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Article ; Online: Emergence of Carbapenem-Resistant

Leung, Eddie Chi-Man / Leung, Polly Hang-Mei / Lai, Raymond Wai-Man

Microbial drug resistance (Larchmont, N.Y.)

2019 Volume 25, Issue 8, Page(s) 1199–1203

Abstract: Aims: ...

Abstract	Aims:
MeSH term(s)	Acinetobacter Infections/drug therapy ; Acinetobacter Infections/microbiology ; Acinetobacter baumannii/genetics ; Acinetobacter baumannii/isolation & purification ; Anti-Bacterial Agents/therapeutic use ; Bacteremia/microbiology ; Bacterial Proteins/genetics ; Carbapenems/therapeutic use ; Cross Infection/drug therapy ; Cross Infection/microbiology ; Cross-Sectional Studies ; Drug Resistance, Bacterial/genetics ; Hong Kong ; Hospitals ; Humans ; Microbial Sensitivity Tests/methods ; Molecular Epidemiology ; Multilocus Sequence Typing/methods ; Retrospective Studies ; beta-Lactamases/genetics
Chemical Substances	Anti-Bacterial Agents ; Bacterial Proteins ; Carbapenems ; beta-Lactamases (EC 3.5.2.6) ; beta-lactamase OXA-23, Acinetobacter baumannii (EC 3.5.2.6)
Language	English
Publishing date	2019-06-03
Publishing country	United States
Document type	Journal Article
ZDB-ID	1290490-9
ISSN	1931-8448 ; 1076-6294
ISSN (online)	1931-8448
ISSN	1076-6294
DOI	10.1089/mdr.2018.0433
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Zs.A 4435: Show issues

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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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Zs.A 1845: Show issues

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Article ; Online: Deep throat saliva as an alternative diagnostic specimen type for the detection of SARS-CoV-2.

Leung, Eddie Chi-Man / Chow, Viola Chi-Ying / Lee, May Kin-Ping / Lai, Raymond Wai-Man

Journal of medical virology

2020 Volume 93, Issue 1, Page(s) 533–536

Abstract: Nasopharyngeal swabs (NPS) are widely accepted as specimens for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the current pandemic of coronavirus disease 2019. However, the collection procedures for NPS specimens causes ...

Abstract	Nasopharyngeal swabs (NPS) are widely accepted as specimens for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the current pandemic of coronavirus disease 2019. However, the collection procedures for NPS specimens causes sneezing and coughing in most patients, which generate droplets or aerosol particles that are hazardous to the healthcare workers collecting these specimens. In this study, 95 patient-matched paired deep throat saliva (DTS) and NPS specimens from 62 patients were analyzed. Samples were tested for SARS-CoV-2 by reverse-transcription polymerase chain reaction (RT-PCR). The rates of detection for DTS (53.7%) and NPS (47.4%) samples were comparable (P = .13). It is important to note that the patients should be clearly instructed or supervised during DTS collection. In conclusion, SARS-CoV-2 detection by RT-PCR was equivalent in DTS and NPS specimens.
MeSH term(s)	COVID-19/diagnosis ; Humans ; Nasopharynx/virology ; Pharynx/virology ; SARS-CoV-2/isolation & purification ; Saliva/virology ; Specimen Handling
Keywords	covid19
Language	English
Publishing date	2020-07-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	752392-0
ISSN	1096-9071 ; 0146-6615
ISSN (online)	1096-9071
ISSN	0146-6615
DOI	10.1002/jmv.26258
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Zs.A 1320: Show issues

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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 of the Xpert Xpress SARS-CoV-2/Flu/RSV Assay for Simultaneous Detection of SARS-CoV-2, Influenza A and B Viruses, and Respiratory Syncytial Virus in Nasopharyngeal Specimens.

Leung, Eddie Chi-Man / Chow, Viola Chi-Ying / Lee, May Kin-Ping / Tang, Kevin Pui-San / Li, Daniel Kwok-Cheung / Lai, Raymond Wai-Man

Journal of clinical microbiology

2021 Volume 59, Issue 4

Abstract: Patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza A (flu A), influenza B (flu B), and respiratory syncytial virus (RSV) have overlapping clinical presentations, but the approaches to treatment and management ... ...

