ABSTRACT
PURPOSE: Although the biliary tract is a common source of invasive infections, the epidemiology of cholangitis- and cholecystitis-associated bloodstream infection (BSI) is not well defined. The objective of this study was to determine the incidence, clinical determinants, microbiology of biliary tract-associated BSI, and predicted adequacy of common empiric therapy regimens. METHODS: All biliary tract-associated BSI in Queensland during 2000-2019 were identified using state-wide data sources. Predicted adequacy of empiric antimicrobial therapy was determined according to microbiological susceptibility data. RESULTS: There were 3,698 episodes of biliary tract-associated BSI occurred in 3,433 patients of which 2,147 (58.1%) episodes were due to cholangitis and 1,551 (41.9%) cholecystitis, for age- and sex-standardized incidence rates of 2.7, and 2.0 per 100,000 population, respectively. An increasing incidence of biliary tract-associated BSI was observed over the study that was attributable to an increase in cholangitis cases. There was a significant increased risk for biliary tract-associated BSI observed with advancing age and male sex. Patients with cholangitis were older, more likely to have healthcare associated infection, and have more comorbidities most notably liver disease and malignancies as compared to patients with cholecystitis. The distribution of infecting pathogens was significantly different with polymicrobial aetiologies more commonly observed with cholangitis (18.4% vs. 10.5%; p < 0.001). The combination of ampicillin/gentamicin/metronidazole was predicted to have the overall highest adequacy (96.1%), whereas amoxicillin/clavulanate had the lowest (77.0%). Amoxicillin/clavulanate (75.2% vs. 79.4%, p:0.03) and ceftriaxone/metronidazole (83.4% vs. 89.6%; p < 0.001) showed significantly inferior predicted adequacy for cholangitis as compared to cholecystitis. CONCLUSIONS: Bloodstream infections related to cholecystitis and cholangitis exhibit different epidemiology, microbiology, and requirements for empiric therapy.
Subject(s)
Anti-Bacterial Agents , Bacteremia , Cholangitis , Humans , Male , Female , Aged , Middle Aged , Cholangitis/epidemiology , Cholangitis/microbiology , Cholangitis/drug therapy , Bacteremia/epidemiology , Bacteremia/drug therapy , Bacteremia/microbiology , Anti-Bacterial Agents/therapeutic use , Incidence , Adult , Aged, 80 and over , Cholecystitis/epidemiology , Cholecystitis/microbiology , Queensland/epidemiology , Young Adult , Adolescent , Risk Factors , Biliary Tract/microbiologyABSTRACT
Introduction: The incidence of biliary system diseases has been continuously increasing in the past decade. Biliary system diseases bring a heavy burden to humanity and society. However, the specific etiology and pathogenesis are still unknown. The biliary system, as a bridge between the liver and intestine, plays an indispensable role in maintaining the physiological metabolism of the body. Therefore, prevention and treatment of biliary diseases are crucial. It is worth noting that the microorganisms participate in the lipid metabolism of the bile duct, especially the largest proportion of intestinal bacteria. Methods: We systematically reviewed the intestinal microbiota in patients with gallstones (GS), non-calculous biliary inflammatory, and biliary tract cancer (BTC). And searched Pubmed, Embase and Web of science for research studies published up to November 2023. Results: We found that the abundance of Faecalibacterium genus is decreased in GS, primary sclerosing cholangitis (PSC), primary biliary cholangitis (PBC) and BTC. Veillonella, Lactobacillus, Streptococcus and Enterococcus genus were significantly increased in PSC, PBC and BTC. Interestingly, we found that the relative abundance of Clostridium was generally reduced in GS, PBC and BTC. However, Clostridium was generally increased in PSC. Discussion: The existing research mostly focuses on exploring the mechanisms of bacteria targeting a single disease. Lacking comparison of multiple diseases and changes in bacteria during the disease process. We hope to provide biomarkers forearly diagnosis of biliary system diseases and provide new directions for the mechanism of intestinal microbiota in biliary diseases.
