Abstract
This chapter contains basic information required for an understanding of subsequent text and is intended primarily for those approaching DNA methodology for the first time; it describes relevant features of nucleic acids and outlines some of the practical and theoretical considerations.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Alito A, Morcillo N, Scipioni S et al (1999) The ÃS6110 restriction fragment length polymorphism in particular multidrug-resistant Mycobacterium tuberculosis strains may evolve too fast for reliable use in outbreak investigation. Journal of Clinical Microbiology 37: 788–791.
Appuhamy S, Parton R, Coote JG and Gibbs HA (1997) Genomic fingerprinting of Haemophilus somnus by a combination of PCR methods. Journal of Clinical Microbiology 35: 288–291.
Boivin G, Handfield J, Toma L et al (1999) Expression of the late cytomegalovirus (CMV) pp150 transcript in leukocytes of AIDS patients is associated with a high viral DNA load in leukocytes and presence of CMV DNA in plasma. Journal of Infectious Diseases 179: 1101–1107.
Bolton LF, Kelley LC, Lee MD et al (1999) Detection of multidrug-resistant Salmonella enterica serotype typhimurium DT104 based on a gene which confers cross-resistance to florfenicol and chloramphenicol. Journal of Clinical Microbiology 37: 1348–1351.
Bougnoux M-E, Dupont C, Mateo J et al (1999) Serum is more suitable than whole blood for diagnosis of systemic candidiasis by nested PCR. Journal of Clinical Microbiology 37: 925–930.
Branigan PJ, Gérard HC, Hudson AP and Schumacher HR (1996) Comparison of synovial tissue and synovial fluid as the source of nucleic acids for detection of Chlamydia trachomatis by polymerase chain reaction. Arthritis & Rheumatism 39: 1740–1746.
Brazier JS, O’Neill GL and Duerden BI (1997) Polymerase chain reaction ribotypes of Clostridium difficile in hospitals in England and Wales. Reviews in Medical Microbiology 8: (supplement 1) S55 - S56.
Cavassini M, Wenger A, Jaton K et al (1999) Evaluation of MRSA-Screen, a simple antiPBP 2a slide latex agglutination kit, for rapid detection of methicillin resistance in Staphylococcus aureus. Journal of Clinical Microbiology 37: 1591–1594.
Cole ST, Brosch R, Parkhill J et al (1998) Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393: 537–544.
Conrads G, Flemmig TF, Seyfarth I et al (1999) Simultaneous detection of Bacteroides forsythus and Prevotella intermedia by 16S rRNA gene-directed multiplex PCR. Journal of Clinical Microbiology 37: 1621–1624.
Cubbon MD, Coia JE, Hanson MF and Thomson-Carter FM (1996) A comparison of immunomagnetic separation, direct culture and polymerase chain reaction for the detection of verocytotoxin-producing BscherichÃa coli 0157 in human faeces. Journal of Medical Microbiology 44: 219–222.
deHaseth, PL, Zupancic ML and Record MT (1998) RNA polymerase-promoter interactions: the comings and goings of RNA polymerase. Journal of Bacteriology 180: 3019–3025.
Dorigo-Zetsma JW, Zaat SAJ, Wertheim-van Dillen PME et al (1999) Comparison of PCR, culture, and serological tests for diagnosis of Mycoplasma pneumoniae respiratory tract infection in children. Journal of Clinical Microbiology 37: 14–17.
Engler KH, Glushkevich T, Mazurova IK et al (1997) A modified Elek test for detection of toxigenic corynebacteria in the diagnostic laboratory. Journal of Clinical Microbiology 35: 495–498.
Espy MJ, Patel R, Paya CV and Smith TF (1995) Comparison of three methods for extraction of viral nucleic acids from blood cultures. Journal of Clinical Microbiology 33: 41–44.
Fang Z, Morrison N, Watt B et al (1998) IS6110 transposition and evolutionary scenario of the direct repeat locus in a group of closely related Mycobacterium tuberculosis strains. Journal of Bacteriology 180: 2102–2109.
Feucht H-H, Zöllner B, Polywka S et al (1997) Prevalence of hepatitis G viremia among healthy subjects, individuals with liver disease, and persons at risk from parenteral transmission. Journal of Clinical Microbiology 35: 767–768.
Gamboa F, Manterola JM, Viflado B et al (1997) Direct detection of Mycobacterium tuberculosis complex in nonrespiratory specimens by Gen-Probe amplified Mycobacterium tuberculosis direct test. Journal of Clinical Microbiology 35: 307–310.
