Microbiological diagnostic procedures for respiratory cystic fibrosis samples in Spain: towards standard of care practices

BMC Microbiology

Rafael Cantón³  Antonio Oliver²  Enrique Gómez-Mampaso¹  Carla López-Causapé²  Marta Cobo¹  Elia Gómez G de la Pedrosa³  Marta Tato³  Rosa del Campo³  Juan de Dios Caballero³ 

[1] Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS), Madrid 28034, Spain;Servicio de Microbiología y Unidad de Investigación, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria de Palma (IdISPa), Palma de Mallorca, Spain;Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain

关键词: Consensus guidelines;    Respiratory samples;    Laboratory procedures;    Microbiology;    Cystic fibrosis;   

Others  :  1090230
DOI  :  10.1186/s12866-014-0335-y

 received in 2014-08-18, accepted in 2014-12-18,  发布年份 2014

【 摘 要 】

Background

The microbiological procedures for cystic fibrosis (CF) samples of 17 participating Spanish centers were examined to verify their compliance with current international and national guidelines and to implement the best standards of care for microbiology practices. A 47-item questionnaire covering different CF microbiology aspects was sent to participant laboratories. Telephone interviews were performed when necessary. Data about samples processing for bacteria, mycobacteria and fungi were collected.

Results

Gene sequencing (71%), MALDI-TOF (59%) or both (94%) were available for most laboratories. Susceptibility testing was performed by automated microdilution systems (94%) and manual diffusion methods (59%). However, a low use of selective media for Staphylococcus aureus (59%) and Burkholderia cepacia complex (71%), and of epidemiological typing methods (41%) was reported.

Conclusions

Most Spanish laboratories are in agreement with consensus guidelines for the processing of CF respiratory samples, but need to improve in the use of specific selective media and typing methods for epidemiologic studies.

【 授权许可】

   
2014 Caballero et al.; licensee BioMed Central.

【 图 表 】

Figure 1.

