Database Authors
Brendan Wilson-Mortier1, Amanda Mackie1, Anahit Penesyan1, Ian Paulsen1, Anamika Kothari2, Peter D Karp2
1Macquarie University, 2SRI International
Summary Klebsiella pneumoniae is a Gram-negative, encapsulated, non-motile and facultatively anaerobic member of the Enterobacteriaceae family, which also includes the well-known genera Escherichia, Salmonella and Shigella [Wyres20, Chang21]. Despite being found in environmental reservoirs and as a commensal member of the gastrointestinal tract or respiratory system of some humans and other mammals, the species is best known for its categorization as an ESKAPE pathogen, and represents a significant emerging threat to public health [Pendleton13, Santajit16, De20]. Traditionally, K. pneumoniae infections (commonly UTIs, pneumonia and wound infections) were largely considered to be confined to cases of opportunistic health-care associated infections (HAIs), referred to as "classical" K. pneumoniae infections, or cKP [Russo11, Russo18]. However, in the mid 1980s, hypervirulent isolates (hvKP) capable of causing community acquired infections (CAIs) in otherwise healthy individuals appeared in Asia, and have since spread worldwide [Hennequin16, Lee17, Russo19, Chen23]. Types of infections caused by hvKP are much broader than cKP, and can include pyogenic liver abscess, endophthalmitis, meningitis, brain abscess, necrotizing fasciitis and more [Russo19, Wyres20, Choby20]. Although antibiotic resistance has represented a clinically significant issue in cKP infections, it is increasingly becoming more prevalent in hvKP infections, increasing mortality rates and rendering treatment challenging [MunozPrice13, Hennequin16, Paczosa16, Lee17, Russo19].

K. pneumoniae is part of a closely related group of species referred to as the Klebsiella pneumoniae species complex (KpSC), which also includes K. quasipneumoniae subsp. similipneumoniae, K. quasipneumoniae subsp. quasipneumoniae, K. quasivariicola, K. africana, K. variicola subsp. tropica, and K. variicola subsp. variicola, each of which shares approximately 95-96% average nucleotide identity (ANI) with K. pneumoniae [Long17, Rodrigues18, Wyres20, Lam22, Morgado22]. Isolates exhibiting ANI scores above this threshold with K. pneumoniae are considered to be a member of the species, with clonal groups (CGs) and sequence types (STs) further defined by core-genome multilocus sequence typing (cgMLST) or core-genome phylogenetic analysis [BialekDavenet14, Holt15, Wyres20, Hennart22]. However, strains of K. pneumoniae can also be categorized based on the variation within the capsule biosynthesis locus (K-locus) and the outer lipopolysaccharide (O-antigen) biosynthesis locus (O-locus) [Lam22]. The genome used for this PGDB belongs to a hypervirulent strain (CG23, ST23 and serotypes O1 and K1) isolated sometime between 1996-2001 from a previously healthy 40-year-old patient suffering from community-acquired primary liver abscess and metastatic meningitis at the National Taiwan University Hospital (NTUH) [Fang04, Wu09].

This Pathway Genome Database (PGDB) was generated by the PathoLogic [Karp16, Karp11] component of Pathway Tools software version 27.5 and MetaCyc [Caspi18] version 27.1 on 04-Apr-2023 21:57:04.

Genome
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NC_0127315,0784,831150975,248,520NCBI Assembly:GCF_000009885.1
pK2044242200042224,152NCBI Assembly:GCF_000009885.1
Total:5,3205,0311501395,472,672
Ortholog data available?Yes
Database Contents
Genes5,320
Pathways437
Enzymatic Reactions2,285
Transport Reactions188
Polypeptides5,035
Protein Complexes252
Enzymes1,418
Transporters623
Compounds1,573
Transcription Units3,560
tRNAs87
Protein Features6,861
GO Terms4,927
Database Version29.0
Synonyms Klebsiella pneumoniae subsp. pneumoniae str. NTUH-K2044
Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Enterobacterales
Enterobacteriaceae
Klebsiella/Raoultella group
Klebsiella
Klebsiella pneumoniae
Klebsiella pneumoniae pneumoniae
Klebsiella pneumoniae pneumoniae NTUH-K2044
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMD00060934
NCBI BioProjectPRJNA224116
NCBI-Taxonomy484021
Environmentisolated from blood of a patient with liver abscess and meningitis
Annotation ProviderNCBI RefSeq
Annotation Date2022-11-3
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version6.3
Annotation CommentBest-placed reference protein set; GeneMarkS-2+

