Culture-based diagnostic microbiology in cystic fibrosis: Can we simplify the complexity?

Journal of Cystic Fibrosis

Volumn 13, Issue 1, 2014, Pages 1-9

  Burns, Jane L ^a   Rolain, Jean Marc ^b  

^a UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^b AIX MARSEILLE UNIVERSITY   (France)

Author keywords

Bacteria; Microbiology; Susceptibility testing

Indexed keywords

ACETYLCYSTEINE; AURAMINE; AZITHROMYCIN; FLUOROCHROME; OXALIC ACID; RHODAMINE; SODIUM HYDROXIDE;

ANTIBIOTIC SENSITIVITY; BACTERIUM CULTURE; BACTERIUM IDENTIFICATION; CLINICAL EVALUATION; CYSTIC FIBROSIS; FLUOROCHROME STAINING; FUNGUS CULTURE; GRAM STAINING; HUMAN; LUNG LAVAGE; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; METAGENOMICS; MICROBIOME; OBSERVATIONAL METHOD; REAL TIME POLYMERASE CHAIN REACTION; RESPIRATORY TRACT INFECTION; REVIEW; SPUTUM CULTURE; STAPHYLOCOCCUS AUREUS; THROAT CULTURE;

BACTERIA; MICROBIOLOGY; SUSCEPTIBILITY TESTING;

CYSTIC FIBROSIS; HUMANS; LUNG DISEASES, FUNGAL; MICROBIOLOGICAL TECHNIQUES; PNEUMONIA, BACTERIAL; REAL-TIME POLYMERASE CHAIN REACTION;

EID: 84890436122     PISSN: 15691993     EISSN: 18735010     Source Type: Journal    
DOI: 10.1016/j.jcf.2013.09.004     Document Type: Review

References (39)