Subject(s)
Biliary Tract Diseases , Gastrointestinal Microbiome , Humans , Biliary Tract Diseases/microbiology , Bacteria/classification , Bacteria/isolation & purification , Bacteria/metabolism , Gallstones/microbiology , Faecalibacterium , Lactobacillus , Biliary Tract/microbiology , Biliary Tract Neoplasms/microbiology , Clostridium/isolation & purification , Cholangitis, Sclerosing/microbiology , Enterococcus , Streptococcus/isolation & purificationABSTRACT
BACKGROUND: Infections caused by multidrug-resistant Pseudomonas aeruginosa (MDRPA) have been on the rise worldwide, and delayed active antimicrobial therapy is associated with high mortality. However, few studies have evaluated increases in P. aeruginosa infections with antimicrobial resistance and risk factors for such antimicrobial resistance in Korea. Here, we analyzed changes in antimicrobial susceptibility associated with P. aeruginosa bacteremia and identified risk factors of antimicrobial resistance. METHODS: The medical records of patients with P. aeruginosa bacteremia who were admitted to a tertiary hospital between January 2009 and October 2020 were retrospectively reviewed. Antibiotic resistance rates were compared among the time periods of 2009-2012, 2013-2016, and 2017-2020 and between the intensive care unit (ICU) and non-ICU setting. Empirical antimicrobial therapy was considered concordant, if the organism was susceptible to antibiotics in vitro, and discordant, if resistant. RESULTS: During the study period, 295 patients with P. aeruginosa bacteremia were identified. The hepatobiliary tract (26.8%) was the most common primary site of infection. The rates of carbapenem-resistant P. aeruginosa (CRPA), MDRPA, and extensively drug-resistant P. aeruginosa (XDRPA) were 24.7%, 35.9%, and 15.9%, respectively. XDRPA showed an increasing trend, and CRPA, MDRPA, and XDRPA were also gradually increasing in non-ICU setting. Previous exposure to fluoroquinolones and glycopeptides and urinary tract infection were independent risk factors associated with CRPA, MDRPA, and XDRPA. Previous exposure to carbapenems was an independent risk factor of CRPA. CRPA, MDRPA, and XDRPA were associated with discordant empirical antimicrobial therapy. CONCLUSION: The identification of risk factors for antimicrobial resistance and analysis of antimicrobial susceptibility might be important for concordant empirical antimicrobial therapy in patients with P. aeruginosa bacteremia.
Subject(s)
Anti-Bacterial Agents/pharmacology , Bacteremia/pathology , Drug Resistance, Multiple, Bacterial , Pseudomonas aeruginosa/drug effects , Aged , Anti-Bacterial Agents/therapeutic use , Bacteremia/drug therapy , Bacteremia/microbiology , Bacteremia/mortality , Biliary Tract/microbiology , Drug Resistance, Multiple, Bacterial/drug effects , Female , Fluoroquinolones/pharmacology , Fluoroquinolones/therapeutic use , Glycopeptides/pharmacology , Glycopeptides/therapeutic use , Hospital Mortality , Humans , Intensive Care Units , Male , Microbial Sensitivity Tests , Middle Aged , Pseudomonas aeruginosa/isolation & purification , Republic of Korea , Retrospective Studies , Risk Factors , Survival Rate , Urinary Tract Infections/diagnosis , Urinary Tract Infections/drug therapy , Urinary Tract Infections/microbiologyABSTRACT
INTRODUCTION: Escherichia coli is the most commonly identified bacteraemia, and causes a broad spectrum of diseases. The range of clinical conditions associated with E. coli bacteraemia mean that antimicrobial therapy is highly variable. This study aimed to determine the workload, efficiency and potential impact of an antimicrobial stewardship (AMS) bundle approach to E. coli bacteraemia. METHODS: An observational cohort study of patients with E. coli bacteraemia was performed, and a review of each case's entire medical record was undertaken. A number of AMS interventions were modelled on this cohort to assess their impact on overall days of antimicrobial therapy and time to optimized antimicrobial therapy. RESULTS: In total, 566 episodes of E. coli bacteraemia were identified. A number of AMS interventions were modelled to assess their impact. The strict implementation of guideline-based therapy was found to increase the number of patients receiving ineffective empirical therapy to 38/266 (14.3%) compared with 27/266 (10.2%) patients when w hen non-guideline-adherent therapy was allowed. A scheduled review by an AMS team on day 3 of empirical therapy could lead to a narrower-spectrum intravenous antibiotic in 237/515 (46%) cases, and 386 cases (68.2% of cohort) could have their duration of therapy reduced by a median of 7 days. CONCLUSION: This study provides detailed description of a large cohort of patients with E. coli bacteraemia. There remains significant variability in empirical treatment, choice of step-down therapy and antimicrobial duration. A significant opportunity exists for AMS programmes to impact the management of E. coli bacteraemia through a bundled approach.
