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

• Published in: Microbial genomics 2024
• Main Authors: Tsang, Kara K, Lam, Margaret M C, Wick, Ryan R, Wyres, Kelly L, Bachman, Michael, Baker, Stephen, Barry, Katherine, Brisse, Sylvain, Campino, Susana, Chiaverini, Alexandra, Cirillo, Daniela Maria, Clark, Taane, Corander, Jukka, Corbella, Marta, Cornacchia, Alessandra, Cuénod, Aline, D'Alterio, Nicola, Di Marco, Federico, Donado-Godoy, Pilar, Egli, Adrian, Farzana, Refath, Feil, Edward J, Fostervold, Aasmund, Gorrie, Claire L, Hassan, Brekhna, Hetland, Marit, Hoa, Le Nguyen Minh, Hoi, Le Thi, Howden, Benjamin, Ikhimiukor, Odion O, Jenney, Adam W J, Kaspersen, Håkon, Khokhar, Fahad, Leangapichart, Thongpan, Ligowska-Marzęta, Małgorzata, Löhr, Iren Høyland, Long, Scott W, Mathers, Amy J, McArthur, Andrew G, Nagaraj, Geetha, Oaikhena, Anderson O, Okeke, Iruka N, Perdigão, João, Parikh, Hardik, Pham, My H, Pomilio, Francesco, Raffelsberger, Niclas Peter, Rakotondrasoa, Andriniaina, Kumar, K L Ravi, Roberts, Leah W, Rodrigues, Carla, Samuelsen, Ørjan, Sands, Kirsty, Sassera, Davide, Seth-Smith, Helena, Shamanna, Varun, Sherry, Norelle L, Sia, Sonia, Spadar, Anton, Stoesser, Nicole, Sunde, Marianne, Sundsfjord, Arnfinn Ståle, Thach, Pham Ngoc, Thomson, Nicholas R, Thorpe, Harry, Torok, M Estée, Trang, Van Dinh, Trung, Nguyen Vu, Vornhagen, Jay, Walsh, Timothy, Warne, Ben, Wilson, Hayley, Wright, Gerard D, Holt, Kathryn E
• Format: Article
• Language: Norwegian
• ISSN: 2057-5858; 2057-5858

Interpreting the phenotypes of blaSHV 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 blaSHV alleles or additional plasmid-borne blaSHV 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 blaSHV-1) is the ancestral chromosomal variant, (ii) ESBL- and BLI-resistant variants have evolved multiple times through parallel substitution mutations, (iii) ESBL variants are mostly mobilized to plasmids and (iv) BLI-resistant variants mostly result from mutations in chromosomal blaSHV. We used matched genome–phenotype data from the KlebNET-GSP AMR Genotype-Phenotype Group to identify 3999 K. pneumoniae isolates carrying one or more blaSHV alleles but no other acquired β-lactamases to assess genotype–phenotype relationships for blaSHV. This collection includes human, animal and environmental isolates collected between 2001 and 2021 from 24 countries. Our analysis supports that mutations at Ambler sites 238 and 179 confer ESBL activity, whilst most omega-loop substitutions do not. Our data also provide support for the WT assignment of 67 protein variants, including 8 that were noted in public databases as ESBL. These eight variants were reclassified as WT because they lack ESBL-associated mutations, and our phenotype data suppor