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Article ; Online: Rapid diagnosis of Aspergillus fumigatus endocarditis using mNGS assay: A case report and review of the literature.

Li, Xiaowei / Li, Dandan / Han, Dongsheng

Diagnostic microbiology and infectious disease

2024 Volume 108, Issue 3, Page(s) 116171

Abstract: Fungal endocarditis is caused mainly by Candida albicans and Aspergillus spp. and was first reported in the 1950s. Natural-valve endocarditis caused by Aspergillus is relatively uncommon. In this case, a 56-year-old male patient was admitted to the ... ...

Abstract	Fungal endocarditis is caused mainly by Candida albicans and Aspergillus spp. and was first reported in the 1950s. Natural-valve endocarditis caused by Aspergillus is relatively uncommon. In this case, a 56-year-old male patient was admitted to the hospital on account of a cough accompanied by chills and fever and ineffective self-medication. Infective endocarditis was initially suspected based on echocardiography (indicating right atrial growth) and clinical manifestations. However, routine pathogen detections were always negative. The patient's condition was identified as Aspergillus fumigatus endocarditis (AFE) and was treated with targeted therapy, considering the detection of significant AFE sequences in the blood through metagenomic next-generation sequencing (mNGS). On this basis, the paper further summarizes the clinical manifestations, diagnosis, treatments, and outcomes of AFE endocarditis cases reported in recent years, aiming to provide a reference to better understand this rare infective disease and guide medical practitioners in choosing the right diagnostic and therapeutic strategy.
MeSH term(s)	Humans ; Male ; Middle Aged ; Aspergillus fumigatus/genetics ; Endocarditis/microbiology ; Endocarditis, Bacterial/diagnosis ; Aspergillus ; High-Throughput Nucleotide Sequencing
Language	English
Publishing date	2024-01-01
Publishing country	United States
Document type	Review ; Case Reports
ZDB-ID	604920-5
ISSN	1879-0070 ; 0732-8893
ISSN (online)	1879-0070
ISSN	0732-8893
DOI	10.1016/j.diagmicrobio.2023.116171
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Article: Lemierre Syndrome: Report of a Case with an Innovative Diagnostic Method and Literature Review.

Xie, Mengxiao / Liu, Jian / Zheng, Jieyuan / Wang, Jingchao / Han, Dongsheng

Infection and drug resistance

2024 Volume 17, Page(s) 1–10

Abstract: Objective: To understand the clinical features, diagnosis and treatment of Lemierre syndrome (LS), a high-risk and low-prevalence infectious disease.: Methods: We present the severe LS case that was diagnosed using metagenomic next-generation ... ...

Abstract	Objective: To understand the clinical features, diagnosis and treatment of Lemierre syndrome (LS), a high-risk and low-prevalence infectious disease. Methods: We present the severe LS case that was diagnosed using metagenomic next-generation sequencing (mNGS) in our hospital, and systematically summarized the diagnosis and treatment strategies of patients that reported LS from 2006 to 2022. Results: The 24-year-old patient in our hospital suffered from cranial nerve paralysis, a neurological complication rarely seen in LS cases. The causative agent ( Conclusion: We summarized the clinical presentation, diagnosis, treatment, and regression of 17 symptomatic cases reported LS to provide clinicians with knowledge about this rare but fatal disease. mNGS assays should be considered as early as possible to identify the responsible pathogens for acute and critically ill patients with suspected infections in order to implement accurate and effective treatment.
Language	English
Publishing date	2024-01-03
Publishing country	New Zealand
Document type	Case Reports
ZDB-ID	2494856-1
ISSN	1178-6973
ISSN	1178-6973
DOI	10.2147/IDR.S439069
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Article ; Online: PCR cloning Intermediated Gibson assembly (PIG) for Constructing DNA Repair Templates in CRISPR-Cas9 Based Gene Editing.

