Microbial ecology of protective isolation room: Air and Surfaces.

INTRODUCTION: Healthcare-associated infections pose a significant public health burden, leading to morbidity, mortality, prolonged hospital stays, and substantial social and economic costs. Immunocompromised patients are at a heightened risk of nosocomial infections. AIM: This prospective study conducted at Mohammed VI University Hospital of Oujda aimed to assess the microbial ecology of surfaces and air in an immunosuppressed patient room compared to a double hospitalization room. METHODS: Microbiological air purity tests were conducted employing both the sedimentation method and the collision method with the assistance of Microflow Alpha. The sedimentation method used Mueller Hinton with 5% human blood, facilitating the free fall of contaminated dust particles. The collection program employed was set for 10 minutes per 1 m3. For surface sampling, swabs were taken from a 25 cm2 surface. The swabs were immediately forwarded to the Microbiology Laboratory. We carried out both macroscopic and microscopic identification of colonies, followed by definitive biochemical identification using the BD phoenixTM system. Antibiotic susceptibility was assessed through agar diffusion on Muller Hinton medium coupled with the determination of the minimum inhibitory concentration. RESULTS: The results revealed a decreased bacterial count within the protective isolation room, in contrast to the standard hospital room. We noted the predominance of coagulase-negative Staphylococcus spp and Bacillus spp. Staphylococcus aureus and Aspergillus spp, common pathogens in healthcare-associated infections, were notably absent in the protective isolation room. The findings underline the pivotal role of hospital environments in the transmission of healthcare-associated infections. CONCLUSION: The protective isolation room demonstrated effective control of microbial contamination, with fewer and less resistant germs. The study highlighted the significance of air treatment systems in preventing the spread of opportunistic infections. Our study underscored the critical role of microbiological cleanliness in preventing nosocomial infections.

Fungal infections in immunocompromised critically ill patients.

Diverse pathogenic fungi can produce severe infections in immunocompromised patients, thereby justifying intensive care unit (ICU) admissions. In some cases, the infections can develop in immunocompromised patients who were previously admitted to the ICU. Aspergillus spp., Pneumocystis jirovecii, Candida spp., and Mucorales are the fungi that are most frequently involved in these infections. Diagnosis continues to be challenging because symptoms and signs are unspecific. Herein, we provide an in-depth review about the diagnosis, with emphasis on recent advances, and treatment of these invasive fungal infections in the ICU setting.

Vaccine-related influenza virus B infection in a child with an undiagnosed B-cell acute lymphoblastic leukemia.

We report a case of Influenza type B (lineage Yamagata) infection in a child who received the live attenuated influenza virus vaccine before being diagnosed with B-cell acute lymphoblastic leukemia. The patient developed a mild disease that persisted for 18 days and resolved without antiviral treatment. The prolonged infection of an attenuated virus in an immunocompromised host might pose a risk of reversion or evolution to a more pathogenic strain. Prompt prevention, identification, and monitoring of similar cases are desirable to avoid the development of severe illness, which could complicate patient management.

Oral Isavuconazole Combined with Nebulized Inhalation and Bronchoscopic Administration of Amphotericin B for the Treatment of Pulmonary Mucormycosis: A Case Report and Literature Review.

Pulmonary mucormycosis (PM) is an invasive and potentially fatal fungal infection, with Rhizopus microsporus (R. microsporus) being the most common pathogen. The routine therapy for this infection includes surgery and antifungal agents. However, the therapeutic effects of single agents are unsatisfactory due to the rapid progression of mucormycosis, while not all patients can tolerate surgery. Innovative treatment methods like combination therapy await validations of their clinical efficacy. We report a case of PM that was diagnosed via metagenomics next-generation sequencing (mNGS) of black drainage fluid from the patient's lung. The patient eventually recovered and was discharged after a combination therapy of oral isavuconazole, inhaled amphotericin B, and local perfusion of amphotericin B through bronchoscopy, which may be a promising strategy for the treatment of PM, especially for cases where surgery is not possible. A retrospective study of 297 cases in a literature review highlights the different treatment methods used in clinical practice.

Identification and assessment of antifungal susceptibility of Candida species based on bronchoalveolar lavage in immunocompromised and critically ill patients.