1. Hauser A.R., Jain M., Bar-Meir M., McColley S.A. Clinical significance of microbial infection and adaptation in cystic fibrosis. Clin Microbiol Rev 2011, 24:29-70.
2. Bittar F., Rolain J.M. Detection and accurate identification of new or emerging bacteria in cystic fibrosis patients. Clin Microbiol Infect 2010, 16:809-820.
3. Lipuma J.J. The changing microbial epidemiology in cystic fibrosis. Clin Microbiol Rev 2010, 23:299-323.
4. Sibley C.D., Grinwis M.E., Field T.R., Eshaghurshan C.S., Faria M.M., Dowd S.E., et al. Culture enriched molecular profiling of the cystic fibrosis airway microbiome. PLoS One 2011, 6:e22702.
5. Carmody L.A., Zhao J., Schloss P.D., Petrosino J.F., Murray S., Young V.B., et al. Changes in cystic fibrosis airway microbiota at pulmonary exacerbation. Ann Am Thorac Soc 2013, 10:179-187.
6. Salipante S.J., Sengupta D.J., Rosenthal C., Costa G., Spangler J., Sims E.H., et al. Rapid 16S rRNA next-generation sequencing of polymicrobial clinical samples for diagnosis of complex bacterial infections. PLoS One 2013, 8:e65226.
7. Sibley C.D., Grinwis M.E., Field T.R., Parkins M.D., Norgaard J.C., Gregson D.B., et al. McKay agar enables routine quantification of the 'Streptococcus milleri' group in cystic fibrosis patients. J Med Microbiol 2010, 59:534-540.
8. Zemanick E.T., Harris J.K., Wagner B.D., Robertson C.E., Sagel S.D., Stevens M.J., et al. Inflammation and airway microbiota during cystic fibrosis pulmonary exacerbations. PLoS One 2013, 8:e62917.
9. Goddard A.F., Staudinger B.J., Dowd S.E., Joshi-Datar A., Wolcott R.D., Aitken M.L., et al. Direct sampling of cystic fibrosis lungs indicates that DNA-based analyses of upper-airway specimens can misrepresent lung microbiota. Proc Natl Acad Sci U S A 2012, 109:13769-13774.
10. Rosenfeld M., Emerson J., Accurso F., Armstrong D., Castile R., Grimwood K., et al. Diagnostic accuracy of oropharyngeal cultures in infants and young children with cystic fibrosis. Pediatr Pulmonol 1999, 28:321-328.
11. Nair B., Stapp J., Stapp L., Bugni L., Van Dalfsen J., Burns J.L. Utility of gram staining for evaluation of the quality of cystic fibrosis sputum samples. J Clin Microbiol 2002, 40:2791-2794.
12. Elborn J.S., Perrett J., Forsman-Semb K., Marks-Konczalik J., Gunawardena K., Entwistle N. Efficacy, safety and effect on biomarkers of AZD9668 in cystic fibrosis. Eur Respir J 2012, 40:969-976.
13. Cystic Fibrosis Trust Laboratory standards for processing microbiological samples from people with cystic fibrosis: report of the UK Cystic Fibrosis Trust Microbiology Laboratory Standards Working Group Retrieved from. https://www.cysticfibrosis.org.uk/media/82034/CD_Laboratory_Standards_Sep_10.pdf.
14. Saiman L., Siegel J. Infection control recommendations for patients with cystic fibrosis: microbiology, important pathogens, and infection control practices to prevent patient-to-patient transmission. Infect Control Hosp Epidemiol 2003, 24:S6-S52.
15. Wright R.M., Moore J.E., Shaw A., Dunbar K., Dodd M., Webb K., et al. Improved cultural detection of Burkholderia cepacia from sputum in patients with cystic fibrosis. J Clin Pathol 2001, 54:803-805.
16. Borman A.M., Palmer M.D., Delhaes L., Carrere J., Favennec L., Ranque S., et al. Lack of standardization in the procedures for mycological examination of sputum samples from CF patients: a possible cause for variations in the prevalence of filamentous fungi. Med Mycol 2010, 48(Suppl. 1):S88-S97.
17. Retsch-Bogart G.Z., Quittner A.L., Gibson R.L., Oermann C.M., McCoy K.S., Montgomery A.B., et al. Efficacy and safety of inhaled aztreonam lysine for airway pseudomonas in cystic fibrosis. Chest 2009, 135:1223-1232.
18. Ramsey B.W., Pepe M.S., Quan J.M., Otto K.L., Montgomery A.B., Williams-Warren J., et al. Intermittent administration of inhaled tobramycin in patients with cystic fibrosis. Cystic Fibrosis Inhaled Tobramycin Study Group. N Engl J Med 1999, 340:23-30.
19. Whittier S., Olivier K., Gilligan P., Knowles M., Della-Latta P. Proficiency testing of clinical microbiology laboratories using modified decontamination procedures for detection of nontuberculous mycobacteria in sputum samples from cystic fibrosis patients. The Nontuberculous Mycobacteria in Cystic Fibrosis Study Group. J Clin Microbiol 1997, 35:2706-2708.
20. Esther C.R., Hoberman S., Fine J., Allen S., Culbreath K., Rodino K., et al. Detection of rapidly growing mycobacteria in routine cultures of samples from patients with cystic fibrosis. J Clin Microbiol 2011, 49:1421-1425.