References

BialekDavenet14: Bialek-Davenet S, Criscuolo A, Ailloud F, Passet V, Jones L, Delannoy-Vieillard AS, Garin B, Le Hello S, Arlet G, Nicolas-Chanoine MH, Decre D, Brisse S (2014). "Genomic definition of hypervirulent and multidrug-resistant Klebsiella pneumoniae clonal groups." Emerg Infect Dis 20(11);1812-20. PMID: 25341126

Caspi18: Caspi R, Billington R, Fulcher CA, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Midford PE, Ong Q, Ong WK, Paley S, Subhraveti P, Karp PD (2018). "The MetaCyc database of metabolic pathways and enzymes." Nucleic Acids Res 46(D1);D633-D639. PMID: 29059334

Chang21: Chang D, Sharma L, Dela Cruz CS, Zhang D (2021). "Clinical Epidemiology, Risk Factors, and Control Strategies of Klebsiella pneumoniae Infection." Front Microbiol 12;750662. PMID: 34992583

Chen23: Chen J, Zhang H, Liao X (2023). "Hypervirulent Klebsiella pneumoniae." Infect Drug Resist 16;5243-5249. PMID: 37589017

Choby20: Choby JE, Howard-Anderson J, Weiss DS (2020). "Hypervirulent Klebsiella pneumoniae - clinical and molecular perspectives." J Intern Med 287(3);283-300. PMID: 31677303

De20: De Oliveira DMP, Forde BM, Kidd TJ, Harris PNA, Schembri MA, Beatson SA, Paterson DL, Walker MJ (2020). "Antimicrobial Resistance in ESKAPE Pathogens." Clin Microbiol Rev 33(3). PMID: 32404435

Fang04: Fang CT, Chuang YP, Shun CT, Chang SC, Wang JT (2004). "A novel virulence gene in Klebsiella pneumoniae strains causing primary liver abscess and septic metastatic complications." J Exp Med 199(5);697-705. PMID: 14993253

Hennart22: Hennart M, Guglielmini J, Bridel S, Maiden MCJ, Jolley KA, Criscuolo A, Brisse S (2022). "A Dual Barcoding Approach to Bacterial Strain Nomenclature: Genomic Taxonomy of Klebsiella pneumoniae Strains." Mol Biol Evol 39(7). PMID: 35700230

Hennequin16: Hennequin C, Robin F (2016). "Correlation between antimicrobial resistance and virulence in Klebsiella pneumoniae." Eur J Clin Microbiol Infect Dis 35(3);333-41. PMID: 26718943

Holt15: Holt KE, Wertheim H, Zadoks RN, Baker S, Whitehouse CA, Dance D, Jenney A, Connor TR, Hsu LY, Severin J, Brisse S, Cao H, Wilksch J, Gorrie C, Schultz MB, Edwards DJ, Nguyen KV, Nguyen TV, Dao TT, Mensink M, Minh VL, Nhu NT, Schultsz C, Kuntaman K, Newton PN, Moore CE, Strugnell RA, Thomson NR (2015). "Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health." Proc Natl Acad Sci U S A 112(27);E3574-81. PMID: 26100894

Karp11: Karp PD, Latendresse M, Caspi R (2011). "The pathway tools pathway prediction algorithm." Stand Genomic Sci 5(3);424-9. PMID: 22675592

Karp16: Karp PD, Latendresse M, Paley SM, Krummenacker M, Ong QD, Billington R, Kothari A, Weaver D, Lee T, Subhraveti P, Spaulding A, Fulcher C, Keseler IM, Caspi R (2016). "Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology." Brief Bioinform 17(5);877-90. PMID: 26454094

Lam22: Lam MMC, Wick RR, Judd LM, Holt KE, Wyres KL (2022). "Kaptive 2.0: updated capsule and lipopolysaccharide locus typing for the Klebsiella pneumoniae species complex." Microb Genom 8(3). PMID: 35311639