Background and Objectives: The presence of fungi in the respiratory tract as mycobiome, particularly Candida species (spp.), remains a serious problem due to increasing numbers of immunocompromised patients. The confirmed reliable existence of these pathogens due to frequent colonization is essential. This investigation aimed to recognize Candida spp. among isolates from bronchoalveolar lavage of immunocompromised and critically ill patients and to evaluate their susceptibility to antimycotic drugs. Materials and Methods: Bronchoalveolar lavage fluid was collected from 161 hospitalized patients presenting with suspected respiratory fungal infection /colonization. The specimens were examined by standard molecular and mycological assays. Candida spp. were recognized with sequence assessment of the D1-D2 section of the large subunit ribosomal DNA. The susceptibility of Candida isolates to common antimycotic drugs was distinguished by standard broth microdilution. Results: Seventy-one clinical isolates of Candida spp. were recognized. Candida albicans was the most frequent, followed by C. glabrata, C. krusei (Pichia kudriavzevii), C. dubliniensis, C. parapsilosis, and C. tropicalis. We found 5.1% of C. albicans isolates and 8% of C. glabrata isolates to show resistance to fluconazole. The whole of the Candida spp. were sensitive to amphotericin B and caspofungin. Conclusion: This study demonstrated that C. albicans and C. glabrata are the most common isolates of bronchoalveolar lavage fluid in patients, and the drug susceptibility screening confirmed that amphotericin B and caspofungin are effective against Candida spp. but some C. glabrata and C. albicans isolates showed resistance to fluconazole.

Orbital aspergillosis in an immunocompromised man with no history of trauma: a case report.

Fungal orbital cellulitis is usually seen in immunocompromised individuals, and opportunistic pathogens are the main etiology. We herein report a case of fungal orbital cellulitis due to Aspergillus in a patient with no history of trauma. A 48-year-old man presented to the emergency room of our hospital with a 2-week history of periorbital swelling, conjunctival hyperemia, and chemosis of his right eye. The visual acuity of his right eye was 6/20, and the intraocular pressure was 44 mmHg. The main clinical findings were proptosis of the right ocular globe with conjunctival hyperemia and a palpable infratemporal orbital mass. Laboratory testing failed to detect the presence of a pathogenic infection, and the lesions on computed tomography images resembled those of a malignant tumor of the orbit. The diagnosis was finally confirmed by postoperative pathological examination, and the patient responded favorably to debridement combined with antifungal therapy. Histopathological examination may help to reveal the nature of this disease. Surgical removal of inflammatory lesions can serve as an important diagnostic and treatment method for fungal orbital cellulitis.

Strategies for prevention and treatment of SARS-COV-2 infection in patients with chronic kidney disease: Literature review.

COVID-19 has proven to be particularly aggressive in patients with chronic kidney disease (CKD). The lower immune response rate and the greater susceptibility to progress to severe forms of the disease have contributed to this phenomenon, which has persisted in the post-vaccination era of the pandemic. Paradoxically, CKD has been excluded from most clinical trials of the main therapeutic tools developed against SARS-CoV-2. However, experience in the use of these drugs has been accumulating in different stages of CKD, supporting their use with guarantees of efficacy and safety. The objective of this review is to gather all treatment indications for COVID-19 in the different phases of the disease, tailored to CKD in its various stages, including renal replacement therapy.

Boosting Vaccine Response in Autoimmune Rheumatic Disease Patients With Inadequate Seroconversion: An Analysis of the Immunogenicity of Vector-Based and Inactivated Vaccines.