Subject(s)
Anti-Bacterial Agents/therapeutic use , Antimicrobial Stewardship/methods , Bacteremia/drug therapy , Escherichia coli Infections/drug therapy , Urinary Tract Infections/drug therapy , Aged , Aged, 80 and over , Anti-Bacterial Agents/administration & dosage , Bacteremia/microbiology , Biliary Tract/microbiology , Escherichia coli/drug effects , Escherichia coli Infections/mortality , Female , Humans , Male , Middle Aged , Retrospective Studies , Urinary Tract Infections/microbiologyABSTRACT
Objective: To investigate the pathogens' distribution and antimicrobial resistance in the bile of acute biliary tract infection patients. Methods: The data of bile bacterial culture and drug sensitivity test of 223 acute biliary tract infection patients who underwent gallbladder puncture or endoscopic retrograde cholangiopancreatography drainage from July 2009 to July 2019 were analyzed retrospectively at Department of General Surgery,Xinhua Hospital,Affiliated to Shanghai Jiao Tong University School of Medicine.There were 141 males and 82 females with age of 67.3 years(range:28 to 93 years).Three to five milliliter of bile was extracted from each patient and sent to the laboratory for bacterial culture,identification and drug sensitivity test.The patients were divided into two groups according to the visiting time: the former group (n=124) was admitted from July 2009 to July 2014,and the latter group(n=99) was admitted from August 2014 to July 2019.The distribution of pathogenic bacteria and the changing trend of drug resistance rate of common bacteria in the two groups were compared.The results of drug sensitivity test were analyzed by WHONET software provided by WHO bacterial surveillance network.The drug resistance rates in different time periods were compared by χ2 test. Results: In this study,there were 147 cases of acute cholangitis and 76 cases of acute cholecystitis.A total of 376 strains of pathogenic bacteria were cultured.Among them,98 strains(26.1%) were gram-positive bacteria,269 strains(71.5%) were gram-negative bacteria and 9 strains(2.4%) were fungi.The top three gram-positive bacteria were Enterococcus faecium (49.0%,48/98),Enterococcus faecalis(20.4%,20/98),and Enterococcus luteus(7.1%,7/98).The top 5 gram-negative bacteria were Escherichia coli(33.5%,90/269),Klebsiella pneumoniae(13.8%,37/269),Pseudomonas aeruginosa(13.0%,35/269),Acinetobacter baumannii (12.6%,34/269),and Enterobacter cloacae(4.8%,13/269).From 2009 to 2019,there was no significant change in the proportion of gram-positive bacteria (former group vs. latter group: 25.3% vs. 28.2%) and gram-negative bacteria(former group vs.latter group: 74.7% vs. 71.8%) in the bile of patients with acute biliary tract infection.Gram-positive bacteria were mainly Enterococci(85.7%,84/98) and gram-negative bacteria were Escherichia coli(33.5%,90/269).Acinetobacter baumannii accounted for 7.8%(11/142) of gram-negative bacteria in the former group and 18.1%(23/127) in the latter group,an increase of 10.3% over previous five years.Pseudomonas aeruginosa had a downward trend,16.9% in the former group(24/142) and 8.7% in the latter group (11/127),the proportion decreased by 8.2%,and the other changes were not significant.The drug resistance rates of common gram-positive bacteria were relatively stable,and the drug resistance rates of Enterococcus faecium to many antibiotics were higher than those of Enterococcus faecalis.The resistance rates of gram-negative bacteria to most antibiotics showed an upward trend,among which Klebsiella pneumoniae showed an upward trend to most of antibiotics(former group: 0/15ï¼4/13, latter group: 55.0%ï¼70.0%; χ2=3.996ï¼16.942, P=0.000ï¼0.046).The drug resistance rates of Acinetobacter baumannii was generally higher,but there were no significant changes in the drug resistance rates of Acinetobacter baumannii between the two groups.The drug resistance rates of Pseudomonas aeruginosa to most antibiotics increased,and the overall drug resistance rates of Escherichia coli were stable and showed a slight upward trend. Conclusions: The main pathogens in bile of patients with acute biliary tract infection are gram-negative bacteria.The constituent ratio of various gram-negative bacteria had no significant change from 2009 to 2019,but the drug resistance rates shows an upward trend.Among the gram-negative bacteria, Escherichia coli is the most important pathogen,and the proportion has no significant change.The proportion of Acinetobacter baumannii in the former group was significantly higher than that in the former group.And the proportion of Pseudomonas aeruginosa has a decreased trend.