Lee17: Lee CR, Lee JH, Park KS, Jeon JH, Kim YB, Cha CJ, Jeong BC, Lee SH (2017). "Antimicrobial Resistance of Hypervirulent Klebsiella pneumoniae: Epidemiology, Hypervirulence-Associated Determinants, and Resistance Mechanisms." Front Cell Infect Microbiol 7;483. PMID: 29209595

Long17: Long SW, Linson SE, Ojeda Saavedra M, Cantu C, Davis JJ, Brettin T, Olsen RJ (2017). "Whole-Genome Sequencing of Human Clinical Klebsiella pneumoniae Isolates Reveals Misidentification and Misunderstandings of Klebsiella pneumoniae, Klebsiella variicola, and Klebsiella quasipneumoniae." mSphere 2(4). PMID: 28776045

Morgado22: Morgado S, Fonseca E, Vicente AC (2022). "Genomics of Klebsiella pneumoniae Species Complex Reveals the Circulation of High-Risk Multidrug-Resistant Pandemic Clones in Human, Animal, and Environmental Sources." Microorganisms 10(11). PMID: 36422351

MunozPrice13: Munoz-Price LS, Poirel L, Bonomo RA, Schwaber MJ, Daikos GL, Cormican M, Cornaglia G, Garau J, Gniadkowski M, Hayden MK, Kumarasamy K, Livermore DM, Maya JJ, Nordmann P, Patel JB, Paterson DL, Pitout J, Villegas MV, Wang H, Woodford N, Quinn JP (2013). "Clinical epidemiology of the global expansion of Klebsiella pneumoniae carbapenemases." Lancet Infect Dis 13(9);785-96. PMID: 23969216

Paczosa16: Paczosa MK, Mecsas J (2016). "Klebsiella pneumoniae: Going on the Offense with a Strong Defense." Microbiol Mol Biol Rev 80(3);629-61. PMID: 27307579

Pendleton13: Pendleton JN, Gorman SP, Gilmore BF (2013). "Clinical relevance of the ESKAPE pathogens." Expert Rev Anti Infect Ther 11(3);297-308. PMID: 23458769

Rodrigues18: Rodrigues C, Passet V, Rakotondrasoa A, Brisse S (2018). "Identification of Klebsiella pneumoniae, Klebsiella quasipneumoniae, Klebsiella variicola and Related Phylogroups by MALDI-TOF Mass Spectrometry." Front Microbiol 9;3000. PMID: 30581423

Russo11: Russo TA, Shon AS, Beanan JM, Olson R, MacDonald U, Pomakov AO, Visitacion MP (2011). "Hypervirulent K. pneumoniae secretes more and more active iron-acquisition molecules than "classical" K. pneumoniae thereby enhancing its virulence." PLoS One 6(10);e26734. PMID: 22039542

Russo18: Russo TA, Olson R, Fang CT, Stoesser N, Miller M, MacDonald U, Hutson A, Barker JH, La Hoz RM, Johnson JR (2018). "Identification of Biomarkers for Differentiation of Hypervirulent Klebsiella pneumoniae from Classical K. pneumoniae." J Clin Microbiol 56(9). PMID: 29925642

Russo19: Russo TA, Marr CM (2019). "Hypervirulent Klebsiella pneumoniae." Clin Microbiol Rev 32(3). PMID: 31092506

Santajit16: Santajit S, Indrawattana N (2016). "Mechanisms of Antimicrobial Resistance in ESKAPE Pathogens." Biomed Res Int 2016;2475067. PMID: 27274985

Wu09: Wu KM, Li LH, Yan JJ, Tsao N, Liao TL, Tsai HC, Fung CP, Chen HJ, Liu YM, Wang JT, Fang CT, Chang SC, Shu HY, Liu TT, Chen YT, Shiau YR, Lauderdale TL, Su IJ, Kirby R, Tsai SF (2009). "Genome sequencing and comparative analysis of Klebsiella pneumoniae NTUH-K2044, a strain causing liver abscess and meningitis." J Bacteriol 191(14);4492-501. PMID: 19447910

Wyres20: Wyres KL, Lam MMC, Holt KE (2020). "Population genomics of Klebsiella pneumoniae." Nat Rev Microbiol 18(6);344-359. PMID: 32055025

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