BACKGROUND: An additional dose of COVID-19 vaccine is being offered to vaccinated people, especially those immunocompromised. The most widely available vaccines in India are the adenoviral vector-based AZD1222 (ChAdOx1 nCoV-19) and the heat-inactivated (BBV152). This study investigated the efficacy of both vaccines in patients with autoimmune rheumatic diseases (AIRD). OBJECTIVES:  To compare final anti-SARS-CoV-2 antibody titers, neutralization of pseudovirions by these antibodies, and T cell responses between patients of AIRD who had received the third dose of AZD1222 and BBV152 vaccines. METHODS: Patients with stable AIRD who had completed two doses of COVID-19 vaccination but had a suboptimal response (anti-receptor binding domain (RBD) antibody<212) were randomized (1:1) to receive either AZD1222 or BBV152 as a booster dose. Patients with previous hybrid immunity or those who developed COVID-19 during the trial were excluded. Antibody titers, neutralization of Wuhan and Omicron pseudovirions, and interferon release by T cells (enzyme-linked immunosorbent spot (ELISpot)) in response to the Spike antigen were measured four weeks after this booster dose. RESULTS: 146 were screened, 91 were randomized, and 67 were analyzed per protocol. The third dose improved antibody titers (p<0.001), neutralization of the Wuhan strain (p<0.001), and T cell interferon release (p<0.001) but not neutralization of the Omicron strain (p=0.24). Antibody titers were higher (p<0.005) after ADZ1222 boost (2,414 IU (interquartile range (IQR): 330-10,315)) than BBV1222 (347.7 IU (0.4-973)). Neutralization of the Wuhan stain was better (AZD1222: 76.6%(23.0-95.45) versus BBV152 (32.7% (0-78.9), p=0.03 by ANCOVA). Neutralization of Omicron (0 (0-28.4) vs 0 (0-4.8)) and T cell interferon release (57.0 IU (23.5-95) vs 50.5 IU (13.2-139)) were similar. CONCLUSION: The third dose improved all parameters of immunogenicity in AIRD patients with previous inadequate responses except Omicron neutralization. The vector-based vaccine exhibits notable efficacy, particularly in antibody titers and neutralizing the Wuhan strain. TRIAL REGISTRATION: CTRI/2021/12/038928.

Estrategias de prevención y tratamiento de la infección por SARS-CoV-2 (Severe Acute Respiratory Coronavirus 2) en pacientes con enfermedad renal crónica: revisión de la literatura / Strategies for prevention and treatment of SARS-CoV-2 infection in patients with chronic kidney disease: Literature review

La COVID-19 ha demostrado ser especialmente agresiva con los pacientes con enfermedad renal crónica (ERC). La menor tasa de respuesta inmunológica y la mayor facilidad para la progresión a formas graves de enfermedad ha propiciado este hecho, que se ha mantenido en la era posvacunal de la pandemia. Paradójicamente, la ERC ha sido excluida de la mayoría de los ensayos clínicos de las principales herramientas terapéuticas desarrolladas frente a SARS-CoV-2. Sin embargo, se ha ido reuniendo experiencia de uso de estos fármacos en distintos estadios de la ERC que avala su uso con garantías de eficacia y seguridad. El objetivo de esta revisión es reunir todas las indicaciones de tratamiento frente a la COVID-19 en los distintos estadios de la enfermedad adaptadas a la ERC en sus distintas fases, incluyendo el tratamiento sustitutivo renal.(AU)

COVID-19 has proven to be particularly aggressive in patients with chronic kidney disease (CKD). The lower immune response rate and the greater susceptibility to progress to severe forms of the disease have contributed to this phenomenon, which has persisted in the post-vaccination era of the pandemic. Paradoxically, CKD has been excluded from most clinical trials of the main therapeutic tools developed against SARS-CoV-2. However, experience in the use of these drugs has been accumulating in different stages of CKD, supporting their use with guarantees of efficacy and safety. The objective of this review is to gather all treatment indications for COVID-19 in the different phases of the disease, tailored to CKD in its various stages, including renal replacement therapy.(AU)

Endoscopic Findings of 'Salmon Roe-like Nodular Lesions' in a Case of Severe Disseminated Strongyloidiasis in a Foreign Resident in Japan.

A Southeast Asian man in his 30s residing in Japan developed severe disseminated strongyloidiasis during long-term steroid therapy. Initially misdiagnosed as gastroenteritis, his condition was later identified as strongyloidiasis by fecal smears and endoscopy. An endoscopic examination revealed salmon roe-like nodular lesions, indicating an advanced stage. Despite treatment, the patient died of the illness. This case underscores the importance of considering the patient's geographical background and immunosuppressive history in medical assessments. It further highlights the need for early and proactive diagnostic approaches, such as stool testing and gastrointestinal endoscopy, to effectively detect and treat imported infectious diseases.

Prolonged viral shedding in an immunocompromised Korean patient infected with hMPXV, sub-lineage B.1.3, with acquired drug resistant mutations during tecovirimat treatment.

