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  1. Article: Evaluation of Two Tests for the Rapid Detection of CTX-M Producers Directly in Urine Samples.

    Tang, Forrest / Lee, Chung-Ho / Li, Xin / Jiang, Shuo / Chow, Kin-Hung / Tse, Cindy Wing-Sze / Ho, Pak-Leung

    Antibiotics (Basel, Switzerland)

    2023  Volume 12, Issue 11

    Abstract: Infections caused by extended-spectrum β-lactamase- ... ...

    Abstract Infections caused by extended-spectrum β-lactamase-producing
    Language English
    Publishing date 2023-11-02
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2681345-2
    ISSN 2079-6382
    ISSN 2079-6382
    DOI 10.3390/antibiotics12111585
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Long-Read Sequencing with Hierarchical Clustering for Antiretroviral Resistance Profiling of Mixed Human Immunodeficiency Virus Quasispecies.

    Ng, Timothy Ting-Leung / Su, Junhao / Lao, Hiu-Yin / Lui, Wui-Wang / Chan, Chloe Toi-Mei / Leung, Amy Wing-Sze / Jim, Stephanie Hoi-Ching / Lee, Lam-Kwong / Shehzad, Sheeba / Tam, Kingsley King-Gee / Leung, Kenneth Siu-Sing / Tang, Forrest / Yam, Wing-Cheong / Luo, Ruibang / Siu, Gilman Kit-Hang

    Clinical chemistry

    2023  Volume 69, Issue 10, Page(s) 1174–1185

    Abstract: Background: HIV infections often develop drug resistance mutations (DRMs), which can increase the risk of virological failure. However, it has been difficult to determine if minor mutations occur in the same genome or in different virions using Sanger ... ...

    Abstract Background: HIV infections often develop drug resistance mutations (DRMs), which can increase the risk of virological failure. However, it has been difficult to determine if minor mutations occur in the same genome or in different virions using Sanger sequencing and short-read sequencing methods. Oxford Nanopore Technologies (ONT) sequencing may improve antiretroviral resistance profiling by allowing for long-read clustering.
    Methods: A new ONT sequencing-based method for profiling DRMs in HIV quasispecies was developed and validated. The method used hierarchical clustering of long amplicons that cover regions associated with different types of antiretroviral drugs. A gradient series of an HIV plasmid and 2 plasma samples was prepared to validate the clustering performance. The ONT results were compared to those obtained with Sanger sequencing and Illumina sequencing in 77 HIV-positive plasma samples to evaluate the diagnostic performance.
    Results: In the validation study, the abundance of detected quasispecies was concordant with the predicted result with the R2 of > 0.99. During the diagnostic evaluation, 59/77 samples were successfully sequenced for DRMs. Among 18 failed samples, 17 were below the limit of detection of 303.9 copies/μL. Based on the receiver operating characteristic analysis, the ONT workflow achieved an F1 score of 0.96 with a cutoff of 0.4 variant allele frequency. Four cases were found to have quasispecies with DRMs, in which 2 harbored quasispecies with more than one class of DRMs. Treatment modifications were recommended for these cases.
    Conclusions: Long-read sequencing coupled with hierarchical clustering could differentiate the quasispecies resistance profiles in HIV-infected samples, providing a clearer picture for medical care.
    MeSH term(s) Humans ; HIV Infections/drug therapy ; Quasispecies/genetics ; HIV-1/genetics ; Anti-Retroviral Agents/pharmacology ; Anti-Retroviral Agents/therapeutic use ; Mutation ; High-Throughput Nucleotide Sequencing/methods ; Cluster Analysis
    Chemical Substances Anti-Retroviral Agents
    Language English
    Publishing date 2023-08-03
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 80102-1
    ISSN 1530-8561 ; 0009-9147
    ISSN (online) 1530-8561
    ISSN 0009-9147
    DOI 10.1093/clinchem/hvad108
    Database MEDical Literature Analysis and Retrieval System OnLINE

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