Cultivation and Genomic Characterization of the Bile Bacterial Species From Cholecystitis Patients

The microbes in human bile are closely related to gallbladder health and other potential disorders. Although the bile microbial community has been investigated by recent studies using amplicon or metagenomic sequencing technologies, the genomic information of the microbial species resident in bile is rarely reported. Herein, we isolated 138 bacterial colonies from the fresh bile specimens of four cholecystitis patients using a culturome approach and genomically characterized 35 non-redundant strains using whole-genome shotgun sequencing. The bile bacterial isolates spanned 3 classes, 6 orders, 10 families, and 14 genera, of which the members of Enterococcus, Escherichia–Shigella, Lysinibacillus, and Enterobacter frequently appeared. Genomic analysis identified three species, including Providencia sp. D135, Psychrobacter sp. D093, and Vibrio sp. D074, which are not represented in existing reference genome databases. Based on the genome data, the functional capacity between bile and gut isolates was compared. The bile strains encoded 5,488 KEGG orthologs, of which 4.9% were specific to the gut strains, including the enzymes involved in biofilm formation, two-component systems, and quorum-sensing pathways. A total of 472 antibiotic resistance genes (ARGs) were identified from the bile genomes including multidrug resistance proteins (42.6%), fluoroquinolone resistance proteins (12.3%), aminoglycoside resistance proteins (9.1%), and β-lactamase (7.2%). Moreover, in vitro experiments showed that some bile bacteria have the capabilities for bile salt deconjugation or biotransformation (of primary bile acids into secondary bile acids). Although the physiological or pathological significance of these bacteria needs further exploration, our works expanded knowledge about the genome, diversity, and function of human bile bacteria.

Biliary Microbiota in Choledocholithiasis and Correlation With Duodenal Microbiota

BackgroundThe pathogenesis of choledocholithiasis is closely related to the role of bacteria. However, little is known about the predictive role of bile bacteria in clinical conditions of patients and the compositional and functional characteristics of biliary microbiota in choledocholithiasis.MethodsTo investigate the predictive value of biliary bacteria, clinical data of 488 patients with choledocholithiasis were collected. The predictive value of common bile bacteria to patients’ clinical conditions was analyzed by logistic regression. Samples of bile and corresponding duodenal juice from 10 selected patients with choledocholithiasis were obtained, and the composition and function of microbial communities were analyzed based on 16S rRNA sequencing and Tax4Fun.ResultsThe clinical conditions of patients with choledocholithiasis, such as recurrence, the severity of acute cholangitis, and duration of hospital stay were closely related to different species of bile bacteria as well as antimicrobial-resistant bacteria. Employing 16S rRNA sequencing, the dominant phyla of biliary and duodenal microbiota were Proteobacteria and Firmicutes. The top three core microbiota at the genus level were Escherichia–Shigella, Fusobacterium, and Enterococcus. Escherichia coli accounted for the most abundant annotated species in both. Differences in composition between biliary and duodenal microbiota were not significant according to the alpha and beta diversities. Differential abundant features were not found in biliary microbiota indicated by A linear discriminant analysis effective size algorithm. The major pathways identified in biliary and duodenal microbiota were related to membrane transport, translation, replication and repair, carbohydrate and amino acid metabolism. However, no significant difference in those major pathways, as well as antimicrobial-resistance patterns, was observed between biliary and duodenal microbiota.ConclusionOur study first demonstrates the predictive contribution of biliary bacteria to the clinical conditions of patients with choledocholithiasis, and then it offers new insights into the compositional and functional features of biliary and duodenal microbiota. Similarities between biliary and duodenal microbiota support the theory of bacterial duodenal–biliary reflux in patients with choledocholithiasis. Meanwhile, when it is impracticable to obtain a bile sample, duodenal juice may be used as an alternative for bacterial culture and susceptibility tests.

Optimizing perioperative antimicrobial therapy for acute cholecystitis using bile Gram stain results

Objective: We aimed to evaluate whether Gram stain results from smear preparations of bile are useful in determining the optimal perioperative antimicrobial agents. Summary of Background Data: Surgical site infections (SSIs) are common complications in emergency cholecystectomy. Methods: A total of 185 patients who underwent emergency cholecystectomy for acute cholecystitis were enrolled (Bell Land General Hospital Ethic Board approval number 2017-0003). Bile was collected from 121 patients. The Gram stain results from bile smear and culture preparations of were evaluated. Furthermore, the antimicrobial resistance was evaluated according to bile Gram stain results. Results: Bile bacteria were detected in 82 patients (67.8%) with the culture preparation and in 72 patients (59.5%) with the smear preparation. The average rate of correspondence in the Gram stain results between smear and culture preparations was 86.3% among patients with bile bacteria in the smear preparation. Cefepime and meropenem had a low antimicrobial resistance rate for all Gram stain results (< 10%). However, the resistance rate of other antimicrobial agents differed according to the Gram stain results. Conclusions: The Gram stain results from the smear preparation appear to be useful in choosing optimal perioperative antimicrobial agents.

Accelerated in vitro model for occlusion of biliary stents: investigating the role played by dietary fibre

BackgroundTo develop a new accelerated in vitro model that has implications for investigating the mechanism of biliary stent occlusion and help in the development of new materials that can alleviate this problem.MethodsWe employ a combination of reconstituted animal bile, bacteria and cellulose fibres optimised to reproducibly generate accelerated occlusion of stents, and produce occlusions that closely mimic those found in clinical studies.ResultsOur model affords repeatable, highly accelerated occlusion (within 2–3 days, compared with between about a week to 2 months in previous models). Our results highlight the role of dietary fibre in blockage of stents and demonstrate their importance in the onset of occlusion.ConclusionsThis accelerated model may have implications for developing biliary stents with enhanced patency.