Genomic Definition of Hypervirulent and Multidrug-Resistant Klebsiella pneumoniae Clonal Groups
Open accessAbstract
Multidrug-resistant and highly virulent Klebsiella pneumoniae isolates are emerging, but the clonal groups (CGs) corresponding to these high-risk strains have remained imprecisely defined. We aimed to identify K. pneumoniae CGs on the basis of genome-wide sequence variation and to provide a simple bioinformatics tool to extract virulence and resistance gene data from genomic data. We sequenced 48 K. pneumoniae isolates, mostly of serotypes K1 and K2, and compared the genomes with 119 publicly available genomes. A total of 694 highly conserved genes were included in a core-genome multilocus sequence typing scheme, and cluster analysis of the data enabled precise definition of globally distributed hypervirulent and multidrug-resistant CGs. In addition, we created a freely accessible database, BIGSdb-Kp, to enable rapid extraction of medically and epidemiologically relevant information from genomic sequences of K. pneumoniae. Although drug-resistant and virulent K. pneumoniae populations were largely nonoverlapping, isolates with combined virulence and resistance features were detected.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
K. pneumoniae strain Kp52.145 was the source for four kpnfepA structural genes: plasmid II locus 0027 [kpniroN] and chromosomal fepA loci 1658, 4984, and 2380.
“K. pneumoniae strain Kp52.145 was the source for four kpnfepA structural genes: plasmid II locus 0027 [kpniroN; GenBank locus CDO11656 (56, 57)] and chromosomal fepA loci 1658, 4984, and 2380.”
From Siderophore-mediated iron acquisition by <i>Klebsiella pneumoniae</i> (2024) · cites this paper as [57]
Materials and Methods (Data Availability; page not specified) identifies CIP 52.145 as a source of chromosome and plasmid sequences. Our copy does not identify the four claimed fepA/iroN genes, their locus numbers, or which is on plasmid II. (LLM, conf=0.82)
Experimental — accuracy not yet measuredKp52.145 harbors plasmid II, a 121.7-kB plasmid that was only found in one other K. pneumoniae strain (B5055).
“Kp52.145 harbors plasmid II, a 121.7-kB plasmid (57) that was only found in one other K. pneu moniae strain (B5055).”
From Siderophore-mediated iron acquisition by <i>Klebsiella pneumoniae</i> (2024) · cites this paper as [57]
The Data Availability section identifies sequences for the CIP 52.145 chromosome and two plasmids, supporting that the strain carries plasmids. Our copy does not identify either as plasmid II, give a size of 121.7 kB, or say it was found only in strain B5055; searches for those terms found no matching passage. (LLM, conf=0.76)
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
1 retracted
Shin, J., & Ko, K. S. (2013) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dkt464 · Cited by 22 · see citing works
RetractedApplication of Phylogenetic Networks in Evolutionary Studies
Huson, D. H., & Bryant, D. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msj030 · Cited by 8,751 · see citing works
Podschun, R., & Ullmann, U. (1998) · Clinical Microbiology Reviews · doi:10.1128/cmr.11.4.589 · Cited by 2,701 · see citing works
BIGSdb: Scalable analysis of bacterial genome variation at the population level
Jolley, K. A., & Maiden, M. C. J. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-595 · Cited by 2,341 · see citing works