Subject(s)
Bile/microbiology , Biliary Tract , Cholangitis , Cholecystitis, Acute/microbiology , Acute Disease , Adult , Aged , Aged, 80 and over , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/therapeutic use , Bile/drug effects , Biliary Tract/microbiology , China , Cholangitis/drug therapy , Cholangitis/microbiology , Cholangitis/surgery , Cholecystitis, Acute/drug therapy , Cholecystitis, Acute/surgery , Drug Resistance, Bacterial/drug effects , Drug Resistance, Bacterial/physiology , Female , Gram-Negative Bacteria/drug effects , Gram-Negative Bacteria/isolation & purification , Humans , Male , Microbial Sensitivity Tests , Middle Aged , Paracentesis , Retrospective StudiesABSTRACT
BACKGROUND: The use of neoadjuvant chemotherapy (NAC) for pancreatic ductal adenocarcinoma (PDAC) has increased in recent years. Limited data exists on the impact of NAC on biliary microbiome. METHODS: Patients who underwent pancreaticoduodenectomy (PD) for PDAC between 2014 and 2017 were reviewed. Patients were stratified into two groups based on their NAC status for comparison. RESULTS: Of 168 patients included, 63 (37.5%) received NAC. Patients who received NAC exhibited significantly increased growth of Gram-negative anaerobic bacteria (p = 0.043). Patients in the non-NAC group were more likely to grow pathogens resistant to ampicillin-sulbactam (47% vs 21%, p = 0.007), cefazolin (49% vs 28%, p = 0.040), cefoxitin (42% vs 11%, p = 0.009) and cefuroxime (26% vs 4%, p = 0.019). NAC status did not impact infectious postoperative outcomes, including SSIs. CONCLUSION: Patients who did not receive NAC were more likely to grow pathogens resistant to cephalosporins. Perioperative antibiotic prophylaxis should be tailored to cover Gram-negative organisms and enterococci.
Subject(s)
Biliary Tract/microbiology , Carcinoma, Pancreatic Ductal/therapy , Neoadjuvant Therapy/methods , Pancreatic Neoplasms/therapy , Surgical Wound Infection/epidemiology , Aged , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/therapeutic use , Antibiotic Prophylaxis , Cephalosporins/pharmacology , Cephalosporins/therapeutic use , Drainage/adverse effects , Drug Resistance, Microbial , Enterococcus/drug effects , Enterococcus/isolation & purification , Female , Gram-Negative Bacteria/drug effects , Gram-Negative Bacteria/isolation & purification , Humans , Male , Microbiota/drug effects , Middle Aged , Pancreaticoduodenectomy , Perioperative Care/methods , Retrospective Studies , Surgical Wound Infection/diagnosis , Surgical Wound Infection/microbiology , Surgical Wound Infection/prevention & controlABSTRACT
BACKGROUND: Postoperative infectious complications after a pancreaticoduodenectomy remain a significant cause of morbidity. Studies have demonstrated that a preoperative biliary stent increases the risk of postoperative infectious complications. Few studies have investigated the specific preoperative biliary stent bacterial sensitivities to preoperative antibiotics and the effect on infectious complications. The goal of this study was to investigate if the presence of a preoperative biliary stent increases the risk of postoperative infectious complications in patients undergoing a pancreaticoduodenectomy. Additionally, we aimed to investigate biliary stent culture sensitivities to preoperative antibiotics and determine if those sensitivities impacted postoperative infectious complications after a pancreaticoduodenectomy. METHODS: A retrospective chart review of patients who had undergone a pancreaticoduodenectomy at a single institution tertiary care center from 2007 to 2018 was performed. Perioperative variables including microbiology cultures from biliary stents were collected and analyzed. RESULTS: A total of 244 patients underwent a pancreaticoduodenectomy. A preoperative biliary stent was present in 45 (18%) patients. Infectious complications occurred in 25% of those patients with a preoperative biliary stent, and 19% of those without (P = .37). Of those patients with a stent that was cultured intraoperatively, 92% grew bacteria and 61% of those were resistant to the preoperative antibiotics administered. Of the patients with a preoperative biliary stent and bacteria resistant to the preoperative antibiotics, 17% developed a postoperative infectious complication, compared with 20% if the bacteria cultured was susceptible to the preoperative antibiotics (P = .64). CONCLUSION: Infectious complications after pancreaticoduodenectomy are a significant cause of morbidity. Stent bacterial sensitivities to preoperative antibiotics did not reduce the postoperative infectious complications in the preoperative biliary stent group suggesting a multifactorial cause of infections.
