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Review

Emerging strategies for the noninvasive diagnosis of nosocomial pneumonia

, &
Pages 523-533 | Received 09 Apr 2019, Accepted 19 Jun 2019, Published online: 25 Jun 2019

References

  • Metersky ML, Wang Y, Klompas M, et al. Trend in ventilator-associated pneumonia rates between 2005 and 2013. JAMA. 2016;316(22):2427–2429.
  • Torres A, Niederman MS, Chastre J, et al. International ERS/ESICM/ESCMID/ALAT guidelines for the management of hospital-acquired pneumonia and ventilator-associated pneumonia: guidelines for the management of hospital-acquired pneumonia (HAP)/ventilator-associated pneumonia (VAP) of the European Respiratory Society (ERS), European Society of Intensive Care Medicine (ESICM), European Society of Clinical Microbiology and Infectious Diseases (ESCMID) and Asociación Latinoamericana del Tórax (ALAT). Eur Respir J. 2017;50(3).pii.1700582.
  • Guillamet CV, Kollef MH. Update on ventilator-associated pneumonia. Curr Opin Crit Care. 2015;21:430–438.
  • Martin-Loeches I, Torres A, Rinaudo M, et al. Resistance patterns and outcomes in intensive care unit (ICU)-acquired pneumonia. Validation of European Centre for Disease Prevention and Control (ECDC) and the Centers for Disease Control and Prevention (CDC) classification of multidrug resistant organisms. J Infect. 2015;70:213–222.
  • Koulenti D, Tsigou E, Rello J. Nosocomial pneumonia in 27 ICUs in Europe: perspectives from the EU-VAP/CAP study. Eur J Clin Microbiol Infect Dis. 2017 Nov;36(11):1999–2006.
  • Kalil AC, Metersky ML, Klompas M, et al. Management of adults with hospital-acquired and ventilator-associated pneumonia: 2016 clinical practice guidelines by the infectious diseases society of America and the American thoracic society. Clin Infect Dis. 2016;63:e61–e111.
  • Micek ST, Wunderink RG, Kollef MH, et al. An international multicenter retrospective study of Pseudomonas aeruginosa nosocomial pneumonia: impact of multidrug resistance. Crit Care. 2015;19:219.
  • Tabah A, Koulenti D, Laupland K, et al. Characteristics and determinants of outcome of hospital-acquired bloodstream infections in intensive care units: the EUROBACT international cohort study. Intensive Care Med. 2012;38(12):1930–1945.
  • Timsit JF, Pilmis B, Zahar JR. How should we treat hospital-acquired and ventilator-associated pneumonia caused by extended-spectrum β-lactamase-producing enterobacteriaceae? Semin Respir Crit Care Med. 2017;38(3):287–300.
  • Niederman MS, Martin-Loeches I, Torres A. The research agenda in VAP/HAP: next steps. Intensive Care Med. 2017;43:1389–1391.
  • Berton DC, Kalil AC, Teixeira PJ. Quantitative versus qualitative cultures of respiratory secretions for clinical outcomes in patients with ventilator-associated pneumonia. Cochrane Database Syst Rev. 2014;10:CD006482.
  • Sole´ Violan J, Fernandez JA, Benıtez AB, et al. Impact of quantitative invasive diagnostic techniques in the management and outcome of mechanically ventilated patients with suspected pneumonia. CritCareMed. 2000;28(8):2737–2741.
  • Martin-Loeches I, Rodriguez AH, Torres A. New guidelines for hospital-acquired pneumonia/ventilator-associated pneumonia: USA vs. Eur Curr Opin Crit Care. 2018;24:347–352.
  • Garnacho-Montero J, Garcia-Garmendia JL, Barrero-Almodovar A, et al. Impact of adequate empirical antibiotic therapy on the outcome of patients admitted to the intensive care unit with sepsis. Crit Care Med. 2003;31:2742–2751.
  • Armand-Lefèvre L, Angebault C, Barbier F, et al. Emergence of imipenem resistant gram-negative bacilli in intestinal flora of intensive care patients. Antimicrob Agents Chemother. 2013;57:1488–1495.
  • Ranzani OT, Senussi T, Idone F, et al. Invasive and non-invasive diagnostic approaches for microbiological diagnosis of hospital-acquired pneumonia. Crit Care. 2019 Feb 18;23(1):51.
  • Russell CD, Koch O, Laurenson IF, et al. Diagnosis and features of hospital-acquired pneumonia: a retrospective cohort study. J Hosp Infect. 2016 Mar;92(3):273–279.
