Survey of clustered regularly interspaced short palindromic repeats and their associated Cas proteins (CRISPR/Cas) systems in multiple sequenced strains of Klebsiella pneumoniae

BMC Research Notes

Volumn 8, Issue 1, 2015, Pages

  Ostria Hernández, Martha Lorena ^a   Sánchez Vallejo, Carlos Javier ^a   Ibarra, J Antonio ^a   Castro Escarpulli, Graciela ^a  

^a INSTITUTO POLITÉCNICO NACIONAL   (Mexico)

Author keywords

Bacterial immune system; Bacteriophages; CRISPR Cas; Multiple drug resistance; Plasmids

Indexed keywords

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; KLEBSIELLA; KLEBSIELLA PNEUMONIAE;

BACTERIAL PROTEIN;

BACTERIAL GENE; BACTERIAL GENOME; BIOLOGICAL MODEL; BIOLOGY; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; CRISPR CAS SYSTEM; DNA SEQUENCE; ESCHERICHIA COLI; GENETIC DATABASE; GENETICS; GENOMICS; KLEBSIELLA PNEUMONIAE; METABOLISM; MOLECULAR WEIGHT; PLASMID; PROCEDURES; PROTEIN DATABASE; VIRULENCE;

BACTERIAL PROTEINS; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEATS; COMPUTATIONAL BIOLOGY; CRISPR-CAS SYSTEMS; DATABASES, GENETIC; DATABASES, PROTEIN; ESCHERICHIA COLI; GENES, BACTERIAL; GENOME, BACTERIAL; GENOMICS; KLEBSIELLA PNEUMONIAE; MODELS, GENETIC; MOLECULAR WEIGHT; PLASMIDS; SEQUENCE ANALYSIS, DNA; VIRULENCE;

EID: 84938386396     PISSN: None     EISSN: 17560500     Source Type: Journal    
DOI: 10.1186/s13104-015-1285-7     Document Type: Article

References (45)

