frequently co-occurring pathogen is the human herpesvirus. Among the case group, 27 patients received a final diagnosis of pneumonia, and 3 patients clinically diagnosed with Whipple's disease demonstrated improvement in both symptoms and imaging after treatment.

Conclusion

NGS revealed a relatively low overall detection rate of TW-positive patients using BALF. TW was more prevalent in middle-aged and elderly male patients characterized by symptoms such as cough, expectoration, shortness of breath, and fever. Chest imaging in these cases typically showed nodules and interstitial changes.

Case report: A patient with HHV-6 and HHV-7 combined with Whipple's trophoblast infection and streptococcal pneumonia

Adult respiratory distress syndrome due to viral pneumonia occurs predominantly in immunodeficient populations; adult respiratory distress syndrome secondary to human herpesvirus HHV-6 and HHV-7 pneumonia is extremely rare. Whipple's disease, caused by Tropheryma whipplei, a Gram-positive bacillus and obligate intracellular pathogen, is clinically challenging to diagnose. Whipple's disease is a chronic multisystem infectious disease caused by T. whipplei, most often affecting the gastrointestinal tract and joints, seldom the lungs. Both pathogens are opportunistic. We report a case of mixed infectious pneumonia in a patient with type 2 diabetes mellitus. The patient presented with dyspnea and intermittent fever. Imaging revealed multiple large patchy consolidations in the left lung. Routine anti-infective therapy was ineffective. Metagenomic next generation sequencing of bronchoalveolar lavage fluid indicated HHV-6 and HHV-7 pneumonia concurrent with T. whipplei and Streptococcus co-infections. Meropenem was administered to improve treatment. This case represents a rare mixed lung infection by multiple uncommon pathogens, and is of particular clinical significance.

Novel Patterns in High-Resolution Computed Tomography in Whipple Pneumonia

With the use of metagenomic next-generation sequencing, patients diagnosed with Whipple pneumonia are being increasingly correctly diagnosed. We report a series of 3 cases in China that showed a novel pattern of movable infiltrates and upper lung micronodules. After treatment, the 3 patients recovered, and lung infiltrates resolved.

Whipple's disease of the respiratory system: A case report

Whipple's disease (WD) is a multiple-system chronic disease caused by Tropheryma whipplei (T. whipplei) infection. The present study describes 3 cases of WD with clinical manifestations of cough, chest pain, headache, dyspnea, sputum, joint pain, abdominal pain, diarrhea and weight loss. Chest computed tomography (CT) showed signs of plaques, nodules and pleural thickening; and bronchoscopic alveolar lavage fluid metagenomic-sequencing indicated that it was T. whipplei. One patient was treated with meropenem as the starting regimen and two patients were treated with ceftriaxone as the starting regimen. Furthermore, two patients were provided with a maintenance regimen of cotrimoxazole and one was given a maintenance regimen of minocycline, which was combined with meropenem and ceftriaxone in order to improve their cough, chest pain, headache and dyspnea symptoms. To the best of our knowledge, there are few reports on WD of the respiratory system caused by T. whipplei, and differential diagnosis is the key to clinical diagnosis. When WD of the respiratory system is difficult to diagnose, metagenomic second-generation sequencing (mNGS) may be a better choice, which can achieve early diagnosis and early treatment. However, its clinical value is still limited; therefore, more research needs to be conducted in the future.

Tropheryma whipplei infection in the lung of a patient with long COVID: a case report

BACKGROUND

Immune dysregulation in individuals with long COVID has been detected. Differential diagnosis of diffuse infiltration on chest CT in long COVID is challenging.

CASE PRESENTATION

A 62-year-old man presented with a 10-month history of dyspnea after COVID-19 infection. Dyspnea became worse in the one month preceding presentation. The chest CT showed multifocal, subpleural, bilateral opacities due to long-COVID, and infiltration around the bronchovascular bundle in the bilateral lower lung field. The pathology for the transbronchial cryobiopsy (TBCB) first reported chronic inflammation (mainly interstitial pneumonia). The patient had positive results on tests for the antibody, RO-52+, EJ+. The presumptive diagnosis of connective tissue disease-interstitial lung disease was made. Prednisone and cyclophosphamide were given. At follow-up one month later, the chest CT showed new diffuse ground-glass infiltration. The previous TBCB specimen was re-evaluated. Foamy macrophages were found in the alveolar air space. Periodic acid-Schiff (PAS) staining was performed. Numerous intracytoplasmic organisms were detected, with morphologic features consistent with those of Tropheryma whipplei. The patient recovered after intravenous ceftriaxone and oral trimethoprim-sulfamethoxazole. The final diagnosis was lung T. whipplei infection and long COVID-19.

