Metagenomic Analysis Identifying a Polymicrobial Pulmonary Infection in a Non-HIV Immunocompromised Patient: A Case Report

Metagenomic Analysis Identifying a Polymicrobial Pulmonary Infection in a Non-HIV Immunocompromised Patient: A Case Report | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Case Report Metagenomic Analysis Identifying a Polymicrobial Pulmonary Infection in a Non-HIV Immunocompromised Patient: A Case Report Jing Duan, Jie Ding, Yingxin Zhang, Zhiqing You, Ding Li, Chao Chen This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-5307741/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 09 Jan, 2025 Read the published version in BMC Pulmonary Medicine → Version 1 posted 4 You are reading this latest preprint version Abstract Background Polymicrobial pulmonary infections, common in immunocompromised patients, often manifest more severe symptoms than monomicrobial infections. Clinical diagnosis delays may lead to mortality, emphasizing the importance of fast and accurate diagnosis for these patients. Metagenomic next-generation sequencing (mNGS), as an unbiased method capable of detecting all microbes, is a valuable tool to identify pathogens, particularly in cases where infections are difficult to diagnosis using conventional methods. Case presentation: A 50-year-old male patient was admitted due to cough, expectoration and dyspnea. CT scan revealed diffuse inflammatory and cavernous lung lesion, and blood examination suggested a polymicrobial infection. However, no etiology was found by routine examination. mNGS of bronchoalveolar lavage simultaneously detected the presence of Pneumocystis jirovecii , Aspergillus fumigates , Nocardia farcinica , Salmonella enterica subsp. enterica , and cytomegalovirus (CMV). The patient was successfully treated with compound sulfamethoxazole, cefoperazone/sulbactam, moxifloxacin, voriconazole, and ganciclovir. The patient recovered after two weeks of anti-infection therapy and maintained good health at a six-month follow-up. Conclusion For immunocompromised patients with multiple infections and atypical symptoms, mNGS emerged as a reliable approach to pathogen detection and guiding antibiotic therapy. mNGS polymicrobial infection immunocompromised patient case report Figures Figure 1 Figure 2 Background Immunocompromised condition, a common problem in Non-HIV patients who have low immunity, thus results in diarrhea, high fever, cough and other pulmonary infections. Immunosuppression is often caused by solid tumors, hematological malignancies, organ transplantation, and autoimmune inflammatory diseases. These individuals are more susceptible to infections caused by opportunistic pathogens. Opportunistic pathogens, such as Nocardia farcinica , Pneumocystis jirovecii , cytomegalovirus (CMV), and so on, are reported to have a higher infection rate in immunosuppressed individuals, and coexisting infections are common[1, 2]. Prompt and accurate diagnosis is critical for effective treatment and outcomes, but conventional diagnostic methods, such as microbial culture, microscopic smear and nucleic acid hybridization, often fall short due to atypical clinical manifestations, which would lead to a poor prognosis[3]. Metagenomic next-generation sequencing (mNGS), an unbiased method capable of detecting all microbes without a prior hypothesis, is suitable for identifying polymicrobial infections caused by difficult-to-culture pathogens. Herein, we reported a case which a variety of pathogens, such as Salmonellas enterica subsp. enteric, Nocardia farcinica , Pneumocystis jirovecii, Aspergillus fumigatus ( A. fumigates ) and CMV, were detected in specimens of an immunocompromised patient. And mNGS played an essential role in the diagnosis and appropriate antibiotic treatment of an immunocompromised patient with a rare polymicrobial pulmonary infection. Case Presentation A 50-year-old male patient was admitted to our hospital on October 17th, 2021. During the 10 days before admission, hard nodules, swollen boils, ulcers, and scabs appeared on several areas of his skin, while 7 days ago the patient began to cough, expectorate and experience dyspnea. Methylprednisolone (48 mg/day, PO) had been administrated for the past three months to treat focal segmental glomerulosclerosis (FSGS). On Admission, the patient’s body temperature was 39.4℃, pulse was 130 beats/min, SpO 2 was 67%, and noninvasive positive pressure ventilation was applied (35 L/min, O 2 60%). CT scan showed diffuse inflammatory and exudative changes in both lungs with multiple lung nodules. Cavernous lesions could be seen in the upper lobe of the right lung (Fig. 1 ). Blood samples were taken for laboratory tests and culture for pathogens. The white blood cell count was 13.42×10 9 /L, CRP was > 200 mg/L, SAA was > 300 mg/L, and procalcitonin was 1.80 ng/ml, all of which were above the upper limit of the biological reference interval. Fungal infection markers (1,3)-β-D-glucan (479.48 pg/ml) and galactomannan (1.019 µg/L) were also out of the normal range. The counts of CD3 + (73 cells/µl), CD4 + (38 cells/µl) and CD8 + T cells (30 cells/µl) were all less than 10% of the lower limit, indicating impairment of the immune function (Table 1 ). Based on the clinical symptoms, imaging results, and laboratory examinations, an infection was suspected. Cefoperazone/sulbactam (3 g q8h, iv, drip), moxifloxacin (0.4 g qd, iv, drip), combined with compound sulfamethoxazole (SMZ 0.8 g-TMP 0.16 g q12 h, PO) were administered to treat gram-negative bacilli, gram-positive cocci, and opportunistic fungi such as P.jirovecii. On the second day of hospitalization, bronchoalveolar lavage was performed. A portion of the BALF was collected for microscopic examination of bacteria, filamentous fungi, mycobacterium tuberculosis, and P.jirovecii. Another part of the BALF was subjected to mNGS and culture. On the third day, Salmonellas enterica subsp. enteric , which was sensitive to moxifloxacin and sulfamethoxazole, was identified by blood culture. P.jirovecii was detected by hexamine silver staining of BALF on the same day. Filamentous gram-positive bacilli resembling Nocardia spp. were also observed under oil lens (Fig. 1 ). As the antibiotic regiments were effective to these pathogens, the patient’s symptoms improved, and no adjustment of antibiotics was necessary. On the 4th day, N.farcinica (1,089 reads), P.jirovecii (6,825 reads), A.fumigatus (3 reads), and CMV (47 reads) were recovered by mNGS (Fig. 2 ). Cefoperazone/sulbactam was discontinued, voriconazole (0.4 g q12 h, iv, drip) was added to treat A. fumigates . Ganciclovir (0.25 g q12h, iv.drip) was added to treat CMV, the dosage of sulfamethoxazole was increased (SMZ 1.2 g-TMP 0.24 g q6h, PO) to treat P. jirovecii and N.farcinica . On the 5th day, N.farcinica was isolated from BALF on blood agar by culture, and the presence of CMV in the BALF was confirmed by Real-time PCR (3.09×10 3 copies/ml). A. fumigates (2 colonies) was isolated by culture on the 6th day. On the 10th day, the patient`s condition improved significantly, while PCR of CMV was negative, so ganciclovir was discontinued. Moxifloxacin was stopped on the 13th day, as the blood culture was negative. After 14 days of treatment, the patient’s condition improved significantly, so he was discharged from the hospital. To prevent any recurrence of the infection, voriconazole (0.2 g q12h, PO) and SMZ-TMP (1.2 g-0.24 g q6h, PO) were prescribed for 3 months. During the 6 month’s follow-up, the patient’s condition remained normal, confirming the effectiveness of the treatment. Table 1 Abnormal laboratory results on admission Indexes Results Normal range Unit Inflammation indexes Leukocyte 13.42×10 9 3.5×10 9 -9.5×10 9 /L CRP > 200 0–10 mg/L SAA > 300 0–10 mg/L Procalcitionin 1.80 0-0.05 ng/ml Fungi marker (1,3)-β-D-glucan 479.48 < 60 pg/ml galactomannan 1.019 < 0.75 µg/L T cell count CD3 + T cell 73 1185–1901 cell/µl CD4 + T cell 38 561–1137 cell/µl CD8 + T cell 30 404–754 cell/µl Discussion and Conclusion Low immunity is frequently encountered among patients undergoing long-term radiotherapy and chemotherapy for cancer, patients with autoimmune diseases, patients with kidney diseases, and others[4, 5]. In our case, this patient has a history of three months of methylprednisolone for kidney disease and exhibits a low CD3 + , CD4 + and CD8 + T cell counts, which is indicative of a compromised immune status. Immunocompromised patients often suffer from a polymicrobial pulmonary infection, such as P. jirovecii, Nocardia farcinica . P. jirovecii is a severe fungal infection that has a high prevalence in immunocompromised individuals, CD4 + lymphocyte counts < 200 cells/ul and corticosteroid use are risk factors for P.jirovecii colonization[6]. Early diagnosis and medication are important for good prognosis, however, diagnosis of P. jirovecii remains challenging due to its atypical clinical manifestations and low sensitivity and specificity of current diagnostic methods[7]. Nocardia farcinica is a weak acidic actinomycete that is widely present in soil, water and air. Inhalation of spores or fragments of hyphae results in pulmonary nocardiosis, about 50 percent of norcardiosis occurs in immunocompromised settings while Nocardia farcinica is more common than other Norcardia species [8–10]. The variable clinical manifestation and the difficulty in pathogen detection often lead to delays in the treatment of norcardiosis patients. Recently, several studies illustrated that compared to conventional methods, mNGS had a satisfactory diagnostic value in P. jirovecii and Norcardia farcinica diagnoses, reducing the detection turnaround time[11–13]. As reported, the application of mNGS corrected misdiagnosed tuberculosis, diagnosed a rare case of multisystem infection and a multi-site infection by Norcardia farcinica , and illustrated the competence of mNGS in the diagnosis of Norcardia spp. [14–16]. The mNGS technique is a promising approach for detecting co-pathogens in mixed pulmonary infection, with key advantages in speed and sensitivity[17]. In cases where multiple pathogens coexist, such as in immunocompromised patients, mNGS can significantly simplify the diagnostic process by identifying bacteria, fungi, parasites, and viruses concurrently. Unlike traditional methods that often rely on prior hypotheses and targeted testing, mNGS is unbiased and can detect even atypical, rare, or emerging pathogens. The high detection sensitivity of mNGS, coupled with its ability to detect unculturable organisms, makes it superior to culture-based methods[18]. In our case, given the history of methylprednisolone usage and the low CD4 + T cells count, they are indeed high-risk factors for opportunistic infection caused by P.jirovecii , A.fumigates, N.farcinica , and CMV. These pathogens are commonly found in immunocompromised individuals, but a simultaneous infection with all four of them is extremely rare. To the best of our knowledge, this is the first reported case of all four pathogens being detected in a single BALF sample using the mNGS technology in China. The conventional diagnostic methods, often struggle with detecting multiple pathogens simultaneously due to their limitations in sensitivity, specificity, throughput, and the need for pre-hypotheses. These limitations can lead to delays in diagnosis and poor prognosis, particularly in cases where multiple pathogens are involved. Although the current gold standard for diagnosing invasive pulmonary aspergillus is based on histopathological evidence and a positive tissue aspergillus polymerase chain reaction (PCR), these two diagnostic methods are invasive. Especially considering the severity of this patient's condition, it is challenging to clinically apply of these invasive diagnostic methods. The rapid and comprehensive pathogen detection capability of mNGS technology can significantly guide the rational use of antibiotics[19, 20]. In this case, the mNGS results assisted clinical doctors in prescribing VCZ for the treatment of Aspergillus fumigatus infection and ganciclovir for the treatment of CMV infection, both of which played a crucial role in the successful management and treatment of the patient’s disease, highlighting the value of mNGS in precision medicine. Given the patient's severe condition and based on clinical experience, the use of VCZ for antifungal treatment is