Abstract	Patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza A (flu A), influenza B (flu B), and respiratory syncytial virus (RSV) have overlapping clinical presentations, but the approaches to treatment and management of infections caused by these viruses are different. Therefore, rapid diagnosis in conjunction with infection prevention measures is important to prevent transmission of the diseases. Recently, a new Xpert Xpress SARS-CoV-2/Flu/RSV (Xpert 4-in-1) assay enables the detection and differentiation of SARS-CoV-2, flu A, flu B, and RSV in upper respiratory tract specimens. In this study, we evaluated the performance of the Xpert 4-in-1 assay by comparing it with that of the Xpert Xpress SARS-CoV-2 and Xpert Xpress Flu/RSV assays for the detection of the four viruses in nasopharyngeal (NP) specimens. A total of 279 NP specimens, including 66, 56, 64, and 53 specimens positive for SARS-CoV-2, flu A, flu B, and RSV, respectively, were included. The Xpert 4-in-1 assay demonstrated high concordance with the comparator assays, with overall agreement for SARS-CoV-2, flu A, flu B, and RSV at 99.64%, 100%, 99.64%, and 100%, respectively, and a high Cohen's kappa (κ) value ranging from 0.99 to 1.00, indicating an almost perfect correlation between assays. The cycle threshold value association between positive samples also showed a good correlation between assays. In conclusion, the overall performance of the Xpert 4-in-1 assay was highly comparable to that of the Xpert SARS-CoV-2 and Xpert Flu/RSV assays for the detection and differentiation of SARS CoV-2, flu A, flu B, and RSV in NP specimens.
MeSH term(s)	COVID-19 ; Herpesvirus 1, Cercopithecine ; Humans ; Influenza A virus/genetics ; Influenza B virus/genetics ; Influenza, Human/diagnosis ; Molecular Diagnostic Techniques ; Nasopharynx ; Respiratory Syncytial Virus Infections ; SARS-CoV-2 ; Sensitivity and Specificity
Language	English
Publishing date	2021-03-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	390499-4
ISSN	1098-660X ; 0095-1137
ISSN (online)	1098-660X
ISSN	0095-1137
DOI	10.1128/JCM.02965-20
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Zs.A 1188: Show issues

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Article ; Online: Deep throat saliva as an alternative diagnostic specimen type for the detection of SARS‐CoV‐2

Leung, Eddie Chi‐man / Chow, Viola Chi‐ying / Lee, May Kin‐ping / 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.26258
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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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: Deep throat saliva as an alternative diagnostic specimen type for the detection of SARS-CoV-2

Leung, Eddie Chi-Man / Chow, Viola Chi-Ying / Lee, May Kin-Ping / Lai, Raymond Wai-Man

J. med. virol

Abstract	Nasopharyngeal swabs (NPS) are widely accepted as specimens for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the current pandemic of coronavirus disease 2019. However, the collection procedures for NPS specimens causes sneezing and coughing in most patients, which generate droplets or aerosol particles that are hazardous to the healthcare workers collecting these specimens. In this study, 95 patient-matched paired deep throat saliva (DTS) and NPS specimens from 62 patients were analyzed. Samples were tested for SARS-CoV-2 by reverse-transcription polymerase chain reaction (RT-PCR). The rates of detection for DTS (53.7%) and NPS (47.4%) samples were comparable (P = .13). It is important to note that the patients should be clearly instructed or supervised during DTS collection. In conclusion, SARS-CoV-2 detection by RT-PCR was equivalent in DTS and NPS specimens.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #630165
Database	COVID19

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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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Zs.A 3790: Show issues

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Article ; Online: Rapid SARS-CoV-2 Variants Enzymatic Detection (SAVED) by CRISPR-Cas12a.

Yang, Jun / Barua, Nilakshi / Rahman, Md Nannur / Li, Carmen / Lo, Norman / Yeong, Kai Yan / Tsang, Tsz Fung / Yang, Xiao / Cheung, Yuk-Yam / Tsang, Alan K L / Chan, Rickjason C W / Leung, Eddie Chi-Man / Chan, Paul K S / Ip, Margaret

Microbiology spectrum

2022 , Page(s) e0326022

Abstract: The continuous and rapid surge of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with high transmissibility and evading neutralization is alarming, necessitating expeditious detection of the variants concerned. Here, we report the ... ...

Abstract	The continuous and rapid surge of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with high transmissibility and evading neutralization is alarming, necessitating expeditious detection of the variants concerned. Here, we report the development of rapid
Language	English
Publishing date	2022-11-07
Publishing country	United States
Document type	Journal Article
ZDB-ID	2807133-5
ISSN	2165-0497 ; 2165-0497
ISSN (online)	2165-0497
ISSN	2165-0497
DOI	10.1128/spectrum.03260-22
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