Han, Dongsheng / Churcher, Scott / Nordman, Jared T

microPublication biology

2023 Volume 2023

Abstract: The CRISPR-Cas9 gene-editing system has revolutionized genome engineering, allowing precise modifications to be made in a wide range of organisms. One significant challenge associated with CRISPR-Cas9 mediated gene editing is the construction of DNA ... ...

Abstract	The CRISPR-Cas9 gene-editing system has revolutionized genome engineering, allowing precise modifications to be made in a wide range of organisms. One significant challenge associated with CRISPR-Cas9 mediated gene editing is the construction of DNA repair templates containing homology arms, a screenable marker and a tag sequence of interest. Here, we present an efficient, two-step strategy to generate DNA repair templates in approximately one week, facilitating rapid and precise genome engineering applications.
Language	English
Publishing date	2023-08-18
Publishing country	United States
Document type	Journal Article
ISSN	2578-9430
ISSN (online)	2578-9430
DOI	10.17912/micropub.biology.000916
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Article ; Online: Clinical usefulness of metagenomic next-generation sequencing for Rickettsia and Coxiella burnetii diagnosis.

Zhang, Xuan / Chen, Huixin / Han, Dongsheng / Wu, Wei

European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology

2023 Volume 42, Issue 6, Page(s) 681–689

Abstract: Rickettsia and Coxiella burnetii are zoonotic tick-borne pathogens that cause febrile illnesses in humans. Metagenomic next-generation sequencing (mNGS) is a new technology used to diagnose infectious diseases. However, clinical experience with applying ... ...

Abstract	Rickettsia and Coxiella burnetii are zoonotic tick-borne pathogens that cause febrile illnesses in humans. Metagenomic next-generation sequencing (mNGS) is a new technology used to diagnose infectious diseases. However, clinical experience with applying the test to rickettsioses and Q fever is relatively limited. Therefore, this study aimed to explore the diagnostic performance of mNGS in detecting Rickettsia and C. burnetii. We retrospectively studied patients with rickettsioses or Q fever between August 2021 and July 2022. Peripheral blood mNGS and polymerase chain reaction (PCR) were performed for all patients. Clinical data were retrieved for analysis. Thirteen patients were included in this study (eleven confirmed cases and two suspected cases). Signs and symptoms included fever (13, 100%), rash (7, 53.8%), muscle soreness (5, 38.5%), headache (4, 30.8%), skin eschar (3, 23.1%), and disturbance of consciousness (2, 15.4%). In addition, eight patients (61.6%) had thrombocytopenia, ten (76.9%) had liver function impairment, and two (15.4%) had renal function impairment. The results of mNGS revealed seven patients with R. japonica (53.8%), five with C. burneti (38.5%), two with R. heilongjiangensis (15.4%), and one with R. honei (7.7%). PCR results were positive in 11 patients (84.6%). After receiving doxycycline-based treatment, 12 (92.3%) patients returned to a normal temperature within 72 h. All patients were discharged in better health. Therefore, mNGS can help diagnose Rickettsia and C. burnetii and shorten the diagnosis time, especially for patients with atypical clinical manifestations and unclear epidemiologic evidence of a tick bite or exposure.
MeSH term(s)	Humans ; Rickettsia/genetics ; Coxiella burnetii/genetics ; Q Fever/diagnosis ; Retrospective Studies ; Rickettsia Infections/diagnosis ; High-Throughput Nucleotide Sequencing
Language	English
Publishing date	2023-03-30
Publishing country	Germany
Document type	Journal Article
ZDB-ID	603155-9
ISSN	1435-4373 ; 0934-9723 ; 0722-2211
ISSN (online)	1435-4373
ISSN	0934-9723 ; 0722-2211
DOI	10.1007/s10096-023-04586-w
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Article ; Online: Prevalence of Asymptomatic SARS-CoV-2 Infection.

