{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,29]],"date-time":"2026-10-29T00:38:25Z","timestamp":1793234305984,"version":"4.5.0"},"reference-count":57,"publisher":"Microbiology Society","issue":"10","license":[{"start":{"date-parts":[[2024,10,21]],"date-time":"2024-10-21T00:00:00Z","timestamp":1729468800000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"crossref","award":["OPP025280"],"award-info":[{"award-number":["OPP025280"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"crossref"}]},{"name":"European Union\u2019s Horizon 2020 Research and Innovation Programme","award":["773830"],"award-info":[{"award-number":["773830"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,10,21]]},"abstract":"<jats:p>\n                    Interpreting the phenotypes of\n                    <jats:italic>bla<\/jats:italic>\n                    <jats:sub>SHV<\/jats:sub>\n                    alleles in\n                    <jats:italic>Klebsiella pneumoniae<\/jats:italic>\n                    genomes is complex. Whilst all strains are expected to carry a chromosomal copy conferring resistance to ampicillin, they may also carry mutations in chromosomal\n                    <jats:italic>bla<\/jats:italic>\n                    <jats:sub>SHV<\/jats:sub>\n                    alleles or additional plasmid-borne\n                    <jats:italic>bla<\/jats:italic>\n                    <jats:sub>SHV<\/jats:sub>\n                    alleles that have extended-spectrum \u03b2-lactamase (ESBL) activity and\/or \u03b2-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 \u03b2-lactamase database (BLDB)] over the specific functionality of individual sulfhydryl variable (SHV) protein variants. Therefore, the identification of ESBL-producing strains from\n                    <jats:italic>K. pneumoniae<\/jats:italic>\n                    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\u2019s 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\n                    <jats:italic>bla<\/jats:italic>\n                    <jats:sub>SHV-1<\/jats:sub>\n                    ) 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\n                    <jats:italic>bla<\/jats:italic>\n                    <jats:sub>SHV<\/jats:sub>\n                    . We used matched genome\u2013phenotype data from the KlebNET-GSP AMR Genotype-Phenotype Group to identify 3999\n                    <jats:italic>K<\/jats:italic>\n                    .\n                    <jats:italic>pneumoniae<\/jats:italic>\n                    isolates carrying one or more\n                    <jats:italic>bla<\/jats:italic>\n                    <jats:sub>SHV<\/jats:sub>\n                    alleles but no other acquired \u03b2-lactamases to assess genotype\u2013phenotype relationships for\n                    <jats:italic>bla<\/jats:italic>\n                    <jats:sub>SHV<\/jats:sub>\n                    . 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\n                    <jats:italic>K. pneumoniae<\/jats:italic>\n                    ), whereby known and novel\n                    <jats:italic>bla<\/jats:italic>\n                    <jats:sub>SHV<\/jats:sub>\n                    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.\n                  <\/jats:p>","DOI":"10.1099\/mgen.0.001294","type":"journal-article","created":{"date-parts":[[2024,10,21]],"date-time":"2024-10-21T12:17:51Z","timestamp":1729513071000},"source":"Crossref","is-referenced-by-count":26,"title":["Diversity, functional classification and genotyping of SHV \u03b2-lactamases in Klebsiella pneumoniae"],"prefix":"10.1099","volume":"10","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7742-8855","authenticated-orcid":false,"given":"Kara K.","family":"Tsang","sequence":"first","affiliation":[{"name":"Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9590-6849","authenticated-orcid":false,"given":"Margaret M. C.","family":"Lam","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, School of Translational Medicine, Monash University, Melbourne, Victoria 3004, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8349-0778","authenticated-orcid":false,"given":"Ryan R.","family":"Wick","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia"},{"name":"Department of Infectious Diseases, School of Translational Medicine, Monash University, Melbourne, Victoria 3004, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4033-6639","authenticated-orcid":false,"given":"Kelly L.","family":"Wyres","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, School of Translational Medicine, Monash University, Melbourne, Victoria 3004, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2507-6987","authenticated-orcid":false,"given":"Michael","family":"Bachman","sequence":"additional","affiliation":[{"name":"University of Michigan, Ann Arbor, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1308-5755","authenticated-orcid":false,"given":"Stephen","family":"Baker","sequence":"additional","affiliation":[{"name":"University of Cambridge, Cambridge, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katherine","family":"Barry","sequence":"additional","affiliation":[{"name":"University of Virginia, Charlottesville, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2516-2108","authenticated-orcid":false,"given":"Sylvain","family":"Brisse","sequence":"additional","affiliation":[{"name":"Institut Pasteur, Universit\u00e9 Paris Cit\u00e9, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1403-6138","authenticated-orcid":false,"given":"Susana","family":"Campino","sequence":"additional","affiliation":[{"name":"Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7412-2164","authenticated-orcid":false,"given":"Alexandra","family":"Chiaverini","sequence":"additional","affiliation":[{"name":"Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise \"G. Caporale\", Teramo, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6415-1535","authenticated-orcid":false,"given":"Daniela Maria","family":"Cirillo","sequence":"additional","affiliation":[{"name":"Ospedale San Raffaele s.r.l. via