Subject(s)
Biliary Tract Surgical Procedures/adverse effects , Pancreatic Neoplasms/surgery , Pancreaticoduodenectomy/adverse effects , Preoperative Care/statistics & numerical data , Surgical Wound Infection/epidemiology , Aged , Anti-Bacterial Agents/therapeutic use , Antibiotic Prophylaxis/methods , Antibiotic Prophylaxis/statistics & numerical data , Biliary Tract/microbiology , Biliary Tract Surgical Procedures/instrumentation , Biliary Tract Surgical Procedures/statistics & numerical data , Drainage/instrumentation , Female , Humans , Intraoperative Care/statistics & numerical data , Male , Microbial Sensitivity Tests/statistics & numerical data , Middle Aged , Preoperative Care/adverse effects , Preoperative Care/instrumentation , Preoperative Care/methods , Retrospective Studies , Stents/microbiology , Surgical Wound Infection/etiology , Surgical Wound Infection/prevention & control , Treatment OutcomeABSTRACT
Staphylococcus aureus is a virulent gram-positive organism, which rarely involves the biliary tract. This study aimed to analyze the clinical characteristics and outcomes of S. aureus bacteremia (SAB) originating from the biliary tract by comparing them with those of catheter-related SAB and biliary Klebsiella pneumoniae bacteremia. A matched case-control study within a prospective observational cohort of patients with SAB was conducted. Biliary SAB was defined as the isolation of S. aureus from blood cultures with symptoms and signs of biliary infection. Biliary SAB patients were matched (1:3) with the control groups: patients with catheter-related SAB and biliary Klebsiella pneumoniae bacteremia. Out of 1818 patients with SAB enrolled in the cohort, 42 (2%) had biliary SAB. Majority of these patients had solid tumors involving the pancreaticobiliary tract or liver, biliary drainage stent, and/or recent broad-spectrum antibiotic exposure. Patients with biliary SAB were more likely to have community-onset SAB, solid tumors, and lower APACHE II score than those with catheter-related SAB. They were less likely to have community-acquired infection and solid tumors and more likely to have lower Charlson comorbidity index and higher APACHE II score as compared with biliary K. pneumoniae bacteremia. The 12-week mortality in the biliary SAB group was higher than those in other control groups (60% vs. 20% and 14%). After adjusting for confounding factors, biliary SAB was independently associated with higher mortality. Biliary SAB is relatively rare. When it is clinically suspected, early aggressive treatment should be considered due to high mortality.
Subject(s)
Bacteremia/epidemiology , Staphylococcal Infections/epidemiology , Staphylococcus aureus/isolation & purification , Aged , Bacteremia/microbiology , Biliary Tract/microbiology , Case-Control Studies , Catheterization/adverse effects , Cohort Studies , Cross Infection/epidemiology , Cross Infection/etiology , Cross Infection/microbiology , Female , Humans , Male , Middle Aged , Prospective Studies , Republic of Korea/epidemiology , Staphylococcal Infections/etiology , Staphylococcal Infections/microbiologyABSTRACT
BACKGROUND: Opportunistic pathogens are important for clinical practice as they often cause antibiotic-resistant infections. However, little is documented for many emerging opportunistic pathogens and their biological characteristics. Here, we isolated a strain of extended-spectrum ß-lactamase-producing Enterobacteriaceae from a patient with a biliary tract infection. We explored the biological and genomic characteristics of this strain to provide new evidence and detailed information for opportunistic pathogens about the co-infection they may cause. RESULTS: The isolate grew very slowly but conferred strong protection for the co-infected cephalosporin-sensitive Klebsiella pneumoniae. As the initial laboratory testing failed to identify the taxonomy of the strain, great perplexity was caused in the etiological diagnosis and anti-infection treatment for the patient. Rigorous sequencing efforts achieved the complete genome sequence of the isolate which we designated as AF18. AF18 is phylogenetically close to a few strains isolated from soil, clinical sewage, and patients, forming a novel species together, while the taxonomic nomenclature of which is still under discussion. And this is the first report of human infection of this novel species. Like its relatives, AF18 harbors many genes related to cell mobility, various genes adaptive to both the natural environment and animal host, over 30 mobile genetic elements, and a plasmid bearing blaCTX-M-3 gene, indicating its ability to disseminate antimicrobial-resistant genes from the natural environment to patients. Transcriptome sequencing identified two sRNAs that critically regulate the growth rate of AF18, which could serve as targets for novel antimicrobial strategies. CONCLUSIONS: Our findings imply that AF18 and its species are not only infection-relevant but also potential disseminators of antibiotic resistance genes, which highlights the need for continuous monitoring for this novel species and efforts to develop treatment strategies.
