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A five-year study of severe community-acquired pneumonia with emphasis on prognosis in patients admitted to an intensive care unit
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An excellent review of the use of molecular techniques to study nosocomial infections
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Brunstein J, Thomas E. Direct screening of clinical specimens for multiple respiratory pathogens using the Genaco Respiratory Panels 1 and 2. Diagn Mol Pathol 2006; 15:169-173. Reports a pilot study of the novel technology of target-enriched multiplex PCR to detect multiple respiratory pathogens.
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Brunstein J, Thomas E. Direct screening of clinical specimens for multiple respiratory pathogens using the Genaco Respiratory Panels 1 and 2. Diagn Mol Pathol 2006; 15:169-173. Reports a pilot study of the novel technology of target-enriched multiplex PCR to detect multiple respiratory pathogens.
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An excellent, thorough review of real-time PCR. Technical aspects of all steps are discussed as well as use of the technique for diagnosis of individual pathogens
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Espy MJ, Uhl JR, Sloan LM, et al. Real-time PCR in clinical microbiology: applications for routine laboratory testing. Clin Microbiol Rev 2006; 19:165-256. An excellent, thorough review of real-time PCR. Technical aspects of all steps are discussed as well as use of the technique for diagnosis of individual pathogens.
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Clin Microbiol Rev
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Espy, M.J.1
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9
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Real-time assays with molecular beacons and other fluorescent nucleic acid hybridization probes
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Marras SA, Tyagi S, Kramer FR. Real-time assays with molecular beacons and other fluorescent nucleic acid hybridization probes. Clin Chim Acta 2006; 363:48-60.
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10
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13744261458
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Diagnostic system for rapid and sensitive differential detection of pathogens
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Briese T, Palacios G, Kokoris M, et al. Diagnostic system for rapid and sensitive differential detection of pathogens. Emerg Infect Dis 2005; 11:310-313.
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11
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33750697985
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MassTag polymerase-chain- reaction detection of respiratory pathogens, including a new rhinovirus genotype, that caused influenza-like illness in New York state during 2004-2005
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This study describes the use of a new technology, MassTag PCR, to detect multiple respiratory pathogens, and reports the detection of a new rhinovirus
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Lamson D, Renwick N, Kapoor V, et al. MassTag polymerase-chain- reaction detection of respiratory pathogens, including a new rhinovirus genotype, that caused influenza-like illness in New York state during 2004-2005. J Infect Dis 2006; 194:1398-1402. This study describes the use of a new technology, MassTag PCR, to detect multiple respiratory pathogens, and reports the detection of a new rhinovirus.
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Lamson, D.1
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12
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33748803652
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Relevance of influenza a virus detection by PCR, shell vial assay, and tube cell culture to rapid reporting procedures
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This paper demonstrates the ability of real-time PCR to diagnose influenza quickly and accurately
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Zitterkopf NL, Leekha S, Espy MJ, et al. Relevance of influenza a virus detection by PCR, shell vial assay, and tube cell culture to rapid reporting procedures. J Clin Microbiol 2006; 44:3366-3367. This paper demonstrates the ability of real-time PCR to diagnose influenza quickly and accurately.
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Zitterkopf, N.L.1
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Espy, M.J.3
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13
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33745700135
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Accuracy and impact of a point-of-care rapid influenza test in young children with respiratory illnesses
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An important study that documents the disease burden of influenza in children using traditional diagnostic techniques, rapid testing and RT-PCR
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Poehling KA, Zhu Y, Tang YW, Edwards K. Accuracy and impact of a point-of-care rapid influenza test in young children with respiratory illnesses. Arch Pediatr Adolesc Med 2006; 160:713-718. An important study that documents the disease burden of influenza in children using traditional diagnostic techniques, rapid testing and RT-PCR.
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Poehling, K.A.1
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14
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33847386509
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Freed NE, Myers CA, Russell KL, et al. Diagnostic discrimination of live attenuated influenza vaccine strains and community-acquired pathogenic strains in clinical samples. Mol Cell Probes 2006; [Epub ahead of print]. An interesting study that reports the development of RT-PCR to distinguish influenza infection from live vaccine.