appropriate. The post-treatment microbiological test results also confirm the effectiveness of the medication. In conclusion, patients in immunocompromised states often suffer from polymicrobial pulmonary infection. Compared to the limitations of traditional diagnostic methods, the mNGS technology has shown significant potential in enhancing the diagnosis and treatment of such complex and challenging infectious cases. Declarations Acknowledgements We would like to express our gratitude to Zhang ran and Li yanhua for their work on microscopic examination. Authors’ contributions Jing Duan and Jie Ding were major contributors in drafting the manuscript, Jing Duan, Zhiqing You and Ding Li participated in the diagnosis of the patient and review of medical records, Yingxin Zhang and Chao Chen participated in revising the manuscript critically. All authors read and approved the final manuscript. Funding This research was supported by the Medical Science and Technology Development Foundation of Department of Health of Shandong Province (2019WS113). Availability of data and materials All data generated or analyzed during this study are included in this published article. Ethics approval and consent to participate As this manuscript is a case report of clinical care provided to a patient, and it does not include any of the patient’s personal identifiers, ethics approval by the institutional review board was not required. Consent for publication The patient provided written informed consent for the publication of the data. Competing interests The authors declare that they have no competing interests. References Kim YK, Sung H, Jung J, Yu SN, Lee JY, Kim SH, et al. Impact of immune status on the clinical characteristics and treatment outcomes of nocardiosis. Diagn Microbiol Infect Dis. 2016;85(4):482-7. Fritzsche C, Riebold D, Munk-Hartig A, Klammt S, Neeck G, Reisinger E. High prevalence of Pneumocystis jirovecii colonization among patients with autoimmune inflammatory diseases and corticosteroid therapy. Scand J Rheumatol. 2012;41(3):208 − 13. Liu Y, Wu W, Xiao Y, Zou H, Hao S, Jiang Y. Application of metagenomic next-generation sequencing and targeted metagenomic next-generation sequencing in diagnosing pulmonary infections in immunocompetent and immunocompromised patients. Front Cell Infect Microbiol. 2024;14:1439472. Tanaka N, Kunihiro Y, Yanagawa N. Infection in Immunocompromised Hosts: Imaging. J Thorac Imaging. 2018;33(5):306 − 21. Mei-Sheng Riley M. Invasive Fungal Infections Among Immunocompromised Patients in Critical Care Settings: Infection Prevention Risk Mitigation. Crit Care Nurs Clin North Am. 2021;33(4):395–405. Avino LJ, Naylor SM, Roecker AM. Pneumocystis jirovecii Pneumonia in the Non-HIV-Infected Population. Ann Pharmacother. 2016;50(8):673-9. Zhang F, Chen J, Huang H, Deng X, Zhang W, Zeng M, et al. Application of metagenomic next-generation sequencing in the diagnosis and treatment guidance of Pneumocystis jirovecii pneumonia in renal transplant recipients. Eur J Clin Microbiol Infect Dis. 2021;40(9):1933-42. McGuinness SL, Whiting SE, Baird R, Currie BJ, Ralph AP, Anstey NM, et al. Nocardiosis in the Tropical Northern Territory of Australia, 1997–2014. Open Forum Infect Dis. 2016;3(4):ofw208. Wang HL, Seo YH, LaSala PR, Tarrand JJ, Han XY. Nocardiosis in 132 patients with cancer: microbiological and clinical analyses. Am J Clin Pathol. 2014;142(4):513 − 23. Wauters G, Avesani V, Charlier J, Janssens M, Vaneechoutte M, Delmee M. Distribution of nocardia species in clinical samples and their routine rapid identification in the laboratory. J Clin Microbiol. 2005;43(6):2624-8. Chen J, He T, Li X, Wang X, Peng L, Ma L. Metagenomic Next-Generation Sequencing in Diagnosis of a Case of Pneumocystis jirovecii Pneumonia in a Kidney Transplant Recipient and Literature Review. Infect Drug Resist. 2020;13:2829-36. Zhang Y, Ai JW, Cui P, Zhang WH, Wu HL, Ye MZ. A cluster of cases of pneumocystis pneumonia identified by shotgun metagenomics approach. J Infect. 2019;78(2):158 − 69. Weng SS, Zhang HY, Ai JW, Gao Y, Liu YY, Xu B, et al. Rapid Detection of Nocardia by Next-Generation Sequencing. Front Cell Infect Microbiol. 2020;10:13. Pan L, Pan XH, Xu JK, Huang XQ, Qiu JK, Wang CH, et al. Misdiagnosed tuberculosis being corrected as Nocardia farcinica infection by metagenomic sequencing: a case report. BMC Infect Dis. 2021;21(1):754. Wu J, Li X, Zhang T, Lin X, Chen YC. Disseminated Nocardia farcinica involves the spinal cord: a case report and review of the literature. BMC Infect Dis. 2021;21(1):1224. Jiao M, Deng X, Yang H, Dong J, Lv J, Li F. Case Report: A Severe and Multi-Site Nocardia farcinica Infection Rapidly and Precisely Identified by Metagenomic Next-Generation Sequencing. Front Med (Lausanne). 2021;8:669552. Wang J, Han Y, Feng J. Metagenomic next-generation sequencing for mixed pulmonary infection diagnosis. BMC Pulm Med. 2019;19(1):252. Miao Q, Ma Y, Wang Q, Pan J, Zhang Y, Jin W, et al. Microbiological Diagnostic Performance of Metagenomic Next-generation Sequencing When Applied to Clinical Practice. Clin Infect Dis. 2018;67(suppl_2):S231-S40. Xu WB, Fu JJ, Yuan XJ, Xian QJ, Zhang LJ, Song PP, et al. Metagenomic next-generation sequencing in the diagnosis of neurocysticercosis: A case report. World J Clin Cases. 2023;11(20):4912-9. Song P, Chen S, Tan X, Gao Y, Fu J, You Z, et al. Metagenomic Analysis Identifying a Rare Leishmania Infection in an Adult With AIDS. Front Cell Infect Microbiol. 