  • Patel IS, Vlahos I, Wilkinson TMA, et al. Bronchiectasis, exacerbation indices, and inflammation in chronic obstructive pulmonary disease. Am J Respir Crit Care Med. 2004;170:400–407.
  • Volpicelli G, Elbarbary M, Blaivas M, et al. International evidence-based recommendations for point-of-care lung ultrasound. Intensive Care Med. 2012;38:577–591.
  • Ellington LE, Gilman RH, Chavez MA, et al. Lung ultrasound as a diagnostic tool for radiographically-confirmed pneumonia in low resource settings. Respir Med. 2017;128:57–64.
  • Bouhemad B, Dransart-Rayé O, Mojoli F, et al. Lung ultrasound for diagnosis and monitoring of ventilator-associated pneumonia. Ann Transl Med. 2018 Nov;6(21):418.
  • Bouhemad B, Liu ZH, Arbelot C, et al. Ultrasound assessment of antibiotic induced pulmonary reaeration in ventilator-associated pneumonia. Crit Care Med. 2010;38:84–92.
  • Viasus D, Calatayud L, McBrown MV, et al. Urinary antigen testing in community-acquired pneumonia in adults: an update. Expert Rev Anti Infect Ther. 2019 Feb;17(2):107–115.
  • Woodhead M, Blasi F, Ewig S, et al. Joint taskforce of the European respiratory society and European society for clinical microbiology and infectious diseases. Guidelines for the management of adult lower respiratory tract infections–full version. Clin Microbiol Infect. 2011 Nov;17(Suppl 6):E1–59.
  • Wunderink RG, Self WH, Anderson EJ, et al. Pneumococcal community-acquired pneumonia detected by serotype-specific urinary antigen detection assays. Clin Infect Dis. 2018 May 2;66(10):1504–1510.
  • Murdoch DR. How recent advances in molecular tests could impact the diagnosis of pneumonia. Expert Rev Mol Diagn. 2016;16(5):533–540.
  • Torres A, Lee N, Cillóniz C, et al. Laboratory diagnosis of pneumonia in the molecullar age. Eur Respir J. 2016;48:1764–1778.
  • Kollef MH, Burnham. C-AD. Ventilator-associated pneumonia: the role of emerging diagnostic technologies. Semin Respir Crit Care Med. 2017;38:253–263.
  • Somerville LK, Ratnamohan VM, Dwyer DE, et al. Molecular diagnosis of respiratory viruses. Pathology. 2015;47:243–249.
  • Blyth CC, Webb SA, Kok J, et al. The impact of bacterial and viral coinfection in severe influenza. Influenza Other Respir Viruses. 2013;7:168–176.
  • Mahony JB. Nucleic acid amplification-based diagnosis of respiratory virus infections. Expert Rev Anti Infect Ther. 2010;8:1273–1292.
  • Diaz MH, Winchell JM. The evolution of advanced molecular diagnostics for the detection and characterization of mycoplasma pneumoniae. Review. 2016 March;7: Article 232:1-17.
  • Martin-Loeches I, Schultz JM, Vincent JL, et al. Influenza. Intensive Care Med. 2017 Jan;43(1):48–58.
  • Ho TH, Huang YC, Lin TY. Evaluation of the BD GeneOhm StaphSR assay for detection of Staphylococcus aureus in patients in intensive care units. J Microbiol Immunol Infect. 2011;44:310–315.
  • Endimiani A, Hujer KM, Hujer AM, et al. Are we ready for novel detection methods to treat respiratory pathogens in hospital-acquired pneumonia? Clin Infect Dis. 2011;52(Suppl 4):S373–S383.
  • Miller S, Moayeri M, Wright C, et al. Comparison of GeneXpert FluA PCR to direct fluorescent antibody and respiratory viral panel PCR assays for detection of 2009 novel H1N1 influenza virus. J Clin Microbiol. 2010;48:4684–4685.
  • Cercenado E, Marın M, Insa R, et al. Rapid detection of Staphylococcus aureus in lower respiratory tract secretions from patients with ventilator-associated pneumonia: evaluation of the Cepheid Xpert MRSA/SA SSTI Assay. J Clin Microbiol. 2012 Dec;50(12):4095–4097.
  • Wassenberg MW, Kluytmans JA, Bosboom RW, et al. Rapid diagnostic testing of methicillin-resistant Staphylococcus aureus carriage at different anatomical sites: costs and benefits of less extensive screening regimens. Clin Microbiol Infect. 2011;17:1704–1710.