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Freed NE, Myers CA, Russell KL, et al. Diagnostic discrimination of live attenuated influenza vaccine strains and community-acquired pathogenic strains in clinical samples. Mol Cell Probes 2006; [Epub ahead of print]. An interesting study that reports the development of RT-PCR to distinguish influenza infection from live vaccine.
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15
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33845299202
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Chutinimitkul S, Suwannakarn K, Chieochansin T, et al. H5N1 Oseltamivir-resistance detection by real-time PCR using two high sensitivity labeled TaqMan probes. J Virol Methods 2007; 139:44-49. Report of a real-time PCR method to detect drug resistance in influenza.
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Chutinimitkul S, Suwannakarn K, Chieochansin T, et al. H5N1 Oseltamivir-resistance detection by real-time PCR using two high sensitivity labeled TaqMan probes. J Virol Methods 2007; 139:44-49. Report of a real-time PCR method to detect drug resistance in influenza.
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16
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24644516529
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Cloning of a human parvovirus by molecular screening of respiratory tract samples
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Allander T, Tammi MT, Eriksson M, et al. Cloning of a human parvovirus by molecular screening of respiratory tract samples. Proc Natl Acad Sci U S A 2005; 102:12891-12896.
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Allander, T.1
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17
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33847408636
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Dare R, Sanghavi S, Bullotta A, et al. Detection of human metapneumovirus (hMPV) infection in immunosuppressed lung transplant recipients and children evaluated for pertussis. J Clin Microbiol 2006; [Epub ahead of print].
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Dare R, Sanghavi S, Bullotta A, et al. Detection of human metapneumovirus (hMPV) infection in immunosuppressed lung transplant recipients and children evaluated for pertussis. J Clin Microbiol 2006; [Epub ahead of print].
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18
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33644840107
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Detection of respiratory syncytial virus in adults with chronic obstructive pulmonary disease
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Falsey AR, Formica MA, Hennessey PA, et al. Detection of respiratory syncytial virus in adults with chronic obstructive pulmonary disease. Am J Respir Crit Care Med 2006; 173:639-643.
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19
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30744470413
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Detection of rhinoviruses by tissue culture and two independent amplification techniques, nucleic acid sequence-based amplification and reverse transcription-PCR, in children with acute respiratory infections during a winter season
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Loens K, Goossens H, De Laat C, et al. Detection of rhinoviruses by tissue culture and two independent amplification techniques, nucleic acid sequence-based amplification and reverse transcription-PCR, in children with acute respiratory infections during a winter season. J Clin Microbiol 2006; 44:166-171.
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Loens, K.1
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20
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33747157239
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Ordas J, Boga JA, Alvarez-Arguelles M, et al. Role of metapneumovirus in viral respiratory infections in young children. J Clin Microbiol 2006; 44:2739-2742. A study of the role of human metapneumovirus in respiratory disease in children, finding that human metapneumovirus is the second most common cause of viral respiratory infection in children less than 1 year old.
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Ordas J, Boga JA, Alvarez-Arguelles M, et al. Role of metapneumovirus in viral respiratory infections in young children. J Clin Microbiol 2006; 44:2739-2742. A study of the role of human metapneumovirus in respiratory disease in children, finding that human metapneumovirus is the second most common cause of viral respiratory infection in children less than 1 year old.
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21
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14844303425
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Respiratory syncytial virus infection in children hospitalized for wheezing: Virus-specific studies from infancy to preschool years
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22
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33744776308
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The authors studied the incidence and clinical characteristics of viral CAP by multiplex RT-PCR and conventional methods
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Angeles Marcos M, Camps M, Pumarola T, et al. The role of viruses in the aetiology of community-acquired pneumonia in adults. Antivir Ther 2006; 11:351-359. The authors studied the incidence and clinical characteristics of viral CAP by multiplex RT-PCR and conventional methods.
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Antivir Ther
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Angeles Marcos, M.1
Camps, M.2
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23
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Comparison of real-time PCR assays with fluorescent-antibody assays for diagnosis of respiratory virus infections in children
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J Clin Microbiol
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Kuypers, J.1
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24
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33749570155
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Comparison of multiplex PCR assays and conventional techniques for the diagnosis of respiratory virus infections in children admitted to hospital with an acute respiratory illness
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Freymuth F, Vabret A, Cuvillon-Nimal D, et al. Comparison of multiplex PCR assays and conventional techniques for the diagnosis of respiratory virus infections in children admitted to hospital with an acute respiratory illness. J Med Virol 2006; 78:1498-1504.