CONCLUSION

This is the first case report of Tropheryma whipplei infection in the lung of a patient with long COVID-19. T. whipplei should be considered as a potential pathogen for diffuse lung infiltration in the post-COVID-19 era.

Acute pneumonia due to Tropheryma whipplei diagnosed by metagenomic next-generation sequencing and pathology: A case report

Tropheryma whipplei (TW) is a rod-shaped, gram-positive bacterium that, when chronically infects humans, can lead to multi-system pathologies, including joint pain, abdominal pain with diarrhea and weight loss, myocarditis, pericarditis, and neurologic inflammation. Moreover, acute infections can lead to bronchopulmonary infections, bacteraemia, and acute diarrhea. However, fewer cases of acute pneumonia due to TW have been reported, and this diagnosis is not well founded. Herein, we report a case of acute pneumonia caused by a TW infection. The patient, a middle-aged man, underwent bronchoscopic alveolar lavage, and the metagenomic next-generation sequencing of the lavage fluid suggested TW infection. A lung puncture biopsy tissue specimen was also positive based on periodic acid-Schiff staining. After confirming the diagnosis, the patient was administered ceftriaxone for anti-infection treatment, improving clinical symptoms and lung imaging results. Therefore, in cases where conventional anti-infective treatment is ineffective for patients with acute pneumonia, we should consider the possibility of TW infection, conduct prompt pathogenetic examination, and provide timely treatment after diagnosis to improve overall patient prognosis.

Routine Metagenomics Service for ICU Patients with Respiratory Infection

Rationale: Respiratory metagenomics (RMg) needs evaluation in a pilot service setting to determine utility and inform implementation into routine clinical practice. Objectives: Feasibility, performance, and clinical impacts on antimicrobial prescribing and infection control were recorded during a pilot RMg service. Methods: RMg was performed on 128 samples from 87 patients with suspected lower respiratory tract infection (LRTI) on two general and one specialist respiratory ICUs at Guy's and St Thomas' NHS Foundation Trust, London. Measurements and Main Results: During the first 15 weeks, RMg provided same-day results for 110 samples (86%), with a median turnaround time of 6.7 hours (interquartile range = 6.1-7.5 h). RMg was 93% sensitive and 81% specific for clinically relevant pathogens compared with routine testing. Forty-eight percent of RMg results informed antimicrobial prescribing changes (22% escalation; 26% deescalation) with escalation based on speciation in 20 out of 24 cases and detection of acquired-resistance genes in 4 out of 24 cases. Fastidious or unexpected organisms were reported in 21 samples, including anaerobes (n = 12), Mycobacterium tuberculosis, Tropheryma whipplei, cytomegalovirus, and Legionella pneumophila ST1326, which was subsequently isolated from the bedside water outlet. Application to consecutive severe community-acquired LRTI cases identified Staphylococcus aureus (two with SCCmec and three with luk F/S virulence determinants), Streptococcus pyogenes (emm1-M1uk clone), S. dysgalactiae subspecies equisimilis (STG62647A), and Aspergillus fumigatus with multiple treatments and public health impacts. Conclusions: This pilot study illustrates the potential of RMg testing to provide benefits for antimicrobial treatment, infection control, and public health when provided in a real-world critical care setting. Multicenter studies are now required to inform future translation into routine service.

Lung cancer patient with Tropheryma whipplei and Nocardia co-infection

A 34-year-old male presented with lung shadow and was asymptomatic during medical examination. The patient had a prior history of thyroid tumors. Imaging manifestation showed a nodule in the medial segment of the right middle lobe, with partial obstruction of the distal bronchus within the lesion. Ground-glass and inflammatory nodules were observed in the anterior segment of the right upper lobe, as well as chronic inflammatory changes in the lower lobe of the right lung. Lung histopathological examination suggested invasive adenocarcinoma. A morphological examination of the bronchoalveolar lavage fluid revealed the presence of Tropheryma whipplei (TW) and Nocardia. Although TW infection has been reported in cancer patients, co-infection with Nocardia is a unique occurrence in this case. Opportunistic pathogens are common in immunocompromised patients but in this case, the patient was a young adult with normal immunity and an early-stage tumor with TW and Nocardia co-infection. We demonstrated the presence of rare microorganisms through imaging findings, combined with different staining methods of bronchoalveolar lavage fluid and lung tissue sections and evaluation of morphological characteristics. The aim of the present study was to provide early diagnosis and treatment of patients by improving microbial morphological detection.

