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Article ; Online: An isothermal CRISPR- based lateral flow assay for detection of Neisseria meningitidis.

Huyen, Dao Thi / Reboud, Julien / Quyen, Dao Thanh / Cooper, Jonathan M / Velavan, Thirumalaisamy P / Trung, Ngo Tat / Song, Le Huu

Annals of clinical microbiology and antimicrobials

2024 Volume 23, Issue 1, Page(s) 28

Abstract: Background: Neisseria meningitidis can cause life-threatening meningococcal meningitis and meningococcemia. Old standard microbiological results from CSF/blood cultures are time consuming. This study aimed to combine the sensitivity of loop-mediated ... ...

Abstract	Background: Neisseria meningitidis can cause life-threatening meningococcal meningitis and meningococcemia. Old standard microbiological results from CSF/blood cultures are time consuming. This study aimed to combine the sensitivity of loop-mediated isothermal nucleic acid amplification (LAMP) with the specificity of CRISPR/Cas12a cleavage to demonstrate a reliable diagnostic assay for rapid detection of N. meningitidis. Methods: A total of n = 139 samples were collected from patients with suspected meningococcal disease and were used for evaluation. The extracted DNA was subjected to qualitative real-time PCR, targeting capsular transporter gene (ctrA) of N. meningitidis. LAMP-specific primer pairs, also targeting the ctrA, were designed and the LAMP products were subjected to CRISPR/Cas12 cleavage reaction. the readout was on a lateral flow strip. Sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of LAMP-CRISPR/Cas was compared with real-time PCR assays. The limit of detection (LOD) was established with serial dilutions of the target N. meningitidis DNA and calculated by Probit regression analysis. Results: Six LAMP assay-specific primers were developed targeting the ctrA gene of N. meningitidis, which is conserved in all meningococcal serogroups. The LAMP primers did not amplify DNA from other bacterial DNA tested, showing 100% specificity. The use of 0.4 M betaine increased the sensitivity and stability of the reaction. LAMP-CRISPR/Cas detected meningococcal serogroups (B, C, W). The assay showed no cross-reactivity and was specific for N. meningitidis. The LOD was 74 (95% CI: 47-311) N. meningitidis copies. The LAMP-CRISPR/Cas performed well compared to the gold standard. In the 139 samples from suspected patients, the sensitivity and specificity of the test were 91% and 99% respectively. Conclusion: This developed and optimized method can complement for the available gold standard for the timely diagnosis of meningococcal meningitis and meningococcemia.
MeSH term(s)	Humans ; Neisseria meningitidis/genetics ; Meningitis, Meningococcal/diagnosis ; Meningitis, Meningococcal/microbiology ; Meningococcal Infections/diagnosis ; Meningococcal Infections/microbiology ; Sensitivity and Specificity ; DNA, Bacterial/genetics ; Sepsis
Chemical Substances	DNA, Bacterial
Language	English
Publishing date	2024-03-30
Publishing country	England
Document type	Journal Article
ZDB-ID	2097873-X
ISSN	1476-0711 ; 1476-0711
ISSN (online)	1476-0711
ISSN	1476-0711
DOI	10.1186/s12941-024-00688-1
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Viral and serological testing of SARS-CoV-2 among health care workers and patients in Vietnam.

Song, Le Huu / Hoan, Nghiem Xuan / Bang, Mai Hong / Kremsner, Peter G / Velavan, Thirumalaisamy P

The Lancet Regional Health. Western Pacific

2021 Volume 8, Page(s) 100113

Language	English
Publishing date	2021-03-02
Document type	Journal Article
ISSN	2666-6065
ISSN (online)	2666-6065
DOI	10.1016/j.lanwpc.2021.100113
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Article ; Online: CRISPR-Cas12a combination to alleviate the false-positive in loop-mediated isothermal amplification-based diagnosis of Neisseria meningitidis.

Trung, Ngo Tat / Son, Le Huu Phuc / Hien, Trinh Xuan / Quyen, Dao Thanh / Bang, Mai Hong / Song, Le Huu

BMC infectious diseases

2022 Volume 22, Issue 1, Page(s) 429

Abstract: Background: Loop isothermal amplification (LAMP) has recently been proposed as a point-of-care diagnostic tool to detect acute infectious pathogens; however, this technique embeds risk of generating false-positive results. Whereas, with abilities to ... ...

