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Article ; Online: Application of digital PCR to determine the reliability of Xpert Xpress SARS-CoV-2 assay with envelope (E) gene negative and nucleocapsid (N2) gene positive results.

Wong, River Chun-Wai / Wong, Ann Han / Ho, Yolanda Iok-Ieng / Siu, Gilman Kit-Hang / Lee, Lam-Kwong / Leung, Eddie Chi-Man / Lai, Raymond Wai-Man

Diagnostic microbiology and infectious disease

2022 Volume 103, Issue 4, Page(s) 115726

Abstract: This study used digital polymerase chain reaction (dPCR) to determine whether envelope (E) gene-negative and nucleocapsid (N2) gene-positive (E-N+) results obtained with the Cepheid Xpert Xpress SARS-CoV-2 assay are reliable. Using droplet digital PCR ... ...

Abstract	This study used digital polymerase chain reaction (dPCR) to determine whether envelope (E) gene-negative and nucleocapsid (N2) gene-positive (E-N+) results obtained with the Cepheid Xpert Xpress SARS-CoV-2 assay are reliable. Using droplet digital PCR results as a reference, 18 of 22 E-N+ samples with a low viral load (81.8%) were identified as true positives.
MeSH term(s)	COVID-19/diagnosis ; COVID-19 Testing ; Clinical Laboratory Techniques/methods ; Humans ; Nasopharynx ; Nucleocapsid/genetics ; Polymerase Chain Reaction ; Reproducibility of Results ; SARS-CoV-2/genetics ; Sensitivity and Specificity
Language	English
Publishing date	2022-05-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	604920-5
ISSN	1879-0070 ; 0732-8893
ISSN (online)	1879-0070
ISSN	0732-8893
DOI	10.1016/j.diagmicrobio.2022.115726
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Article ; Online: Performance evaluation of Panther Fusion SARS-CoV-2 assay for detection of SARS-CoV-2 from deep throat saliva, nasopharyngeal, and lower-respiratory-tract specimens.

Wong, River Chun-Wai / Wong, Ann Han / Ho, Yolanda Iok-Ieng / Leung, Eddie Chi-Man / Lai, Raymond Wai-Man

Journal of medical virology

2020 Volume 93, Issue 3, Page(s) 1226–1228

MeSH term(s)	Adult ; Aged ; Biological Assay/methods ; COVID-19/diagnosis ; COVID-19/virology ; Clinical Laboratory Techniques/methods ; Female ; Humans ; Male ; Middle Aged ; Nasopharynx/virology ; Pharynx/virology ; SARS-CoV-2/genetics ; Saliva/virology
Keywords	covid19
Language	English
Publishing date	2020-10-08
Publishing country	United States
Document type	Letter
ZDB-ID	752392-0
ISSN	1096-9071 ; 0146-6615
ISSN (online)	1096-9071
ISSN	0146-6615
DOI	10.1002/jmv.26574
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Article: The clinical utility of Nanopore 16S rRNA gene sequencing for direct bacterial identification in normally sterile body fluids.

Lao, Hiu-Yin / Wong, Lily Lok-Yee / Hui, Yan / Ng, Timothy Ting-Leung / Chan, Chloe Toi-Mei / Lo, Hazel Wing-Hei / Yau, Miranda Chong-Yee / Leung, Eddie Chi-Man / Wong, River Chun-Wai / Ho, Alex Yat-Man / Yip, Kam-Tong / Lam, Jimmy Yiu-Wing / Chow, Viola Chi-Ying / Luk, Kristine Shik / Que, Tak-Lun / Chow, Franklin Wang Ngai / Siu, Gilman Kit-Hang

Frontiers in microbiology

2024 Volume 14, Page(s) 1324494

Abstract: The prolonged incubation period of traditional culture methods leads to a delay in diagnosing invasive infections. Nanopore 16S rRNA gene sequencing (Nanopore 16S) offers a potential rapid diagnostic approach for directly identifying bacteria in infected ...