[Pulmonary Mucinous Adenocarcinoma Combined with Bronchial Squamous Cell Papilloma and Infection with Tropheryma Whipplei: A Case Report]

Simultaneous multiple primary tumors on the same side of the lung with Tropheryma whipplei (TW) infection are rare. We reviewed the clinical data, imaging manifestations, pathological results, diagnosis and treatment of a primary pulmonary mucinous adenocarcinoma (PPMA) patient with bronchial squamous cell papilloma (BSCP) and TW infection, and discussed our treatment experience. The patient mainly presented with chronic cough and sputum, and computed tomography (CT) showed inflammatory changes with multiple nodular shadows. Biopsy of the lower lobe of the right lung showed PPMA, and right lung sub-branchial nodules discovered during bronchoscope revealed BSCP. Metagenomics next generation sequencing (mNGS) of bronchoalveolar lavage fluid showed mixed infection of Streptococcus pneumoniae and TW with a poor anti-infective effect. No clear genetic mutation was detected, and the patient was treated with chemotherapy and regularly followed up. We should improve the awareness of multiple pulmonary pathologies during clinical practice, avoid missed diagnosis and misdiagnosis, and carry out comprehensive treatment after clarifying the diagnosis as soon as possible.
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Tropheryma whipplei-induced plastic bronchitis in children: a case report

This article reports a case of a 7-year-old child with severe pneumonia whose chest CT showed pulmonary consolidation, and bronchoscopy revealed plastic bronchitis. The metagenomic Next-Generation Sequencing (NGS) of the pulmonary lavage fluid suggested the infection of Tropheryma whipplei (T whipplei). The patient was treated with bronchial lavage to remove sputum plugs, intravenous azithromycin, and piperacillin-tazobactam and was discharged after eight days of hospitalization without any recurrence during follow-up. This article aims to raise clinical awareness of T whipplei infection and suggests that NGS for rare pathogens should be performed early for unexplained plastic bronchitis.

Experience in the diagnosis and treatment of pneumonia caused by infection with Tropheryma whipplei: A case series

Tropheryma whipplei (TW) is the root cause of Whipple's disease (WD), a rare infectious illness leading to multi-organ impairment. A prominent feature of WD is acute pneumonia, which can be exceedingly challenging to diagnose clinically due to the pathogen's surreptitious nature. However and significantly, with the advent of metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF), it offers clinicians a potent tool at their disposal to detect TW infections. The present study conducted a retrospective analysis of clinical data gleaned from five patients in Hunan Province in China. Findings in this study demonstrated the potential of BALF-mNGS in diagnosing pneumonia caused by TW infection.

Whipple's disease presenting as weight gain and constipation in a Chinese woman

BACKGROUND

Whipple's disease is a chronic infection due to Tropheryma whipplei, commonly reported in the Caucasian but not in the Chinese population.

CASE PRESENTATION

A 52-year-old female with good past health, was diagnosed with Whipple's disease, presenting with constipation, unintentional weight gain, and fleeting polyarthralgia. Investigations prior to admission showed raised CA125 and computed tomography of the abdomen showed multiple retroperitoneal mesenteric lymphadenopathies. Extensive investigations performed on secondary causes of weight gain were unrevealing. Subsequent PET-CT scan revealed generalized lymphadenopathy involving the left deep cervical, supraclavicular, and retroperitoneal mesenteric area. Excisional biopsy of the left supraclavicular lymph node was performed, with histology showing infiltrations of Periodic acid-Schiff positive foamy macrophages. T. whipplei DNA was detected in her serum, saliva, stool, and lymph node by PCR targeting the 16S ribosomal RNA gene. She was started on intravenous ceftriaxone, and then stepped down to oral antibiotics for a total of 44 months. The recurrence of fever after 12 days of ceftriaxone raised the suspicion of Immune Reconstitution Inflammatory Syndrome (IRIS). Serial imaging showed a gradual reduction in the size of retroperitoneal lymphadenopathies. Literature review on Whipple's disease in the Chinese population identified 13 reports of detectable T. whipplei DNA in clinical specimens. The majority of the cases were pneumonia, followed by culture-negative endocarditis, encephalitis, and skin and soft tissue infection. However, most patients with pneumonia were diagnosed based on next generation sequencing alone, with the resolution of pulmonary infiltrates without adequate duration of antibiotics, suggesting the possibility of colonization instead of infection. The recommendation of long-term doxycycline suppression after treatment may be supported by the slow response of retroperitoneal lymphadenopathies to antibiotics in our patient.

CONCLUSIONS

Unintentional weight gain and constipation could be atypical presentations of Whipple's disease. It is a rare disease in the Chinese population despite the advancement of molecular techniques in the diagnosis of infections. A prolonged course of antibiotics may be required due to slow clinical response as documented by serial imaging in our case. The possibility of IRIS should be considered in patients with breakthrough fever during treatment of Whipple's disease.