Han, Dongsheng / Li, Jinming

Annals of internal medicine

2021 Volume 174, Issue 2, Page(s) 284

MeSH term(s)	Asymptomatic Diseases ; COVID-19 ; Coronavirus Infections ; Humans ; Prevalence ; SARS-CoV-2
Language	English
Publishing date	2021-02-15
Publishing country	United States
Document type	Letter ; Comment
ZDB-ID	336-0
ISSN	1539-3704 ; 0003-4819
ISSN (online)	1539-3704
ISSN	0003-4819
DOI	10.7326/L20-1281
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Article: Clinical Performance of Self-Collected Purified Water Gargle for Detection of Influenza a Virus Infection by Real-Time RT-PCR.

Li, Guiling / Tan, Tianyang / Chen, Luting / Bao, Jiaqi / Han, Dongsheng / Yu, Fei

Infection and drug resistance

2024 Volume 17, Page(s) 1903–1910

Abstract: Purpose: Self-collected specimens are increasingly being used as alternatives to swab-based methods for the detection of respiratory viruses. While saliva is well accepted, gargle specimens are a potential alternative with characteristics that are more ... ...

Abstract	Purpose: Self-collected specimens are increasingly being used as alternatives to swab-based methods for the detection of respiratory viruses. While saliva is well accepted, gargle specimens are a potential alternative with characteristics that are more favorable for laboratory handling. This study assessed the performance of gargle specimens in the detection of influenza A viruses (IAVs). Patients and methods: We performed a prospective head-to-head comparison between combined nasopharyngeal and oropharyngeal swabs (NPS&OPS) and purified water gargle (PWG) among adult outpatients with febrile respiratory symptoms to detect IAVs using real-time RT-PCR during two influenza seasons. Results: During study periods 1 (July 13 to 26, 2022, H3N2 predominated) and 2 (February 25 to March 10, 2023, H1N1 pdm09 predominated), a total of 459 patients were recruited. The overall agreement between the NPS&OPS and PWG was 85.0% (390/459, κ = 0.697), with 88.0% in period 1 and 82.6% in period 2. The detection rate of IAVs in PWG (51.6%, 237/459) was lower than that in NPS&OPS (62.3%, 286/459) (p < 0.0001). The overall sensitivity and specificity were 96.6% (93.7-98.3%) and 100% (97.1-100%) in NPS&OPS and were 80.1% (75.0-84.4%) and 100% (97.1-100%) in PWG, respectively. Among the 227 pairs of concordant positive specimens, cycle threshold (Ct) values were significantly lower in NPS&OPS than in PWG (median Ct values: 24.2, 28.2, p < 0.0001). Conclusion: Although self-collected PWG specimens offer acceptable performance for IAVs molecular testing, NPS&OPS remain a reliable option. Given the convenience of collection, nonviscous gargles are recommended for viral detection during emergencies or under specific conditions.
Language	English
Publishing date	2024-05-14
Publishing country	New Zealand
Document type	Journal Article
ZDB-ID	2494856-1
ISSN	1178-6973
ISSN	1178-6973
DOI	10.2147/IDR.S450991
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Article ; Online: Fatal multiple organ dysfunction caused by commensal bacteria of urogenital tract infection in adult lung transplant recipients: two case reports

Tian, Manman / Han, Dongsheng / Ma, Subo / Liu, Tingting / Yang, Wu / Zheng, Xia

Virol J. 2023 Dec., v. 20, no. 1 p.24-24

2023

Abstract: BACKGROUND: Infection following lung transplantation has been the focus of clinical concerns. The colonization rate of commensal bacteria of the urogenital tract, including Mycoplasma hominis, Ureaplasma urealyticum (UU), and herpes simplex virus type-2 ( ...