Subject(s)
Coinfection/microbiology , Drug Resistance, Multiple, Bacterial/genetics , Enterobacteriaceae/genetics , Gene Expression Regulation, Bacterial/genetics , beta-Lactamases/metabolism , Anti-Bacterial Agents/pharmacology , Biliary Tract/microbiology , Coculture Techniques , Enterobacteriaceae/cytology , Enterobacteriaceae/pathogenicity , Enterobacteriaceae/ultrastructure , Humans , Klebsiella pneumoniae/genetics , Klebsiella pneumoniae/metabolism , Klebsiella pneumoniae/pathogenicity , Microscopy, Electron, Scanning , Phylogeny , RNA, Untranslated/genetics , RNA, Untranslated/metabolism , RNA-Seq , Transcriptome/genetics , Whole Genome Sequencing , beta-Lactamases/geneticsABSTRACT
The microbiome plays a crucial role in maintaining the homeostasis of the organism. Recent evidence has provided novel insights for understanding the interaction between the microbiota and the host. However, the vast majority of such studies have analyzed the interactions taking place in the intestinal tract. The biliary tree has traditionally been considered sterile under normal conditions. However, the advent of metagenomic techniques has revealed an unexpectedly rich bacterial community in the biliary tract. Associations between specific microbiological patterns and inflammatory biliary diseases and cancer have been recently described. Hence, biliary dysbiosis may be a primary trigger in the pathogenesis of biliary diseases. In particular, recent studies have suggested that microorganisms could play a significant role in the development of gallstones, pathogenesis of autoimmune cholangiopathies and biliary carcinogenesis. Moreover, the intimate connection between the biliary tract, liver and pancreas, could reveal hidden influences on the development of diseases of these organs. Further studies are needed to deepen the comprehension of the influence of the biliary microbiota in human pathology. This knowledge could lead to the formulation of strategies for modulating the biliary microbiota in order to treat and prevent these pathological conditions.
Subject(s)
Biliary Tract/microbiology , Liver Diseases/microbiology , Humans , MicrobiotaABSTRACT
BACKGROUND AND OBJECTIVE: The distal cholangiocarcinoma (dCCA) is associated with many factors: genes, environment, infection, etc. The current changes in biliary flora are thought to be involved in the formation of many gastrointestinal tract (GIT) diseases, like colon adenocarcinoma. Therefore we want to investigate whether the dCCA has a certain correlation with biliary microecology, and to detect specific strains. METHODS: A total of 68 adults were enrolled, of whom 8 with dCCA, 16 with recurrent choledocholithiasis, and 44 with the onset of common bile duct stones. Endoscopic Retrograde Cholangiopancretography (ERCP) was utilized to collect bile samples for DNA extraction and 16S rRNA gene sequencing, followed by analysis of bile microbiota composition. RESULTS: First, Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria are the most dominant phyla in the bile of patients with dCCA and the onset of common bile duct stoes. Secondly, compared with the onset of common bile duct stones patients, we got a significant increase in the phylum Gemmatimonadetes, Nitrospirae, Chloroflexi, Latescibacteria, and Planctomycetes in dCCA patients. Finally, at the genus level, we obtained sequencing results of 252 bacterial genera from patients with dCCA, recurrent choledocholithiasis, and the new onset of common bile duct stones, revealing heterogeneity among individuals. CONCLUSION: To the best of our knowledge, this is the first study of the dysbiosis of bile flora in patients with dCCA. This micro-ecological disorder may be a decisive factor in the formation of dCCA. At the same time, for the first time, this study provides a test chart of biliary microbial populations that may be associated with recurrent choledocholithiasis. The compositional changes of the core microbial group of the biliary tract have potentially important biological and medical significance for the microbiological biliary disorders of dCCA.