Abstract	The prolonged incubation period of traditional culture methods leads to a delay in diagnosing invasive infections. Nanopore 16S rRNA gene sequencing (Nanopore 16S) offers a potential rapid diagnostic approach for directly identifying bacteria in infected body fluids. To evaluate the clinical utility of Nanopore 16S, we conducted a study involving the collection and sequencing of 128 monomicrobial samples, 65 polymicrobial samples, and 20 culture-negative body fluids. To minimize classification bias, taxonomic classification was performed using 3 analysis pipelines: Epi2me, Emu, and NanoCLUST. The result was compared to the culture references. The limit of detection of Nanopore 16S was also determined using simulated bacteremic blood samples. Among the three classifiers, Emu demonstrated the highest concordance with the culture results. It correctly identified the taxon of 125 (97.7%) of the 128 monomicrobial samples, compared to 109 (85.2%) for Epi2me and 102 (79.7%) for NanoCLUST. For the 230 cultured species in the 65 polymicrobial samples, Emu correctly identified 188 (81.7%) cultured species, compared to 174 (75.7%) for Epi2me and 125 (54.3%) for NanoCLUST. Through ROC analysis on the monomicrobial samples, we determined a threshold of relative abundance at 0.058 for distinguishing potential pathogens from background in Nanopore 16S. Applying this threshold resulted in the identification of 107 (83.6%), 117 (91.4%), and 114 (91.2%) correctly detected samples for Epi2me, Emu, and NanoCLUST, respectively, in the monomicrobial samples. Nanopore 16S coupled with Epi2me could provide preliminary results within 6 h. However, the ROC analysis of polymicrobial samples exhibited a random-like performance, making it difficult to establish a threshold. The overall limit of detection for Nanopore 16S was found to be about 90 CFU/ml.
Language	English
Publishing date	2024-01-09
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2023.1324494
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Article ; Online: Evaluation on testing of deep throat saliva and lower respiratory tract specimens with Xpert Xpress SARS-CoV-2 assay.

Wong, River Chun-Wai / Wong, Ann Han / Ho, Yolanda Iok-Ieng / Leung, Eddie Chi-Man / Lai, Raymond Wai-Man

Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology

2020 Volume 131, Page(s) 104593

Abstract: Background: Xpert® Xpress SARS-CoV-2 assay is only validated on nasopharyngeal specimens for detection of SARS-CoV-2. Other specimen types such as deep throat saliva (DTS), also known as posterior oropharyngeal saliva and lower-respiratorytract ... ...

Abstract	Background: Xpert® Xpress SARS-CoV-2 assay is only validated on nasopharyngeal specimens for detection of SARS-CoV-2. Other specimen types such as deep throat saliva (DTS), also known as posterior oropharyngeal saliva and lower-respiratorytract specimens (LRT) including sputum, tracheal aspirate and bronchoalveolar lavage are not validated. These non-validated specimen types, however, do have significant diagnostic value. Objective: Evaluate the performance of Xpert Xpress SARS-CoV-2 assay for detection of SARS-CoV-2 from DTS and LRT specimens. Methods: 162 specimens from 158 patients with suspected COVID-19 disease were tested with Xpert Xpress SARS-CoV-2 assay. These included 120 DTS and 42 LRT specimens i.e. 35 sputum, 6 tracheal aspirate and one bronchoalveolar lavage. Results were compared to those by the TIB-Molbiol LightMix® SarbecoV E-gene assay. Results: Xpert Xpress SARS-CoV-2 assay has satisfactory performance when compared with reference method. The positive percent agreement (PPA) of DTS and LRT specimens were 98.86 % & 100 % respectively while the negative percent agreement (NPA) was 100 % for both DTS and LRT specimens. Conclusions: This study demonstrated with appropriate sample pre-treatment, Xpert Xpress SARS-CoV-2 assay can be used to test on non-validated specimen types including DTS & LRT specimens.
MeSH term(s)	Adult ; Betacoronavirus ; COVID-19 ; COVID-19 Testing ; Clinical Laboratory Techniques ; Coronavirus Infections/diagnosis ; Female ; Humans ; Male ; Middle Aged ; Molecular Diagnostic Techniques ; Nasopharynx/virology ; Oropharynx/virology ; Pandemics ; Pharynx/virology ; Pneumonia, Viral/diagnosis ; Reagent Kits, Diagnostic ; Respiratory System/virology ; SARS-CoV-2 ; Saliva/virology ; Sensitivity and Specificity ; Specimen Handling/methods
Chemical Substances	Reagent Kits, Diagnostic
Keywords	covid19
Language	English
Publishing date	2020-08-16
Publishing country	Netherlands
Document type	Evaluation Study ; Journal Article
ZDB-ID	1446080-4
ISSN	1873-5967 ; 1386-6532
ISSN (online)	1873-5967
ISSN	1386-6532
DOI	10.1016/j.jcv.2020.104593
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Article ; Online: Evaluation on testing of deep throat saliva and lower respiratory tract specimens with Xpert Xpress SARS-CoV-2 assay

Wong, River Chun-Wai / Wong, Ann Han / Ho, Yolanda Iok-Ieng / Leung, Eddie Chi-Man / Lai, Raymond Wai-Man

Journal of Clinical Virology

2020 Volume 131, Page(s) 104593

Keywords	Virology ; Infectious Diseases ; covid19
Language	English
Publisher	Elsevier BV
Publishing country	us
Document type	Article ; Online
ZDB-ID	1446080-4
ISSN	1873-5967 ; 1386-6532
ISSN (online)	1873-5967
ISSN	1386-6532
DOI	10.1016/j.jcv.2020.104593
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Performance evaluation of Panther Fusion SARS-CoV-2 assay for detection of SARS-CoV-2 from deep throat saliva, nasopharyngeal, and lower-respiratory-tract specimens