Abstract	BACKGROUND: Infection following lung transplantation has been the focus of clinical concerns. The colonization rate of commensal bacteria of the urogenital tract, including Mycoplasma hominis, Ureaplasma urealyticum (UU), and herpes simplex virus type-2 (HSV-2), is high, which may cause secondary infection after transplantation. CASE PRESENTATION: Twenty-three-year-old and 67-year-old women underwent lung transplantation for different causes. Shortly after the operation, they developed perineal skin ulcers, hypoxia, and intractable epilepsy. Subsequent computed tomography (CT) of the chest showed lung consolidation, and cranial CT showed shallowing sulci and gyri. UU and HSV-2 were detected in bronchoalveolar lavage fluid by next-generation sequencing, and HSV-2 was shown in the cerebrospinal fluid of both patients. Despite active treatment, both suffered irreversible brain function damage within 72 h of the seizure. CONCLUSIONS: Clinicians should know that commensal bacteria of urogenital tract infections can lead to fatal multiple organ dysfunction after lung transplantation.
Keywords	Mycoplasma hominis ; Ureaplasma urealyticum ; adults ; brain ; cerebrospinal fluid ; chest ; computed tomography ; epilepsy ; herpes simplex ; hypoxia ; lungs ; secondary infection ; viruses
Language	English
Dates of publication	2023-12
Size	p. 24.
Publishing place	BioMed Central
Document type	Article ; Online
ZDB-ID	2160640-7
ISSN	1743-422X
ISSN	1743-422X
DOI	10.1186/s12985-022-01958-0
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Article ; Online: Fatal multiple organ dysfunction caused by commensal bacteria of urogenital tract infection in adult lung transplant recipients: two case reports.

Tian, Manman / Han, Dongsheng / Ma, Subo / Liu, Tingting / Yang, Wu / Zheng, Xia

Virology journal

2023 Volume 20, Issue 1, Page(s) 24

Abstract: Background: Infection following lung transplantation has been the focus of clinical concerns. The colonization rate of commensal bacteria of the urogenital tract, including Mycoplasma hominis, Ureaplasma urealyticum (UU), and herpes simplex virus type-2 ...

Abstract	Background: Infection following lung transplantation has been the focus of clinical concerns. The colonization rate of commensal bacteria of the urogenital tract, including Mycoplasma hominis, Ureaplasma urealyticum (UU), and herpes simplex virus type-2 (HSV-2), is high, which may cause secondary infection after transplantation. Case presentation: Twenty-three-year-old and 67-year-old women underwent lung transplantation for different causes. Shortly after the operation, they developed perineal skin ulcers, hypoxia, and intractable epilepsy. Subsequent computed tomography (CT) of the chest showed lung consolidation, and cranial CT showed shallowing sulci and gyri. UU and HSV-2 were detected in bronchoalveolar lavage fluid by next-generation sequencing, and HSV-2 was shown in the cerebrospinal fluid of both patients. Despite active treatment, both suffered irreversible brain function damage within 72 h of the seizure. Conclusions: Clinicians should know that commensal bacteria of urogenital tract infections can lead to fatal multiple organ dysfunction after lung transplantation.
MeSH term(s)	Humans ; Adult ; Female ; Young Adult ; Mycoplasma Infections/complications ; Mycoplasma Infections/drug therapy ; Mycoplasma Infections/microbiology ; Transplant Recipients ; Multiple Organ Failure ; Ureaplasma urealyticum ; Bacteria ; Lung/diagnostic imaging
Language	English
Publishing date	2023-02-08
Publishing country	England
Document type	Case Reports ; Journal Article
ZDB-ID	2160640-7
ISSN	1743-422X ; 1743-422X
ISSN (online)	1743-422X
ISSN	1743-422X
DOI	10.1186/s12985-022-01958-0
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Article: Diagnostic Performance of Metagenomic Next-Generation Sequencing in Central Nervous System Cryptococcosis Using Cerebrospinal Fluid.

Zhang, Xuan / Lin, Yaqing / Chen, Huixin / Hu, Jianhua / Zhao, Hong / Yang, Meifang / Han, Dongsheng

Infection and drug resistance

2023 Volume 16, Page(s) 6175–6183

Abstract: Purpose: Metagenomic next-generation sequencing (mNGS) has been widely used to diagnose infectious diseases. However, there are few studies on its diagnostic performance in the central nervous system (CNS) cryptococcosis. This study examined the ... ...

