Skip to content
1887

Microbial Genomics logo Microbial Genomics

Volume 10, Issue 10

Diversity, functional classification and genotyping of SHV β-lactamases in Open Access

Abstract

Interpreting the phenotypes of alleles in genomes is complex. Whilst all strains are expected to carry a chromosomal copy conferring resistance to ampicillin, they may also carry mutations in chromosomal alleles or additional plasmid-borne 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 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 ) 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 . We used matched genome–phenotype data from the KlebNET-GSP AMR Genotype-Phenotype Group to identify 3999 . isolates carrying one or more alleles but no other acquired β-lactamases to assess genotype–phenotype relationships for . 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 ), whereby known and novel 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.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): AMR , BLI resistance , extended-spectrum β-lactamase (ESBL) , genotype , K. pneumoniae , prediction , SHV and β-lactamase
Funding
This study was supported by the:
  • European Union’s Horizon 2020 Research and Innovation Programme (Award 773830)
    • Principal Award Recipient: SylvainBrisse
  • Bill and Melinda Gates Foundation (Award OPP025280)
    • Principal Award Recipient: KathrynE. Holt
© 2024 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
Loading

Article metrics loading...

/content/journal/mgen/10.1099/mgen.0.001294
2024-10-21
2025-11-16

Metrics

Loading full text...

Full text loading...

/deliver/fulltext/mgen/10/10/mgen001294.html?itemId=/content/journal/mgen/10.1099/mgen.0.001294&mimeType=html&fmt=ahah