Abstract	Background: Loop isothermal amplification (LAMP) has recently been proposed as a point-of-care diagnostic tool to detect acute infectious pathogens; however, this technique embeds risk of generating false-positive results. Whereas, with abilities to accurately recognize specific sequence, the CRISPR/Cas12a can forms complexes with cognate RNA sensors and cleave pathogen's DNA targets complimerntary to its cognate RNA, afterward acquiring the collateral activity to unbiasedly cut nearby off-target fragments. Therefore, if relevant fluorescent-quencher-nucleic probes are present in the reaction, the non-specific cleavage of probes releases fluorescences and establish diagnostic read-outs. Methods: The MetA gene of N. meningitidis was selected as target to optimize the LAMP reaction, whereas pseudo-dilution series of N. meningitidis gemonics DNA was used to establish the detection limit of LAMP/Cas12a combination assay. The diagnostic performance of established LAMP/Cas12a combination assay was validated in comparation with standard real-time PCR on 51 CSF samples (14 N. meningitidis confirmed patients and 37 control subjects). Results: In relevant biochemical conditions, CRISPR-Cas12a and LAMP can work synchronously to accurately identify genetics materials of Nesseria menitigistis at the level 40 copies/reaction less than 2 h. Conclusions: In properly optimized conditions, the CRISPR-Cas12a system helps to alleviate false positive result hence enhancing the specificity of the LAMP assays.
MeSH term(s)	CRISPR-Cas Systems ; DNA ; Humans ; Molecular Diagnostic Techniques ; Neisseria meningitidis/genetics ; Nucleic Acid Amplification Techniques/methods ; RNA
Chemical Substances	RNA (63231-63-0) ; DNA (9007-49-2)
Language	English
Publishing date	2022-05-04
Publishing country	England
Document type	Journal Article
ZDB-ID	2041550-3
ISSN	1471-2334 ; 1471-2334
ISSN (online)	1471-2334
ISSN	1471-2334
DOI	10.1186/s12879-022-07363-w
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Article ; Online: PCR-based Sepsis@Quick test is superior in comparison with blood culture for identification of sepsis-causative pathogens.

Trung, Ngo Tat / Thau, Nguyen Sy / Bang, Mai Hong / Song, Le Huu

Scientific reports

2019 Volume 9, Issue 1, Page(s) 13663

Abstract: Sepsis is an acute, often fatal syndrome that requires early diagnosis and proper treatment. Blood culture (BC) is the gold standard for the identification of pathogens, however it has marked limitations, including that it is time-consuming (delaying ... ...

Abstract	Sepsis is an acute, often fatal syndrome that requires early diagnosis and proper treatment. Blood culture (BC) is the gold standard for the identification of pathogens, however it has marked limitations, including that it is time-consuming (delaying treatment) and can only detect microbes that readily grow under culture conditions. Alternatively, non-culture-based methodologies like polymerase chain reaction (PCR) are faster but also have limitations; e.g., the reaction is often inhibited by the abundance of human DNA and thus can only detect limited known target pathogens. In our previous publication, we have demonstrated a proof-of-concept of a simple pre-analytical tool to remove human DNA from patients' blood specimens, hence allowing downstream PCRs to detect rare bacterial genetic materials. In the current study, we reported a better performance of a novel prototype diagnosis kit named Sepsis@Quick that combines human DNA removal step with real-time PCRs compared to blood-culture for identifying sepsis causative bacteria. Our data showed that Sepsis@Quick is superior to blood culture in which the novel diagnostic kit could identify more pathogens and even polymicrobial infection, faster and less influenced by the empirical administration of broad spectrum antibiotic therapy (single administration or combination of cephalosporin III and fluoroquinolon). Additionally, for the first time, we demonstrated that positive results achieved by Sepsis@Quick are significantly associated with a reduction of sepsis-related mortality.
MeSH term(s)	Adult ; Aged ; Aged, 80 and over ; Bacteria/genetics ; Bacteria/growth & development ; Bacteria/isolation & purification ; Bacterial Infections/diagnosis ; Blood Culture/methods ; DNA, Bacterial/genetics ; Early Diagnosis ; Female ; Humans ; Male ; Middle Aged ; Polymerase Chain Reaction/methods ; RNA, Ribosomal, 16S/genetics ; Reagent Kits, Diagnostic ; Sensitivity and Specificity ; Sepsis/blood ; Sepsis/microbiology
Chemical Substances	DNA, Bacterial ; RNA, Ribosomal, 16S ; Reagent Kits, Diagnostic
Language	English
Publishing date	2019-09-20
Publishing country	England
Document type	Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-019-50150-y
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Article ; Online: Markers of prolonged hospitalisation in severe dengue.