Following the worldwide surge in mpox (monkeypox) in 2022, cases have persisted in Asia, including South Korea, and sexual contact is presumed as the predominant mode of transmission, with a discernible surge in prevalence among immunocompromised patients. Drugs such as tecovirimat can result in drug-resistant mutations, presenting obstacles to treatment. This study aimed to ascertain the presence of tecovirimat-related resistant mutations through genomic analysis of the monkeypox virus isolated from a reported case involving prolonged viral shedding in South Korea. Here, tecovirimat-resistant mutations, previously identified in the B.1 clade, were observed in the B.1.3 clade, predominant in South Korea. These mutations exhibited diverse patterns across different samples from the same patient and reflected the varied distribution of viral subpopulations in different anatomical regions. The A290V and A288P mutant strains we isolated hold promise for elucidating these mechanisms, enabling a comprehensive analysis of viral pathogenesis, replication strategies, and host interactions. Our findings imply that acquired drug-resistant mutations, may present a challenge to individual patient treatment. Moreover, they have the potential to give rise to transmitted drug-resistant mutations, thereby imposing a burden on the public health system. Consequently, the meticulous genomic surveillance among immunocompromised patients, conducted in this research, assumes paramount importance.

'The Year of Living Dangerously': Successful Rhodococcus Equi Therapy in an Immunosuppressed Patient with Minimal Toxicity by One Year of Continuous Intravenous Vancomycin Therapy Combined with Oral Levofloxacin And Rifampicin.

Background: Rhodococcus equi is a Gram-positive microorganism that causes infections, particularly in immunocompromised patients. Treatment duration can be prolonged. While vancomycin is an effective drug in this scenario, its use may lead to renal damage. Studies have shown that continuous vancomycin infusion appears to be a safe strategy in terms of adverse effects compared to bolus administration. Case description: We present the case of a 71-year-old female liver transplant recipient. After being diagnosed with a mediastinal infection caused by Rhodococcus equi with poor response to initial therapy, she required 12 months of continuous intravenous domiciliary infusion of vancomycin combined with oral levofloxacin and rifampicin. There was no drug-related complication throughout the follow-up. Conclusions: The use of continuous vancomycin infusion has emerged as a safer, more efficient, and cost-effective alternative to intermittent administration. We want to emphasise the uniqueness of this case, where despite the unprecedented treatment duration, no adverse effects occurred. LEARNING POINTS: Vancomycin therapy based on continuous infusion represents a safer and cheaper strategy than classic intermittent administration.The use of continuous infusion facilitates the management of complex infections with outpatient antimicrobial therapy.

Recombinant mannan-binding lectin magnetic beads increase pathogen detection in immunocompromised patients.

The microbiological diagnosis of infection for hematological malignancy patients receiving chemotherapy or allogeneic hematopoietic stem cell transplantation (allo-HSCT) patients relies primarily on standard microbial culture, especially blood culture, which has many shortcomings, such as having low positive rates, being time-consuming and having a limited pathogenic spectrum. In this prospective observational self-controlled test accuracy study, blood, cerebrospinal fluid (CSF), and bronchoalveolar lavage fluid (BALF) samples were collected from chemotherapy or allo-HSCT patients with clinical symptoms of infections who were hospitalized at Peking University First Hospital. Possible pathogens were detected by the method based on recombinant mannan-binding lectin (MBL) magnetic bead enrichment (M1 method) and simultaneously by a standard method. The analytical sensitivity of M1 method was close to that of standard culture method. Besides, the turn-around time of M1-method was significantly shorter than that of standard culture method. Moreover, the M1 method also added diagnostic value through the detection of some clinically relevant microbes missed by the standard method. M1 method could significantly increase the detection efficiency of pathogens (including bacteria and fungi) in immunocompromised patients. KEY POINTS: • The detection results of M1-method had a high coincidence rate with that of standard method • M1 method detected many pathogens which had not been found by standard clinic method.

Bell's palsy: a case report of unusual presentation in a patient with rhino-orbital cerebral mucormycosis.

BACKGROUND: Mucormycosis is a fungal infection caused by the Mucorales order of fungi. This fungus is commonly found in soil and can cause disease in immunocompromised patients. On the other hand, Bell's palsy is an idiopathic condition that results in the sudden onset of unilateral facial muscle weakness, affecting the facial nerve. CASE PRESENTATION: A 51-year-old Persian housewife with a history of poorly controlled diabetes mellitus presented with a splitting headache that had been ongoing for 1 week and an inability to close her left eye or make facial expressions on the left side of her face. The patient's vital signs were normal, but physical examination revealed a yellow-grey scar on the left side of her hard palate and Bell's palsy on the left side. A neurological examination showed that she could move both eyes but could not close her left eye, move up her left eyebrow, or smile. Further investigations were performed, including laboratory tests, radiologic imaging, and functional endoscopic sinus surgery. The patient underwent three rounds of debridement for bony erosion in the medial and posterior walls of the left maxillary sinus and the hard palate. Pathological examination confirmed mucormycosis infection in the hard palate and mucosa. CONCLUSION: Fungal infection must be considered a potential diagnosis for immunocompromised adults who exhibit symptoms of Bell's palsy.