  • Caliendo AM. Multiplex PCR and emerging technologies for the detection of respiratory pathogens. Clin Infect Dis. 2011 May;52(Suppl 4):S326–30.
  • Babady NE. The FilmArray1 respiratory panel: an automated, broadly multiplexed molecular test for the rapid and accurate detection of respiratory pathogens. Expert Rev Mol Diagn. 2013;13:779–788.
  • Sansot M, Fradin E, Chenouard R, et al. Performance of the extended use of the FilmArray® BCID panel kit for bronchoalveolar lavage analysis. Mol Biol Rep. 2019 Feb 23;46:2685–2692.
  • Shorr AF, Zilberberg MD, Micek ST, et al. Viruses are prevalent in non-ventilated hospital-acquired pneumonia. Respir Med. 2017 Jan;122:76–80.
  • Pulido MR, Moreno-Martínez P, González-Galán V, et al. Application of biofire filmarray blood culture identification panel for rapid identification of the causative agents of ventilator-associated pneumonia. Clin Microbiol Infect. 2018 Nov;24(11):1213.e1-1213.
  • Baudel JL, Tankovic J, Dahoumane R, et al. Multiplex PCR performed of bronchoalveolar lavage fluid increases pathogen identification rate in critically ill patients with pneumonia: a pilot study. Ann Intensive Care. 2014;4:35.
  • Seng P, Rolain JM, Fournier PE, et al. MALDI-TOF-mass spectrometry applications in clinical microbiology. Future Microbiol 2010; 5:1733–1754.
  • Seng P, Drancourt M, Gouriet F, et al. Ongoing revolution in bacteriology: routine identification of bacteria by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Clin Infect Dis. 2009;49:543–551.
  • Huang AM, Newton D, Kunapuli A, et al. Impact of rapid organism identification via matrix-assisted laser desorption/ionization time-of-flight combined with antimicrobial stewardship team intervention in adult patients with bacteremia and candidemia. Clin Infect Dis. 2013;57(9):1237–1245.
  • Fiori B, D’ Inzeo T, Giaquinto A, et al. Optimized use of the MALDI biotyper system and the filmarray BCID panel for direct identification of microbial pathogens from positive blood cultures. J Clin Microbiol. 2016;54:576–584.
  • Chen L, Mediavilla JR, Endimiani A, et al. Multiplex real-time PCR assay for detection and classification of Klebsiella pneumoniae carbapenemase gene (blaKPC) variants. J Clin Microbiol. 2011;49:579–585.
  • Lung ML, Codina G. Molecular diagnosis in HAP/VAP. Curr Opin Crit Care. 2012;18:487–494.
  • Strålin K, Ehn F, Giske CG, et al. The IRIDICA PCR/electrospray ionization-mass spectrometry assay on bronchoalveolar lavage for bacterial etiology in mechanically ventilated patients with suspected pneumonia. PLoS One. 2016 Jul 27;11(7):e0159694.
  • Ullberg M, Lüthje P, Mölling P, et al. Broad-range detection of microorganisms directly from bronchoalveolar lavage specimens by PCR/electrospray ionization-mass spectrometry. PLoS One. 2017 Jan 13;12(1):e0170033.
  • Huttner A, Emonet S, Harbarth S, et al. Polymerase chain reaction/electrospray ionization-mass spectrometry for the detection of bacteria and fungi in bronchoalveolar lavage fluids: a prospective observational study. Clin Microbiol Infect. 2014;20:O1059–66.
  • Wolk DM, Kaleta EJ, Wysocki VH.PCR-electrospray ionization mass spectrometry: the potential to change infectious disease diagnostics in clinical and public health laboratories. J Mol Diagn. 2012;14(4):295-304.
  • Dodémont M, De Mendonça R, Nonhoff C, et al. Evaluation of verigene gam-positive blood culture assay performance for bacteremic patients. Eur J Clin Microbial Infect Dis. 2015;34:473–477.
  • Alby K, Daniels LM, Weber DJ, et al. Development of a treatment algorithm for streptococci and enterococci from positive blood cultures identified with the Verigene Gram-positive blood culture assay. J ClinMicrobiol. 2013;51(11):3869–3871.
  • [cited 2017 Feb 17]. https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfPMN/pmn.cfm?ID=K163260
  • Sutherland A, Thomas M, Brandon RA, et al. Development and validation of a novel molecular biomarker diagnostic test for the early detection of sepsis. Crit Care. 2011;15:R149.
