Association of diverse bacterial communities in human bile samples with biliary tract disorders: a survey using culture and polymerase chain reaction-denaturing gradient gel electrophoresis methods

Abstract

Bacterial infection is considered a predisposing factor for disorders of the biliary tract. This study aimed to determine the diversity of bacterial communities in bile samples and their involvement in the occurrence of biliary tract diseases. A total of 102 bile samples were collected during endoscopic retrograde cholangiopancreatography (ERCP). Characterization of bacteria was done using culture and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) methods. Antimicrobial susceptibility of the isolates was determined based on the Clinical and Laboratory Standards Institute (CLSI) guidelines and identity of the nucleotide sequences of differentiated bands from the DGGE gels was determined based on GenBank data. In total, 41.2 % (42/102) of the patients showed bacterial infection in their bile samples. This infection was detected in 21 % (4/19), 45.4 % (5/11), 53.5 % (15/28), and 54.5 % (24/44) of patients with common bile duct stone, microlithiasis, malignancy, and gallbladder stone, respectively. Escherichia coli showed a significant association with gallstones. Polymicrobial infection was detected in 48 % of the patients. While results of the culture method established coexistence of biofilm-forming bacteria (Pseudomonas aeruginosa, E. coli, Klebsiella pneumoniae, Enterococcus spp., and Acinetobacter spp.) in different combinations, the presence of Capnocytophaga spp., Lactococcus spp., Bacillus spp., Staphylococcus haemolyticus, Enterobacter or Citrobacter spp., Morganella spp., Salmonella spp., and Helicobacter pylori was also characterized in these samples by the PCR-DGGE method. Multidrug resistance phenotypes (87.5 %) and resistance to third- and fourth-generation cephalosporins and quinolones were common in these strains, which could evolve through their selection by bile components. Ability for biofilm formation seems to be a need for polymicrobial infection in this organ.

Phylogeny, Resistome, and Virulome of Escherichia coli Causing Biliary Tract Infections

“…In Spain, the analysis of a total of 1429 E. coli isolates causing intra-abdominal infections in a surveillance study called SMART (Study for Monitoring Antimicrobial Resistance Trends) between 2016 and 2017 revealed that ciprofloxacin and amoxicillin-clavulanic acid presented resistance rates of 27.6% and 18.5%, respectively [36]. However, in Iran, the MDR pattern was detected in 95.5% of the E. coli recovered from bile, reporting different antimicrobial resistance rates in comparison with our results, mainly in the case of third generation cephalosporins (82% vs. 0%), carbapenems (≈70% vs. 0%), gentamicin (36.4% vs. 6.6%), and ciprofloxacin (45.5% vs. 13.3%), respectively [37].…”

Co-infections with liver fluke and Helicobacter species: A paradigm change in pathogenesis of opisthorchiasis and cholangiocarcinoma?

“…H. pylori and other species of Helicobacter can survive at the alkaline pH of the bile as they can be detected in bile sampled from biliary diseases including CCA [36, 37]. Most of the H. pylori and other bacteria in the bile are coccoid form that may reflect responses to bile acids [38].…”

“…Most of the H. pylori and other bacteria in the bile are coccoid form that may reflect responses to bile acids [38]. In addition, biofilm formation by the bacteria in the bile seems facilitate survival in the environment within the human biliary tract [36]. Interestingly, an increased abundance of H. pylori virulence genes, i.e.…”

Effect of Periampullary Diverticulum on Biliary Flora and the Formation of Common Bile Duct Stone

“…Bacterial infection and abnormal bilirubin metabolism will cause calcium bilirubin to deposit and accumulate into nucleation in the biliary tract, resulting in the formation of stones, especially the formation of pigment stones is more thought to be caused by a bacterial infection. Through the study of people without biliary diseases, it has been proved that the biliary tract is sterile under normal conditions [24], while bacteria grow in the bile culture of almost all patients with choledocholithiasis. And all bile samples in this study were also detected by high-throughput sequencing.…”