Comprehensive Molecular Testing for Respiratory Pathogens in Community-Acquired Pneumonia

Naomi J Gadsby, Clark D Russell, Martin P McHugh, Harriet Mark, Andrew Conway Morris, Ian F Laurenson, Adam T Hill, Kate E Templeton, Naomi J Gadsby, Clark D Russell, Martin P McHugh, Harriet Mark, Andrew Conway Morris, Ian F Laurenson, Adam T Hill, Kate E Templeton

Abstract

Background: The frequent lack of a microbiological diagnosis in community-acquired pneumonia (CAP) impairs pathogen-directed antimicrobial therapy. This study assessed the use of comprehensive multibacterial, multiviral molecular testing, including quantification, in adults hospitalized with CAP.

Methods: Clinical and laboratory data were collected for 323 adults with radiologically-confirmed CAP admitted to 2 UK tertiary care hospitals. Sputum (96%) or endotracheal aspirate (4%) specimens were cultured as per routine practice and also tested with fast multiplex real-time polymerase-chain reaction (PCR) assays for 26 respiratory bacteria and viruses. Bacterial loads were also calculated for 8 bacterial pathogens. Appropriate pathogen-directed therapy was retrospectively assessed using national guidelines adapted for local antimicrobial susceptibility patterns.

Results: Comprehensive molecular testing of single lower respiratory tract (LRT) specimens achieved pathogen detection in 87% of CAP patients compared with 39% with culture-based methods. Haemophilus influenzae and Streptococcus pneumoniae were the main agents detected, along with a wide variety of typical and atypical pathogens. Viruses were present in 30% of cases; 82% of these were codetections with bacteria. Most (85%) patients had received antimicrobials in the 72 hours before admission. Of these, 78% had a bacterial pathogen detected by PCR but only 32% were culture-positive (P < .0001). Molecular testing had the potential to enable de-escalation in number and/or spectrum of antimicrobials in 77% of patients.

Conclusions: Comprehensive molecular testing significantly improves pathogen detection in CAP, particularly in antimicrobial-exposed patients, and requires only a single LRT specimen. It also has the potential to enable early de-escalation from broad-spectrum empirical antimicrobials to pathogen-directed therapy.

Keywords: PCR; bacterial load; community-acquired pneumonia; molecular testing; viral.

© The Author 2016. Published by Oxford University Press for the Infectious Diseases Society of America.