2021;11:764142. Additional Declarations No competing interests reported. Cite Share Download PDF Status: Published Journal Publication published 09 Jan, 2025 Read the published version in BMC Pulmonary Medicine → Version 1 posted Editorial decision: Revision requested 28 Oct, 2024 Editor assigned by journal 28 Oct, 2024 Submission checks completed at journal 25 Oct, 2024 First submitted to journal 21 Oct, 2024 You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-5307741","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Case Report","associatedPublications":[],"authors":[{"id":370438584,"identity":"0e448558-a681-4eef-ae8b-5b3b02d0da1f","order_by":0,"name":"Jing Duan","email":"","orcid":"","institution":"Liaocheng People’s Hospital, Shandong First Medical University","correspondingAuthor":false,"prefix":"","firstName":"Jing","middleName":"","lastName":"Duan","suffix":""},{"id":370438585,"identity":"4da825d2-fb6f-4d84-b5ae-aa36a9e4cac1","order_by":1,"name":"Jie Ding","email":"","orcid":"","institution":"Liaocheng People’s Hospital and Liaocheng School of Clinical Medicine, Shandong First Medical University","correspondingAuthor":false,"prefix":"","firstName":"Jie","middleName":"","lastName":"Ding","suffix":""},{"id":370438586,"identity":"43d27df9-3126-4d23-9db7-973aa0853740","order_by":2,"name":"Yingxin Zhang","email":"","orcid":"","institution":"Liaocheng People’s Hospital and Liaocheng School of Clinical Medicine, Shandong First Medical University","correspondingAuthor":false,"prefix":"","firstName":"Yingxin","middleName":"","lastName":"Zhang","suffix":""},{"id":370438587,"identity":"cd3dd3b6-5cbc-4c8c-a1ad-4c8cdedefafc","order_by":3,"name":"Zhiqing You","email":"","orcid":"","institution":"Liaocheng People’s Hospital, Shandong First Medical University","correspondingAuthor":false,"prefix":"","firstName":"Zhiqing","middleName":"","lastName":"You","suffix":""},{"id":370438588,"identity":"6cdf0581-ad1e-4a65-b107-be1fe6395146","order_by":4,"name":"Ding Li","email":"","orcid":"","institution":"Liaocheng People’s Hospital, Shandong First Medical University","correspondingAuthor":false,"prefix":"","firstName":"Ding","middleName":"","lastName":"Li","suffix":""},{"id":370438589,"identity":"acf93eb2-25c4-4d20-b589-e1c4a75201d8","order_by":5,"name":"Chao Chen","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA9UlEQVRIiWNgGAWjYDACCSBmbAASPIyNDz7+seHh528gWgtzs+HMhjQZyRkHiNbC3ibN23DYxqAhAb8O/tnNxx783GEnx89zsE1y5o7zPAYMBxg/fMzBY8mdY+mGvWeSjSV7G5stPp65zWPO3MAsOXMbbi0GEjlm0oxtzIkbzjM23pzBdpvHsuEAGzMvXi3534Ba6kFaGqR52M7xGBxIIKQlhw2o5XDihrONTdK8bQcIa5G4kWYm2dt23Fiy52Cz4YwzyTySMw424/UL/4zkZxI/26qBIZb+8MGHCjt7fv7mgx8+4tGCDYCjaRSMglEwCkYBJQAAYP9VF04IHQIAAAAASUVORK5CYII=","orcid":"","institution":"Liaocheng People’s Hospital and Liaocheng School of Clinical Medicine, Shandong First Medical University","correspondingAuthor":true,"prefix":"","firstName":"Chao","middleName":"","lastName":"Chen","suffix":""}],"badges":[],"createdAt":"2024-10-22 02:38:15","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-5307741/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-5307741/v1","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1186/s12890-024-03473-0","type":"published","date":"2025-01-09T15:58:01+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":67652256,"identity":"e59d4ddb-a340-4560-9519-2f09444b02ce","added_by":"auto","created_at":"2024-10-28 11:52:38","extension":"jpg","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":872699,"visible":true,"origin":"","legend":"\u003cp\u003eClinical course and laboratory examination results of the patients.\u003c/p\u003e","description":"","filename":"Fig1clinicalcourseofthepatient.jpg","url":"https://assets-eu.researchsquare.com/files/rs-5307741/v1/f76489fbdbd26668a6da8ff7.jpg"},{"id":67652258,"identity":"fb1db42e-1dad-4397-8ad8-d1b9b0703236","added_by":"auto","created_at":"2024-10-28 11:52:38","extension":"jpg","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":342653,"visible":true,"origin":"","legend":"\u003cp\u003eThe follow-up diagnosis of polymicrobial pulmonary infection by Metagenomic next-generation sequencing (mNGS). (A) Mapping of \u003cem\u003eNocardia farcinica\u003c/em\u003e reads on the genome. (B) Reads distribution of \u003cem\u003eP.jirovecii\u003c/em\u003e in the BALF sample. (C) Distribution of \u003cem\u003eAspergillus fumigatus\u003c/em\u003e reads in the BALF sample. (D) Reads Distribution of CMV on the genome.\u003c/p\u003e","description":"","filename":"Fig2.jpg","url":"https://assets-eu.researchsquare.com/files/rs-5307741/v1/d487dce415f22c9dcb61140f.jpg"},{"id":73694770,"identity":"3ef2f3d7-acdb-4370-bf94-cc2af378bbc2","added_by":"auto","created_at":"2025-01-13 16:14:03","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1663859,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-5307741/v1/b29e38fa-709f-4291-8609-bdbd683a578d.pdf"}],"financialInterests":"No competing interests reported.","formattedTitle":"Metagenomic Analysis Identifying a Polymicrobial Pulmonary Infection in a Non-HIV Immunocompromised Patient: A Case Report","fulltext":[{"header":"Background","content":"\u003cp\u003eImmunocompromised condition, a common problem in Non-HIV patients who have low immunity, thus results in diarrhea, high fever, cough and other pulmonary infections. Immunosuppression is often caused by solid tumors, hematological malignancies, organ transplantation, and autoimmune inflammatory diseases. These individuals are more susceptible to infections caused by opportunistic pathogens. Opportunistic pathogens, such as \u003cem\u003eNocardia farcinica\u003c/em\u003e, \u003cem\u003ePneumocystis jirovecii\u003c/em\u003e, cytomegalovirus (CMV), and so on, are reported to have a higher infection rate in immunosuppressed individuals, and coexisting infections are common[1, 2]. Prompt and accurate diagnosis is critical for effective treatment and outcomes, but conventional diagnostic methods, such as microbial culture, microscopic smear and nucleic acid hybridization, often fall short due to atypical clinical manifestations, which would lead to a poor prognosis[3].\u003c/p\u003e \u003cp\u003eMetagenomic next-generation sequencing (mNGS), an unbiased method capable of detecting all microbes without a prior hypothesis, is suitable for identifying polymicrobial infections caused by difficult-to-culture pathogens. Herein, we reported a case which a variety of pathogens, such as \u003cem\u003eSalmonellas enterica subsp. enteric, Nocardia farcinica\u003c/em\u003e, \u003cem\u003ePneumocystis jirovecii, Aspergillus fumigatus\u003c/em\u003e (\u003cem\u003eA. fumigates\u003c/em\u003e) and CMV, were detected in specimens of an immunocompromised patient. And mNGS played an essential role in the diagnosis and appropriate antibiotic treatment of an immunocompromised patient with a rare polymicrobial pulmonary infection.