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

Caballero et al. - Microbiological diagnostic procedures for respiratory cystic fibrosis samples in Spain: towards standard of care practices Open Access Microbiological diagnostic procedures for respiratory cystic fibrosis samples in Spain: towards standard of care practices Juan de Dios Caballero1,2, Rosa del Campo1,2, Marta Tato1,2, Elia Gmez G de la Pedrosa1,2, Marta Cobo1, Carla Lpez-Causap2,3, Enrique Gmez-Mampaso1, Antonio Oliver2,3, Rafael Cantn1,2* and Spanish Network for Cystic Fibrosis Microbiology Laboratories 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. Background Cystic fibrosis (CF) disease is produced by mutations in the CF transmembrane conductance regulator gene (CFTR). Altered CFTR leads to the production of viscous secretions in respiratory airways that cannot be cleared by the mucociliary system and patients get chronically colonized by different microorganisms (bacteria, mycobacteria and fungi) which cause inflammation, progressive lung destruction and, finally, death by respiratory failure [1]. Microbiological diagnosis of CF has evolved far beyond the isolation and identification of classic pathogens such as Pseudomonas aeruginosa and Staphylococcus aureus [2]. Early diagnosis of CF disease and better strategies of patient management have substantially increased * Correspondence: 1Servicio de Microbiologa, Hospital Universitario Ramn y Cajal and Instituto Ramn y Cajal de Investigaciones Sanitarias (IRYCIS), Madrid 28034, Spain 2Red Espaola de Investigacin en Patologa Infecciosa (REIPI), Madrid, Spain Full list of author information is available at the end of the article patients life expectancy with a subsequent impact on CF pathogens epidemiology [2,3]. Continuous follow-up of microbial colonization represents a challenge to clinical laboratories for its complexity and has become a standard of care in patient management. Recommendations for the CF microbiology laboratory management have been included in the European Cystic Fibrosis Society (ECFS) guidelines, as part of the framework of a specialized CF center [4,5]. High antibiotic pressure and the special environment of the CF lung allow the establishment of multi-drug resistant bacteria that require special techniques for their isolation and/or identification, such as Burkholderia cepacia complex (BCC), other non-fermenting Gram negative rods (NFGNR) and nontuberculous-mycobacteria (NTM) [2,3]. In addition, commonly isolated pathogens such as P. aeruginosa or S. aureus can exhibit altered phenotypic characteristics as a result of time-dependent adaptive 2014 Caballero et al.; licensee BioMed Central. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. phenotypic changes to the CF lung, including smallcolony variants (SCVs) and hyper-mutable and mucoid strains variants. Correct diagnosis of these phenotypic variants is difficult and has clinical relevance as there is growing evidence that correlates them with multi-drug resistance, persistency phenomena and poorer lung function [6-9]. Moreover, accurate isolation, identification and susceptibility testing of CF pathogens are critical for ensuring appropriate treatment and implementation of infection control measures, and also for improving our understanding of CF microbiology [10-14]. Laboratories working with CF samples need special procedures and installations as well as specialized microbiologists to provide a correct patient assessment for clinicians [4,10-14]. Adherence to consensus guidelines is also important for laboratories to obtain comparable results and for their adaptation to the best standards of care in CF patients [4,10,14]. The aim of this work was to compile information about the microbiological procedures of the Spanish Hospitals with CF Units in order to assess their compliance with recent consensus guidelines and to implement general recommendations for CF samples processing. Results Hospitals and laboratories Seventeen hospital microbiology laboratories covering all the Spanish territory were requested to participate by answering to our questionnaire (Table 1) and all of them agreed. These centers, which are reference CF Units in their corresponding geographic areas, were selected due to their collaboration with us in another multicenter study focused on CF microbial colonization patterns. Although the precise number of CF patients in our country is unknown since no national patient registry exists, centers included in this survey attend to the majority of the Spanish CF population. The total population attended by these hospitals is approximately 7,150,000 people (mean 420,502). The total number of hospital beds is 15,183 (mean 893) and 1,037 (mean 61) for intensive care units (ICU). The number of CF patients attended by these centers is 2,315 (Table 1), which represents 75% of the CF Spanish population according with the last ECFS report [15]. The number of CF samples processed weekly by each laboratory varies from 10 to 20 in the majority of cases (n = 7, 41%, Figure 1). Only 5 laboratories (29.4%) have a CF section exclusively dedicated for the CF samples processing, although in all cases the final report to clinicians was under the responsibility of a clinical microbiologist. Sixteen laboratories (94%) have written protocols for processing CF samples. More than half are certified by a Quality Management System (n = 10, 58.8%), the most commonly implemented being ISO9001 (n = 8; 80%) followed by other national or regional systems (n = 2 (...truncated)