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25
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33747151669
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Experimental evaluation of the FluChip diagnostic microarray for influenza virus surveillance
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Townsend MB, Dawson ED, Mehlmann M, et al. Experimental evaluation of the FluChip diagnostic microarray for influenza virus surveillance. J Clin Microbiol 2006; 44:2863-2871.
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Mehlmann, M.3
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26
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33645464302
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Broad-spectrum respiratory tract pathogen identification using resequencing DNA microarrays
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The authors describe the technique of a microarray-based method to detect multiple pathogens and pilot the test with clinical samples
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Lin B, Wang Z, Vora GJ, et al. Broad-spectrum respiratory tract pathogen identification using resequencing DNA microarrays. Genome Res 2006; 16:527-535. The authors describe the technique of a microarray-based method to detect multiple pathogens and pilot the test with clinical samples.
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Lin, B.1
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27
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29
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Evaluation of real-time reverse transcriptase-PCR and real-time loop-mediated amplification assays for severe acute respiratory syndrome coronavirus detection
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31
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33747157582
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Multicenter comparison of nucleic acid extraction methods for detection of severe acute respiratory syndrome coronavirus RNA in stool specimens
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The authors conducted a multicenter study to evaluate different RNA extraction methods to maximize sensitivity of real-time PCR for diagnosis of SARS
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Petrich A, Mahony J, Chong S, et al. Multicenter comparison of nucleic acid extraction methods for detection of severe acute respiratory syndrome coronavirus RNA in stool specimens. J Clin Microbiol 2006; 44:2681-2688. The authors conducted a multicenter study to evaluate different RNA extraction methods to maximize sensitivity of real-time PCR for diagnosis of SARS.
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J Clin Microbiol
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Petrich, A.1
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Development of a method for concentrating and purifying SARS coronavirus RNA by a magnetic bead capture system
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Hei, A.L.1
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33751239459
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Oner AF, Bay A, Arslan S, et al. Avian influenza A (H5N1) infection in eastern Turkey in 2006. N Engl J Med 2006; 355:2179-2185. This important paper reports a human outbreak of avian influenza.
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Oner AF, Bay A, Arslan S, et al. Avian influenza A (H5N1) infection in eastern Turkey in 2006. N Engl J Med 2006; 355:2179-2185. This important paper reports a human outbreak of avian influenza.
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34
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84921707493
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Centers for Disease Control and Prevention. New laboratory assay for diagnostic testing of avian influenza A/H5 (Asian Lineage). MMWR Morb Mortal Wkly Rep 2006; 55: 127. Report of the FDA approval of a real-time RT-PCR for diagnosis of avian influenza.
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Centers for Disease Control and Prevention. New laboratory assay for diagnostic testing of avian influenza A/H5 (Asian Lineage). MMWR Morb Mortal Wkly Rep 2006; 55: 127. Report of the FDA approval of a real-time RT-PCR for diagnosis of avian influenza.
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35
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30644470391
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Single step multiplex real-time RT-PCR for H5N1 influenza A virus detection
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Payungporn S, Chutinimitkul S, Chaisingh A, et al. Single step multiplex real-time RT-PCR for H5N1 influenza A virus detection. J Virol Methods 2006; 131:143-147.
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36
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29144481982
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A 5′-nuclease real-time reverse transcriptase-polymerase chain reaction assay for the detection of a broad range of influenza A subtypes, including H5N1
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Whiley DM, Sloots TP. A 5′-nuclease real-time reverse transcriptase-polymerase chain reaction assay for the detection of a broad range of influenza A subtypes, including H5N1. Diagn Microbiol Infect Dis 2005; 53:335-337.
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37
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33645473329
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Specific detection of H5N1 avian influenza A virus in field specimens by a one-step RT-PCR assay
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Ng LF, Barr I, Nguyen T, et al. Specific detection of H5N1 avian influenza A virus in field specimens by a one-step RT-PCR assay. BMC Infect Dis 2006; 6:40.
