Diversity, functional classification and genotyping of SHV β-lactamases in Klebsiella pneumoniae
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 Andrea Klokkhammer , 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 , 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 , Thach Pham Ngoc , Thomson Nicholas R. , Thorpe Harry A. , Torok M. Estée , Trang Van Dinh , Trung Nguyen Vu , Vornhagen Jay , Walsh Timothy , Warne Ben , Wilson Hayley , Wright Gerard D. , Holt Kathryn E. ,   KlebNET-GSP AMR Genotype-Phenotype Group
Published: October 2024

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 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 bla
SHV. We used matched genome–phenotype data from the KlebNET-GSP AMR Genotype-Phenotype Group to identify 3999 K. pneumoniae isolates carrying one or more bla
SHV alleles but no other acquired β-lactamases to assess genotype–phenotype relationships for bla
SHV. 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 support susceptibility to third-generation cephalosporins (SHV-27, SHV-38, SHV-40, SHV-41, SHV-42, SHV-65, SHV-164 and SHV-187). The approach and results outlined here have been implemented in Kleborate v2.4.1 (a software tool for genotyping K. pneumoniae), whereby known and novel bla
SHV alleles are classified based on causative mutations. Kleborate v2.4.1 was updated to include ten novel protein variants from the KlebNET-GSP dataset and all alleles in public databases as of November 2023. This study demonstrates the power of sharing AMR phenotypes alongside genome data to improve the understanding of resistance mechanisms.