olgettina, Milano, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8985-9265","authenticated-orcid":false,"given":"Taane","family":"Clark","sequence":"additional","affiliation":[{"name":"Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7752-1942","authenticated-orcid":false,"given":"Jukka","family":"Corander","sequence":"additional","affiliation":[{"name":"University of Oslo, Oslo, Norway"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0969-6484","authenticated-orcid":false,"given":"Marta","family":"Corbella","sequence":"additional","affiliation":[{"name":"Microbiology and Virology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4240-468X","authenticated-orcid":false,"given":"Alessandra","family":"Cornacchia","sequence":"additional","affiliation":[{"name":"Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise \"G. Caporale\", Teramo, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8522-6134","authenticated-orcid":false,"given":"Aline","family":"Cu\u00e9nod","sequence":"additional","affiliation":[{"name":"Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicola","family":"D'Alterio","sequence":"additional","affiliation":[{"name":"Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise \"G. 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J.","family":"Jenney","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9559-1303","authenticated-orcid":false,"given":"H\u00e5kon","family":"Kaspersen","sequence":"additional","affiliation":[{"name":"Norwegian Veterinary Institute, \u00c5s, Norway"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fahad","family":"Khokhar","sequence":"additional","affiliation":[{"name":"University of Cambridge, Cambridge, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6358-5902","authenticated-orcid":false,"given":"Thongpan","family":"Leangapichart","sequence":"additional","affiliation":[{"name":"Norwegian Veterinary Institute, \u00c5s, Norway"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ma\u0142gorzata","family":"Ligowska-Marz\u0119ta","sequence":"additional","affiliation":[{"name":"Statens Serum Institut, Copenhagen, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8847-0044","authenticated-orcid":false,"given":"Iren H\u00f8yland","family":"L\u00f6hr","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3043-5307","authenticated-orcid":false,"given":"Scott W.","family":"Long","sequence":"additional","affiliation":[{"name":"Houston Methodist, Weill Cornell Medical College, New York, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3533-6351","authenticated-orcid":false,"given":"Amy J.","family":"Mathers","sequence":"additional","affiliation":[{"name":"University of Virginia, Charlottesville, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1142-3063","authenticated-orcid":false,"given":"Andrew G.","family":"McArthur","sequence":"additional","affiliation":[{"name":"Michael G. DeGroote Institute for Infectious Disease Research and Department of Biochemistry & Biomedical Sciences, McMaster University, Hamilton, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8099-7493","authenticated-orcid":false,"given":"Geetha","family":"Nagaraj","sequence":"additional","affiliation":[{"name":"Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8803-5077","authenticated-orcid":false,"given":"Anderson O.","family":"Oaikhena","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Microbiology, University of Ibadan, Ibadan, Nigeria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1694-7587","authenticated-orcid":false,"given":"Iruka N.","family":"Okeke","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Microbiology, University of Ibadan, Ibadan, Nigeria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0339-1305","authenticated-orcid":false,"given":"Jo\u00e3o","family":"Perdig\u00e3o","sequence":"additional","affiliation":[{"name":"University of Lisbon, Lisbon, Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5621-7343","authenticated-orcid":false,"given":"Hardik","family":"Parikh","sequence":"additional","affiliation":[{"name":"University of Virginia, Charlottesville, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"My H.","family":"Pham","sequence":"additional","affiliation":[{"name":"Wellcome Sanger Institute, Hinxton, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6946-8603","authenticated-orcid":false,"given":"Francesco","family":"Pomilio","sequence":"additional","affiliation":[{"name":"Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise \"G. 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Ravi","family":"Kumar","sequence":"additional","affiliation":[{"name":"Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1024-0564","authenticated-orcid":false,"given":"Leah W.","family":"Roberts","sequence":"additional","affiliation":[{"name":"Queensland University of Technology, Brisbane, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9608-2404","authenticated-orcid":false,"given":"Carla","family":"Rodrigues","sequence":"additional","affiliation":[{"name":"Institut Pasteur, Universit\u00e9 Paris Cit\u00e9, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5525-2614","authenticated-orcid":false,"given":"\u00d8rjan","family":"Samuelsen","sequence":"additional","affiliation":[{"name":"Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Troms\u00f8, Norway"},{"name":"Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Troms\u00f8, Norway"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5049-4481","authenticated-orcid":false,"given":"Kirsty","family":"Sands","sequence":"additional","affiliation":[{"name":"Ineos-Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0442-5252","authenticated-orcid":false,"given":"Davide","family":"Sassera","sequence":"additional","affiliation":[{"name":"Department of Biology and Biotechnology, University of Pavia, Pavia, Italy"},{"name":"Microbiology and Virology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6082-5114","authenticated-orcid":false,"given":"Helena","family":"Seth-Smith","sequence":"additional","affiliation":[{"name":"Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2775-2280","authenticated-orcid":false,"given":"Varun","family":"Shamanna","sequence":"additional","affiliation":[{"name":"Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, 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