Subject(s)
Bile Duct Neoplasms/microbiology , Biliary Tract/microbiology , Cholangiocarcinoma/microbiology , Gallstones/microbiology , Microbiota , Adult , Aged , Aged, 80 and over , Bacteria/classification , Bacteria/genetics , Bacteria/isolation & purification , Biodiversity , China , Choledocholithiasis/microbiology , Female , Humans , Male , Microbiota/genetics , Middle Aged , Neoplasm Recurrence, Local , RNA, Ribosomal, 16SABSTRACT
The standardized application of antibacterial agents in the treatment of biliary tract diseases is of great significance.On the basis of international and domestic guidelines and consensuses, combining with the actual situation of Chinese biliary tract infection, Study Group of biliary Tract Surgery in Chinese Society of Surgery of Chinese Medical Association and Enhanced Recovery After Surgery Committee of Chinese Research Hospital Association and Editorial Board of Chinese Journal of Surgery organized experts to make recommendations which adopted a problem-oriented approach on the severity grade of biliary tract infection, the protocol of specimen examination, the use of antibiotics, the indication of drug withdrawal, the agents application strategy of drug-resistant bacteria infection and special situation to guide surgeons getting the accurate judgement of the severity of biliary tract infection and the formulation of standard protocols for the use of antibacterial agents on the premise of following the bacteriological and drug resistance monitoring information.
Subject(s)
Anti-Bacterial Agents/standards , Anti-Bacterial Agents/therapeutic use , Bacterial Infections/drug therapy , Bile Duct Diseases/drug therapy , Biliary Tract Surgical Procedures , Biliary Tract/microbiology , Bacterial Infections/microbiology , Bacterial Infections/prevention & control , Bile Duct Diseases/microbiology , Bile Duct Diseases/prevention & control , Consensus , HumansABSTRACT
Background: Patients with periampullary tumors frequently undergo endoscopic biliary investigations and biliary drainage (BD) prior to surgery. Recent literature shows a shift of the biliary microbiome toward more resistant bacteria in patients having BD. This study aimed to evaluate the local microbiome and changes induced by BD and related antibiotic exposure and to consider the choice of antibiotic for peri-operative prophylaxis. Methods: A single-center retrospective cohort study included patients operated on for periampullary tumors between January 2013 and November 2017. All patients had intra-operative bile samples taken for culture and peri-operative antibiotic use as well as documentation of complications according to the Dindo-Clavien classification. Results: A total of 37 patients were included. All received pre-operative endoscopy, and 29 (78%) had BD preceded by administration of ceftriaxone or metronidazole. Intra-operative antibiotic prophylaxis consisted of cefuroxime (92%) or ceftriaxone (13%) combined with metronidazole (100%). Bacterial contamination of bile samples was more common in the BD group than in the no biliary drainage (NBD) group (93% vs 38%; p < 0.01). A shift was observed from bile containing mainly Escherichia coli and Streptococcus spp. toward Enterococcus faecalis (0 in the NBD group versus 44.8% in the BD group; p < 0.01), Enterococcus faecium (0 versus 23%; p = 0.3), and Candida albicans (0 versus 34.5%; p = 0.08). Post-operative antibiotic modifications were common. No difference was found regarding Dindo-Clavien complications, post-operative stay, or antibiotic use in the two groups, although one patient in the NBD group who had pre-operative biliary endoscopy with antibiotic prophylaxis developed a fatal septic clot caused by Escherichia coli resistant to cefuroxime. Conclusions: We observed a significant change toward colonization by enterococci and fungi in the microbiome of patients who had pre-operative biliary investigations or drainage with antibiotic prophylaxis. These findings indicate that bile samples should be obtained systematically during surgery for periampullary tumors to guide any post-operative antibiotic therapy and peri-operative antibiotic prophylaxis and might need adaptation to target the modified microbiome.