Recker, Mario / Fleischmann, Wim A / Nghia, Trinh Huu / Truong, Nguyen Van / Nam, Le Van / Duc Anh, Do / Song, Le Huu / The, Nguyen Trong / Anh, Chu Xuan / Hoang, Nguyen Viet / My Truong, Nhat / Toan, Nguyen Linh / Kremsner, Peter G / Velavan, Thirumalaisamy P

PLoS neglected tropical diseases

2024 Volume 18, Issue 1, Page(s) e0011922

Abstract: Background: Dengue is one of the most common diseases in the tropics and subtropics. Whilst mortality is a rare event when adequate supportive care can be provided, a large number of patients get hospitalised with dengue every year that places a heavy ... ...

Abstract	Background: Dengue is one of the most common diseases in the tropics and subtropics. Whilst mortality is a rare event when adequate supportive care can be provided, a large number of patients get hospitalised with dengue every year that places a heavy burden on local health systems. A better understanding of the support required at the time of hospitalisation is therefore of critical importance for healthcare planning, especially when resources are limited during major outbreaks. Methods: Here we performed a retrospective analysis of clinical data from over 1500 individuals hospitalised with dengue in Vietnam between 2017 and 2019. Using a broad panel of potential biomarkers, we sought to evaluate robust predictors of prolonged hospitalisation periods. Results: Our analyses revealed a lead-time bias, whereby early admission to hospital correlates with longer hospital stays - irrespective of disease severity. Importantly, taking into account the symptom duration prior to hospitalisation significantly affects observed associations between hospitalisation length and previously reported risk markers of prolonged stays, which themselves showed marked inter-annual variations. Once corrected for symptom duration, age, temperature at admission and elevated neutrophil-to-lymphocyte ratio were found predictive of longer hospitalisation periods. Conclusion: This study demonstrates that the time since dengue symptom onset is one of the most significant predictors for the length of hospital stays, independent of the assigned severity score. Pre-hospital symptom durations need to be accounted for to evaluate clinically relevant biomarkers of dengue hospitalisation trajectories.
MeSH term(s)	Humans ; Severe Dengue/diagnosis ; Severe Dengue/epidemiology ; Retrospective Studies ; Hospitalization ; Length of Stay ; Biomarkers
Chemical Substances	Biomarkers
Language	English
Publishing date	2024-01-30
Publishing country	United States
Document type	Journal Article
ZDB-ID	2429704-5
ISSN	1935-2735 ; 1935-2735
ISSN (online)	1935-2735
ISSN	1935-2735
DOI	10.1371/journal.pntd.0011922
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Article ; Online: Association of Human Leukocyte Antigen Haplotypes With End-Stage Renal Disease in Vietnamese Patients Prior to First Transplantation.

Hieu, Ho Trung / Ha, Nguyen Thu / Song, Le Huu / Nghi, Tran Hong

Transplantation proceedings

2019 Volume 51, Issue 8, Page(s) 2549–2554

Abstract: Introduction: The prevalence of chronic kidney failure is significantly increasing in Vietnam, causing a burden for health care. This study assessed the relationship of HLA-A, -B, and -DRB1 alleles with end-stage renal disease (ESRD).: Method: A ... ...