  • McHugh L, Seldon TA, Brandon RA, et al. A molecular host response assay to discriminate between sepsis and infection-negative systemic inflammation in critically ill patients: discovery and validation in independent cohorts. PLoS Med. 2015;12:e1001916.
  • Roisin S, Huang TD, de Mendonça R, et al. Prospective evaluation of a high multiplexing real-time polymerase chain reaction array for the rapid identification and characterization of bacteria causative of nosocomial pneumonia from clinical specimens: a proof-of-concept study. Eur J Clin Microbiol Infect Dis. 2018 Jan;37(1):109–116.
  • Naas T, Cuzon G, Bogaerts P, et al. Evaluation of a DNA microarray (Check-MDR CT102) for rapid detection of TEM, SHV, and CTX-M extended-spectrum β-lactamases and of KPC, OXA-48, VIM, IMP, and NDM-1 carbapenemases. J Clin Microbiol. 2011;49:1608–1613.
  • Endimiani A, Hujer AM, Hujer KM, et al. Evaluation of a commercial microarray system for detection of SHV-, TEM-, CTX-M-, and KPC-type β-lactamase genes in Gram-negative isolates. J Clin Microbiol. 2010;48:2618–2622.
  • Fishbain JT, Sinyavskiy O, Riederer K, et al. Detection of extended-spectrum β-lactamase and Klebsiella pneumoniae carbapenemase genes directly from blood cultures by use of a nucleic acid microarray. J Clin Microbiol. 2012;50:2901–2904.
  • Mahony J, Chong S, Bulir D, et al. Development of a sensitive loop-mediated isothermal amplification assay that provides specimen-to-result diagnosis of respiratory syncytial virus infection in 30 minutes. J Clin Microbiol. 2013;51:2696–2701.
  • Bell J, Bonner A, Cohen DM, et al. Multicenter clinical evaluation of the novel AlereTM i Influenza A and B isothermal nucleic acid amplification test. J Clin Virol. 2014;61:81–86.
  • Zhang W, Chen C, Cui J, et al. Application of loop-mediated isothermal amplification (LAMP) assay for the rapid diagnosis of pathogenic bacteria in clinical sputum specimens of acute exacerbation of COPD (AECOPD). Int J Clin Exp Med. 2015;8:7881–7889.
  • Yamamoto N, Hamaguchi S, Akeda Y, et al. Clinical specimen-direct LAMP: a useful tool for the surveillance of blaOXA-23-positive carbapenem-resistant Acinetobacter baumannii. PLoS One. 2015;10:e0133204.
  • Yu J, Liu J, Li Y, et al. Rapid detection of carbapenemase activity of Enterobacteriaceae isolated from positive blood cultures by MALDI-TOF MS. Ann Clin Microbiol Antimicrob. 2018 May 18;17(1):22.
  • Choquet M, Guiheneuf R, Castelain S, et al. Comparison of MALDI-ToF MS with the Rapidec Carba NP test for the detection of carbapenemase-producing enterobacteriaceae. Eur J Clin Microbiol Infect Dis. 2018 Jan;37(1):149–155.
  • Vincent JL, Brealey D, Libert N, et al. Rapid diagnosis of infections in the critically Ill team. Rapid diagnosis of infection in the critically ill, a multicenter study of molecular detection in bloodstream infections, pneumonia, and sterile site infections. Crit Care Med. 2015;43:2283–2291.
  • Burnham CA, Frobel RA, Herrera ML, et al. Rapid ertapenem susceptibility testing and Klebsiella pneumoniae carbapenemase phenotype detection in Klebsiella pneumoniae isolates by use of automated microscopy of immobilized live bacterial cells. J Clin Microbiol. 2014;52(3):982–986.
  • Douglas IS, Price CS, Overdier KH, et al. Rapid automated microscopy for microbiological surveillance of ventilator-associated pneumonia. Am J Respir Crit Care Med. 2015;191:566–573.
  • Metzger S, Frobel RA, Dunne WM Jr. Rapid simultaneous identification and quantitation of Staphylococcus aureus and Pseudomonas aeruginosa directly from bronchoalveolar lavage specimens using automated microscopy. Diagn Microbiol Infect Dis. 2014;79:160–165.
  • Douglas IS. New diagnostic methods for pneumonia in the ICU. Curr Opin Infect Dis. 2016 Apr;29(2):197–204.