Federal Funding for the Study of Antimicrobial Resistance in Nosocomial Pathogens: No ESKAPE
Rice, L. B. (2008) · The Journal of Infectious Diseases · doi:10.1086/533452 · Cited by 2,328 · see citing works
Multilocus Sequence Typing of Klebsiella pneumoniae Nosocomial Isolates
Diancourt, L., Passet, V., Verhoef, J., Grimont, P. A. D., & Brisse, S. (2005) · Journal of Clinical Microbiology · doi:10.1128/jcm.43.8.4178-4182.2005 · Cited by 1,342 · see citing works
Self-citationHypervirulent (hypermucoviscous) Klebsiella pneumoniae
Shon, A. S. Y., Bajwa, R. P. S., & Russo, T. A. (2013) · Virulence · doi:10.4161/viru.22718 · Cited by 1,175 · see citing works
Woodford, N., Turton, J. F., & Livermore, D. M. (2011) · FEMS Microbiology Reviews · doi:10.1111/j.1574-6976.2011.00268.x · Cited by 881 · see citing works
Snitkin, E. S., Zelazny, A. M., Thomas, P. J., Stock, F., Program, N. C. S., Henderson, D. K., Palmore, T. N., & Segre, J. A. (2012) · Science Translational Medicine · doi:10.1126/scitranslmed.3004129 · Cited by 863 · see citing works
Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain
Jolley, K. A., Bliss, C. M., Bennett, J. S., Bratcher, H. B., Brehony, C., Colles, F. M., Wimalarathna, H. M. L., Harrison, O. B., Sheppard, S. K., Cody, A. J., et al. (2012) · Microbiology · doi:10.1099/mic.0.055459-0 · Cited by 652 · see citing works
Fang, C., Lai, S.-Y., Yi, W., Hsueh, P., Liu, K., & Chang, S. (2007) · Clinical Infectious Diseases · doi:10.1086/519262 · Cited by 648 · see citing works
Routine Use of Microbial Whole Genome Sequencing in Diagnostic and Public Health Microbiology
Köser, C. U., Ellington, M. J., Cartwright, E. J. P., Gillespie, S. H., Brown, N. M., Farrington, M., Holden, M. T. G., Gordon Dougan, B., Bentley, S. D., Parkhill, J., et al. (2012) · PLoS Pathogens · doi:10.1371/journal.ppat.1002824 · Cited by 545 · see citing works
Brisse, S., Fèvre, C., Passet, V., Issenhuth-Jeanjean, S., Tournebize, R., Diancourt, L., & Grimont, P. A. D. (2009) · PLoS ONE · doi:10.1371/journal.pone.0004982 · Cited by 493 · see citing works
Self-citationVallenet, D., Belda, E., Calteau, A., Cruveiller, S., Engelen, S., Lajus, A., Fèvre, F. L., Longin, C., Mornico, D., Roche, D., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1194 · Cited by 385 · see citing works
Sequencing and analysis of the large virulence plasmid pLVPK of Klebsiella pneumoniae CG43
Chen, Y.-T., Chang, H.-Y., Lai, Y.-C., Pan, C.-C., Tsai, S.-F., & Peng, H.-L. (2004) · Gene · doi:10.1016/j.gene.2004.05.008 · Cited by 351 · see citing works
Li, W., Sun, G., Yu, Y., Li, N., Chen, M., Jin, R., Jiao, Y., & Wu, H. (2013) · Clinical Infectious Diseases · doi:10.1093/cid/cit675 · Cited by 304 · see citing works
Siu, L.-K. K., Fung, C., Chang, F., Lee, N. L. S., Yeh, K., Koh, T. H., & Ip, M. (2011) · Journal of Clinical Microbiology · doi:10.1128/jcm.00977-11 · Cited by 230 · see citing works
Plasmid-Encoded Multidrug Efflux Pump Conferring Resistance to Olaquindox in Escherichia coli
Hansen, L. H., Johannesen, E., Burmølle, M., Sørensen, A. H., & Sørensen, S. J. (2004) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.48.9.3332-3337.2004 · Cited by 214 · see citing works
Decré, D., Verdet, C., Emirian, A., Gourrierec, T. L., Petit, J., Offenstadt, G., Maury, É., Brisse, S., & Arlet, G. (2011) · Journal of Clinical Microbiology · doi:10.1128/jcm.00676-11 · Cited by 182 · see citing works