\u003c/p\u003e"},{"header":"Case Presentation","content":"\u003cp\u003eA 50-year-old male patient was admitted to our hospital on October 17th, 2021. During the 10 days before admission, hard nodules, swollen boils, ulcers, and scabs appeared on several areas of his skin, while 7 days ago the patient began to cough, expectorate and experience dyspnea. Methylprednisolone (48 mg/day, PO) had been administrated for the past three months to treat focal segmental glomerulosclerosis (FSGS). On Admission, the patient’s body temperature was 39.4℃, pulse was 130 beats/min, SpO\u003csub\u003e2\u003c/sub\u003e was 67%, and noninvasive positive pressure ventilation was applied (35 L/min, O\u003csub\u003e2\u003c/sub\u003e 60%). CT scan showed diffuse inflammatory and exudative changes in both lungs with multiple lung nodules. Cavernous lesions could be seen in the upper lobe of the right lung (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003e). Blood samples were taken for laboratory tests and culture for pathogens. The white blood cell count was 13.42×10\u003csup\u003e9\u003c/sup\u003e/L, CRP was \u0026gt; 200 mg/L, SAA was \u0026gt; 300 mg/L, and procalcitonin was 1.80 ng/ml, all of which were above the upper limit of the biological reference interval. Fungal infection markers (1,3)-β-D-glucan (479.48 pg/ml) and galactomannan (1.019 µg/L) were also out of the normal range. The counts of CD3\u003csup\u003e+\u003c/sup\u003e (73 cells/µl), CD4\u003csup\u003e+\u003c/sup\u003e (38 cells/µl) and CD8\u003csup\u003e+\u003c/sup\u003e T cells (30 cells/µl) were all less than 10% of the lower limit, indicating impairment of the immune function (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e). Based on the clinical symptoms, imaging results, and laboratory examinations, an infection was suspected. Cefoperazone/sulbactam (3 g q8h, iv, drip), moxifloxacin (0.4 g qd, iv, drip), combined with compound sulfamethoxazole (SMZ 0.8 g-TMP 0.16 g q12 h, PO) were administered to treat gram-negative bacilli, gram-positive cocci, and opportunistic fungi such as \u003cem\u003eP.jirovecii.\u003c/em\u003e On the second day of hospitalization, bronchoalveolar lavage was performed. A portion of the BALF was collected for microscopic examination of bacteria, filamentous fungi, mycobacterium tuberculosis, and \u003cem\u003eP.jirovecii.\u003c/em\u003e Another part of the BALF was subjected to mNGS and culture. On the third day, \u003cem\u003eSalmonellas enterica subsp. enteric\u003c/em\u003e, which was sensitive to moxifloxacin and sulfamethoxazole, was identified by blood culture. \u003cem\u003eP.jirovecii\u003c/em\u003e was detected by hexamine silver staining of BALF on the same day. Filamentous gram-positive bacilli resembling \u003cem\u003eNocardia spp.\u003c/em\u003e were also observed under oil lens (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003e). As the antibiotic regiments were effective to these pathogens, the patient’s symptoms improved, and no adjustment of antibiotics was necessary. On the 4th day, \u003cem\u003eN.farcinica\u003c/em\u003e (1,089 reads), \u003cem\u003eP.jirovecii\u003c/em\u003e (6,825 reads), \u003cem\u003eA.fumigatus\u003c/em\u003e (3 reads), and CMV (47 reads) were recovered by mNGS (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003e). Cefoperazone/sulbactam was discontinued, voriconazole (0.4 g q12 h, iv, drip) was added to treat \u003cem\u003eA. fumigates\u003c/em\u003e. Ganciclovir (0.25 g q12h, iv.drip) was added to treat CMV, the dosage of sulfamethoxazole was increased (SMZ 1.2 g-TMP 0.24 g q6h, PO) to treat \u003cem\u003eP. jirovecii and N.farcinica\u003c/em\u003e. On the 5th day, \u003cem\u003eN.farcinica\u003c/em\u003e was isolated from BALF on blood agar by culture, and the presence of CMV in the BALF was confirmed by Real-time PCR (3.09×10\u003csup\u003e3\u003c/sup\u003e copies/ml). \u003cem\u003eA. fumigates\u003c/em\u003e (2 colonies) was isolated by culture on the 6th day. On the 10th day, the patient`s condition improved significantly, while PCR of CMV was negative, so ganciclovir was discontinued. Moxifloxacin was stopped on the 13th day, as the blood culture was negative. After 14 days of treatment, the patient’s condition improved significantly, so he was discharged from the hospital. To prevent any recurrence of the infection, voriconazole (0.2 g q12h, PO) and SMZ-TMP (1.2 g-0.24 g q6h, PO) were prescribed for 3 months. During the 6 month’s follow-up, the patient’s condition remained normal, confirming the effectiveness of the treatment.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e\u003cdiv class=\"gridtable\"\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c5\" colnum=\"5\"\u003e\u003c/div\u003e\u003ctable float=\"Yes\" id=\"Tab1\" border=\"1\"\u003e\u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 1\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003eAbnormal laboratory results on admission\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e\u003ccolgroup cols=\"5\"\u003e\u003c/colgroup\u003e\u003cthead\u003e\u003ctr\u003e\u003cth align=\"left\" colname=\"c1\"\u003e\u0026nbsp;\u003c/th\u003e\u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003eIndexes\u003c/p\u003e \u003c/th\u003e\u003cth align=\"left\" colname=\"c3\"\u003e \u003cp\u003eResults\u003c/p\u003e \u003c/th\u003e\u003cth align=\"left\" colname=\"c4\"\u003e \u003cp\u003eNormal range\u003c/p\u003e \u003c/th\u003e\u003cth align=\"left\" colname=\"c5\"\u003e \u003cp\u003eUnit\u003c/p\u003e \u003c/th\u003e\u003c/tr\u003e\u003c/thead\u003e\u003ctbody\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\" morerows=\"3\" rowspan=\"4\"\u003e \u003cp\u003eInflammation\u003c/p\u003e \u003cp\u003eindexes\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eLeukocyte\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e13.42×10\u003csup\u003e9\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e3.5×10\u003csup\u003e9\u003c/sup\u003e-9.5×10\u003csup\u003e9\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e/L\u003c/p\u003e \u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eCRP\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u0026gt; 200\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e0–10\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003emg/L\u003c/p\u003e \u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eSAA\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u0026gt; 300\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e0–10\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003emg/L\u003c/p\u003e \u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eProcalcitionin\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e1.80\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e0-0.05\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eng/ml\u003c/p\u003e \u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eFungi marker\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e(1,3)-β-D-glucan\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e479.48\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e\u0026lt; 60\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003epg/ml\u003c/p\u003e \u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u0026nbsp;\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003egalactomannan\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e1.019\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e\u0026lt; 0.75\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eµg/L\u003c/p\u003e \u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eT cell count\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eCD3\u003csup\u003e+\u003c/sup\u003e T cell\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e73\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e1185–1901\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003ecell/µl\u003c/p\u003e \u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u0026nbsp;\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eCD4\u003csup\u003e+\u003c/sup\u003e T cell\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e38\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e561–1137\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003ecell/µl\u003c/p\u003e \u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u0026nbsp;\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eCD8\u003csup\u003e+\u003c/sup\u003e T cell\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e30\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e404–754\u003c/p\u003e \u003c/td\u003e\u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003ecell/µl\u003c/p\u003e \u003c/td\u003e\u003c/tr\u003e\u003c/tbody\u003e\u003c/table\u003e\u003c/div\u003e "},{"header":"Discussion and Conclusion","content":"\u003cp\u003eLow immunity is frequently encountered among patients undergoing long-term radiotherapy and chemotherapy for cancer, patients with autoimmune diseases, patients with kidney diseases, and others[4, 5]. In our case, this patient has a history of three months of methylprednisolone for kidney disease and exhibits a low CD3\u003csup\u003e+\u003c/sup\u003e, CD4\u003csup\u003e+\u003c/sup\u003e and CD8\u003csup\u003e+\u003c/sup\u003e T cell counts, which is indicative of a compromised immune status. Immunocompromised patients often suffer from a polymicrobial pulmonary infection, such as \u003cem\u003eP. jirovecii, Nocardia farcinica\u003c/em\u003e. \u003cem\u003eP. jirovecii\u003c/em\u003e is a severe fungal infection that has a high prevalence in immunocompromised individuals, CD4\u003csup\u003e+\u003c/sup\u003e lymphocyte counts \u0026lt; 200 cells/ul and corticosteroid use are risk factors for \u003cem\u003eP.jirovecii\u003c/em\u003e colonization[6]. Early diagnosis and medication are important for good prognosis, however, diagnosis of \u003cem\u003eP. jirovecii\u003c/em\u003e remains challenging due to its atypical clinical manifestations and low sensitivity and specificity of current diagnostic methods[7]. \u003cem\u003eNocardia farcinica\u003c/em\u003e is a weak acidic actinomycete that is widely present in soil, water and air. Inhalation of spores or fragments of hyphae results in pulmonary nocardiosis, about 50 percent of norcardiosis occurs in immunocompromised settings while \u003cem\u003eNocardia farcinica\u003c/em\u003e is more common than other \u003cem\u003eNorcardia\u003c/em\u003e species [8–10]. The variable clinical manifestation and the difficulty in pathogen detection often lead to delays in the treatment of norcardiosis patients. Recently, several studies illustrated that compared to conventional methods, mNGS had a satisfactory diagnostic value in \u003cem\u003eP. jirovecii\u003c/em\u003e and \u003cem\u003eNorcardia farcinica\u003c/em\u003e diagnoses, reducing the detection turnaround time[11–13]. As reported, the application of mNGS corrected misdiagnosed tuberculosis, diagnosed a rare case of multisystem infection and a multi-site infection by \u003cem\u003eNorcardia farcinica\u003c/em\u003e, and illustrated the competence of mNGS in the diagnosis of \u003cem\u003eNorcardia spp.\u003c/em\u003e [14–16].\u003c/p\u003e\u003cp\u003eThe mNGS technique is a promising approach for detecting co-pathogens in mixed pulmonary infection, with key advantages in speed and sensitivity[17]. In cases where multiple pathogens coexist, such as in immunocompromised patients, mNGS can significantly simplify the diagnostic process by identifying bacteria, fungi, parasites, and viruses concurrently. Unlike traditional methods that often rely on prior hypotheses and targeted testing, mNGS is unbiased and can detect even atypical, rare, or emerging pathogens. The high detection sensitivity of mNGS, coupled with its ability to detect unculturable organisms, makes it superior to culture-based methods[18].