Gamboa F, Fernandez G, Padilla E et al (1998a) Comparative evaluation of initial and new versions of the Gen-Probe Amplified Mycobacterium Tuberculosis Direct Test for direct detection of Mycobacterium tuberculosis in respiratory and nonrespiratory specimens. Journal of Clinical Microbiology 36: 684–689.
Gamboa F, Dominguez J, Padilla E et al (1998b) Rapid diagnosis of extrapulmonary tuberculosis by ligase chain reaction amplification. Journal of Clinical Microbiology 36: 1324–1329.
Geha DJ, Uhl JR, Gustaferro CA and Persing DH (1994) Multiplex PCR for identification of methicillin-resistant staphylococci in the clinical laboratory. Journal of Clinical Microbiology 32: 1768–1772.
Gillespie SH, McHugh TD and Newport LE (1997) Specificity of IS6110-based amplification assays for Mycobacterium tuberculosis complex [letter]. Journal of Clinical Microbiology 35: 799–800.
Githui WA, Wilson SM and Drobniewski FA (1999) Specificity of IS6110-based DNA fingerprinting and diagnostic techniques for Mycobacterium tuberculosis complex. Journal of Clinical Microbiology 37: 1224–1226.
Gleissberg V (1999) The threat of multidrug resistance: is tuberculosis ever untreatable or uncontrollable? Lancet 353: 998–999.
Govan V, Allsopp M and Davison S (1999) A PCR detection method for rapid identification of Paenibacillus larvae. Applied and Environmental Microbiology 65: 2243–2245.
Grant IR, Ball HJ and Rowe MT (1998) Isolation of Mycobacterium paratuberculosis from milk by immunomagnetc separation. Applied and Environmental Microbiology 64: 3153–3158.
Guerasimova A, Ivanov I and Lehrach H (1999) A method of one-step enzyme labelling of short oligonucleotide probes for filter hybridization. Nucleic Acids Research 27: 703–705.
Hellyer TJ, DesJardin LE, Assaf MK et al (1997) Authors’ reply to comment on the specificity of IS6110-based assays [letter]. Journal of Clinical Microbiology 35: 800–801.
Hellyer TJ, DesJardin LE, Hehman GJ et al (1999a) Quantitative analysis of mRNA as a marker for viability of Mycobacterium tuberculosis. Journal of Clinical Microbiology 37: 290–295.
Hellyer TJ, DesJardin LE, Teixeira L et al (1999b) Detection of viable Mycobacterium tuberculosis by reverse transcriptase-strand displacement amplification of mRNA. Journal of Clinical Microbiology 37: 518–523.
Hinrikson HP, Dutly F and Altwegg M (1999) Homogeneity of 16S–23S ribosomal intergenic spacer regions of Tropheryma whippelii in Swiss patients with Whipple’s disease. Journal of Clinical Microbiology 37: 152–156.
Horst J-P, Wu T-h and Marinus MG (1999) Escherichia coli mutator genes. Trends in Microbiology 7: 29–36.
Hultman T, Bergh S, Moks T and Uhlén M (1991) Bidirectional solid phase sequencing of in vitro-amplified plasmid DNA. BioTechniques 10: 84–93.
Jensen JS, Bruun B and Gahrn-Hansen B (1999) Unexpected cross-reaction with Fuso-bacterium necrophorum in a PCR for detection of mycoplasmas. Journal of Clinical Microbiology 37: 828–829.
Jersek B, Gilot P, Gubina M et al (1999) Typing of Listeria monocytogenes strains by repetitive element sequence-based PCR. Journal of Clinical Microbiology 37: 103–109.
Jorgensen JH, Salinas JR, Paxson R et al (1999) False-positive Gen-Probe Direct Mycobacterium tuberculosis Amplification Test results from patients with pulmonary M. kansasii and M. avium infections. Journal of Clinical Microbiology 37: 175–178.
Kauppinen J, Mäntyjärvi R and Katila M-L (1999) Mycobacterium malmoense-specific nested PCR based on a conserved sequence detected in random amplified polymorphic DNA fingerprints. Journal of Clinical Microbiology 37: 1454–1458.
Kawamura S, Maesaki S, Noda T et al (1999) Comparison between PCR and detection of antigen in sera for diagnosis of pulmonary aspergillosis. Journal of Clinical Microbiology 37: 218–220.