Self-citationSamuelsen, Ø., Naseer, U., Tofteland, S., Skutlaberg, D. H., Onken, A., Hjetland, R., Sundsfjord, A., & Giske, C. G. (2009) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dkp018 · Cited by 171 · see citing works
Diversity and Evolution of the Class A Chromosomal Beta-Lactamase Gene inKlebsiella pneumoniae
Haeggman, S., Löfdahl, S., Paauw, A., Verhoef, J., & Brisse, S. (2004) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.48.7.2400-2408.2004 · Cited by 164 · see citing works
Self-citationTurton, J. F., Englender, H., Gabriel, S. N., Turton, S. E., Kaufmann, M. E., & Pitt, T. L. (2007) · Journal of Medical Microbiology · doi:10.1099/jmm.0.46964-0 · Cited by 159 · see citing works
A Gene-By-Gene Approach to Bacterial Population Genomics: Whole Genome MLST of Campylobacter
Sheppard, S. K., Jolley, K. A., & Maiden, M. C. J. (2012) · Genes · doi:10.3390/genes3020261 · Cited by 150 · see citing works
Breurec, S., Guessennd, N., Timinouni, M., et al. (2012) · Clinical Microbiology and Infection · doi:10.1111/j.1469-0691.2012.03805.x · Cited by 118 · see citing works
Comparative Genomics of Klebsiella pneumoniae Strains with Different Antibiotic Resistance Profiles
Kumar, V. D., Sun, P., Vamathevan, J. J., Li, Y., Ingraham, K. A., Palmer, L. M., Huang, J., & Brown, J. R. (2011) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.00052-11 · Cited by 113 · see citing works
Huang, T.-W., Chen, T.-L., Chen, Y.-T., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0062774 · Cited by 90 · see citing works
Jolley, K. A., Hill, D. M. C., Bratcher, H. B., et al. (2012) · Journal of Clinical Microbiology · doi:10.1128/jcm.01312-12 · Cited by 80 · see citing works
Pérez, F., Rudin, S. D., Marshall, S. H., et al. (2013) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.00725-13 · Cited by 68 · see citing works
Warburg, G., Hidalgo‐Grass, C., Partridge, S. R., Tolmasky, M. E., Temper, V., Moses, A. E., Block, C., & Strahilevitz, J. (2012) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dkr552 · Cited by 66 · see citing works
Sung Weon, J. U. N. G., Chae, H., PARK, Y. J., et al. (2012) · Epidemiology and Infection · doi:10.1017/s0950268812000933 · Cited by 64 · see citing works
Fèvre, C., Passet, V., Weill, F., et al. (2005) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.49.12.5149-5152.2005 · Cited by 61 · see citing works
Self-citationFrom molecular to genomic epidemiology: transforming surveillance and control of infectious diseases
Struelens, M. J., & Brisse, S. (2013) · Eurosurveillance · doi:10.2807/ese.18.04.20386-en · Cited by 60 · see citing works
Self-citationBaraniak, A., Izdebski, R., Fiett, J., Sadowy, E., Adler, A., Kazma, M., Salomon, J., Lawrence, C., Rossini, A., Salvia, A., et al. (2013) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.02571-12 · Cited by 53 · see citing works
Dolejská, M., Villa, L., Dobiašová, H., et al. (2012) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.01886-12 · Cited by 48 · see citing works
Multidrug resistance determinants from NDM-1-producing Klebsiella pneumoniae in the USA
Łęski, T. A., Vora, G. J., & Taitt, C. R. (2012) · International Journal of Antimicrobial Agents · doi:10.1016/j.ijantimicag.2012.05.019 · Cited by 40 · see citing works
Primary liver abscess due to CC23-K1 virulent clone of Klebsiella pneumoniae in France
Merlet, A., Cazanave, C., Dutronc, H., et al. (2012) · Clinical Microbiology and Infection · doi:10.1111/j.1469-0691.2012.03953.x · Cited by 38 · see citing works