Whipple's disease review, prevalence, mortality, and characteristics in the United States: A cross-sectional national inpatient study

Whipple's disease is a rare multiorgan systemic disease caused by Tropheryma whipplei infection that may present with a wide range of signs and symptoms. This study aim to comprehensively review and determine the inpatient prevalence, mortality, risk factors, and reasons for hospitalization of patients with Whipple's disease. ICD-10 codes were used to identify admissions with Whipple's disease during the years 2016 to 2018. Characteristics of admissions with and without Whipple's disease were compared. The most common reasons for hospitalization were identified in admissions with Whipple's disease. The prevalence of Whipple's disease was 4.6 per 1 million hospitalizations during the study period. Whipple's disease admissions were significantly older than other hospitalizations, with a mean age of 60.2 ± 1.6 years compared to 50.0 ± 0.1. Males were more likely to have Whipple's disease and represented approximately two-thirds of hospitalizations. A disproportionate number of admissions occurred in the Midwest. Patients with Whipple's disease were most commonly admitted for gastrointestinal disease, followed by systemic infection, cardiovascular/circulatory disease, musculoskeletal disease, respiratory disease, and neurological disease. High mortality was seen in admissions for central nervous system (CNS) disease. Whipple's disease has heterogeneous presentations for inpatient admissions, and disproportionately affects older males. High hospitalization rates in the Midwest support environmental and occupational disease transmission likely from the soil. Hospitalists should be aware of the various acute, subacute, and chronic presentations of this disease, and that acute presentations may be more common in the inpatient setting.

Tropheryma whipplei detection by metagenomic next-generation sequencing in bronchoalveolar lavage fluid: A cross-sectional study

Tropheryma whipplei is the bacterium associated with Whipple’s disease (WD), a chronic systemic infectious disease primarily involving the gastrointestinal tract. T. whipplei can also be detected in different body site of healthy individuals, including saliva and feces. Traditionally, Tropheryma whipplei has a higher prevalence in bronchoalveolar lavage fluid (BALF) of immunocompromised individuals. Few studies have explored the significance of the detection of T. whipplei in BALF. Herein, we retrospectively reviewed 1725 BALF samples which detected for metagenomic next-generation sequencing (mNGS) from March 2019 to April 2022 in Zhuhai, China. Seventy BALs (70/1725, 4.0%) from 70 patients were positive for T. whipplei. Forty-four patients were male with an average age of 50 years. The main symptoms included cough (23/70), expectoration (13/70), weight loss (9/70), and/or dyspnea (8/70), but gastrointestinal symptoms were rare. Chronic liver diseases were the most common comorbidity (n=15, 21.4%), followed by diabetes mellitus (n=13, 18.6%). Only nine patients (12.9%) were immunocompromised. Twenty-four patients (34.3%) were finally diagnosed with reactivation tuberculosis and 15 patients (21.4%) were diagnosed with lung tumors, including 13 primary lung adenocarcinoma and two lung metastases. Fifteen patients (21.4%) had pneumonia. Among the 20 samples, T. whipplei was the sole agent, and Mycobacterium tuberculosis complex was the most common detected other pathogens. Among the non-tuberculosis patients, 31 (31/46, 67.4%) had ground glass nodules or solid nodules on chest CT. Our study indicates that T. whipplei should be considered as a potential contributing factor in some lung diseases. For non-immunocompromised patients, the detection of T. whipplei also needs attention. The mNGS technology improves the detection and attention of rare pathogens. In the future, the infection, colonization, and prognosis of T. whipplei in lung still need to be studied.

Tropheryma whipplei Detection by Nanopore Sequencing in Patients With Interstitial Lung Disease

Tropheryma whipplei is a bacterium associated with Whipple's disease, which commonly manifests as weight loss, arthralgia, and diarrhea. The most frequently involved organs comprise the heart and eyes, in addition to the central nervous system. Few studies have explored the relationship between T. whipplei and pneumonia. Herein, we report three patients with interstitial lung disease (ILD) of unknown cause, whose bronchoalveolar lavage fluid (BALF) were evaluated via Nanopore sequencing. In our in-house BALF Nanopore platform, human DNA was removed with saponin, to improve the reads ratio of microorganisms/host. T. whipplei was the sole or most abundant pathogen in all the patients, comprising 1,385, 826, and 285 reads. The positive result was confirmed via quantitative polymerase chain reaction (PCR) with two pairs of primers (cycle threshold value: 33.26/36.29; 31.68/32.01; 28.82/28.80) and Sanger sequencing. To our knowledge, this is the first report of T. whipplei detection using Nanopore-based sequencing. The turnaround time was approximately 6-8 h in clinical laboratories, including less than 1 h for analysis. In conclusion, the results of this study confirm that Nanopore sequencing can rapidly detect rare pathogens, to improve clinical diagnosis. In addition, diagnosis of Whipple's disease should be combined other laboratory findings, such as periodic acid-Schiff (PAS) staining, and considered a possibility in middle-aged men presenting with ILD and a clinical history of unexplained arthralgia and/or fever.