Abstract	Introduction: The prevalence of chronic kidney failure is significantly increasing in Vietnam, causing a burden for health care. This study assessed the relationship of HLA-A, -B, and -DRB1 alleles with end-stage renal disease (ESRD). Method: A retrospective, cross-sectional study and a comparative study using secondary data analysis were conducted on 196 ESRD patients and 187 controls from 2009 to 2017. The patient and donor profiles were collected from medical records, including age, sex, etiology of renal failure, and HLA phenotypes. HLA-A, -B, and -DRB1* typing were done by polymerase chain reaction-sequence specific primers. Result: The most frequent HLA alleles in Vietnamese patients with ESRD were HLA-A02, -A11, -B15, -B46, -DRB104, -DRB109, and -DRB112. The haplotypes HLA-A0233 (odds ratio [OR] = 0.40, 95% CI: 0.15-0.98) had a negative association for ESRD. The haplotypes HLA-B1515 (OR = 4.14, 95% CI: 1.52-11.26) and HLA-DRB11212 (OR = 2.01, 95% CI: 1.06-3.81) had a positive association for ESRD. The haplotypes HLA-B1515 (OR = 4.69, 95% CI: 1.69-13.03) and -DRB11212 (OR = 2.15, 95% CI: 1.10-4.21) had a positive association for ESRD related to glomerulonephritis. The HLA-B1557 (OR = 17.34, 95% CI: 2.70-11.49) had a positive association for ESRD related to hypertension. Conclusion:* The haplotypes of HLA class I and II had significant relationships with ESRD. The results of our study should be confirmed in further investigations.
MeSH term(s)	Adult ; Cross-Sectional Studies ; Female ; Gene Frequency ; Glomerulonephritis/genetics ; Glomerulonephritis/immunology ; Haplotypes/genetics ; Histocompatibility Antigens Class I/genetics ; Humans ; Kidney Failure, Chronic/genetics ; Kidney Failure, Chronic/immunology ; Kidney Failure, Chronic/surgery ; Kidney Transplantation ; Male ; Middle Aged ; Odds Ratio ; Phenotype ; Preoperative Period ; Retrospective Studies ; Vietnam
Chemical Substances	Histocompatibility Antigens Class I
Language	English
Publishing date	2019-08-28
Publishing country	United States
Document type	Evaluation Study ; Journal Article
ZDB-ID	82046-5
ISSN	1873-2623 ; 0041-1345
ISSN (online)	1873-2623
ISSN	0041-1345
DOI	10.1016/j.transproceed.2019.03.067
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Article ; Online: High Hepatitis E Virus (HEV) Seroprevalence and No Evidence of HEV Viraemia in Vietnamese Blood Donors.

Cao, Le Chi / Martin, Vanessa / Linh, Le Thi Kieu / Giang, Tran Thi / Chau, Ngo Thi Minh / Anh, Ton Nu Phuong / Nghia, Vu Xuan / The, Nguyen Trong / My, Truong Nhat / Sy, Bui Tien / Toan, Nguyen Linh / Song, Le Huu / Bock, C-Thomas / Velavan, Thirumalaisamy P

Viruses

2023 Volume 15, Issue 10

Abstract: The prevalence of hepatitis E virus (HEV) in the Vietnamese population remains underestimated. The aim of the present study was to investigate the seroprevalence of HEV IgG/IgM antibodies and the presence of HEV RNA in blood donors as a part of ... ...

Abstract	The prevalence of hepatitis E virus (HEV) in the Vietnamese population remains underestimated. The aim of the present study was to investigate the seroprevalence of HEV IgG/IgM antibodies and the presence of HEV RNA in blood donors as a part of epidemiological surveillance for transfusion-transmitted viruses. Serum samples from blood donors (
MeSH term(s)	Male ; Humans ; Female ; Hepatitis E virus/genetics ; Blood Donors ; Seroepidemiologic Studies ; Viremia/epidemiology ; Southeast Asian People ; Vietnam/epidemiology ; Hepatitis E ; Hepatitis Antibodies ; RNA, Viral/genetics ; Immunoglobulin G ; Immunoglobulin M
Chemical Substances	Hepatitis Antibodies ; RNA, Viral ; Immunoglobulin G ; Immunoglobulin M
Language	English
Publishing date	2023-10-11
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v15102075
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Article ; Online: Aetiologies and clinical presentation of central nervous system infections in Vietnamese patients: a prospective study.

Gabor, Julian Justin / Anh, Chu Xuan / Sy, Bui Tien / Hoan, Phan Quoc / Quyen, Dao Thanh / The, Nguyen Trong / Kuk, Salih / Kremsner, Peter G / Meyer, Christian G / Song, Le Huu / Velavan, Thirumalaisamy P

Scientific reports

2022 Volume 12, Issue 1, Page(s) 18065

Abstract: Knowledge of the clinical presentation of central nervous system (CNS) infections and the causative pathogens is crucial for appropriate diagnosis and rapid initiation of appropriate treatment to prevent severe neurological sequelae. The aim of this ... ...