Kim B-J, Kim S-Y, Park B-H et al (1997) Mutations in the rpoB gene of Mycobacterium tuberculosis that interfere with PCR-single-strand conformation polymorphism analysis for rifampin susceptibility testing. Journal of Clinical Microbiology 35: 492–494.
Kimura M, Miyake H, Kim H-S et al (1995) Species-specific PCR detection of malaria parasites by microtiter plate hybridization: clinical study with malaria patients. Journal of Clinical Microbiology 33: 2342–2346.
Kwok S, Kellogg DE, McKinney N et al (1990) Effects of primer-template mismatches on the polymerase chain reaction: human immunodeficiency virus type 1 model studies. Nucleic Acids Research 18: 999–1005.
Lu J-J, Perng C-L, Shyu R-Y et al (1999) Comparison of five PCR methods for detection of Helicobacter pylori in gastric juices. Journal of Medical Microbiology 37: 772–774.
Luk JM, Kongmuang U, Tsang RSW and Lindberg AA (1997) An enzyme-linked immunosorbent assay to detect PCR products of the rfbS gene from serogroup D salmonellae: a rapid screening prototype. Journal of Clinical Microbiology 35: 714–718.
Majlessi M, Nelson NC and Becker M (1998) Advantages of 2’-0-methyl oligoribonucleotide probes for detecting RNA targets. Nucleic Acids Research 26: 2224–2229.
Mangan JA, Sole KM, Mitchison DA and Butcher PD (1997) An effective method of RNA extraction from bacteria refractory to disruption, including mycobacteria. Nucleic Acids Research 25: 675–676.
Mangiapan G, Vokurka M, Schouls L et al (1996) Sequence capture-PCR improves detection of mycobacterial DNA in clinical specimens. Journal of Clinical Microbiology 34: 1209–1215.
Marcos JY, Soriano AC, Salazar MS et al (1999) Rapid identification and typing of Staphylococcus aureus by PCR-restriction fragment length polymorphism analysis of the aroA gene. Journal of Clinical Microbiology 37: 570–574.
Mikosza ASJ, La T, Brooke CJ et al (1999) PCR amplification from fixed tissue indicates frequent involvement of Brachyspira aalborgi in human intestinal spirochetosis. Journal of Clinical Microbiology 37: 2093–2098.
Monteiro L, Bonnemaison D, Vekris A et al (1997) Complex polysaccharides as PCR inhibitors in feces: Helicobacter pylori model. Journal of Clinical Microbiology 35: 995–998.
Mooney RA, Artsimovitch and Landick R (1998) Information processing by RNA polymerase: recognition of regulatory signals during RNA chain elongation. Journal of Bacteriology 180: 3265–3275.
Nakao H & Popovic T (1997) Development of a direct PCR assay for detection of the diphtheria toxin gene. Journal of Clinical Microbiology 35: 1651–1655.
Olsvik O, Popovic T, Skjerve E et al (1994) Magnetic separation techniques in diagnostic microbiology. Clinical Microbiology Reviews 7: 43–54.
Pagratis NC (1996) Rapid preparation of single stranded DNA from PCR products by streptavidin induced electrophoretic mobility shift. Nucleic Acids Research 24: 3645–3646.
Pfyffer GE, Funke-Kissling P, Rundler E and Weber R (1999) Performance characteristics of the BDProbeTec system for direct detection of Mycobacterium tuberculosis complex in respiratory specimens. Journal of Clinical Microbiology 37: 137–140.
Piersimoni C, Callegaro A, Nista D et al (1997) Comparative evaluation of two commercial amplification assays for direct detection of Mycobacterium tuberculosis complex in respiratory specimens. Journal of Clinical Microbiology 35: 193–196.
Pozzi G, Meloni M, Iona E et al (1999) rpoB mutations in multidrug-resistant strains of Mycobacterium tuberculósis isolated in Italy. Journal of Clinical Microbiology 37: 1197–1199.
Ratcliff R, Donnellan S, Lanser J et al (1997) Interspecies sequence differences in the Mip protein from the genus Legionella: implications for function and evolutionary relatedness. Molecular Microbiology 25: 1149–1158.
Ratcliff R, Lanser J, Manning P and Heuzenroeder M (1998) Sequence-based classification scheme for the genus Legionella targeting the mip gene. Journal of Clinical Microbiology 36: 1560–1567.