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BMC Infect Dis
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38
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33744955035
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Genotypic identification of presumptive Streptococcus pneumoniae by PCR using four genes highly specific for S. pneumoniae
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Suzuki N, Yuyama M, Maeda S, et al. Genotypic identification of presumptive Streptococcus pneumoniae by PCR using four genes highly specific for S. pneumoniae. J Med Microbiol 2006; 55:709-714.
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J Med Microbiol
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Suzuki, N.1
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39
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33751205368
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Pneumolysin polymerase chain reaction for diagnosis of pneumococcal pneumonia and empyema in children
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Lahti E, Mertsola J, Kontiokari T, et al. Pneumolysin polymerase chain reaction for diagnosis of pneumococcal pneumonia and empyema in children. Eur J Clin Microbiol Infect Dis 2006; 25:783-789.
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(2006)
Eur J Clin Microbiol Infect Dis
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Lahti, E.1
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40
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33846010198
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Penicillin- nonsusceptible Streptococcus pneumoniae in Poland - phenotypic and molecular analysis
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Sadowy E, Izdebski R, Skoczynska A, et al. Penicillin- nonsusceptible Streptococcus pneumoniae in Poland - phenotypic and molecular analysis. Antimicrob Agents Chemother 2006; 51:40-47.
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41
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29144492142
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Evaluation and selection of tandem repeat loci for Streptococcus pneumoniae MLVA strain typing
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Koeck JL, Njanpop-Lafourcade BM, Cade S, et al. Evaluation and selection of tandem repeat loci for Streptococcus pneumoniae MLVA strain typing. BMC Microbiol 2005; 5:66.
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BMC Microbiol
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Koeck, J.L.1
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42
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33747177786
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Aguiar-Alves F, Medeiros F, Fernandes O, et al. New Staphylococcus aureus genotyping method based on exotoxin (set) genes. J Clin Microbiol 2006; 44:2728-2732. Report of a novel method for detecting methicillin resistance using sequencebased genotyping of exotoxin genes to provide an alternative to RFLP-based methods.
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Aguiar-Alves F, Medeiros F, Fernandes O, et al. New Staphylococcus aureus genotyping method based on exotoxin (set) genes. J Clin Microbiol 2006; 44:2728-2732. Report of a novel method for detecting methicillin resistance using sequencebased genotyping of exotoxin genes to provide an alternative to RFLP-based methods.
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43
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33745169634
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Virtual digest identification of secondary enzymes for use in pulsed-field gel electrophoresis of Staphylococcus aureus
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Roberts JC, Cannons AC, Amuso PT, Cattani J. Virtual digest identification of secondary enzymes for use in pulsed-field gel electrophoresis of Staphylococcus aureus. J Microbiol Methods 2006; 66:362-368.
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J Microbiol Methods
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44
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30744437462
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Vindel A, Trincado P, Gomez E, et al. Prevalence and evolution of methicillin-resistant Staphylococcus aureus in Spanish hospitals between 1996 and 2002. J Clin Microbiol 2006; 44:266-270. An interesting study that tested over 2000 methicillin-resistant S. aureus strains over a 7-year period to determine predominant genetic profiles.
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Vindel A, Trincado P, Gomez E, et al. Prevalence and evolution of methicillin-resistant Staphylococcus aureus in Spanish hospitals between 1996 and 2002. J Clin Microbiol 2006; 44:266-270. An interesting study that tested over 2000 methicillin-resistant S. aureus strains over a 7-year period to determine predominant genetic profiles.
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46
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33746216125
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Assignment of Staphylococcus isolates to groups by spa typing, SmaI macrorestriction analysis, and multilocus sequence typing
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Strommenger B, Kettlitz C, Weniger T, et al. Assignment of Staphylococcus isolates to groups by spa typing, SmaI macrorestriction analysis, and multilocus sequence typing. J Clin Microbiol 2006; 44:2533-2540.
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47
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2442556167
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New real-time PCR assay for rapid detection of methicillin-resistant Staphylococcus aureus directly from specimens containing a mixture of staphylococci
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Huletsky A, Giroux R, Rossbach V, et al. New real-time PCR assay for rapid detection of methicillin-resistant Staphylococcus aureus directly from specimens containing a mixture of staphylococci. J Clin Microbiol 2004; 42:1875-1884.