References

  1. Ford PJ, Avison MB. Evolutionary mapping of the SHV beta-lactamase and evidence for two separate IS26-dependent blaSHV mobilization events from the Klebsiella pneumoniae chromosome. J Antimicrob Chemother 2004; 54:69–75 [View Article] [PubMed]
     [Google Scholar]
  2. Heritage J, M’Zali FH, Gascoyne-Binzi D, Hawkey PM. Evolution and spread of SHV extended-spectrum beta-lactamases in gram-negative bacteria. J Antimicrob Chemother 1999; 44:309–318 [View Article] [PubMed]
     [Google Scholar]
  3. Hammond DS, Schooneveldt JM, Nimmo GR, Huygens F, Giffard PM bla. bla(SHV) genes in Klebsiella pneumoniae: different allele distributions are associated with different promoters within individual isolates. Antimicrob Agents Chemother 2005; 49:256–263 [View Article] [PubMed]
     [Google Scholar]
  4. Pitton J-S. Mechanisms of bacterial resistance to antibiotics. Ergebnisse der Physiol Rev Physiol 1972; 65:15–93 [View Article]
     [Google Scholar]
  5. Matthew M, Hedges RW, Smith JT. Types of beta-lactamase determined by plasmids in gram-negative bacteria. J Bacteriol 1979; 138:657–662 [View Article] [PubMed]
     [Google Scholar]
  6. Nugent ME, Hedges RW. The nature of the genetic determinant for the SHV-1 beta-lactamase. Mol Gen Genet 1979; 175:239–243 [View Article] [PubMed]
     [Google Scholar]
  7. Kliebe C, Nies BA, Meyer JF, Tolxdorff-Neutzling RM, Wiedemann B. Evolution of plasmid-coded resistance to broad-spectrum cephalosporins. Antimicrob Agents Chemother 1985; 28:302–307 [View Article] [PubMed]
     [Google Scholar]
  8. Knothe H, Shah P, Krcmery V, Antal M, Mitsuhashi S. Transferable resistance to cefotaxime, cefoxitin, cefamandole and cefuroxime in clinical isolates of Klebsiella pneumoniae and Serratia marcescens. Infection 1983; 11:315–317 [View Article] [PubMed]
     [Google Scholar]
  9. Barthélémy M, Péduzzi J, Ben Yaghlane H, Labia R. Single amino acid substitution between SHV-1 beta-lactamase and cefotaxime-hydrolyzing SHV-2 enzyme. FEBS Lett 1988; 231:217–220 [View Article] [PubMed]
     [Google Scholar]
  10. Liakopoulos A, Mevius D, Ceccarelli D. A review of SHV extended-spectrum β-lactamases: neglected yet ubiquitous. Front Microbiol 2016; 7:1374 [View Article] [PubMed]
     [Google Scholar]
  11. Alcock BP, Huynh W, Chalil R, Smith KW, Raphenya AR et al. CARD 2023: expanded curation, support for machine learning, and resistome prediction at the comprehensive antibiotic resistance database. Nucleic Acids Res 2023; 51:D690–D699 [View Article] [PubMed]
     [Google Scholar]
  12. Podbielski A, Schönling JA, Melzer B, Warnatz K. Molecular cloning and nucleotide sequence of a new plasmid-coded Klebsiella pneumoniae beta-lactamase gene (SHV-2a) responsible for high-level cefotaxime resistance. Zentralbl Bakteriol 1991; 275:369–373 [View Article] [PubMed]
     [Google Scholar]
  13. Rasheed JK, Jay C, Metchock B, Berkowitz F, Weigel L et al. Evolution of extended-spectrum beta-lactam resistance (SHV-8) in a strain of Escherichia coli during multiple episodes of bacteremia. Antimicrob Agents Chemother 1997; 41:647–653 [View Article] [PubMed]
     [Google Scholar]
  14. Kurokawa H, Yagi T, Shibata N, Shibayama K, Kamachi K et al. A new SHV-derived extended-spectrum beta-lactamase (SHV-24) that hydrolyzes ceftazidime through A single-amino-acid substitution (D179G) in the -loop. Antimicrob Agents Chemother 2000; 44:1725–1727 [View Article] [PubMed]
     [Google Scholar]
  15. Ma L, Alba J, Chang F-Y, Ishiguro M, Yamaguchi K et al. Novel SHV-derived extended-spectrum beta-lactamase, SHV-57, that confers resistance to ceftazidime but not cefazolin. Antimicrob Agents Chemother 2005; 49:600–605 [View Article] [PubMed]
     [Google Scholar]
  16. Arpin C, Labia R, Andre C, Frigo C, El Harrif Z et al. SHV-16, a beta-lactamase with a pentapeptide duplication in the omega loop. Antimicrob Agents Chemother 2001; 45:2480–2485 [View Article] [PubMed]
     [Google Scholar]
  17. Prinarakis EE, Miriagou V, Tzelepi E, Gazouli M, Tzouvelekis LS. Emergence of an inhibitor-resistant beta-lactamase (SHV-10) derived from an SHV-5 variant. Antimicrob Agents Chemother 1997; 41:838–840 [View Article] [PubMed]
     [Google Scholar]
  18. Dubois V, Poirel L, Arpin C, Coulange L, Bebear C et al. SHV-49, a novel inhibitor-resistant beta-lactamase in a clinical isolate of Klebsiella pneumoniae. Antimicrob Agents Chemother 2004; 48:4466–4469 [View Article] [PubMed]
     [Google Scholar]
  19. Dubois V, Poirel L, Demarthe F, Arpin C, Coulange L et al. Molecular and biochemical characterization of SHV-56, a novel inhibitor-resistant beta-lactamase from Klebsiella pneumoniae. Antimicrob Agents Chemother 2008; 52:3792–3794 [View Article] [PubMed]
     [Google Scholar]