  • Vrioni G, Mamali V, Zarkotou O, et al. Performance of the β LACTA™ test for rapid detection of expanded-spectrum cephalosporin-non-susceptible Enterobacteriaceae. J Glob Antimicrob Resist. 2017;10:285–288.
  • Garnier M, Rozencwajg S, Pham T, et al. Evaluation of early antimicrobial therapy adaptation guided by the BetaLACTA(R) test: a case-control study. Crit Care. 2017;21:161.
  • Gallah Y, Benzerara J, Tankovic P, et al. β LACTA test performance for detection of extended-spectrum β-lactamase-producing Gram-negative bacilli directly on bronchial aspirates samples: a validation study. Clin Microbiol Infect. 2018 April;24(4):402–408.
  • Filipiak W, Beer R, Sponring A, et al. Breath analysis for in vivo detection of pathogens related to ventilator-associated pneumonia in intensive care patients: a prospective pilot study. J Breath Res. 2015;9:016004.
  • Schnabel R, Fijten R, Smolinska A, et al. Analysis of volatile organic compounds in exhaled breath to diagnose ventilator-associated pneumonia. Sci Rep. 2015;5:17179.
  • May AK, Brady JS, Romano-Keeler J, et al. A pilot study of the noninvasive assessment of the lung microbiota as a potential tool for the early diagnosis of ventilator-associated pneumonia. Chest. 2015 Jun;147(6):1494–1502.
  • van Oort PM, Nijsen T, Weda H, et al. BreathDx consortium. BreathDx - molecular analysis of exhaled breath as a diagnostic test for ventilator-associated pneumonia: protocol for a European multicenter observational study. BMC Pulm Med. 2017;17:1.
  • Bouza E, Martínez-Alarcón J, Maseda E, et al. “Diagnóstico Etiológico de la Neumonía Asociada a Ventilación Mecánica (DENEVEM)” – etiologic diagnosis of VAP – study Group. Quality of the aetiological diagnosis of ventilator-associated pneumonia in Spain in the opinion of intensive care specialists and microbiologists. Enferm Infecc Microbiol Clin. 2017 Mar;35(3):153–164.
  • Douglas IS. Pulmonary infections in critical/intensive care - rapid diagnosis and optimizing antimicrobial usage. Curr Opin Pulm Med. 2017 May;23(3):198–203.
  • Mok JH, Eom JS, Jo EJ, et al. Clinical utility of rapid pathogen identification using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry in ventilated patients with pneumonia: a pilot study. Respirology. 2016;21:321–328.
  • 2002. http://www.biosyn.com/Images/ArticleImages/pdf/PNA-Fluorescent-in-Situ-Hybridization-for-Rapid-Microbiology.pdf
  • Tsalik EL, Bonomo RA, Fowler VG Jr. New molecular diagnostic approaches to bacterial infections and antibacterial resistance. Annu Rev Med. 2018 Jan 29;69:379–394.
  • 2015. https://www.sciencedirect.com/topics/neuroscience/sanger-sequencing
  • Basnayake TL1, Waterer GW. Rapid diagnostic tests for defining the cause of community-acquired pneumonia. Curr Opin Infect Dis. 2015 Apr;28(2):185–192.
  • Conway Morris A, Gadsby N, McKenna JP, et al. 16S pan-bacterial PCR can accurately identify patients with ventilator-associated pneumonia. Thorax. 2017 Nov;72(11):1046–1048.
  • Nguyen EV, Gharib SA, Palazzo SJ, et al. Proteomic profiling of bronchoalveolar lavage fluid in critically ill patients with ventilator-associated pneumonia. PLoS One. 2013;8:e58782.
  • Kothari N, Bogra J, Abbas H, et al. Tumor necrosis factor gene polymorphism results in high TNF level in sepsis and septic shock. Cytokine. 2013;61:676–681.
  • Kelly BJ, Imai I, Bittinger K, et al. Composition and dynamics of the respirator tract microbiome in intubated patients. Microbiome. 2016;4:7.
  • Khadempar S, Familghadakchi S, Motlagh RA, et al. CRISPR-Cas9 in genome editing: its function and medical applications. J Cell Physiol. 2019 May;234(5):5751–5761.
  • Torres-Ruiz R, Rodriguez-Perales S. CRISPR-Cas9 technology: applications and human disease modelling. Brief Funct Genomics. 2017 Jan;16(1):4–12.
  • Dickson RP, Erb-Downward JR, Martinez FJ, et al. The microbiome and the respiratory tract. Annu Rev Physiol. 2016;78:481–504.

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