Identification of Vaccine targets in Klebsiella pneumonia using Violin

Author Name(s): *Swathi K, Swetha C, Uma sree G, Kavitha, Janardhan K
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Klebsiella pneumoniae causes community acquired, nosocomial infections & other diseases like bacteremia, hepatic abscess, meningitis, respiratory & urinary tract infections worldwide. This organism is rod shaped, gram-negative, non-motile encapsulated, lactose fermenting facultative anaerobic bacterium, found as the normal flora on the mouth, skin and intestine. Klebsiella pneumoniae belonging to the Enterobacterceae family typically expresses 2 types of antigens –O antigen a component of Lipopolysaccharide & -K antigen a capsular polysaccharide. Many antibiotics are recommended for the treatment, but the organism is showing resistance making the treatment challenging. The solution could be use of vaccines; a polyvalent pneumococcal polysaccharide vaccine was licensed for the treatment of pneumococcal infections during late 1977, but there were reports of its failure. VIOLIN a web-based vaccine tool integrates vaccine literature data mining, vaccine research data curation & storage & curated vaccine data analysis for vaccines & vaccine candidates developed against various pathogens of high priority in public health & biological safety. VIOLIN also provides a program for vaccine target prediction. In our study we have used this tool for the detection of vaccine targets for K.pneumoniae NTUH-K2044 and it was found that the putative outer membrane can be synthesized in vivo and can be used as a potent protein sub-unit protein against Klebsiella infections.


Antibiotics, vaccine, polysaccharide, VIOLIN


The start of the “vaccine” by Jenner’s description of small pox has revolutionized the world of immunology in preventing infectious diseases (E. Jenner 1798) [1]. Critical advances in the field of vaccine took place in 19th and early 20th century by the scientists like Pasteur, Koch, Von Behring, Calmette, Guerin and Ehrlich by the development of antiserum, antitoxins and live- attenuated vaccines (M. R. Hilleman 2000) [2]. Further advances in cell cultures, molecular biology and immunology have led to the modern-era of “subunit” vaccine development. The recombinant hepatitis B vaccine is one of the first licensed sub-unit vaccines for human use. The advent of computers and informatics has facilitated vaccine-research and development. ImmunoInformatics targets the mathematical and computational approaches to address immunological questions. Since 1980’s many Immunoinformatics methods have been used to predict T-Cells and B-Cells immune epitopes, [3]. The experimentally verified immune epitopes are stored in web-based databases like the Immune Epitope Database and Analysis Resource (IEDA) and few others [4].
The molecular and sequencing technologies, bioinformatics analysis has allowed in silico selection of vaccine targets [5]. A novel approach called REVERSE VACCINOLOGY or IMMUNOME DERIVED VACCINE DESIGN [6]. This algorithm was first used against Neisseria meningitides for the identification of vaccine targets in it [7]. The Vaccine Investigation OnLine Information Network (VIOLIN) the first Immunoinformatics tool for vaccine design was developed in 1980’s by DeLisi and Berzofsky and others [8], it is a web based central resource, allowing easy curation, comparison and analysis of vaccine-related research data. VIOLIN is publicly available at contains information regarding microbial pathogenesis, host ranges, host specificities, as well as vaccine – specific information such as vaccine type, methodology, genetic engineered genes.
Klebsiella pneumonia is one of the species of the genera KLEBSIELLA, and is a gram negative facultative anaerobe belonging to the phylum PROTEOBACTERIA, and exhibits close genetic resemblance to the other bacteria of Enterobacteriaceae like Escherichia, salmonella, shigella, and Yesinia [9]. The community acquired Pyogenic Liver Abscesses (PLA) is caused by Klebsiella pneumoniae complicated with metastatic meningitis and endophthalmitis have been found globally [10]. For the study of vaccine targets in the genus Klebsiella we have chosen the strain Klebsiella
pneumoniae NTUH-K2044. The sequencing for this organism was done by Keh-Ming Wu, Ling–Hui Li, etal at the Institute of Biomedical Informatics, Taiwan. This organism was found to have the circular chromosome and the length of genome is 52, 48,520 kb with an extra-chromosomal circular plasmid of length 2, 24,152 kb by name PK2044. The complete genome of this strain is available in the NCBI genome under the accession number NC_012731.
The bacterium overcomes the innate immunity through several means; the capsule which is the first pathogenic determinant is also called K antigen. The capsule is composed of complex acidic polysaccharides which is so massive that it prevents the phagocytosis by PolyMorphoNuclear (PMN) granulocytes and also prevents the cell death by the bactericidal serum mediated complement proteins of the host [11].
Based on the symptoms and tests the physician may confirm that the patient is suffering from the Klebsiella infections and may suggest the drugs like Cefotaxime Carbapenem Ceftizoxime Gentamicin Tobramycin which have bactericidal activity of inhibiting the cell wall synthesis by binding to the Penicillin Binding Proteins (PBP) which inhibits the peptidoglycan synthesis.
The prudent use of antibiotics has led to the resistance of the antibiotics by the microbes as said by Dr.Dilip Mathai, the President of Clinical Infectious Diseases Society. This is an unusual nature of Klebsiella to show resistance to structurally unrelated antibiotics like nalidixic acid, timethoprim and chloramphenicol and is also known to have developed resistance to the class of antibiotics known as Carbapene and has developed into a multidrug-resistant mutant.
The Klebsiella species bearing resistance to this class of antibiotic are called KPC producing Organisms or Carbapenem resistance Klebsiella pneumoniae (CRKP). These organisms produce an enzyme carbapenemase which helps in drawing resistance against Carbapenem and the study on the multiresistant CRKP was done in Los Angeles Country by the Department of Public Healthcare.


Klebsiella pneumoniae being a ubiquitous microbe is the major cause of the urinary infections was first explored by Friedlander after which Keh Ming etal have sequenced the genome of Klebsiella pneumoniae NTUH-K2044. This microbe is known to contain 5.2Mbp which is used for its survival.
There are many treatments available for treating these infections. The major one is the usage of antibiotics and drugs. As with evolutionary progress this microbe has shown resistance to the antibiotics and drugs which has made the treatment to patients miserable as there is no available treatment to these diseases.
The only solution could be the use of vaccines. Vaccine is the part of the pathogen which triggers immune response in the host. Thus vaccine acts as the epitope to the host’s immune system. Vaccine Informatics is an emerging research that focuses on the development and application of bioinformatics methods that can be used to facilitate every aspect of the preclinical, clinical vaccine enterprise. Many Immunoinformatics algorithms have been developed to predict T and B- cell immune epitopes for epitope vaccine development. This process of identification is called Reverse Vaccinology. By using this tool we have found that several regions can be used as vaccines for the human consumption, the regions like Mag A encoding genes can be used. And after the detailed study on the organism it was found that the genes like Mag A, rmp A, capsular serotypes and hypermucoviscosity were involved in the virulence of the strain. The putative outer membrane can be synthesized in vivo and can be used as a protein sub-unit protein against Klebsiella infections.

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