Comprehensive Diagnosis of Bacterial Infection Associated with Acute Cholecystitis Using Metagenomic Approach

Abstract

Acute cholecystitis (AC), which is strongly associated with retrograde bacterial infection, is an inflammatory disease that can be fatal if inappropriately treated. Currently, bacterial culture testing, which is basically recommended to detect the etiological agent, is a time-consuming (4–6 days), non-comprehensive approach. To rapidly detect a potential pathogen and predict its antimicrobial susceptibility, we undertook a metagenomic approach to characterize the bacterial infection associated with AC. Six patients (P1–P6) who underwent cholecystectomy for AC were enrolled in this study. Metagenome analysis demonstrated possible single or multiple bacterial infections in four patients (P1, P2, P3, and P4) with 24-h experimental procedures; in addition, the CTX-M extended-spectrum ß-lactamase (ESBL) gene was identified in two bile samples (P1 and P4). Further whole genome sequencing of Escherichia coli isolates suggested that CTX-M-27-producing ST131 and CTX-M-14-producing novel-ST were identified in P1 and P4, respectively. Metagenome analysis of feces and saliva also suggested some imbalance in the microbiota for more comprehensive assessment of patients with AC. In conclusion, metagenome analysis was useful for rapid bacterial diagnostics, including assessing potential antimicrobial susceptibility, in patients with AC.

Understanding the Promises and Hurdles of Metagenomic Next-Generation Sequencing as a Diagnostic Tool for Infectious Diseases

“…Currently, the turnaround time for mNGS has been reported to be anywhere from approximately 6 hours to 7 days (average of 48 hours) from specimen receipt depending on the sequencing technology, methods, and bioinformatics programs exploited [9,22,25,41,42]. In general, mNGS methodologies are labor intensive and require several steps from nucleic acid extraction, library preparation, and sequencing to data analysis.…”

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

“…To the best of our knowledge, this is the first study that uses NGS for microbial characterization of bile samples from patients with acute cholecystitis, with the exception of a small study on six patients. 21 This is also the first study to describe the bacteriology of severe acute cholecystitis according to the TG18/TG13 severity grading. 5 , 8 Although bactobilia is considered a negative prognostic factor in acute cholecystitis, there is, with the exception of the aforementioned Israeli study, 7 little evidence on the clinical importance of the individual bacterial species.…”

Metagenome Analysis as a Tool to Study Bacterial Infection Associated with Acute Surgical Abdomen

“…This method is based on the amplification and analysis of bacterial 16S rRNA genes with massively parallel processing [ 11 ]. Millions of DNA/RNA molecules in a specimen are sequenced in parallel and pathogens can be identified by matching the sequences to a reference database without bacterial cultivation [ 12 , 13 ]. This technology has allowed researchers to identify previously uncharacterized bacteria or viruses that cause infectious diseases [ 10 , 14 , 15 ] and also to investigate organisms previously thought to be inaccessible, including obligate anaerobes and other microorganisms that cannot survive outside their hosts without symbionts [ 11 ].…”