PNA-based microbial pathogen identification and resistance marker detection: An accurate, isothermal rapid assay based on genome-specific features

Artificial DNA: PNA and XNA

Volumn 1, Issue 2, 2010, Pages 76-82

  Smolina, Irina ^a   Miller, Nancy S ^b   Frank Kamenetskii, Maxim D ^a  

^a Boston University   (United States)

^b BOSTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Bacteral detection; Drug resistance; PNA; RCA; S. aureus

Indexed keywords

BIOLOGICAL MARKER; FLUORESCENT DYE; GENOMIC DNA; METICILLIN; PEPTIDE NUCLEIC ACID;

ACCURACY; ANTIBIOTIC RESISTANCE; ANTIBIOTIC SENSITIVITY; ARTICLE; BACTERIUM IDENTIFICATION; FLUORESCENCE IN SITU HYBRIDIZATION; GENE AMPLIFICATION; GENE SEQUENCE; GENETIC MARKER; METHICILLIN RESISTANT STAPHYLOCOCCUS AUREUS; MICROBIAL IDENTIFICATION; MULTIDRUG RESISTANCE; NONHUMAN; POLYMERASE CHAIN REACTION; PSEUDOMONAS AERUGINOSA; ROLLING CIRCLE AMPLIFICATION; SENSITIVITY AND SPECIFICITY; STAPHYLOCOCCUS AUREUS;

BACTERIA (MICROORGANISMS); STAPHYLOCOCCUS AUREUS;

EID: 79952166943     PISSN: 1949095X     EISSN: 19490968     Source Type: Journal    
DOI: 10.4161/adna.1.2.13256     Document Type: Article

References (26)

1. Mothershed EA, Whitney AM. Nucleic acid-based methods for the detection of bacterial pathogens:Present and future considerations for the clinical laboratory. Clinica Chimica Acta 2006; 363:206-20.
2. Procop GW. In situ hybridization for the detection of infectious agents. Clinical Microbiolog Newsletter 2002; 24:121-5.
3. Mothershed M, Horn M, Daims H. Fluorescence in situ hybridization for the identification and characterization of prokaryotes. Curr Opinion Microbol 2003; 6:302-9.
4. Moter A, Gobel UB. Fluorescence in situ hybridization (FISH) for direct visualization of microorganisms. J Microbiol Methods 2000; 41:85-112.
5. Zwirglmaier K. Fluorescence in situ hybridization (FISH)-the next generation. FEMS Microbiol Lett 2005; 246:151-8.
6. Smolina IV, Lee C, Frank-Kamenetskii MD. Detection of low copy genomic DNA sequences in individual bacterial cells using PNA-assisted rolling circle amplification and fluorescence in situ hybridization. Appl Environ Microbiol 2007; 73:2324-8.
7. Smolina IV, Kuhn H, Lee C, Frank-Kamenetskii MD. Fluorescence-based detection of short DNA sequences under non-denaturing conditions. Bioorg Med Chem 2008; 16:84-93.
8. Beekmann SE, Diekema DJ, Chapin KC, Doern GV. Effects of Rapid Detection of Bloodstream Infections on Length of Hospitalization and Hospital Charges. J Clin Microbiol 2003; 41:3119-25.
9. Harbarth S, Samore MH. Antimicrobial resistance determinants and future control. Emerg Infect Diseases 2005; 11:794-801.
10. Nielsen PE, Egholm M, Berg RH, Buchardt O. Sequence-selective recognition of DNA by strand displacement with a thymine-substituted polyamide. Science 1991; 254:1497-500.
11. pH-independent-independent sequence-specific DNA binding by pseudoisocytosine- containing bis-PNA. Nucleic Acids Res 1995; 23:217-22.
12. Demidov VV, Frank-Kamenetskii MD. Two sides of the coin: affinity and specificity of nucleic acid interactions. Trends Biochem Sci 2004; 29:62-71.
13. Kuhn H, Demidov VV, Frank-Kamenetskii MD, Nielsen PE. Kinetic Sequence Discrimination of Cationic bis-PNAs upon Targeting of Double-Stranded DNA. Nucleic Acids Res 1998; 26:582-7.
14. Bukanov NO, Demidov VV, Nielsen PE, Frank- Kamenetskii MD. PD-loop: a complex of duplex DNA with an oligonucleotide. Proc Natl Acad Sci USA 1998; 95:5516-20.
15. Nilsson M. Lock and roll: single-molecule genotyping in situ using padlock probes and rolling-circle amplification. Histochem Cell Biol 2006; 126:159-64.
16. Kuhn H, Demidov VV, Frank-Kamenetskii MD. An earring for the double helix: Assembly of topological links comprising duplex DNA and a circular oligodeoxynucleotide. J Biomol Struct Dyn 2000; 11:221-5.
17. Demidov VV, Kuhn H, Lavrentieva-Smolina IV, Frank-Kamenetskii MD. Peptide nucleic acid-assisted topological labeling of duplex DNA. Methods 2001; 23:123-31
18. Kuhn H, Demidov VV, Frank-Kamenetskii MD. Topological links between duplex DNA and a circular DNA single strand. Angewandte Chemie Int Ed 1999; 38:1446-9.
19. Baner J, Gyarmati P, Yacoub A, Hakhverdyan M, Stenberg J, et al. Microarray-based molecular detection of foot-and-mouth disease, vesicular stomatitis and swine vesicular disease viruses, using padlock probes. J Virol Methods 2007; 143:200-6.
20. Deurenberg RH, Vink C, Kalenic S, Friedrich AW, Bruggeman CA, Stobberingh EE. The molecular evolution of methicillin-resistant Staphylococcus aureus. Clin Microbiol Infect 2007; 13:222-35.
21. Wellinghausen N, Siegel D, Gebert S, Winter J. Rapid detection of Staphylococcus aureus bacteremia and methicillin resistance by real-time PCR in whole blood samples. Eur J Clin Microbiol Infect Diseases 2009; 28:1001-5.
22. Oliveira K, Procop GW, Wilson D, Coull J, Stender H. Rapid identification of Staphylococcus aureus directly from blood cultures by fluorescence in situ hybridization with peptide nucleic acid probes. J Clin Microbiol 2002; 40:247-51.
23. Jarvius J, Melin J, Göransson J, Stenberg J, Fredriksson S, Gonzalez-Rey C, et al. Digital quantification using amplified single-molecule detection. Nature Methods 2006; 3:725-7.
24. Sundsfjord A, Simonsen GS, Haldosen BC, Haaheim H, Hjelmevoll SO, et al. Genetic methods for detection of antimicrobial resistance. APMIS 2004; 112:815-37.
25. Mothershed EA, Whitney AM. Nucleic acid-based methods for the detection of bacterial pathogens: Present and future considerations for the clinical laboratory. Clinica Chimica Acta 2006; 363:206-20.
26. Espy MJ, Uhl JR, Sloan LM, Buckwalter SP, Jones MF, et al. Real-time PCR in clinical microbiology: applications for routine laboratory testing. Clin Microbiol Rev 2006; 19:165-256