Seattle Children's Hospital, University of Washington School of Medicine, Department of Pediatrics, Division of Infectious Diseases, Seattle, WA, USA.
Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), CNRS-IRD UMR 6236, Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France.
J Cyst Fibros. 2014 Jan;13(1):1-9. doi: 10.1016/j.jcf.2013.09.004. Epub 2013 Oct 3.
Cystic fibrosis (CF) diagnostic microbiology has evolved from a focus on Staphylococcus aureus as primary pathogen to identification of the contribution of Pseudomonas aeruginosa and other non-fermenting gram negatives; studies of the lung microbiome have added new complexity. This review summarizes state-of-the art culture methods and makes recommendations for addition of non-culture based methods in the diagnostic laboratory. Plating on selective media is recommended, with organism identification by matrix assisted laser desorption-time of flight mass spectroscopy and real-time polymerase chain reaction (PCR) supplanting both biochemical identification and other less accurate and more time-consuming molecular methods. Conventional antibiotic susceptibility testing, possibly at less frequent intervals, remains the standard but more CF-relevant methods may arise in the future. There is a role for direct identification of organisms in clinical samples using quantitative real-time PCR, next generation sequencing, and metagenomic studies for the re-examination of samples that do not yield traditional CF pathogens.
囊性纤维化 (CF) 诊断微生物学已经从关注金黄色葡萄球菌作为主要病原体演变为鉴定铜绿假单胞菌和其他非发酵革兰氏阴性菌的作用；对肺部微生物组的研究增加了新的复杂性。本综述总结了最先进的培养方法，并为诊断实验室中添加非培养方法提出了建议。建议在选择性培养基上进行平板培养，通过基质辅助激光解吸时间飞行质谱和实时聚合酶链反应 (PCR) 进行微生物鉴定，取代生化鉴定和其他准确性较低且耗时较长的分子方法。传统的抗生素药敏试验，可能间隔时间较短，仍然是标准，但未来可能会出现更适合 CF 的方法。使用定量实时 PCR、下一代测序和宏基因组研究直接在临床样本中鉴定微生物，对于未检出传统 CF 病原体的样本进行重新检测，这是有作用的。
