Diversity, functional classification and genotyping of SHV β-lactamases in Klebsiella pneumoniae

作者：Kara K. Tsang, Margaret M. C. Lam, Ryan R. Wick, Kelly L. Wyres, Michael A. Bachman, Stephen G. Baker, Katherine Barry, Sylvain Brisse, Susana G. Campino, Alexandra Chiaverini, Daniela María Cirillo, Taane Gregory Clark, Jukka Corander, Marta Corbella, Alessandra Cornacchia, Aline Cuénod, Nicola D’Alterio, Federico Di Marco, Pilar Donado-Godoy, Adrian Egli, Refath Farzana, Edward J. Feil, Aasmund Fostervold, Claire L. Gorrie, Brekhna Hassan, Marit Andrea Klokkhammer Hetland, Le Nguyen Minh Hoa, Le Thi Hoi, Benjamin P. Howden, Odion O. Ikhimiukor, Adam W. J. Jenney, Håkon Pedersen Kaspersen, Fahad Khokhar, Thongpan Leangapichart, Małgorzata Ligowska-Marzęta, Iren Høyland Löhr, Scott Wesley Long, Amy J. Mathers, Andrew G. McArthur, Geetha Nagaraj, Anderson O. Oaikhena, Iruka N. Okeke, João Perdigão, Hardik I. Parikh, My H. Pham, Francesco Pomilio, Niclas Raffelsberger, Andriniaina Rakotondrasoa, K. L. Ravi Kumar, Leah Wendy Roberts, Carla Rodrigues, Ørjan Samuelsen, Kirsty M. Sands, Davide Sassera, Helena M. B. Seth-Smith, Varun Shamanna, Norelle L. Sherry, Sonia B. Sia, Anton Spadar, Nicole E Stoesser, Marianne Sunde, Arnfinn Sundsfjord, Phạm Ngọc Thạch, Nicholas R. Thomson, Harry A. Thorpe, M. Estée Török, Van Dinh Trang, Nguyen Vu Trung, Jay Vornhagen, Timothy Rutland Walsh, Ben Warne, Hayley J. Wilson, Gerard D. Wright, Kathryn E. Holt, KlebNET-GSP AMR Genotype-Phenotype Group · 发表于：Microbial Genomics · 年份：2024 · DOI：10.1099/mgen.0.001294 · 被引用次数：22 · 研究领域：Antibiotic Resistance in Bacteria、Bacteriophages and microbial interactions、Bacterial biofilms and quorum sensing

Interpreting the phenotypes of bla SHV alleles in Klebsiella pneumoniae genomes is complex. Whilst all strains are expected to carry a chromosomal copy conferring resistance to ampicillin, they may also carry mutations in chromosomal bla SHV alleles or additional plasmid-borne bla SHV alleles that have extended-spectrum β-lactamase (ESBL) activity and/or β-lactamase inhibitor (BLI) resistance activity. In addition, the role of individual mutations/a changes is not completely documented or understood. This has led to confusion in the literature and in antimicrobial resistance (AMR) gene databases [e.g. the National Center for Biotechnology Information (NCBI) Reference Gene Catalog and the β-lactamase database (BLDB)] over the specific functionality of individual sulfhydryl variable (SHV) protein variants. Therefore, the identification of ESBL-producing strains from K. pneumoniae genome data is complicated. Here, we reviewed the experimental evidence for the expansion of SHV enzyme function associated with specific aa substitutions. We then systematically assigned SHV alleles to functional classes (WT, ESBL and BLI resistant) based on the presence of these mutations. This resulted in the re-classification of 37 SHV alleles compared with the current assignments in the NCBI’s Reference Gene Catalog and/or BLDB (21 to WT, 12 to ESBL and 4 to BLI resistant). Phylogenetic and comparative genomic analyses support that (i) SHV-1 (encoded by bla SHV-1 ) is the ancestral chromosomal var...