OBJECTIVES Guidelines for antibiotic treatment of acute cholecystitis are based on studies using culture techniques for microbial identification. Microbial culture has well described limitations and more comprehensive data on the microbial spectrum may support adjustments of these recommendations. We used next generation sequencing to conduct a thorough microbiological characterization of bile-samples from patients with moderate and severe acute cholecystitis. METHODS We prospectively included patients with moderate and severe acute cholecystitis, undergoing percutaneous or perioperative drainage of the gall bladder. Bile samples were analyzed using both culture and deep sequencing of bacterial 16S rRNA and rpoB genes and the fungal ITS2-segment. Clinical details were evaluated by medical record review. RESULTS Thirty-six patients with moderate and severe acute cholecystitis were included. Bile from 31 (86%) of these contained bacteria (29) and/or fungi (5) as determined by sequencing. Culture identified only 40 (38%) of the 106 microbes identified by sequencing. In none of the 15 polymicrobial samples did culture detect all present microbes. Frequently identified bacteria often missed by culture included oral streptococci, anaerobic bacteria, enterococci and Enterobacteriaceae other than Klebsiella spp. and Escherichia coli. CONCLUSIONS Culture techniques display decreased sensitivity for the microbial diagnostics of acute cholecystitis leaving possible pathogens undetected.

中文翻译：

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急性胆囊炎中的细菌和真菌。将下一代测序与培养进行比较的前瞻性研究。

目的急性胆囊炎的抗生素治疗指南基于使用培养技术进行微生物鉴定的研究。微生物培养已充分描述了局限性，有关微生物谱的更全面的数据可能支持对这些建议的调整。我们使用下一代测序对中度和重度急性胆囊炎患者的胆汁样本进行了全面的微生物学表征。方法我们的研究对象包括中度和重度急性胆囊炎，经皮或围手术期胆囊引流的患者。使用细菌16S rRNA和rpoB基因以及真菌ITS2段的培养和深度测序对胆汁样品进行分析。通过病历审查评估临床细节。结果纳入了36例中重度急性胆囊炎患者。通过测序确定，其中31种（86％）的胆汁中含有细菌（29）和/或真菌（5）。在测序鉴定的106种微生物中，培养仅鉴定出40种（38％）。在15种微生物样品中，没有一种能检测到所有存在的微生物。经常被培养物遗漏的常见细菌包括口腔链球菌，厌氧菌，肠球菌和肠杆菌科（除克雷伯菌属以外）。和大肠杆菌。结论培养技术对急性胆囊炎的微生物诊断显示出降低的敏感性，从而未发现可能的病原体。在测序鉴定的106种微生物中，培养仅鉴定出40种（38％）。在15种微生物样品中，没有一种能检测到所有存在的微生物。经常被培养物遗漏的常见细菌包括口腔链球菌，厌氧菌，肠球菌和肠杆菌科（除克雷伯菌属以外）。和大肠杆菌。结论培养技术对急性胆囊炎的微生物诊断显示出降低的敏感性，从而未发现可能的病原体。在测序鉴定的106种微生物中，培养仅鉴定出40种（38％）。在15种微生物样品中，没有一种能检测到所有存在的微生物。经常被培养物遗漏的常见细菌包括口腔链球菌，厌氧菌，肠球菌和肠杆菌科（除克雷伯菌属以外）。和大肠杆菌。结论培养技术对急性胆囊炎的微生物诊断显示出降低的敏感性，从而未发现可能的病原体。