Bacteria and fungi in acute cholecystitis. A prospective study comparing next generation sequencing to culture

• Published in: The Journal of infection Vol. 80; no. 1; pp. 16 - 23
• Main Authors: Dyrhovden, Ruben, Øvrebø, Kjell Kåre, Nordahl, Magnus Vie, Nygaard, Randi M., Ulvestad, Elling, Kommedal, Øyvind
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 01.01.2020
• Subjects: 16S; Acute cholecystitis; Bacteria - genetics; Bile; Cholecystitis, Acute - surgery; Fungi - genetics; High-Throughput Nucleotide Sequencing; Humans; ITS; Massive parallel sequencing; Next generation sequencing; Prospective Studies; RNA, Ribosomal, 16S - genetics; rpoB; Massive parallel sequencing; rpoB; Acute cholecystitis; ITS; Next generation sequencing; 16S; Bile
• ISSN: 0163-4453; 1532-2742
• DOI: 10.1016/j.jinf.2019.09.015

•Culture leaves more than 60% of the microbes undetected in acute cholecystitis.•Anaerobic bacteria, Enterobacteriaceae and enterococci among those often missed.•Culture independent approaches are needed in routine diagnostics of cholecystitis.•Studies on the microbiology of cholecystitis must include metagenomic sequencing.•Treatment recommendations must take into account limitations of bacterial culture. 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. 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. 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. Culture techniques display decreased sensitivity for the microbial diagnostics of acute cholecystitis leaving possible pathogens undetected.