Mahboubi Mona A, Carmody Lisa A, Foster Bridget K, Kalikin Linda M, VanDevanter Donald R, LiPuma John J
Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, Michigan, USA.
Department of Pediatrics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA.
J Clin Microbiol. 2016 Mar;54(3):613-9. doi: 10.1128/JCM.02299-15. Epub 2015 Dec 23.
Cystic fibrosis (CF) is characterized by chronic infection and inflammation of the airways. In vitro culture of select bacterial species from respiratory specimens has been used to guide antimicrobial therapy in CF for the past few decades. More recently, DNA sequence-based, culture-independent approaches have been used to assess CF airway microbiology, although the role that these methods will (or should) have in routine microbiologic analysis of CF respiratory specimens is unclear. We performed DNA sequence analyses to detect bacterial species in 945 CF sputum samples that had been previously analyzed by selective CF culture. We determined the concordance of results based on culture and sequence analysis, highlighting the comparison of the results for the most prevalent genera. Although overall prevalence rates were comparable between the two methods, results varied by genus. While sequence analysis was more likely to detect Achromobacter, Stenotrophomonas, and Burkholderia, it was less likely to detect Staphylococcus. Streptococcus spp. were rarely reported in culture results but were the most frequently detected species by sequence analysis. A variety of obligate and facultative anaerobic species, not reported by culture, was also detected with high prevalence by sequence analysis. Sequence analysis indicated that in a considerable proportion of samples, taxa not reported by selective culture constituted a relatively high proportion of the total bacterial load, suggesting that routine CF culture may underrepresent significant segments of the bacterial communities inhabiting CF airways.
囊性纤维化（CF）的特征是气道的慢性感染和炎症。在过去几十年中，从呼吸道标本中体外培养特定细菌物种已被用于指导CF的抗菌治疗。最近，基于DNA序列的、不依赖培养的方法已被用于评估CF气道微生物群，尽管这些方法在CF呼吸道标本常规微生物分析中所起的作用尚不清楚。我们对945份先前通过选择性CF培养分析过的CF痰液样本进行了DNA序列分析，以检测细菌物种。我们根据培养和序列分析确定了结果的一致性，重点比较了最常见属的结果。虽然两种方法的总体患病率相当，但结果因属而异。序列分析更有可能检测到无色杆菌属、嗜麦芽窄食单胞菌属和伯克霍尔德菌属，而检测到葡萄球菌属的可能性较小。链球菌属在培养结果中很少报告，但却是序列分析中最常检测到的物种。通过序列分析还高患病率地检测到了多种未在培养中报告的专性和兼性厌氧物种。序列分析表明，在相当一部分样本中，选择性培养未报告的分类群在总细菌负荷中占相对较高的比例，这表明常规CF培养可能未能充分代表居住在CF气道中的细菌群落的重要部分。