Abstract	Knowledge of the clinical presentation of central nervous system (CNS) infections and the causative pathogens is crucial for appropriate diagnosis and rapid initiation of appropriate treatment to prevent severe neurological sequelae. The aim of this study is to understand the aetiology of CNS infections based on the clinical presentation of Vietnamese patients. A prospective hospital-based cohort study was conducted between May 2014 and May 2017. We screened 137 patients with clinically suspected CNS infection for fungal, bacterial and viral pathogens using their cerebrospinal fluid (CSF) and blood cultures. In addition, DNA or RNA extracted from CSF samples were subjected to nucleic acid testing (NAT) with a selective panel of bacterial, viral and fungal pathogens. At least one pathogen could be detected in 41% (n = 56) of the patients. The main pathogens causing CNS infections were Streptococcus suis (n = 16; 12%) and Neisseria meningitidis (n = 9; 7%), followed by Herpes simplex virus 1/2 (n = 4; 3%) and Klebsiella pneumoniae (n = 4; 3%). Other pathogens were only identified in a few cases. Patients with bacterial CNS infections were significantly older, had a worse outcome, a lower Glasgow Coma Scale (GCS), a higher rate of speech impairment and neck stiffness than patients with viral or tuberculous CNS infections. In northern Vietnam, adults are mostly affected by bacterial CNS infections, which have a severe clinical course and worse outcomes compared to viral or tuberculous CNS infections. Clinicians should be aware of the regional occurrence of pathogens to initiate rapid and appropriate diagnosis and treatment.
MeSH term(s)	Adult ; Humans ; Prospective Studies ; Cohort Studies ; Vietnam/epidemiology ; Central Nervous System Infections/diagnosis ; Central Nervous System Infections/epidemiology ; Central Nervous System Infections/cerebrospinal fluid ; Central Nervous System Bacterial Infections ; Asian People
Language	English
Publishing date	2022-10-27
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-022-23007-0
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Article ; Online: Author Correction: Genetic variants of programmed cell death 1 are associated with HBV infection and liver disease progression.

Hoan, Nghiem Xuan / Huyen, Pham Thi Minh / Binh, Mai Thanh / Trung, Ngo Tat / Giang, Dao Phuong / Linh, Bui Thuy / Dung, Dang Thi Ngoc / Pallerla, Srinivas Reddy / Kremsner, Peter G / Velavan, Thirumalaisamy P / Bang, Mai Hong / Song, Le Huu

Scientific reports

2022 Volume 12, Issue 1, Page(s) 2034

Language	English
Publishing date	2022-02-01
Publishing country	England
Document type	Published Erratum
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-022-06068-z
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Article ; Online: SARS-CoV-2 viral dynamics of the first 1000 sequences from Vietnam and neighbouring ASEAN countries.

Hoan, Nghiem Xuan / Pallerla, Srinivas Reddy / Huy, Pham Xuan / Krämer, Hannah / My, Truong Nhat / Tung, Tran Thanh / Hoan, Phan Quoc / Toan, Nguyen Linh / Song, Le Huu / Velavan, Thirumalaisamy P

IJID Regions (Online)

2022 Volume 2, Page(s) 175–179

Abstract: Objective: The regional distribution and transmissibility of existing COVID-19 variants of concern (VOC) has led to concerns about increasing transmission, given the ability of VOCs to evade immunity as breakthrough infections become more prevalent.: ... ...

Abstract	Objective: The regional distribution and transmissibility of existing COVID-19 variants of concern (VOC) has led to concerns about increasing transmission, given the ability of VOCs to evade immunity as breakthrough infections become more prevalent. Methods: SARS-CoV-2 genomes ( Results: Between January and November 8, 2021, VOCs, including alpha (B.1.1.7), beta (B.1.351), gamma (P.1), and delta (B.1.617.2), were observed across the ASEAN countries. While alpha and delta were the major VOCs in nine ASEAN countries, delta was predominant. The alpha VOC was first reported by Singapore, beta by Malaysia, gamma by the Philippines, and delta by Singapore. Of the first 1000 genomes analysed from Vietnam, alpha and delta were the most represented, with delta being the dominant VOC from May 2021. The delta variant was introduced in early January 2021, and formed a large cluster within the representative genomes. Conclusion: Spatial and temporal monitoring of SARS-CoV-2 variants is critical to the understanding of viral phylodynamics, and will provide useful guidance to policy makers for infection prevention and control.
Language	English
Publishing date	2022-01-20
Publishing country	England
Document type	Journal Article
ISSN	2772-7076
ISSN (online)	2772-7076
DOI	10.1016/j.ijregi.2022.01.008
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