COVID-19 mRNA Vaccination Trends Among Immunocompromised Patients.

INTRODUCTION: Immunocompromised patients are at increased risk of contracting severe COVID-19 infection. The purpose of this study was to assess COVID-19 vaccination trends of immunocompromised patients at a large, urban primary care setting. METHODS: A retrospective chart review of immunocompromised patients who had a visit between 1/1/2021 and 5/15/2022 at Thomas Jefferson University's Department of Family and Community Medicine (DFCM) was conducted. Patient charts were reviewed for demographics, number of visits to the DFCM, immunocompromising diagnoses, and COVID-19 mRNA vaccination status, including vaccination type and number of vaccine doses received. Descriptive statistics were calculated. Paired t tests were conducted to assess relationships between immunocompromised patients with ≥3 mRNA vaccine doses and those with ≤2 mRNA vaccine doses. RESULTS: A total of 887 patients were included. Most patients were Black (66.7%), above the age of 50 (82.1%), and male (55.9%). Solid tumor cancers (62.6%) and HIV/AIDS (23.8%) were the most represented immunocompromising diagnoses. Overall, 556 patients received ≥3 mRNA vaccine doses (62.7%) and 331 patients received ≤2 mRNA vaccine doses (37.3%). Eighty-three patients (9.4%) had no COVID-19 vaccines on record. Of the 591 Black patients, 248 (42%) received ≤2 mRNA vaccine doses. CONCLUSION: Despite the majority of the sample receiving ≥3 mRNA vaccine doses, disparities in vaccination rates exist, especially when comparing White and Black patients. Vaccination rates in immunocompromised patients should be improved, and primary care providers should prioritize outreach efforts focusing on patient-centered COVID-19 vaccine education in these populations.

Higher Levels of SARS-CoV-2 Genetic Variation in Immunocompromised Patients: A Retrospective Case-Control Study.

BACKGROUND: A severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection lasts longer in immunocompromised hosts than in immunocompetent patients. Prolonged infection is associated with a higher probability of selection for novel SARS-CoV-2 mutations, particularly in the spike protein, a critical target for vaccines and therapeutics. METHODS: From December 2020 to September 2022, respiratory samples from 444 immunocompromised patients and 234 health care workers positive for SARS-CoV-2, diagnosed at 2 hospitals in Paris, France, were analyzed using whole-genome sequencing using Nanopore technology. Custom scripts were developed to assess the SARS-CoV-2 genetic diversity between the 2 groups and within the host. RESULTS: Most infections were SARS-CoV-2 Delta or Omicron lineages. Viral genetic diversity was significantly higher in infections of immunocompromised patients than those of controls. Minor mutations were identified in viruses sequenced from immunocompromised individuals, which became signature mutations for newer SARS-CoV-2 variants as the epidemic progressed. Two patients were coinfected with Delta and Omicron variants. The follow-up of immunocompromised patients revealed that the SARS-CoV-2 genome evolution differed in the upper and lower respiratory tracts. CONCLUSIONS: This study found that SARS-CoV-2 infection in immunocompromised patients is associated with higher genetic diversity, which could lead to the emergence of new SARS-CoV-2 variants with possible immune evasion or different virulence characteristics.

Hairy Cell Leukemia (HCL) Presenting As Severe Acute Respiratory Distress Syndrome (ARDS) With Legionella pneumophila: Coincidence or Causation?

Due to a low index of suspicion coupled with specific growth conditions and non-specific clinical manifestations, Legionella (L.) pneumophila is a frequently misdiagnosed cause of pneumonia in immunocompromised patients, especially those with hematological malignancies. We present a case of severe acute respiratory distress syndrome (ARDS) secondary to Legionnaire's disease in a patient with newly diagnosed hairy cell leukemia (HCL) to highlight the importance of early recognition, diagnosis, and treatment of Legionnaire's disease to reduce morbidity and mortality.