Abstract	Purpose: Metagenomic next-generation sequencing (mNGS) has been widely used to diagnose infectious diseases. However, there are few studies on its diagnostic performance in the central nervous system (CNS) cryptococcosis. This study examined the diagnostic efficacy of mNGS in identifying Patients and methods: From March 2021 to March 2023, 290 patients with suspected CNS infection were recruited from the First Affiliated Hospital, School of Medicine, Zhejiang University, and 74 patients were ultimately included in the study. Lastly, 22 patients with CNS cryptococcosis were included. Of these patients, 25 CSF samples were enrolled. The diagnostic performance of conventional assays [including India ink, cryptococcal antigen (CrAg) testing, and culture] and mNGS was evaluated for CNS cryptococcosis. Results: In the 25 samples collected, the coincidence rates of mNGS with India ink, CrAg, and culture were 64.0% (16/25), 80.0% (20/25), and 80.0% (20/25), respectively. Without antifungal drug exposure, the coincidence rates were increased to 66.7% (10/15), 100.0% (15/15), and 93.3% (14/15), respectively. The coincidence rates after antifungal therapy were all decreased to 60.0% (6/10), 50.0% (5/10), and 60.0% (6/10), respectively. Moreover, in the 25 samples, the sensitivity of mNGS reached 80.0%, and of India ink, CrAg testing, and culture were 68.0, 100.0, and 60.0%, respectively. The mNGS showed an excellent positive rate (100.0%) in the 15 samples collected without antifungal drug exposure, which was significantly higher than the antifungal drug-exposed group (n = 10) (50.0%) ( Conclusion: mNGS is an effective tool for diagnosing CNS cryptococcosis using CSF; however, its sensitivity decreases considerably in patients who have been effectively treated with antifungal drugs.
Language	English
Publishing date	2023-09-13
Publishing country	New Zealand
Document type	Journal Article
ZDB-ID	2494856-1
ISSN	1178-6973
ISSN	1178-6973
DOI	10.2147/IDR.S425463
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Article ; Online: Metagenomics next-generation sequencing tests take the stage in the diagnosis of lower respiratory tract infections.

Diao, Zhenli / Han, Dongsheng / Zhang, Rui / Li, Jinming

Journal of advanced research

2021 Volume 38, Page(s) 201–212

Abstract: Metagenomic next-generation sequencing (mNGS) has changed the diagnosis landscape of lower respiratory tract infections (LRIs). With the development of newer sequencing assays, it is now possible to assess all microorganisms in a sample using a single ... ...

Abstract	Metagenomic next-generation sequencing (mNGS) has changed the diagnosis landscape of lower respiratory tract infections (LRIs). With the development of newer sequencing assays, it is now possible to assess all microorganisms in a sample using a single mNGS analysis. The applications of mNGS for LRIs span a wide range of areas including LRI diagnosis, airway microbiome analyses, human host response analyses, and prediction of drug resistance. mNGS is currently in an exciting transitional period; however, before implementation in a clinical setting, there are several barriers to overcome, such as the depletion of human nucleic acid, discrimination between colonization and infection, high costs, and so on. Aim of Review: In this review, we summarize the potential applications and challenges of mNGS in the diagnosis of LRIs to promote the integration of mNGS into the management of patients with respiratory tract infections in a clinical setting. Key Scientific Concepts of Review: Once its analytical validation, clinical validation and clinical utility been demonstrated, mNGS will become an important tool in the field of infectious disease diagnosis.
MeSH term(s)	High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; Metagenomics ; Microbiota/genetics ; Respiratory Tract Infections/diagnosis
Language	English
Publishing date	2021-09-29
Publishing country	Egypt
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	2541849-X
ISSN	2090-1224 ; 2090-1224
ISSN (online)	2090-1224
ISSN	2090-1224
DOI	10.1016/j.jare.2021.09.012
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