\u003c/p\u003e\u003cp\u003eIn our case, given the history of methylprednisolone usage and the low CD4\u003csup\u003e+\u003c/sup\u003e T cells count, they are indeed high-risk factors for opportunistic infection caused by \u003cem\u003eP.jirovecii\u003c/em\u003e, \u003cem\u003eA.fumigates, N.farcinica\u003c/em\u003e, and CMV. These pathogens are commonly found in immunocompromised individuals, but a simultaneous infection with all four of them is extremely rare. To the best of our knowledge, this is the first reported case of all four pathogens being detected in a single BALF sample using the mNGS technology in China. The conventional diagnostic methods, often struggle with detecting multiple pathogens simultaneously due to their limitations in sensitivity, specificity, throughput, and the need for pre-hypotheses. These limitations can lead to delays in diagnosis and poor prognosis, particularly in cases where multiple pathogens are involved. Although the current gold standard for diagnosing invasive pulmonary aspergillus is based on histopathological evidence and a positive tissue aspergillus polymerase chain reaction (PCR), these two diagnostic methods are invasive. Especially considering the severity of this patient's condition, it is challenging to clinically apply of these invasive diagnostic methods.\u003c/p\u003e\u003cp\u003eThe rapid and comprehensive pathogen detection capability of mNGS technology can significantly guide the rational use of antibiotics[19, 20]. In this case, the mNGS results assisted clinical doctors in prescribing VCZ for the treatment of \u003cem\u003eAspergillus fumigatus\u003c/em\u003e infection and ganciclovir for the treatment of CMV infection, both of which played a crucial role in the successful management and treatment of the patient’s disease, highlighting the value of mNGS in precision medicine. Given the patient's severe condition and based on clinical experience, the use of VCZ for antifungal treatment is appropriate. The post-treatment microbiological test results also confirm the effectiveness of the medication.\u003c/p\u003e\u003cp\u003eIn conclusion, patients in immunocompromised states often suffer from polymicrobial pulmonary infection. Compared to the limitations of traditional diagnostic methods, the mNGS technology has shown significant potential in enhancing the diagnosis and treatment of such complex and challenging infectious cases.\u003c/p\u003e"},{"header":"Declarations","content":"\u003cp\u003e\u003cstrong\u003eAcknowledgements\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eWe would like to express our gratitude to Zhang ran and Li yanhua for their work on microscopic examination.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAuthors\u0026rsquo; contributions\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eJing Duan and\u0026nbsp;Jie Ding\u0026nbsp;were major contributors in drafting the manuscript, Jing Duan, Zhiqing You and Ding Li participated in the diagnosis of the patient and review of medical records, Yingxin Zhang and Chao Chen participated in revising the manuscript critically. All authors read and approved the final manuscript.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eFunding\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThis research was supported by the Medical Science and Technology Development Foundation of Department of Health of Shandong Province (2019WS113).\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAvailability of data and materials\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eAll data generated or analyzed during this study are included in this published article.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eEthics approval and consent to participate\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eAs this manuscript is a case report of clinical care provided to a patient, and it does not include any of the patient\u0026rsquo;s personal identifiers, ethics approval by the institutional review board was not required.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConsent for publication\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe patient provided written informed consent for the publication of the data.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eCompeting interests\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe authors declare that they have no competing interests.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\n \u003cli\u003e\u003cspan\u003eKim YK, Sung H, Jung J, Yu SN, Lee JY, Kim SH, et al. Impact of immune status on the clinical characteristics and treatment outcomes of nocardiosis. Diagn Microbiol Infect Dis. 2016;85(4):482-7.\u003c/span\u003e\u003c/li\u003e\n \u003cli\u003e\u003cspan\u003eFritzsche C, Riebold D, Munk-Hartig A, Klammt S, Neeck G, Reisinger E. High prevalence of Pneumocystis jirovecii colonization among patients with autoimmune inflammatory diseases and corticosteroid therapy. Scand J Rheumatol. 2012;41(3):208\u0026thinsp;\u0026minus;\u0026thinsp;13.\u003c/span\u003e\u003c/li\u003e\n \u003cli\u003e\u003cspan\u003eLiu Y, Wu W, Xiao Y, Zou H, Hao S, Jiang Y. Application of metagenomic next-generation sequencing and targeted metagenomic next-generation sequencing in diagnosing pulmonary infections in immunocompetent and immunocompromised patients. Front Cell Infect Microbiol. 2024;14:1439472.\u003c/span\u003e\u003c/li\u003e\n \u003cli\u003e\u003cspan\u003eTanaka N, Kunihiro Y, Yanagawa N. Infection in Immunocompromised Hosts: Imaging. J Thorac Imaging. 2018;33(5):306\u0026thinsp;\u0026minus;\u0026thinsp;21.\u003c/span\u003e\u003c/li\u003e\n \u003cli\u003e\u003cspan\u003eMei-Sheng Riley M. Invasive Fungal Infections Among Immunocompromised Patients in Critical Care Settings: Infection Prevention Risk Mitigation. Crit Care Nurs Clin North Am. 2021;33(4):395\u0026ndash;405.\u003c/span\u003e\u003c/li\u003e\n \u003cli\u003e\u003cspan\u003eAvino LJ, Naylor SM, Roecker AM. Pneumocystis jirovecii Pneumonia in the Non-HIV-Infected Population. Ann Pharmacother. 2016;50(8):673-9.\u003c/span\u003e\u003c/li\u003e\n \u003cli\u003e\u003cspan\u003eZhang F, Chen J, Huang H, Deng X, Zhang W, Zeng M, et al. Application of metagenomic next-generation sequencing in the diagnosis and treatment guidance of Pneumocystis jirovecii pneumonia in renal transplant recipients. Eur J Clin Microbiol Infect Dis. 2021;40(9):1933-42.\u003c/span\u003e\u003c/li\u003e\n \u003cli\u003e\u003cspan\u003eMcGuinness SL, Whiting SE, Baird R, Currie BJ, Ralph AP, Anstey NM, et al. Nocardiosis in the Tropical Northern Territory of Australia, 1997\u0026ndash;2014. Open Forum Infect Dis. 2016;3(4):ofw208.\u003c/span\u003e\u003c/li\u003e\n \u003cli\u003e\u003cspan\u003eWang HL, Seo YH, LaSala PR, Tarrand JJ, Han XY. Nocardiosis in 132 patients with cancer: microbiological and clinical analyses. Am J Clin Pathol. 