Skip to main content Accessibility help

We use cookies to distinguish you from other users and to provide you with a better experience on our websites. Close this message to accept cookies or find out how to manage your cookie settings.

Close cookie message
×
Hostname: page-component-78c5997874-m6dg7 Total loading time: 0 Render date: 2024-11-09T07:21:16.637Z Has data issue: false hasContentIssue false

11 - Polymerase chain reaction and infectious diseases

Published online by Cambridge University Press:  25 January 2011

By
Jim Huggett
Edited by
Stephen A. Bustin
Stephen A. Bustin
Affiliation:
Queen Mary University of London
Get access

Summary

As in numerous other areas, the comparatively simple technique of polymerase chain reaction (PCR) has revolutionized the field of infectious diseases. Whether this is through sequencing the genomes of key pathogens or developing vaccines by genetic manipulation, PCR-driven molecular biology has stamped its mark on infectious diseases. It is particularly fascinating to consider how PCR has influenced, and continues to influence, disease management and to realize how influential this research technology has become as a practical diagnostic tool.

Its role in this context can be broadly split into diagnosis, epidemiology, and prognostic monitoring. However, before considering the utility of the PCR, it is useful to discuss infectious diseases and the additional considerations required for using PCR for their management.

Infectious diseases can be broadly split into groups corresponding to the causative pathogen: bacterial (tuberculosis [TB], pseudomembranous colitis [PMC], sepsis) and viral (acquired immunodeficiency syndrome [AIDS], hepatitis C, influenza) are two simple groupings. Viral pathogens are the most common causes of infectious diseases worldwide (e.g., common cold with numerous viral causes), with bacterial pathogens often being more serious when they strike. The remaining categories are more complex and include the eukaryotes. A major group are the Protozoa, including the causes of many classical tropical diseases (e.g., malaria and sleeping sickness). The fungal pathogens (Pneumocystis pneumonia [PCP]) are frequently opportunistic, causing infections worldwide in individuals with reduced or impaired immunity.

Type
Chapter
Information
The PCR Revolution
Basic Technologies and Applications
 , pp. 173 - 188
Publisher: Cambridge University Press
Print publication year: 2009