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Huletsky, A.1
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48
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33749526099
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Evaluation of a single-locus real-time polymerase chain reaction as a screening test for specific detection of methicillin-resistant Staphylococcus aureus in ICU patients
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This study examines the diagnostic value of a real-time PCR assay for rapid detection of methicillin resistance
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Oberdorfer K, Pohl S, Frey M, et al. Evaluation of a single-locus real-time polymerase chain reaction as a screening test for specific detection of methicillin-resistant Staphylococcus aureus in ICU patients. Eur J Clin Microbiol Infect Dis 2006; 25:657-663. This study examines the diagnostic value of a real-time PCR assay for rapid detection of methicillin resistance.
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(2006)
Eur J Clin Microbiol Infect Dis
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Oberdorfer, K.1
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Morozumi M, Ito A, Murayama SY, et al. Assessment of real-time PCR for diagnosis of Mycoplasma pneumoniae pneumonia in pediatric patients. Can J Microbiol 2006; 52:125-129. A large-scale study examining the use of real-time PCR to detect M. pneumoniae in children with CAP. Real-time PCR detected more cases than standard diagnostic techniques.
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53
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54
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The use of multiplex PCR for diagnosis of patients with CAP was compared to respiratory culture. Sensitivity was quite variable depending on the organism and the sample type
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Stralin K, Tornquist E, Kaltoff MS, et al. Etiologic diagnosis of adult bacterial pneumonia by culture and PCR applied to respiratory tract samples. J Clin Microbiol 2006; 44:643-645. The use of multiplex PCR for diagnosis of patients with CAP was compared to respiratory culture. Sensitivity was quite variable depending on the organism and the sample type.
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56
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A well-conducted study that examines the use of real-time PCR to detect various bacterial pathogens in patients with lower respiratory infection. It is one of the few studies to include a control group
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Kais M, Spindler C, Kalin M, et al. Quantitative detection of Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis in lower respiratory tract samples by real-time PCR. Diagn Microbiol Infect Dis 2006; 55:169-178. A well-conducted study that examines the use of real-time PCR to detect various bacterial pathogens in patients with lower respiratory infection. It is one of the few studies to include a control group.
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59
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Pai M, Kalantri S, Dheda K. New tools and emerging technologies for the diagnosis of tuberculosis: part II. Active tuberculosis and drug resistance. Expert Rev Mol Diagn 2006; 6:423-432. A comprehensive review of nucleic acid amplification tests for diagnosis of active tuberculosis and detection of drug resistance.
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Agranoff D, Fernandez-Reyes D, Papadopoulos MC, et al. Identification of diagnostic markers for tuberculosis by proteomic fingerprinting of serum. Lancet 2006; 368:1012-1021. An intriguing study reporting the use of serum proteomic fingerprinting to identify patients with tuberculosis. Diagnostic accuracy was good for discrimination of patients with tuberculosis compared to those with similar clinical symptoms.
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61
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Greco S, Girardi E, Navarra A, Saltini C. Current evidence on diagnostic accuracy of commercially based nucleic acid amplification tests for the diagnosis of pulmonary tuberculosis. Thorax 2006; 61:783-790. This paper is an important meta-analysis of commercial nucleic acid amplification tests for tuberculosis diagnosis. It reports sensitivity and specificity of various tests and factors that improve diagnostic odds ratios.
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63
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An excellent review of diagnostic techniques for diagnosis and detection of drug resistance in tuberculosis
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Palomino JC. Newer diagnostics for tuberculosis and multidrug resistant tuberculosis. Curr Opin Pulm Med 2006; 12:172-178. An excellent review of diagnostic techniques for diagnosis and detection of drug resistance in tuberculosis.
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71
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Linssen CF, Jacobs JA, Beckers P, et al. Inter-laboratory comparison of three different real-time PCR assays for the detection of Pneumocystis jiroveci in bronchoalveolar lavage fluid samples. J Med Microbiol 2006; 55:1229-1235. An important study that compares the performance of real-time PCR assays for Pneumocystis in different laboratories.
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74
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