2014;142(4):513\u0026thinsp;\u0026minus;\u0026thinsp;23.\u003c/span\u003e\u003c/li\u003e\n \u003cli\u003e\u003cspan\u003eWauters G, Avesani V, Charlier J, Janssens M, Vaneechoutte M, Delmee M. Distribution of nocardia species in clinical samples and their routine rapid identification in the laboratory. J Clin Microbiol. 2005;43(6):2624-8.\u003c/span\u003e\u003c/li\u003e\n \u003cli\u003e\u003cspan\u003eChen J, He T, Li X, Wang X, Peng L, Ma L. Metagenomic Next-Generation Sequencing in Diagnosis of a Case of Pneumocystis jirovecii Pneumonia in a Kidney Transplant Recipient and Literature Review. Infect Drug Resist. 2020;13:2829-36.\u003c/span\u003e\u003c/li\u003e\n \u003cli\u003e\u003cspan\u003eZhang Y, Ai JW, Cui P, Zhang WH, Wu HL, Ye MZ. A cluster of cases of pneumocystis pneumonia identified by shotgun metagenomics approach. J Infect. 2019;78(2):158\u0026thinsp;\u0026minus;\u0026thinsp;69.\u003c/span\u003e\u003c/li\u003e\n \u003cli\u003e\u003cspan\u003eWeng SS, Zhang HY, Ai JW, Gao Y, Liu YY, Xu B, et al. Rapid Detection of Nocardia by Next-Generation Sequencing. Front Cell Infect Microbiol. 2020;10:13.\u003c/span\u003e\u003c/li\u003e\n \u003cli\u003e\u003cspan\u003ePan L, Pan XH, Xu JK, Huang XQ, Qiu JK, Wang CH, et al. Misdiagnosed tuberculosis being corrected as Nocardia farcinica infection by metagenomic sequencing: a case report. 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Clin Infect Dis. 2018;67(suppl_2):S231-S40.\u003c/span\u003e\u003c/li\u003e\n \u003cli\u003e\u003cspan\u003eXu WB, Fu JJ, Yuan XJ, Xian QJ, Zhang LJ, Song PP, et al. Metagenomic next-generation sequencing in the diagnosis of neurocysticercosis: A case report. World J Clin Cases. 2023;11(20):4912-9.\u003c/span\u003e\u003c/li\u003e\n \u003cli\u003e\u003cspan\u003eSong P, Chen S, Tan X, Gao Y, Fu J, You Z, et al. Metagenomic Analysis Identifying a Rare Leishmania Infection in an Adult With AIDS. Front Cell Infect Microbiol. 2021;11:764142.\u003c/span\u003e\u003c/li\u003e\n\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"bmc-pulmonary-medicine","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"pulm","sideBox":"Learn more about [BMC Pulmonary Medicine](http://bmcpulmmed.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/pulm/default.aspx","title":"BMC Pulmonary Medicine","twitterHandle":"BMC_series","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true},"keywords":"mNGS, polymicrobial infection, immunocompromised patient, case report","lastPublishedDoi":"10.21203/rs.3.rs-5307741/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-5307741/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003ch2\u003eBackground\u003c/h2\u003e \u003cp\u003ePolymicrobial pulmonary infections, common in immunocompromised patients, often manifest more severe symptoms than monomicrobial infections. Clinical diagnosis delays may lead to mortality, emphasizing the importance of fast and accurate diagnosis for these patients. Metagenomic next-generation sequencing (mNGS), as an unbiased method capable of detecting all microbes, is a valuable tool to identify pathogens, particularly in cases where infections are difficult to diagnosis using conventional methods.\u003c/p\u003e\u003ch2\u003eCase presentation:\u003c/h2\u003e \u003cp\u003eA 50-year-old male patient was admitted due to cough, expectoration and dyspnea. CT scan revealed diffuse inflammatory and cavernous lung lesion, and blood examination suggested a polymicrobial infection. However, no etiology was found by routine examination. mNGS of bronchoalveolar lavage simultaneously detected the presence of \u003cem\u003ePneumocystis jirovecii\u003c/em\u003e, \u003cem\u003eAspergillus fumigates\u003c/em\u003e, \u003cem\u003eNocardia farcinica\u003c/em\u003e, \u003cem\u003eSalmonella enterica subsp. enterica\u003c/em\u003e, and cytomegalovirus (CMV). The patient was successfully treated with compound sulfamethoxazole, cefoperazone/sulbactam, moxifloxacin, voriconazole, and ganciclovir. The patient recovered after two weeks of anti-infection therapy and maintained good health at a six-month follow-up.\u003c/p\u003e\u003ch2\u003eConclusion\u003c/h2\u003e \u003cp\u003eFor immunocompromised patients with multiple infections and atypical symptoms, mNGS emerged as a reliable approach to pathogen detection and guiding antibiotic therapy.\u003c/p\u003e","manuscriptTitle":"Metagenomic Analysis Identifying a Polymicrobial Pulmonary Infection in a Non-HIV Immunocompromised Patient: A Case Report","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2024-10-28 11:52:34","doi":"10.21203/rs.3.rs-5307741/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2024-10-28T10:28:32+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2024-10-28T06:23:58+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2024-10-25T14:00:14+00:00","index":"","fulltext":""},{"type":"submitted","content":"BMC Pulmonary Medicine","date":"2024-10-22T02:28:22+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"bmc-pulmonary-medicine","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"pulm","sideBox":"Learn more about [BMC Pulmonary Medicine](http://bmcpulmmed.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/pulm/default.aspx","title":"BMC Pulmonary Medicine","twitterHandle":"BMC_series","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"a11d87b3-52df-46c6-9925-707e911c2f24","owner":[],"postedDate":"October 28th, 2024","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[],"tags":[],"updatedAt":"2025-01-13T16:11:19+00:00","versionOfRecord":{"articleIdentity":"rs-5307741","link":"https://doi.org/10.1186/s12890-024-03473-0","journal":{"identity":"bmc-pulmonary-medicine","isVorOnly":false,"title":"BMC Pulmonary Medicine"},"publishedOn":"2025-01-09 15:58:01","publishedOnDateReadable":"January 9th, 2025"},"versionCreatedAt":"2024-10-28 11:52:34","video":"","vorDoi":"10.1186/s12890-024-03473-0","vorDoiUrl":"https://doi.org/10.1186/s12890-024-03473-0","workflowStages":[]},"version":"v1","identity":"rs-5307741","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-5307741","identity":"rs-5307741","version":["v1"]},"buildId":"qtupq5eGEP_6zYnWcrvyt","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}