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Wat, D., The common cold: a review of the literature. Eur J Intern Med 15(2), 79 (2004).CrossRefGoogle ScholarPubMed
Huggett, J. F., McHugh, T. D., and Zumla, A., Tuberculosis: amplification-based clinical diagnostic techniques. Int J Biochem Cell Biol 35(10), 1407 (2003).CrossRefGoogle ScholarPubMed
Perrin, F. M., Lipman, M. C., McHugh, T. D. et al., Biomarkers of treatment response in clinical trials of novel antituberculosis agents. Lancet Infect Dis 7(7), 481 (2007).CrossRefGoogle ScholarPubMed
Zuckerman, J. N. and Zuckerman, A. J., Hepatitis, Viral. In: Cook, G. C. and Zumla, A. I. (eds), Manson's Tropical Diseases. Elsevier Science, London, 2003.Google Scholar
Barbour, J. D. and Grant, R. M., The role of viral fitness in HIV pathogenesis. Curr HIV/AIDS Rep 2(1), 29 (2005).CrossRefGoogle ScholarPubMed
Drosten, C., Panning, M., Drexler, J. F. et al., Ultrasensitive monitoring of HIV-1 viral load by a low-cost real-time reverse transcription-PCR assay with internal control for the 5′ long terminal repeat domain. Clin Chem 52(7), 1258 (2006).CrossRefGoogle ScholarPubMed
Gottesman, B. S., Grosman, Z., Lorber, M. et al., Measurement of HIV RNA in patients infected by subtype C by assays optimized for subtype B results in an underestimation of the viral load. J Med Virol 73(2), 167 (2004).CrossRefGoogle Scholar
Eccles, R., Understanding the symptoms of the common cold and influenza. Lancet Infect Dis 5(11), 718 (2005).CrossRefGoogle ScholarPubMed
,Writing Committee of the Second World Health Organization Consultation on Clinical Aspects of Human Infection with Avian Influenza A (H5N1) Virus, Abdel-Ghafar, A. N., Chotpitayasunondh, T., Gao, Z. et al., Update on avian influenza A (H5N1) virus infection in humans. N Engl J Med 358(3), 261 (2008).Google ScholarPubMed
Mody, L. and Cinti, S., Pandemic influenza planning in nursing homes: are we prepared?J Am Geriatr Soc 55(9), 1431 (2007).CrossRefGoogle ScholarPubMed
Chapin, K. C., Molecular tests for detection of the sexually-transmitted pathogens Neisseria gonorrhoeae and Chlamydia trachomatis. Med Health R I 89(6), 202 (2006).Google ScholarPubMed
Miller, M. B., Molecular diagnosis of infectious diseases. N C Med J 68(2), 115 (2007).Google ScholarPubMed
Ling, D. I., Flores, L. L., Riley, L. W. et al., Commercial nucleic-acid amplification tests for diagnosis of pulmonary tuberculosis in respiratory specimens: meta-analysis and meta-regression. PLoS ONE 3(2), e1536 (2008).CrossRefGoogle ScholarPubMed
Ling, D. I., Zwerling, A. A., and Pai, M., GenoType MTBDR assays for the diagnosis of multidrug-resistant tuberculosis: a meta-analysis. Eur Respir J 32(5), 1165 (2008).CrossRefGoogle Scholar
Stubbs, S. L., Brazier, J. S., O'Neill, G. L. et al., PCR targeted to the 16S-23S rRNA gene intergenic spacer region of Clostridium difficile and construction of a library consisting of 116 different PCR ribotypes. J Clin Microbiol 37(2), 461 (1999).Google ScholarPubMed
Berg, R. J., Schaap, I., Templeton, K. E. et al., Typing and subtyping of Clostridium difficile isolates by using multiple-locus variable-number tandem-repeat analysis. J Clin Microbiol 45(3), 1024 (2007).CrossRefGoogle ScholarPubMed
Supply, P., Lesjean, S., Savine, E. et al., Automated high-throughput genotyping for study of global epidemiology of Mycobacterium tuberculosis based on mycobacterial interspersed repetitive units. J Clin Microbiol 39(10), 3563 (2001).CrossRefGoogle ScholarPubMed
Crubezy, E., Ludes, B., Poveda, J. D. et al., Identification of Mycobacterium DNA in an Egyptian Pott's disease of 5,400 years old. C R Acad Sci III 321(11), 941 (1998).CrossRefGoogle Scholar
Crawford, J. T., Genotyping in contact investigations: a CDC perspective. Int J Tuberc Lung Dis 7 (12 Suppl 3), S453 (2003).Google ScholarPubMed
Brazma, A., Hingamp, A., Quackenbush, J. et al., Minimum information about a microarray experiment (MIAME) – toward standards for microarray data. Nat Genet 29(4), 365 (2001).CrossRefGoogle ScholarPubMed
Noordhoek, G. T., Mulder, S., Wallace, P. et al., Multicentre quality control study for detection of Mycobacterium tuberculosis in clinical samples by nucleic amplification methods. Clin Microbiol Infect 10(4), 295 (2004).CrossRefGoogle ScholarPubMed
Noordhoek, G. T., Embden, J. D., and Kolk, A. H., Reliability of nucleic acid amplification for detection of Mycobacterium tuberculosis: an international collaborative quality control study among 30 laboratories. J Clin Microbiol 34(10), 2522 (1996).Google ScholarPubMed
Padley, D. J., Heath, A. B., Sutherland, C. et al., Establishment of the 1st World Health Organization International Standard for Plasmodium falciparum DNA for nucleic acid amplification technique (NAT)-based assays. Malar J 7, 139 (2008).CrossRefGoogle ScholarPubMed
Huggett, J. F., Taylor, M. S., Kocjan, G. et al., Development and evaluation of a real-time PCR assay for detection of Pneumocystis jirovecii DNA in bronchoalveolar lavage fluid of HIV-infected patients. Thorax (2008) Feb; 63(2):154–9.CrossRefGoogle ScholarPubMed
Mens, P. F., Schoone, G. J., Kager, P. A. et al., Detection and identification of human Plasmodium species with real-time quantitative nucleic acid sequence-based amplification. Malar J 5, 80 (2006).CrossRefGoogle ScholarPubMed
Hänscheid, T. and Grobusch, M. P., How useful is PCR in the diagnosis of malaria?Trends Parasitol 18(9), 395 (2002).CrossRefGoogle Scholar
Mens, P., Spieker, N., Omar, S. et al., Is molecular biology the best alternative for diagnosis of malaria to microscopy? A comparison between microscopy, antigen detection and molecular tests in rural Kenya and urban Tanzania. Trop Med Int Health 12(2), 238 (2007).Google ScholarPubMed
Bejon, P., Andrews, L., Hunt-Cooke, A. et al., Thick blood film examination for Plasmodium falciparum malaria has reduced sensitivity and underestimates parasite density. Malar J 5, 104 (2006).CrossRefGoogle ScholarPubMed
Andrews, L., Andersen, R. F., Webster, D. et al., Quantitative real-time polymerase chain reaction for malaria diagnosis and its use in malaria vaccine clinical trials. Am J Trop Med Hyg 73(1), 191 (2005).Google ScholarPubMed
Klatser, P. R., Kuijper, S., Ingen, C. W. et al., Stabilized, freeze-dried PCR mix for detection of mycobacteria. J Clin Microbiol 36(6), 1798 (1998).Google Scholar
Tansuphasiri, U., Chinrat, B., and Rienthong, S., Evaluation of culture and PCR-based assay for detection of Mycobacterium tuberculosis from sputum collected and stored on filter paper. Southeast Asian J Trop Med Public Health 32(4), 844 (2001).Google ScholarPubMed
Boehme, C. C., Nabeta, P., Henostroza, G. et al., Operational feasibility of using loop-mediated isothermal amplification for diagnosis of pulmonary tuberculosis in microscopy centers of developing countries. J Clin Microbiol 45(6), 1936 (2007).Google Scholar
Quezada, C. M., Kamanzi, E., Mukamutara, J. et al., Implementation validation performed in Rwanda to determine whether the INNO-LiPA Rif.TB line probe assay can be used for detection of multidrug-resistant Mycobacterium tuberculosis in low-resource countries. J Clin Microbiol 45(9), 3111 (2007).CrossRefGoogle ScholarPubMed
Cannas, A., Goletti, D., Girardi, E. et al., Mycobacterium tuberculosis DNA detection in soluble fraction of urine from pulmonary tuberculosis patients. Int J Tuberc Lung Dis 12(2), 146 (2008).Google ScholarPubMed
Ho, H. A., Dore, K., Boissinot, M. et al., Direct molecular detection of nucleic acids by fluorescence signal amplification. J Am Chem Soc 127(36), 12673 (2005).CrossRefGoogle ScholarPubMed

Save book to Kindle

To save this book to your Kindle, first ensure [email protected] is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about saving to your Kindle.

Note you can select to save to either the @free.kindle.com or @kindle.com variations. ‘@free.kindle.com’ emails are free but can only be saved to your device when it is connected to wi-fi. ‘@kindle.com’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

Find out more about the Kindle Personal Document Service.

Available formats
×

Save book to Dropbox

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Dropbox.

Available formats
×

Save book to Google Drive

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Google Drive.

Available formats
×