Pseudomonas otitidis bacteremia in an immunocompromised patient with cellulitis: case report and literature review.

BACKGROUND: Pseudomonas otitidis belongs to the genus Pseudomonas and causes various infections, including ear, skin, and soft tissue infections. P. otitidis has a unique susceptibility profile, being susceptible to penicillins and cephalosporins but resistant to carbapenems, due to the production of the metallo-ß-lactamase called POM-1. This revealed genetic similarities with Pseudomonas aeruginosa, which can sometimes lead to misidentification. CASE PRESENTATION: We report the case of a 70-year-old Japanese male who developed cellulitis and bacteremia during chemotherapy for multiple myeloma. He was initially treated with meropenem, but blood culture later revealed gram-negative bacilli identified as P. otitidis using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Carbapenem resistance was predicted from previous reports; therefore, we switched to dual therapy with levofloxacin and cefepime, and favorable treatment results were obtained. CONCLUSION: This is the first reported case of P. otitidis cellulitis and bacteremia in an immunocompromised patient. Carbapenems are typically used in immunocompromised patients and P. otitidis is often resistant to it. However, its biochemical properties are similar to those of Pseudomonas aeruginosa; therefore, its accurate identification is critical. In the present study, we rapidly identified P. otitidis using MALDI-TOF MS and switched from carbapenems to an appropriate antimicrobial therapy, resulting in a successful outcome.

HIV Patient With a Complicated and Unique Presentation of the Monkeypox Virus.

Monkeypox virus presents a concerning challenge, as it is known for its ability to spread through a diverse range of transmission routes, including established pathways like direct contact and shared living spaces, with the spectrum of potential methods appearing to be limitless. This immunocompromised 43-year-old HIV patient presented to the emergency department (ED) in the United States with shortness of breath, cough, and painful lesions for several months. Numerous consults and a full panel of testing revealed an odd case of the monkeypox virus that strayed away from the predefined classifications for the disease. The case sheds light on the need for further research in immunocompromised patient populations as their presentations may be different from what research currently suggests.

Clinical Efficiency of Metagenomic Next-Generation Sequencing in Sputum for Pathogen Detection of Patients with Pneumonia According to Disease Severity and Host Immune Status.

Purpose: Severe pneumonia causes the highest mortality rate in immunocompromised patients. This study aimed to investigate the pathogen diagnostic efficacy of metagenomic next-generation sequencing (mNGS) using sputum sample in patients with pneumonia according to patients' disease severity and immune conditions. Patients and Methods: A total of 180 patients suffering from pneumonia were recruited, and sputum samples were collected in duplicate for pathogen detection by both conventional microbiological tests (CMT) and mNGS. Then, the performance of pathogen identification was examined between two methods, according to disease severity and patients' immune status. Results: In comparison to CMT, mNGS had higher positivity rates in all patients with pneumonia (85.0% vs 62.2%, P=9.445e-07). The most commonly detected microorganism in sputum of pneumonia patients was Acinetobacter baumannii (42/180, 23.3%) in bacterum level, Candida albicans in fungus level (44/180, 24.4%), and Human herpesvirus 1 (39/180, 27.5%) in virus level. However, for mNGS results, Candida albicans in 34.9% of positive patients, and Human herpesvirus 1 in 7.7% of positive cases were confirmed as pathogens causing pneumonia. Acinetobacter baumannii detected by mNGS in 75% of positive patients was diagnosed as pathogen of pneumonia. The microorganism profile of sputum mNGS differed according to disease severity and immune status of patients. Pneumocystis jirovecii was more likely to infect immunocompromised patients (P=0.002). Pseudomonas aeruginosa (14.8% vs 0.0%, P=0.008) and Human herpesvirus 1 (26.1% vs 5.3%, P=0.004) had higher infection rate in patients with severe pneumonia compared with non-severe cases. mNGS had overwhelming advantages over CMT in detecting a lot of microorganisms including Streptococcus pneumoniae, Enterococcus faecium, Pneumocystis jirovecii, and majority of viruses. Conclusion: mNGS is a complementary tool of CMT for detecting suspected pathogens for patients with lower respiratory infections. The interpretation of opportunistic pathogens identified by mNGS is challenging, and needs comprehensive consideration of sequencing data and clinical factors.