Wong, River Chun-Wai / Wong, Ann Han / Ho, Yolanda Iok-Ieng / Leung, Eddie Chi-Man / Lai, Raymond Wai-Man

J. med. virol

Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #806519
Database	COVID19

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Article ; Online: Performance evaluation of Panther Fusion SARS‐CoV‐2 assay for detection of SARS‐CoV‐2 from deep throat saliva, nasopharyngeal, and lower‐respiratory‐tract specimens

Wong, River Chun‐Wai / Wong, Ann Han / Ho, Yolanda Iok‐Ieng / Leung, Eddie Chi‐Man / Lai, Raymond Wai‐Man

Journal of Medical Virology ; ISSN 0146-6615 1096-9071

2020

Keywords	Virology ; Infectious Diseases ; covid19
Language	English
Publisher	Wiley
Publishing country	us
Document type	Article ; Online
DOI	10.1002/jmv.26574
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Evaluation on testing of deep throat saliva and lower respiratory tract specimens with Xpert Xpress SARS-CoV-2 assay

Wong, River Chun-Wai / Wong, Ann Han / Ho, Yolanda Iok-Ieng / Leung, Eddie Chi-Man / Lai, Raymond Wai-Man

J Clin Virol

Abstract: BACKGROUND: Xpert® Xpress SARS-CoV-2 assay is only validated on nasopharyngeal specimens for detection of SARS-CoV-2. Other specimen types such as deep throat saliva (DTS), also known as posterior oropharyngeal saliva and lower-respiratorytract specimens ...

Abstract	BACKGROUND: Xpert® Xpress SARS-CoV-2 assay is only validated on nasopharyngeal specimens for detection of SARS-CoV-2. Other specimen types such as deep throat saliva (DTS), also known as posterior oropharyngeal saliva and lower-respiratorytract specimens (LRT) including sputum, tracheal aspirate and bronchoalveolar lavage are not validated. These non-validated specimen types, however, do have significant diagnostic value. OBJECTIVE: Evaluate the performance of Xpert Xpress SARS-CoV-2 assay for detection of SARS-CoV-2 from DTS and LRT specimens. METHODS: 162 specimens from 158 patients with suspected COVID-19 disease were tested with Xpert Xpress SARS-CoV-2 assay. These included 120 DTS and 42 LRT specimens i.e. 35 sputum, 6 tracheal aspirate and one bronchoalveolar lavage. Results were compared to those by the TIB-Molbiol LightMix® SarbecoV E-gene assay. RESULTS: Xpert Xpress SARS-CoV-2 assay has satisfactory performance when compared with reference method. The positive percent agreement (PPA) of DTS and LRT specimens were 98.86 % & 100 % respectively while the negative percent agreement (NPA) was 100 % for both DTS and LRT specimens. CONCLUSIONS: This study demonstrated with appropriate sample pre-treatment, Xpert Xpress SARS-CoV-2 assay can be used to test on non-validated specimen types including DTS & LRT specimens.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #714455
Database	COVID19

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Article ; Online: CTX-M type beta-lactamases among fecal Escherichia coli and Klebsiella pneumoniae isolates in non-hospitalized children and adults.

Ho, Pak-Leung / Wong, River Chun-Wai / Chow, Kin-Hung / Yip, Kenneth / Wong, Samson Sai-Yin / Que, Tak-Lun

Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi

2008 Volume 41, Issue 5, Page(s) 428–432

Abstract: We investigated the occurrence and diversity of extended-spectrum beta-lactamase (ESBL) enzymes among antibiotic-resistant Escherichia coli and Klebsiella pneumoniae isolates obtained from human feces. All ESBL-positive isolates were characterized at the ...