  20. Mendonça N, Manageiro V, Robin F, Salgado MJ, Ferreira E et al. The Lys234Arg substitution in the enzyme SHV-72 is a determinant for resistance to clavulanic acid inhibition. Antimicrob Agents Chemother 2008; 52:1806–1811 [View Article] [PubMed]
     [Google Scholar]
  21. Manageiro V, Ferreira E, Cougnoux A, Albuquerque L, Caniça M et al. Characterization of the inhibitor-resistant SHV β-lactamase SHV-107 in a clinical Klebsiella pneumoniae strain coproducing GES-7 enzyme. Antimicrob Agents Chemother 2012; 56:1042–1046 [View Article] [PubMed]
     [Google Scholar]
  22. Feldgarden M, Brover V, Gonzalez-Escalona N, Frye JG, Haendiges J et al. AMRFinderPlus and the reference gene catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence. Sci Rep 2021; 11:12728 [View Article] [PubMed]
     [Google Scholar]
  23. Naas T, Oueslati S, Bonnin RA, Dabos ML, Zavala A et al. Beta-lactamase database (BLDB) - structure and function. J Enzyme Inhib Med Chem 2017; 32:917–919 [View Article] [PubMed]
     [Google Scholar]
  24. Bradford PA, Bonomo RA, Bush K, Carattoli A, Feldgarden M et al. Consensus on β-lactamase nomenclature. Antimicrob Agents Chemother 2022; 66:e0033322 [View Article] [PubMed]
     [Google Scholar]
  25. Lin T-L, Tang S-I, Fang C-T, Hsueh P-R, Chang S-C et al. Extended-spectrum beta-lactamase genes of Klebsiella pneumoniae strains in Taiwan: recharacterization of shv-27, shv-41, and tem-116. Microb Drug Resist 2006; 12:12–15 [View Article] [PubMed]
     [Google Scholar]
  26. Neubauer S, Madzgalla S, Marquet M, Klabunde A, Büttner B et al. A Genotype-phenotype correlation study of SHV β-lactamases offers new insight into SHV resistance profiles. Antimicrob Agents Chemother 2020; 64:e02293-19 [View Article] [PubMed]
     [Google Scholar]
  27. Lam MMC, Wick RR, Watts SC, Cerdeira LT, Wyres KL et al. A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex. Nat Commun 2021; 12:4188 [View Article] [PubMed]
     [Google Scholar]
  28. Fajardo-Lubián A, Ben Zakour NL, Agyekum A, Qi Q, Iredell JR. Host adaptation and convergent evolution increases antibiotic resistance without loss of virulence in a major human pathogen. PLOS Pathog 2019; 15:e1007218 [View Article] [PubMed]
     [Google Scholar]
  29. Hasman H, Saputra D, Sicheritz-Ponten T, Lund O, Svendsen CA et al. Rapid whole-genome sequencing for detection and characterization of microorganisms directly from clinical samples. J Clin Microbiol 2014; 52:139–146 [View Article] [PubMed]
     [Google Scholar]
  30. Katoh K, Misawa K, Kuma K, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 2002; 30:3059–3066 [View Article] [PubMed]
     [Google Scholar]
  31. Zhou Z, Alikhan N-F, Sergeant MJ, Luhmann N, Vaz C et al. GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens. Genome Res 2018; 28:1395–1404 [View Article] [PubMed]
     [Google Scholar]
  32. Yu G. Using ggtree to Visualize data on tree‐like structures. CP Bioinform 2020; 69: [View Article]
     [Google Scholar]
  33. Zhu Q, Gao S, Xiao B, He Z, Hu S. Plasmer: an accurate and sensitive bacterial plasmid prediction tool based on machine learning of shared k-mers and genomic features. Microbiol Spectr 2023; 11:e0464522 [View Article] [PubMed]
     [Google Scholar]
  34. Darling ACE, Mau B, Blattner FR, Perna NT. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 2004; 14:1394–1403 [View Article] [PubMed]
     [Google Scholar]
  35. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
     [Google Scholar]
  36. Gilchrist CLM, Chooi Y-H. Clinker & clustermap.js: automatic generation of gene cluster comparison figures. Bioinformatics 2021; 37:2473–2475 [View Article] [PubMed]
     [Google Scholar]
  37. Thorn AV, Aarestrup FM, Munk P. Flankophile: a bioinformatic pipeline for prokaryotic genomic synteny analysis. Microbiol Spectr 2024; 12:e0241323 [View Article] [PubMed]
     [Google Scholar]
  38. Fu L, Niu B, Zhu Z, Wu S, Li W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 2012; 28:3150–3152 [View Article] [PubMed]
     [Google Scholar]
  39. Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M. ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res 2006; 34:D32–6 [View Article] [PubMed]
     [Google Scholar]
  40. Inouye M, Dashnow H, Raven L-A, Schultz MB, Pope BJ et al. SRST2: rapid genomic surveillance for public health and hospital microbiology labs. Genome Med 2014; 6:90 [View Article] [PubMed]
     [Google Scholar]
  41. Mazzariol A, Roelofsen E, Koncan R, Voss A, Cornaglia G. Detection of a new SHV-type extended-spectrum beta-lactamase, SHV-31, in a Klebsiella pneumoniae strain causing a large nosocomial outbreak in The Netherlands. Antimicrob Agents Chemother 2007; 51:1082–1084 [View Article] [PubMed]
     [Google Scholar]