Coexistence of qnrB4 and qnrS1 in a clinical strain of Klebsiella pneumoniae
Hu, F., Xu, X., Zhu, D., et al. (2008) · Acta Pharmacologica Sinica · doi:10.1111/j.1745-7254.2008.00757.x · Cited by 38 · see citing works
Coexistence of qnrB4 and qnrS1 in a clinical strain of Klebsiella pneumoniae
Fu-pin, Hu, Xiaogang, et al. (2008) · 中国药理学报：英文版 · Cited by 29 · see citing works
Characterization of a Transmissible Plasmid Encoding VEB-1 and VIM-1 in Proteus mirabilis
Papagiannitsis, C. C., Miriagou, V., Kotsakis, S. D., et al. (2012) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.00470-12 · Cited by 24 · see citing works
Bialek-Davenet, S., Nicolas-Chanoine, M.-H., Decré, D., & Brisse, S. (2012) · Epidemiology and Infection · doi:10.1017/s0950268812002051 · Cited by 14 · see citing works
Self-citationBroberg, C. A., Palacios, M., & Miller, V. L. (2013) · Genome Announcements · doi:10.1128/genomea.00312-13 · Cited by 10 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Pu, D., Zhao, J., Chang, K., Zhuo, X., & Cao, B. (2023) · Science Bulletin · doi:10.1016/j.scib.2023.09.040 · Cited by 194 · see citing works
Siderophore-mediated iron acquisition by <i>Klebsiella pneumoniae</i>
Kumar, A., Chakravorty, S., Yang, T., Russo, T. A., Newton, S. M., & Klebba, P. E. (2024) · Journal of Bacteriology · doi:10.1128/jb.00024-24 · Cited by 42 · see citing works
- Authors
- Bialek-Davenet, S., Criscuolo, A., Ailloud, F., Passet, V., Jones, L., Delannoy-Vieillard, A.-S., Garin, B., Le Hello, S., Arlet, G., Nicolas-Chanoine, M.-H., Decré, D., & Brisse, S.
- Affiliations
- Centre National de la Recherche Scientifique (FR)
- Institut Pasteur (FR)
- Inserm (FR)
- Corresponding author
- Brisse, Sylvain
- ORCID
- Venue
- Emerging Infectious Diseases
- Published
- 2014-11
- Volume
- 20
- Issue
- 11
- Pages
- 1812-1820
- ISSN
- 1080-6040 (ISSN-L)
- 1080-6059
- PMC
- PMC4214299
- OpenAlex
- W1976819345
- Cited by
- 481
- References
- 41
- Citations by year
- 2026: 33 · 2025: 51 · 2024: 38 · 2023: 51 · 2022: 50 · 2021: 39 · 2020: 52 · 2019: 40 · 2018: 41 · 2017: 36 · 2016: 29 · 2015: 18 · 2014: 2
- FWCI
- 12.93
- Type
- journal article
- Language
- en
- Open access
- diamond
- doi.org
- Licence
- cc-by
- Locations
- Emerging infectious diseases (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- HAL (submittedVersion, cc-by-nc-nd)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Greater South Information System
- Funders
- Agence Nationale de la Recherche (10-LABX-62-IBEID, ANR‐10‐LABX‐62‐IBEID, ANR-10, ANR-10-LABX-0062, ANR-10-LABX-62)
- Conseil Régional, Île-de-France
- Assistance publique-Hôpitaux de Paris
- Centers for Disease Control and Prevention
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Medicine › Antibiotic Resistance in Bacteria
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Endocrinology › Enterobacteriaceae and Cronobacter Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Endocrinology › Escherichia coli research studies
- Keywords
- Klebsiella pneumoniae, hypervirulent strains, multidrug resistance, clonal groups, core genome multilocus sequence typing, virulence genes, antimicrobial resistance genes, biological databases
- MeSH terms
- Anti-Bacterial Agents, Humans, Klebsiella Infections, Klebsiella pneumoniae, Phylogeny, Serotyping, Virulence, Cluster Analysis, Genome, Bacterial, Genomics, Drug Resistance, Multiple, Bacterial, Multilocus Sequence Typing
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