Abstract	We investigated the occurrence and diversity of extended-spectrum beta-lactamase (ESBL) enzymes among antibiotic-resistant Escherichia coli and Klebsiella pneumoniae isolates obtained from human feces. All ESBL-positive isolates were characterized at the molecular level by polymerase chain reaction, sequencing and pulsed-field gel electrophoresis (PFGE). Eight of 46 antibiotic-resistant E. coli (6 from children and 2 from adults) and 4 of 8 K. pneumoniae (all from adults) isolates were found to be ESBL-positive by the double-disk synergy test. Seven isolates were found to have CTX-M-14, 2 each had CTX-M-24 and CTX-M-38, and 1 had CTX-M-9. In addition, 8 isolates were found to carry TEM-1b or TEM-1c. No SHV-type enzyme was found among the E. coli strains. In 9 strains, the plasmidic bla(CTX-M) determinants were transferable to E. coli by conjugation. Analysis by PFGE showed evidence of clonal and non-clonal spread. The present study shows fecal carriage of organisms producing bla(CTX-M) determinants and underscores the role that commensals could play as a reservoir for their dissemination.
MeSH term(s)	Cephalosporin Resistance/genetics ; Cephalosporinase/genetics ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli/enzymology ; Escherichia coli/genetics ; Escherichia coli/isolation & purification ; Feces/microbiology ; Humans ; Klebsiella pneumoniae/enzymology ; Klebsiella pneumoniae/genetics ; Klebsiella pneumoniae/isolation & purification ; Microbial Sensitivity Tests ; Polymerase Chain Reaction ; beta-Lactam Resistance/genetics ; beta-Lactamases/genetics
Chemical Substances	Cephalosporinase (EC 3.5.2.-) ; beta-Lactamases (EC 3.5.2.6)
Language	English
Publishing date	2008-10
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1497590-7
ISSN	1995-9133 ; 1684-1182 ; 0253-2662
ISSN (online)	1995-9133
ISSN	1684-1182 ; 0253-2662
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Article ; Online: Determinants for asthma control, quality of life and use of complementary and alternative medicine in asthmatic pediatric patients in four cities.

Hon, Kam Lun / Bao, Yan Min / Chan, Kate C / Chau, Kin Wai / Chen, Rong-Shan / Cheok, Kun Tat Gary / Chiu, Wa Keung / Deng, Li / He, Chun-Hui / Ieong, Kin Mui / Kung, Jeng Sum C / Lam, Ping / Lam, Shu Yan David / Lee, Qun Ui / Lee, So Lun / Leung, Ting Fan / Leung, Theresa N H / Shi, Lei / Siu, Ka Ka /

Tan, Wei-Ping / Wang, Maggie Haitian / Wong, Tak Wai / Wu, Bao-Jing / Yip, Ada Y F / Zheng, Yue-Jie / Ng, Daniel K

World journal of pediatrics : WJP

2018 Volume 14, Issue 5, Page(s) 482–491

Abstract: ... a multi-center study to survey asthma control and QoL in four cities in the Pearl River Delta.: Methods ...

Abstract	Background: Asthma is a significant chronic health problem worldwide. Management aims at disease control by reducing functional impairment and exacerbations and improving quality of life (QoL). We report a multi-center study to survey asthma control and QoL in four cities in the Pearl River Delta. Methods: The conjoint survey involved ten Hong Kong pediatric hospitals/units, two Shenzhen hospitals, two Macau hospitals, and two Guangzhou hospitals on asthma control (using Asthma Control Test) and QoL (Pediatric Allergic Disease Quality of Life Questionnaire, PADQLQ). Acceptability of a treatment is graded as very good/good/fair/poor. Results: Good asthma control was only reported in 80% subjects in Hong Kong, but higher in sister cities (85-94%, P < 0.001). Allergic rhinitis, "incense burning", and "smoker in family" were prevalent among the four cities. Logistic regression showed better control of asthma was associated with better PADQLQ (B = - 0.029, P < 0.001), better acceptability of bronchodilator (B = - 1.488, P = 0.025), negatively with "smoker in family" (B = - 0.83, P = 0.015) and various PADQLQ domains. Conversely, worse PADQLQ was associated with allergic rhinitis severity (B = 4.77, P < 0.001), poor control of asthma (B = 7.56, P < 0.001), increased frequency of traditional Chinese medicine use (B = 1.7, P < 0.05), increased frequency of bronchodilator usage (B = 1.05, P < 0.05), "smoker in family" (B = 4.05, P < 0.05), and incense burning at home (B = 3.9, P < 0.05). Conclusions: There are some clinical and cultural differences among the four southern Chinese cities within the Guangdong province. This study identifies potentially modifiable environmental and treatment factors associated with poor asthma control and QoL for health-care interventions. Having a smoker in the family is independently associated with poor asthma control and QoL.
MeSH term(s)	Adolescent ; Asthma/diagnosis ; Asthma/psychology ; Asthma/therapy ; Child ; Cities ; Complementary Therapies/methods ; Cross-Sectional Studies ; Female ; Hong Kong ; Humans ; Logistic Models ; Male ; Multivariate Analysis ; Pediatrics ; Quality of Life ; Risk Assessment ; Severity of Illness Index ; Surveys and Questionnaires ; Treatment Outcome ; Urban Population
Language	English
Publishing date	2018-07-25
Publishing country	Switzerland
Document type	Journal Article ; Multicenter Study
ZDB-ID	2236681-7
ISSN	1867-0687 ; 1708-8569
ISSN (online)	1867-0687
ISSN	1708-8569
DOI	10.1007/s12519-018-0167-1
Database	MEDical Literature Analysis and Retrieval System OnLINE

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