【 参考文献 】

• [1]Rosenstein BJ, Zeitlin PL: Cystic fibrosis. Lancet 1998, 351:277-282.
• [2]Gilligan PH: Infections in patients with cystic fibrosis: diagnostic microbiology update. Clin Lab Med 2014, 34:197-217.
• [3]Lipuma JJ: The changing microbial epidemiology in cystic fibrosis. Clin Microbiol Rev 2010, 23(2):299-323.
• [4]Conway S, Balfour-Lynn IM, De Rijcke K, Drevinek P, Foweraker J, Havermans T, Heijerman H, Lannefors L, Lindblad A, Macek M, Madge S, Moran M, Morrison L, Morton A, Noordhoek J, Sands D, Vertommen A, Peckham D: European cystic fibrosis society standards of care: framework for the cystic fibrosis centre. J Cyst Fibros 2014, 13(Suppl 1):S3-S22.
• [5]Stern M, Bertrand DP, Bignamini E, Corey M, Dembski B, Goss CH, Pressler T, Rault G, Viviani L, Elborn JS, Castellani C: European cystic fibrosis society standards of care: quality management in cystic fibrosis. J Cyst Fibros 2014, 13(Suppl 1):S43-S59.
• [6]Oliver A: Mutators in cystic fibrosis chronic lung infection: prevalence, mechanisms, and consequences for antimicrobial therapy. Int J Med Microbiol 2010, 300:563-572.
• [7]Oliver A, Mena A: Bacterial hypermutation in cystic fibrosis, not only for antibiotic resistance. Clin Microbiol Infect 2010, 16:798-808.
• [8]Besier S, Smaczny C, von Mallinckrodt C, Krahl A, Ackermann H, Brade V, Wichelhaus TA: Prevalence and clinical significance of Staphylococcus aureus small-colony variants in cystic fibrosis lung disease. J Clin Microbiol 2007, 45:168-172.
• [9]Wolter DJ, Emerson JC, McNamara S, Buccat AM, Qin X, Cochrane E, Houston LS, Rogers GB, Marsh P, Prehar K, Pope CE, Blackledge M, Déziel E, Bruce KD, Ramsey BW, Gibson RL, Burns JL, Hoffman LR: Staphylococcus aureus small-colony variants are independently associated with worse lung disease in children with cystic fibrosis. Clin Infect Dis 2013, 57:384-391.
• [10]Saiman L, Siegel JD, LiPuma JJ, Brown RF, Bryson EA, Chambers MJ, Downer VS, Fliege J, Hazle LA, Jain M, Marshall BC, O’Malley C, Pattee SR, Potter-Bynoe G, Reid S, Robinson KA, Sabadosa KA, Schmidt HJ, Tullis E, Webber J, Weber DJ: Infection prevention and control guideline for cystic fibrosis: 2013 update. Infect Control Hosp Epidemiol 2014, 35(Suppl 1):S1-S67.
• [11]Shreve MR, Butler S, Kaplowitz HJ, Rabin HR, Stokes D, Light M, Regelmann WE: Impact of microbiology practice on cumulative prevalence of respiratory tract bacteria in patients with cystic fibrosis. J Clin Microbiol 1999, 37:753-757.
• [12]Häfner L, Peters G, Kahl BC: Assessment of microbiological diagnostic procedures for respiratory specimens from cystic fibrosis patients in German laboratories by use of a questionnaire. J Clin Microbiol 2014, 52:977-979.
• [13]Zhou J, Garber E, Desai M, Saiman L: Compliance of clinical microbiology laboratories in the United States with current recommendations for processing respiratory tract specimens from patients with cystic fibrosis. J Clin Microbiol 2006, 44:1547-1549.
• [14]Alarcón T, Caballero T, Cantón R, Oliver A: Diagnóstico de la colonización-infección broncopulmonar en el paciente con fibrosis quística. In Procedimientos en microbiología clínica 2007. cap. 28. Edited by Cercenado E, Cantón R. Available from Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica (SEIMC): http://www.seimc.org/contenidos/documentoscientificos/procedimientosmicrobiologia/seimc-procedimientomicrobiologia28.pdf
• [15]European Cystic Fibrosis Society Patient Registry: 2010 Annual Data Report. 2014.
• [16]Cantón R, Máiz L, Escribano A, Oliveira C, Oliver A, Asensio O, Gartner S, Roma E, Quintana-Gallego E, Salcedo A, Girón R, Barrio MI, Pastor MD, Prados MC, Martínez-Martínez MT, Barberán J, Castón J, Martínez-Martínez L, Poveda JL, Vázquez C, de Gracia J, Solé A: Consenso español para la prevención y el tratamiento de la infección bronquial por Pseudomonas aeruginosa en el paciente con fibrosis quística.Arch Bronconeumol 2015, accepted for publication.
• [17]Balke B, Schmoldt S, Häussler S, Suerbaum S, Heesemann J, Hogardt M: A German external quality survey of diagnostic microbiology of respiratory tract infections in patients with cystic fibrosis. J Cyst Fibros 2008, 7:7-14.
• [18]Miller MB, Gilligan PH: Laboratory aspects of management of chronic pulmonary infections in patients with cystic fibrosis. J Clin Microbiol 2003, 41:4009-4015.
• [19]Maciá MD, Borrell N, Pérez JL, Oliver A: Detection and susceptibility testing of hypermutable Pseudomonas aeruginosa strains with the Etest and disk diffusion. Antimicrob Agents Chemother 2004, 48:2665-2672.
• [20]Smyth AR, Bell SC, Bojcin S, Bryon M, Duff A, Flume P, Kashirskaya N, Munck A, Ratjen F, Schwarzenberg SJ, Sermet-Gaudelus I, Southern KW, Taccetti G, Ullrich G, Wolfe S: European cystic fibrosis society standards of care: best practice guidelines. J Cyst Fibros 2014, 13(Suppl 1):S23-S42.
• [21]Shelly DB, Spilker T, Gracely EJ, Coenye T, Vandamme P, LiPuma JJ: Utility of commercial systems for identification of Burkholderia cepacia complex from cystic fibrosis sputum culture. J Clin Microbiol 2000, 38:3112-3115.
• [22]Fernández-Olmos A, García-Castillo M, Morosini MI, Lamas A, Máiz L, Cantón R: MALDI-TOF MS improves routine identification of non-fermenting Gram negative isolates from cystic fibrosis patients. J Cyst Fibros 2012, 11:59-62.
• [23]Lambiase A, Del Pezzo M, Cerbone D, Raia V, Rossano F, Catania MR: Rapid identification of Burkholderia cepacia complex species recovered from cystic fibrosis patients using matrix-assisted laser desorption ionization time-of-flight mass spectrometry. J Microbiol Methods 2013, 92:145-149.
• [24]Posteraro B, De Carolis E, Vella A, Sanguinetti M: MALDI-TOF mass spectrometry in the clinical mycology laboratory: identification of fungi and beyond. Expert Rev Proteomics 2013, 10:151-164.
• [25]Chen JH, Yam WC, Ngan AH, Fung AM, Woo WL, Yan MK, Choi GK, Ho PL, Cheng VC, Yuen KY: Advantages of using matrix-assisted laser desorption ionization-time of flight mass spectrometry as a rapid diagnostic tool for identification of yeasts and mycobacteria in the clinical microbiological laboratory. J Clin Microbiol 2013, 51:3981-3987.
• [26]Burns JL, Saiman L, Whittier S, Larone D, Krzewinski J, Liu Z, Marshall SA, Jones RN: Comparison of agar diffusion methodologies for antimicrobial susceptibility testing of Pseudomonas aeruginosa isolates from cystic fibrosis patients. J Clin Microbiol 2000, 38:1818-1822.
• [27]Wainwright CE, France MW, O’Rourke P, Anuj S, Kidd TJ, Nissen MD, Sloots TP, Coulter C, Ristovski Z, Hargreaves M, Rose BR, Harbour C, Bell SC, Fennelly KP: Cough-generated aerosols of Pseudomonas aeruginosa and other Gram-negative bacteria from patients with cystic fibrosis. Thorax 2009, 64:926-931.
• [28]Bryant JM, Grogono DM, Greaves D, Foweraker J, Roddick I, Inns T, Reacher M, Haworth CS, Curran MD, Harris SR, Peacock SJ, Parkhill J, Floto RA: Whole-genome sequencing to identify transmission of Mycobacterium abscessus between patients with cystic fibrosis: a retrospective cohort study. Lancet 2013, 381:1551-1560.
• [29]Leung JM, Olivier KN: Nontuberculous mycobacteria: the changing epidemiology and treatment challenges in cystic fibrosis. Curr Opin Pulm Med 2013, 19:662-669.
• [30]De Bel A, De Geyter D, De Schutter I, Mouton C, Wellemans I, Hanssens L, Schelstraete P, Malfroot A, Pierard D: Sampling and decontamination method for culture of nontuberculous mycobacteria in respiratory samples of cystic fibrosis patients. J Clin Microbiol 2013, 51:4204-4206.
• [31]Middleton PG, Chen SC, Meyer W: Fungal infections and treatment in cystic fibrosis. Curr Opin Pulm Med 2013, 19:670-675.
• [32]Borman AM, Palmer MD, Delhaes L, Carrère J, Favennec L, Ranque S, Gangneux JP, Horré R, Bouchara JP: 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.