References

    1. Lim WS, Baudouin SV, George RC et al. . BTS guidelines for the management of community acquired pneumonia in adults: update 2009. Thorax 2009; 64:iii1–55.
    1. Jokinen C, Heiskanen L, Juvonen H et al. . Incidence of community-acquired pneumonia in the population of four municipalities in eastern Finland. Am J Epidemiol 1993; 137:977–88.
    1. Myint PK, Kwok CS, Majumdar SR et al. . The International Community-Acquired Pneumonia (CAP) Collaboration Cohort (ICCC) study: rationale, design and description of study cohorts and patients. BMJ Open 2012; 2:e001030.
    1. Jain S, Self WH, Wunderink RG et al. . Community-acquired pneumonia requiring hospitalization among U.S. adults. N Engl J Med 2015; 373:415–22.
    1. Mandell LA, Wunderink RG, Anzueto A et al. . Infectious Diseases Society of America/American Thoracic Society consensus guidelines on the management of community-acquired pneumonia in adults. Clin Infect Dis 2007; 44:S27–72.
    1. Chalmers JD, Taylor JK, Singanayagam A et al. . Epidemiology, antibiotic therapy, and clinical outcomes in health care associated pneumonia: a UK cohort study. Clin Infect Dis 2011; 53:107–13.
    1. Musher DM, Roig IL, Cazares G, Stager CE, Logan N, Safar H. Can an etiologic agent be identified in adults who are hospitalized for community-acquired pneumonia: results of a one-year study. J Infect 2013; 67:11–8.
    1. Jain S, Williams DJ, Arnold SR et al. . Community-acquired pneumonia requiring hospitalization among U.S. children. N Engl J Med 2015; 372:835–45.
    1. Musher DM, Thorner AR. Community-acquired pneumonia. N Engl J Med 2014; 371:1619–28.
    1. Templeton KE, Scheltinga SA, Graffelman AW et al. . Comparison and evaluation of real-time PCR, real-time nucleic acid sequence-based amplification, conventional PCR, and serology for diagnosis of Mycoplasma pneumoniae. J Clin Microbiol 2003; 41:4366–71.
    1. Templeton KE, Scheltinga SA, Sillekens P et al. . Development and clinical evaluation of an internally controlled, single-tube multiplex real-time PCR assay for detection of Legionella pneumophila and other Legionella species. J Clin Microbiol 2003; 41:4016–21.
    1. Heim A, Ebnet C, Harste G, Pring-Åkerblom P. Rapid and quantitative detection of human adenovirus by real-time PCR. J Med Virol 2003; 70:228–39.
    1. Templeton KE, Scheltinga SA, Beersma MF, Kroes AC, Claas EC. Rapid and sensitive method using multiplex real-time PCR for diagnosis of infections by influenza A and influenza B viruses, respiratory syncytial virus, and parainfluenza viruses 1, 2, 3, and 4. J Clin Microbiol 2004; 42:1564–9.
    1. Scheltinga SA, Templeton KE, Beersma MF, Claas EC. Diagnosis of human metapneumovirus and rhinovirus in patients with respiratory tract infections by an internally controlled multiplex real-time RNA PCR. J Clin Virol 2005; 33:306–11.
    1. Gaunt ER, Hardie A, Claas EC, Simmonds P, Templeton KE. Epidemiology and clinical presentations of the four human coronaviruses 229E, HKU1, NL63, and OC43 detected over 3 years using a novel multiplex real-time PCR method. J Clin Microbiol 2010; 48:2940–7.
    1. Yang S, Lin S, Khalil A et al. . Quantitative PCR assay using sputum samples for rapid diagnosis of pneumococcal pneumonia in adult emergency department patients. J Clin Microbiol 2005; 43:3221–6.
    1. Apfalter P, Stoiser B, Barousch W, Nehr M, Kramer L, Burgmann H. Community-acquired bacteria frequently detected by means of quantitative polymerase chain reaction in nosocomial early-onset ventilator-associated pneumonia. Crit Care Med 2005; 33:1492–8.
    1. Kais M, Spindler C, Kalin M, Ortqvist A, Giske CG. Quantitative detection of Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis in lower respiratory tract samples by real-time PCR. Diagn Microbiol Infect Dis 2006; 55:169–78.
    1. Bayram A, Kocoglu E, Balci I, Filiz A, Eksi F. Real-time polymerase chain reaction assay for detection of Streptococcus pneumoniae in sputum samples from patients with community-acquired pneumonia. J Microbiol Immunol Infect 2006; 39:452–7.
    1. Abdeldaim GM, Stralin K, Olcen P, Blomberg J, Herrmann B. Toward a quantitative DNA-based definition of pneumococcal pneumonia: a comparison of Streptococcus pneumoniae target genes, with special reference to the Spn9802 fragment. Diagn Microbiol Infect Dis 2008; 60:143–50.
    1. Johansson N, Kalin M, Tiveljung-Lindell A, Giske CG, Hedlund J. Etiology of community-acquired pneumonia: increased microbiological yield with new diagnostic methods. Clin Infect Dis 2010; 50:202–9.
    1. Rios-Licea MM, Bosques FJ, Arroliga AC, Galindo-Galindo JO, Garza-Gonzalez E. Quadruplex real-time quantitative PCR assay for the detection of pathogens related to late-onset ventilator-associated pneumonia: a preliminary report. J Microbiol Methods 2010; 81:232–4.
    1. Ost DE, Poch D, Fadel A, Wettimuny S, Ginocchio C, Wang XP. Mini-bronchoalveolar lavage quantitative polymerase chain reaction for diagnosis of methicillin-resistant Staphylococcus aureus pneumonia. Crit Care Med 2010; 38:1536–41.