1. Frost LS, Leplae R, Summers AO, Toussaint A (2005) Mobile genetic elements: the agents of open source of evolution. Nat Rev Microbiol 3:722-732
2. Stern A, Keren L, Wurtzel O, Amitai G, Sorek R (2010) Self-targeting by CRISPR: gene regulation or autoinmunity? Trends Genet 26:335-340
3. Weinberger AD, Gilmore MS (2012) CRISPR/Cas: to take up DNA or not- that is the question. Cell Host Microbe 12:125-126
4. Deveau H, Garneau JE, Moineau S (2010) CRISPR/cas system and its role in phage-bacteria interactions. Annu Rev Microbiol 64:475-493
5. Bikard D, Hatoum-Aslan A, Mucida D, Marraffini LA (2012) CRISPR interference can prevent natural transformation and virulence acquisition during in vivo bacterial infection. Cell Host Microbe 12:177-186
6. Szczepankowska A (2012) Role of CRISPR/cas system in the development of bacteriophage resistance. Adv Virus Res 82:289-338
7. Makarova KS, Haft DH, Barrangou R, Brouns SJ, Charpentier E, Horvath P et al (2011) Evolution and classification of the CRISPR- Cas systems. Nat Rev Microbiol 9:467-477
8. Richter C, Chang JT, Fineran PC (2012) Function and regulation of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated (Cas) system. Viruses 4:2291-2311
9. Labrie SJ, Samson JE, Moineau S (2010) Bacteriophage resistance mechanisms. Nat Rev Microbiol 8:317-327
10. Pul Ü, Wurm R, Arslan Z, Geißen R, Hofmann N, Wagner R (2010) Identification and characterization of E. coli CRISPR-cas promoters and their silencing by H-NS. Mol Microbiol 75:1495-1512
11. Mojica FJ, Díez-Villaseñor C (2010) The on-off switch of CRISPR immunity against phages in Escherichia coli. Mol Microbiol 77:1341-1345
12. Westra ER, Pul U, Heidrich N, Jore MM, Lundgren M, Stratmann T et al (2010) H-NS-mediated repression of CRISPR-based immunity in Escherichia coli K12 can be relieved by the transcription activator LeuO. Mol Microbiol 77:1380-1393
13. Medina-Aparicio L, Rebollar-Flores JE, Gallego-Hernández AL, Vázquez A, Olvera L, Gutiérrez-Ríos RM et al (2011) The CRISPR/Cas immune system is an operon regulated by LeuO, H-NS, and leucine-responsive regulatory protein in Salmonella enterica serovar Typhi. J Bacteriol 193:2396-2407
14. Hatoum-Aslan A, Marraffini LA (2014) Impact of CRISPR immunity on the emergence and virulence of bacterial pathogens. Curr Opin Microbiol 17:82-90
15. Louwen R, Staals RH, Endtz HP, van Baarlen P, van der Oost J (2014) The role of CRISPR-Cas systems in virulence of pathogenic bacteria. Microbiol Mol Biol Rev 78:74-88
16. Palmer KL, Gilmore MS (2010) Multidrug-resistant enterococci lack CRISPR-cas. MBio 1:1-10
17. El Fertas-Aissani R, Messai Y, Alouache S, Bakour R (2013) Virulence profiles and antibiotic susceptibility patterns of Klebsiella pneumoniae strains isolated from different clinical specimens. Pathol Biol 61:209-216
18. Baquero F, Tedim AP, Coque TM (2013) Antibiotic resistance shaping multi-level population biology of bacteria. Front Microbiol 4:1-15
19. García-Fernández A, Villa L, Carta C, Venditti C, Giordano A, Venditti M et al (2012) Klebsiella pneumoniae ST258 producing KPC-3 identified in Italy carries novel plasmids and OmpK36/OmpK35 porin variants. Antimicrob Agents Chemother 56:2143-2145
20. Grissa I, Vergnaud G, Pourcel C (2007) CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res 35:W52-W57
21. Lin AC, Liao TL, Lin YC, Lai YC, Lu MC, Chen YT (2012) Complete Genome Sequence of Klebsiella pneumoniae 1084, a Hypermucoviscosity-Negative K1 Clinical Strain. J Bacteriol 194:6316
22. Lin YC, Lu MC, Tang HL, Liu HC, Chen CH, Liu KS et al (2011) Assessment of hypermucoviscosity as a virulence factor for experimental Klebsiella pneumoniae infections: comparative virulence analysis with hypermucoviscosity-negative strain. BMC Microbiol 11:50
23. Wu KM, Li LH, Yan JJ, Tsao N, Liao TL, Tsai HC et al (2009) Genome sequencing and comparative analysis of Klebsiella pneumoniae NTUH-K2044, a strain causing liver abscess and meningitis. J Bacteriol 191:4492-4501
24. Xie G, Ramirez MS, Marshall SH, Hujer KM, Lo CC, Johnson S et al (2013) Genome sequences of two Klebsiella pneumoniae isolates from different geographical regions, Argentina (strain JHCK1) and the United States (strain VA360). Genome Announc 1:e00168-e00213
25. Ramirez MS, Xie G, Marshall SH, Hujer KM, Chain PS, Bonomo RA et al (2012) Multidrug resistant (MDR) Klebsiella pneumoniae clinical isolates: a zone of high heterogeneity (HHZ) as a tool for epidemiological studies. Clin Microbiol Infect 18:E254-E258
26. Marcoleta A, Gutiérrez-Cortez S, Maturana D, Monasterio O, Lagos R (2013) Whole-genome sequence of the microcin E492-producing strain Klebsiella pneumoniae RYC492. Genome Announc 1:e00178-e00213
27. De Lorenzo V, Martínez JL, Asensio C (1984) Microcin-mediated interactions between Klebsiella pneumoniae and Escherichia coli strains. J Gen Microbiol 130:391-400
28. Mojica FJ, Díez-Villaseñor C, García-Martínez J, Soria E (2005) Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J Mol Evol 60:174-182
29. Bondy-Denomy J, Davidson A (2014) To acquire or resist: the complex biological effects of CRISPR-Cas systems. Trends Microbiol 22:218-225
30. Rüden H, Gastmeier P, Daschner FD, Schumacher M (1997) Nosocomial and community-acquired infections in Germany. Summary of the results of the first national prevalence study (NIDEP). Infection 25:199-202
31. Diekema DJ, Beekmann SE, Chapin KC, Morel KA, Munson E, Doern GV (2003) Epidemiology and outcome of nosocomial and community-onset bloodstream infection. J Clin Microbiol 41:3655-3660
32. Sader HS, Jones RN, Gales AC, Silva JB, Pignatari AC (2004) SENTRY antimicrobial surveillance program report: latin American and Brazilian results for 1997 through 2001. Braz J Infect Dis 8:25-79
33. Balkhy HH, Cunningham G, Chew FK, Francis C, Al Nakhli DJ, Almuneef MA et al (2006) Hospital- and community-acquired infections: a point prevalence and risk factors survey in a tertiary care center in Saudi Arabia. Int J Infect Dis 10:326-333
34. Boucher HW, Talbot GH, Bradley JS, Edwards JE, Gilbert D, Rice LB et al (2009) Bad bugs, no drugs: no ESKAPE! An update from the Infectious Diseases Society of America. Clin Infect Dis 48:1-12
35. Djordjevic Z, Jankovic S, Gajovic O, Djonovic N, Folic N, Bukumiric Z (2012) Hospital infections in a neurological intensive care unit: incidence, causative agents and risk factors. J Infect Dev Ctries 6:798-805
36. Pleckaityte M, Zilnyte M, Zvirbliene A (2012) Insights into the CRISPR/Cas system of Gardnerella vaginalis. BMC Microbiol 12:301
37. Tasaki E, Hirayama J, Tazumi A, Hayashi K, Hara Y, Ueno H et al (2012) Molecular identification and characterization of clustered regularly interspaced short palindromic repeats (CRISPRs) in a urease-positive thermophilic Campylobacter sp. (UPTC). World J Microbiol Biotechnol 28:713-720
38. Marraffini LA (2010) Impact of CRIPSR immunity on the emergence of bacterial pathogens. Future Microbiol 5:693-695
39. Thomas-Chollier M, Defrance M, Medina-Rivera A, Sand O, Herrmann C, Thieffry D et al (2011) RSAT 2011:regulatory sequence analysis. Nucleic Acids Res 39:W86-W91
40. Caspi R, Altman T, Billington R, Dreher K, Foerster H, Fulcher CA et al (2014) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res 42:D459-D471
41. Darling AE, Mau B, Perna NT (2010) progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 5:e11147
42. Katoh K, Toh H (2008) Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform 9:286-298
43. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H et al (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947-2948
44. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792-1797
45. Crooks GE, Hon G, Chandonia JM, Brenner SE (2004) WebLogo: a sequence logo generator. Genome Res 14:1188-1190