21. Seng P., Abat C., Rolain J.M., Colson P., Lagier J.C., Gouriet F., et al. Identification of rare pathogenic bacteria in a clinical microbiology laboratory: impact of MALDI-TOF mass spectrometry. J Clin Microbiol 2013, 51:2182-2194.
22. Spilker T., Vandamme P., Lipuma J.J. Identification and distribution of Achromobacter species in cystic fibrosis. J Cyst Fibros 2013, 12:298-301.
23. Leao S.C., Tortoli E., Euzeby J.P., Garcia M.J. Proposal that Mycobacterium massiliense and Mycobacterium bolletii be united and reclassified as Mycobacterium abscessus subsp. bolletii comb. nov., designation of Mycobacterium abscessus subsp. abscessus subsp. nov. and emended description of Mycobacterium abscessus. Int J Syst Evol Microbiol 2011, 61:2311-2313.
24. Blauwendraat C., Dixon G.L., Hartley J.C., Foweraker J., Harris K.A. The use of a two-gene sequencing approach to accurately distinguish between the species within the Mycobacterium abscessus complex and Mycobacterium chelonae. Eur J Clin Microbiol Infect Dis 2012, 31:1847-1853.
25. Desai A.P., Stanley T., Atuan M., McKey J., Lipuma J.J., Rogers B., et al. Use of matrix assisted laser desorption ionisation-time of flight mass spectrometry in a paediatric clinical laboratory for identification of bacteria commonly isolated from cystic fibrosis patients. J Clin Pathol 2012, 65:835-838.
26. Del Chierico F., Masotti A., Onori M., Fiscarelli E., Mancinelli L., Ricciotti G., et al. MALDI-TOF MS proteomic phenotyping of filamentous and other fungi from clinical origin. J Proteomics 2012, 75:3314-3330.
27. Saleeb P.G., Drake S.K., Murray P.R., Zelazny A.M. Identification of mycobacteria in solid-culture media by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol 2011, 49:1790-1794.
28. Bittar F., Cassagne C., Bosdure E., Stremler N., Dubus J.C., Sarles J., et al. Outbreak of Corynebacterium pseudodiphtheriticum infection in cystic fibrosis patients, France. Emerg Infect Dis 2010, 16:1231-1236.
29. Wolter D.J., Emerson J.C., McNamara S., Buccat A.M., Qin X., Cochrane E., et al. Staphylococcus aureus small-colony variants are independently associated with worse lung disease in children with cystic fibrosis. Clin Infect Dis 2013, 57:384-391.
30. Burns J.L., Saiman L., Whittier S., Larone D., Krzewinski J., Liu Z., et al. Comparison of agar diffusion methodologies for antimicrobial susceptibility testing of Pseudomonas aeruginosa isolates from cystic fibrosis patients. J Clin Microbiol 2000, 38:1818-1822.
31. Foweraker J.E., Laughton C.R., Brown D.F., Bilton D. Phenotypic variability of Pseudomonas aeruginosa in sputa from patients with acute infective exacerbation of cystic fibrosis and its impact on the validity of antimicrobial susceptibility testing. J Antimicrob Chemother 2005, 55:921-927.
32. Etherington C., Hall M., Conway S., Peckham D., Denton M. Clinical impact of reducing routine susceptibility testing in chronic Pseudomonas aeruginosa infections in cystic fibrosis. J Antimicrob Chemother 2008, 61:425-427.
33. Waters V., Ratjen F. Combination antimicrobial susceptibility testing for acute exacerbations in chronic infection of Pseudomonas aeruginosa in cystic fibrosis. Cochrane Database Syst Rev 2008, CD006961.
34. Moskowitz S.M., Emerson J.C., McNamara S., Shell R.D., Orenstein D.M., Rosenbluth D., et al. Randomized trial of biofilm testing to select antibiotics for cystic fibrosis airway infection. Pediatr Pulmonol 2011, 46:184-192.
35. Zankari E., Hasman H., Kaas R.S., Seyfarth A.M., Agerso Y., Lund O., et al. Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing. J Antimicrob Chemother 2013, 68:771-777.
36. Dunne W.M., Westblade L.F., Ford B. Next-generation and whole-genome sequencing in the diagnostic clinical microbiology laboratory. Eur J Clin Microbiol Infect Dis 2012, 31:1719-1726.
37. Fodor A.A., Klem E.R., Gilpin D.F., Elborn J.S., Boucher R.C., Tunney M.M., et al. The adult cystic fibrosis airway microbiota is stable over time and infection type, and highly resilient to antibiotic treatment of exacerbations. PLoS One 2012, 7:e45001.
38. Zhao J., Schloss P.D., Kalikin L.M., Carmody L.A., Foster B.K., Petrosino J.F., et al. Decade-long bacterial community dynamics in cystic fibrosis airways. Proc Natl Acad Sci U S A 2012, 109:5809-5814.
39. Zemanick E.T., Wagner B.D., Sagel S.D., Stevens M.J., Accurso F.J., Harris J.K. Reliability of quantitative real-time PCR for bacterial detection in cystic fibrosis airway specimens. PLoS One 2010, 5:e15101.