    1. Feizabadi MM, Majnooni A, Nomanpour B et al. . Direct detection of Pseudomonas aeruginosa from patients with healthcare associated pneumonia by real time PCR. Infect Genet Evol 2010; 10:1247–51.
    1. Werno AM, Anderson TP, Murdoch DR. Association between pneumococcal load and disease severity in adults with pneumonia. J Med Microbiol 2012; 61:1129–35.
    1. Kwon SJ, Jeon T, Seo D et al. . Quantitative PCR for etiologic diagnosis of methicillin-resistant Staphylococcus aureus pneumonia in intensive care unit. Tuberc Respir Dis (Seoul) 2012; 72:293–301.
    1. Bogaerts P, Hamels S, de Mendonca R et al. . Analytical validation of a novel high multiplexing real-time PCR array for the identification of key pathogens causative of bacterial ventilator-associated pneumonia and their associated resistance genes. J Antimicrob Chemother 2013; 68:340–7.
    1. Abdeldaim GM, Strålin K, Olcén P, Blomberg J, Mölling P, Herrmann B. Quantitative fucK gene polymerase chain reaction on sputum and nasopharyngeal secretions to detect Haemophilus influenzae pneumonia. Diagn Microbiol Infect Dis 2013; 76:141–6.
    1. Strålin K, Herrmann B, Abdeldaim G, Olcén P, Holmberg H, Mölling P. Comparison of sputum and nasopharyngeal aspirate samples and of the PCR gene targets lytA and Spn9802 for quantitative PCR for rapid detection of pneumococcal pneumonia. J Clin Microbiol 2014; 52:83–9.
    1. Jamal W, Al Roomi E, Abdul Aziz LR, Rotimi VO. Evaluation of Curetis Unyvero, a multiplex PCR-based testing system, for rapid detection of bacteria and antibiotic resistance and impact of the assay on management of severe nosocomial pneumonia. J Clin Microbiol 2014; 52:2487–92.
    1. Huijskens EG, Koopmans M, Palmen FM, van Erkel AJ, Mulder PG, Rossen JW. The value of signs and symptoms in differentiating between bacterial, viral and mixed aetiology in patients with community-acquired pneumonia. J Med Microbiol 2014; 63:441–52.
    1. Edin A, Granholm S, Koskiniemi S, Allard A, Sjöstedt A, Johansson A. Development and laboratory evaluation of a real-time PCR assay for detecting viruses and bacteria of relevance for community-acquired pneumonia. J Mol Diagn 2015; 17:315–24.
    1. Gadsby NJ, McHugh MP, Russell CD et al. . Development of two real-time multiplex PCR assays for the detection and quantification of eight key bacterial pathogens in lower respiratory tract infection. Clin Microbiol Infect 2015; 21:788.e1–13.
    1. American Thoracic Society, Infectious Diseases Society of America. Guidelines for the management of adults with hospital-acquired, ventilator-associated, and healthcare-associated pneumonia. Am J Respir Crit Care Med 2005; 171:388–416.
    1. Public Health England. Investigation of Bronchoalveolar Lavage, Sputum and Associated Specimens. UK Standards for Microbiology Investigations. 2015. B 57 Issue 3.1 Available at: . Accessed 12 January 2016.
    1. Templeton KE, Scheltinga SA, van den Eeden WC, Graffelman AW, van den Broek PJ, Claas EC. Improved diagnosis of the etiology of community-acquired pneumonia with real-time polymerase chain reaction. Clin Infect Dis 2005; 41:345–51.
    1. Hohenthal U, Vainionpää R, Meurman O et al. . Aetiological diagnosis of community acquired pneumonia: utility of rapid microbiological methods with respect to disease severity. Scand J Infect Dis 2008; 40:131–8.
    1. Jennings LC, Anderson TP, Beynon KA et al. . Incidence and characteristics of viral community-acquired pneumonia in adults. Thorax 2008; 63:42–8.
    1. Charles PG, Whitby M, Fuller AJ et al. . The etiology of community-acquired pneumonia in Australia: why penicillin plus doxycycline or a macrolide is the most appropriate therapy. Clin Infect Dis 2008; 46:1513–21.
    1. Johnstone J, Majumdar SR, Fox JD, Marrie TJ. Viral infection in adults hospitalized with community-acquired pneumonia: prevalence, pathogens, and presentation. Chest 2008; 134:1141–8.
    1. Sangil A, Calbo E, Robles A et al. . Aetiology of community-acquired pneumonia among adults in an H1N1 pandemic year: the role of respiratory viruses. Eur J Clin Microbiol Infect Dis 2012; 31:2765–72.
    1. Gadsby NJ, Reynolds AJ, McMenamin J et al. . Increased reports of Mycoplasma pneumoniae from laboratories in Scotland in 2010 and 2011—impact of the epidemic in infants. Euro Surveill 2012; 17:pii:20110.
    1. Self WH, Williams DJ, Zhu Y et al. . Respiratory viral detection in children and adults: comparing asymptomatic controls and patients with community-acquired pneumonia. J Infect Dis 2015; 10.1093/infdis/jiv323.
    1. Albrich WC, Madhi SA, Adrian PV et al. . Use of a rapid test of pneumococcal colonization density to diagnose pneumococcal pneumonia. Clin Infect Dis 2012; 54:601–9.
    1. Davey P, Brown E, Charani E et al. . Interventions to improve antibiotic prescribing practices for hospital inpatients. Cochrane Database Syst Rev 2013; 4:CD003543.
    1. Oosterheert JJ, van Loon AM, Schuurman R et al. . Impact of rapid detection of viral and atypical bacterial pathogens by real-time polymerase chain reaction for patients with lower respiratory tract infection. Clin Infect Dis 2005; 41:1438–44.

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