Rauhut R and Klug G (1999) mRNA degradation in bacteria. FEMS Microbiology Reviews 23: 353–370.
Read SJ, Jeffery KJM and Bangham CRM (1997) Aseptic meningitis and encephalitis: the role of PCR in the diagnostic laboratory. Journal of Clinical Microbiology 35: 691–696.
Roth WK, Weber M and Seifreid E (1999) Feasibility and efficacy of routine PCR screening of blood donations for hepatitis C virus, hepatitis B virus, and HIV-1 in a blood-bank setting. Lancet 353: 359–363.
Rudi K, Kroken M, Dahlberg OJ et al (1997) Rapid, universal method to isolate PCR-ready DNA using magnetic beads. BioTechniques 22: 506–511.
Schlötterer C and Wolff C (1996) Ml3mtvh: an improved M13 vector for rapid and simple cloning of PCR products. Trends in Genetics 12: 286–287.
Schmitz F-J, MacKenzie CR, Hofmann B et al (1997) Specific information concerning taxonomy, pathogenicity and methicillin resistance of staphylococci obtained by a multiplex PCR. Journal of Medical Microbiology 46: 773–778.
Schmitz F-J, Steiert M, Hofmann B et al (1998a) Development of a multiplex-PCR for direct detection of the genes for enterotoxin B and C, and toxic shock syndrome toxin-1 in Staphylococcus aureus isolates. Journal of Medical Microbiology 47: 335–340.
Schmitz F-J, Steiert M, Tichy H-V et al (1998b) Typing of methicillin-resistant Staphylococcus aureus isolates from Düsseldorf by six genotypic methods. Journal of Medical Microbiology 47: 341–351.
Shaio M-F, Lin P-R and Liu J-Y (1997) Colorimetric one-tube nested PCR for detection of Trichomonas vaginales in vaginal discharge. Journal of Clinical Microbiology 35: 132–138.
Sidhu H, Holmes RP, Allison MJ and Peck AB (1999) Direct quantification of the enteric bacterium Oxalobacter formigenes in human faecal samples by quantitative competitive-template PCR. Journal of Clinical Microbiology 37: 1503–1509.
Soumet C, Ermel G, Rose N et al (1999) Evaluation of a multiplex PCR assay for simultaneous identification of Salmonella sp., Salmonella Enteritidis and Salmonella Typhimurium from environmental swabs of poultry houses. Letters in Applied Microbiology 28: 113–117.
Talbot EA, Williams DL and Frothingham R (1997) PCR identification of Mycobacterium bovis BCG. Journal of Clinical Microbiology 35: 566–569.
Tham JM, Lee SH, Tan TMC et al (1999) Detection and species determination of malaria parasites by PCR: comparison with microscopy and with ParaSight-F and ICT malaria tests in a clinical environment. Journal of Clinical Microbiology 37: 1269–1273.
Weller TMA (1999) The distribution of mecA, mecRl and mecl and sequence analysis of mecl and the mec promoter region in staphylococci expressing resistance to methicillin. Journal of Antimicrobial Chemotherapy 43: 15–22.
Whitby JE, Heaton PR, Whitby HE et al (1997) Rapid detection of rabies and rabies-related viruses by RT-PCR and enzyme-linked immunosorbent assay. Journal of Virological Methods 69: 63–72.
Wollenhaupt J, Schnarr S and Kuipers JG (1998) Bacterial antigens in reactive arthritis and spondarthritis. Rational use of laboratory testing in diagnosis and follow-up. Baillière’s Clinical Rheumatology 12: 627–647.
Ye B-C, Ikebukuro K and Karube I (1998) Quantitative analysis of polymerase chain reaction using anisotropy ratio and relative hydrodynamic volume of fluorescence polarization method. Nucleic Acids Research 26: 3614–3615.
Rights and permissions
Copyright information
© 2000 Springer Science+Business Media Dordrecht
About this chapter
Cite this chapter
Singleton, P. (2000). Nucleic Acids (The Essentials); Target Sequences; Choice and Handling of Specimens. In: DNA Methods in Clinical Microbiology. Springer, Dordrecht. https://doi.org/10.1007/978-94-017-1286-6_2
Download citation
DOI: https://doi.org/10.1007/978-94-017-1286-6_2
Publisher Name: Springer, Dordrecht
Print ISBN: 978-90-481-5456-2
Online ISBN: 978-94-017-1286-6
eBook Packages: Springer Book Archive