  42. Ling B-D, Liu G, Xie Y-E, Zhou Q-X, Zhao T-K et al. Characterisation of a novel extended-spectrum beta-lactamase, SHV-70, from a clinical isolate of Enterobacter cloacae in China. Int J Antimicrob Agents 2006; 27:355–356 [View Article] [PubMed]
     [Google Scholar]
  43. Nicolas MH, Jarlier V, Honore N, Philippon A, Cole ST. Molecular characterization of the gene encoding SHV-3 beta-lactamase responsible for transferable cefotaxime resistance in clinical isolates of Klebsiella pneumoniae. Antimicrob Agents Chemother 1989; 33:2096–2100 [View Article] [PubMed]
     [Google Scholar]
  44. Levison ME, Mailapur YV, Pradhan SK, Jacoby GA, Adams P et al. Regional occurrence of plasmid-mediated SHV-7, an extended-spectrum beta-lactamase, in Enterobacter cloacae in Philadelphia Teaching Hospitals. Clin Infect Dis 2002; 35:1551–1554 [View Article] [PubMed]
     [Google Scholar]
  45. Szabó D, Melan MA, Hujer AM, Bonomo RA, Hujer KM et al. Molecular analysis of the simultaneous production of two SHV-type extended-spectrum beta-lactamases in a clinical isolate of Enterobacter cloacae by using single-nucleotide polymorphism genotyping. Antimicrob Agents Chemother 2005; 49:4716–4720 [View Article] [PubMed]
     [Google Scholar]
  46. Heritage J, Chambers PA, Tyndall C, Buescher ES. SHV-34: an extended-spectrum beta-lactamase encoded by an epidemic plasmid. J Antimicrob Chemother 2003; 52:1015–1017 [View Article] [PubMed]
     [Google Scholar]
  47. Lavilla S, González-López JJ, Sabaté M, García-Fernández A, Larrosa MN et al. Prevalence of qnr genes among extended-spectrum beta-lactamase-producing enterobacterial isolates in Barcelona, Spain. J Antimicrob Chemother 2008; 61:291–295 [View Article] [PubMed]
     [Google Scholar]
  48. Moradigaravand D, Martin V, Peacock SJ, Parkhill J. Evolution and epidemiology of multidrug-resistant Klebsiella pneumoniae in the United Kingdom and Ireland. mBio 2017; 8:e01976-16 [View Article] [PubMed]
     [Google Scholar]
  49. Sherry NL, Lane CR, Kwong JC, Schultz M, Sait M et al. Genomics for molecular epidemiology and detecting transmission of carbapenemase-producing Enterobacterales in Victoria, Australia, 2012 to 2016. J Clin Microbiol 2019; 57: [View Article]
     [Google Scholar]
  50. Chang FY, Siu LK, Fung CP, Huang MH, Ho M. Diversity of SHV and TEM beta-lactamases in Klebsiella pneumoniae: gene evolution in Northern Taiwan and two novel beta-lactamases, SHV-25 and SHV-26. Antimicrob Agents Chemother 2001; 45:2407–2413 [View Article] [PubMed]
     [Google Scholar]
  51. Huletsky A, Couture F, Levesque RC. Nucleotide sequence and phylogeny of SHV-2 beta-lactamase. Antimicrob Agents Chemother 1990; 34:1725–1732 [View Article] [PubMed]
     [Google Scholar]
  52. Newire EA, Ahmed SF, House B, Valiente E, Pimentel G. Detection of new SHV-12, SHV-5 and SHV-2a variants of extended spectrum beta-lactamase in Klebsiella pneumoniae in Egypt. Ann Clin Microbiol Antimicrob 2013; 12:16 [View Article] [PubMed]
     [Google Scholar]
  53. Chaves J, Ladona MG, Segura C, Coira A, Reig R et al. SHV-1 beta-lactamase is mainly a chromosomally encoded species-specific enzyme in Klebsiella pneumoniae. Antimicrob Agents Chemother 2001; 45:2856–2861 [View Article] [PubMed]
     [Google Scholar]
  54. Haeggman S, Löfdahl S, Paauw A, Verhoef J, Brisse S. Diversity and evolution of the class A chromosomal beta-lactamase gene in Klebsiella pneumoniae. Antimicrob Agents Chemother 2004; 48:2400–2408 [View Article] [PubMed]
     [Google Scholar]
  55. Kuzin AP, Nukaga M, Nukaga Y, Hujer AM, Bonomo RA et al. Structure of the SHV-1 beta-lactamase. Biochemistry 1999; 38:5720–5727 [View Article] [PubMed]
     [Google Scholar]
  56. Sampson JM, Ke W, Bethel CR, Pagadala SRR, Nottingham MD et al. Ligand-dependent disorder of the Omega loop observed in extended-spectrum SHV-type beta-lactamase. Antimicrob Agents Chemother 2011; 55:2303–2309 [View Article] [PubMed]
     [Google Scholar]
  57. Giakkoupi P, Miriagou V, Gazouli M, Tzelepi E, Legakis NJ et al. Properties of mutant SHV-5 β-lactamases constructed by substitution of isoleucine or valine for methionine at position 69. Antimicrob Agents Chemother 1998; 42:1281–1283 [View Article]
     [Google Scholar]
/content/journal/mgen/10.1099/mgen.0.001294
Loading
Diversity, functional classification and genotyping of SHV β-lactamases in Klebsiella pneumoniae
M Gen 10, 001294 (2024); https://doi.org/10.1099/mgen.0.001294
/content/journal/mgen/10.1099/mgen.0.001294
/content/journal/mgen/10.1099/mgen.0.001294
Loading

Data & Media loading...

Supplements

Supplementary material 1

EXCEL

Supplementary material 2

PDF

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An error occurred
Approval was partially successful, following selected items could not be processed due to error