Subject(s)
Anti-Bacterial Agents/administration & dosage , Antibiotic Prophylaxis/methods , Biliary Tract/microbiology , Drainage/adverse effects , Pancreaticoduodenectomy/methods , Preoperative Care/methods , Surgical Wound Infection/prevention & control , Aged , Aged, 80 and over , Bacteria/classification , Bacteria/isolation & purification , Biliary Tract Neoplasms/diagnosis , Biliary Tract Neoplasms/surgery , Endoscopy/adverse effects , Female , Fungi/classification , Fungi/isolation & purification , Humans , Male , Microbiota , Middle Aged , Retrospective StudiesABSTRACT
OBJECTIVES: The aim of this study was to perform a detailed genomic characterisation of IncR plasmids from China. METHODS: Three IncR plasmids (p13190-tetA, p02085-tetA and p30860-tetA) from clinical isolates ofKlebsiella pneumoniae, Citrobacter freundii and Enterobacter cloacae, respectively, were fully sequenced using high-throughput genome sequencing and were compared with five previously sequenced IncR plasmids (pHN84KPC, pSH-01, pK245, pKPC_P16 and pKPC-LK30) from China. RESULTS: The eight IncR plasmids from China possessed conserved IncR backbones composed of repB, parAB, umuCD, retA and resD. Resistance accessory modules integrated into the IncR backbones included multidrug resistance (MDR) regions in p30860-tetA, p02085-tetA, p13190-tetA and pK245, blaKPC-2 regions in pHN84KPC, pKPC-LK30 and pKPC_P16, and the ΔTn1721-sil region in pSH-01. These resistance accessory modules were inserted at a site between retA and vagD, resulting in loss of the backbone genes vagCD in some of the plasmids. The resistance accessory modules differed dramatically from one another and carried distinct profiles of resistance markers. In particular, all of p13190-tetA, p02085-tetA, p30860-tetA, pHN84KPC, pSH-01 and pK245 carried tetracycline resistance tet gene modules, and the carbapenemase gene blaKPC-2 was identified in pHN84KPC, pKPC-LK30 and pKPC_P16. In addition, one or more regions responsible for plasmid replication and/or maintenance were found in some of the resistance accessory modules, facilitating stable replication of corresponding IncR plasmids at steady-state copy numbers. CONCLUSIONS: This detailed comparative genomics analysis of IncR plasmids from China provides a deeper insight into the diversification and evolution of IncR plasmids.
Subject(s)
Citrobacter freundii/genetics , Enterobacter cloacae/genetics , Genetic Variation , Genome, Bacterial , Klebsiella pneumoniae/genetics , Plasmids/genetics , Aged , Bacteremia/microbiology , Biliary Tract/microbiology , China , Genomics , High-Throughput Nucleotide Sequencing , Humans , Male , Middle Aged , Sputum/microbiologyABSTRACT
BACKGROUND: Neoadjuvant therapy for pancreatic cancer is being employed more commonly. Most of these patients undergo biliary stenting which results in bacterial colonization and more surgical site infections (SSIs). However, the influence of neoadjuvant therapy on the biliary microbiome has not been studied. METHODS: From 2007 to 2017, patients at our institution who underwent pancreatoduodenectomy (PD) and had operative bile cultures were studied. Patient demographics, stent placement, bile cultures, bacterial sensitivities, SSIs and clinically-relevant postoperative pancreatic fistulas (CR-POPF) were analyzed. Patients who underwent neoadjuvant therapy were compared to those who went directly to surgery. Standard statistical analyses were performed. RESULTS: Eighty-three patients received neoadjuvant therapy while 89 underwent surgery alone. Patients who received neoadjuvant therapy were more likely to have enterococci (45 vs 22%, p < 0.01), and Klebsiella (37 vs 19%, p < 0.01) in their bile. Resistance to cephalosporins was more common in those who received neoadjuvant therapy (76 vs 60%, p < 0.05). Neoadjuvant therapy did not affect the incidence of SSIs or CR-POPFs. CONCLUSION: The biliary microbiome is altered in patients undergoing pancreatoduodenectomy (PD) after neoadjuvant therapy. Most patients undergoing PD with a biliary stent have microorganisms resistant to cephalosporins. Antibiotic prophylaxis in these patients should cover enterococci and gram-negative bacteria.
Subject(s)
Biliary Tract/microbiology , Carcinoma, Pancreatic Ductal/therapy , Microbiota , Neoadjuvant Therapy , Pancreatic Neoplasms/therapy , Adult , Aged , Aged, 80 and over , Bile/microbiology , Chemoradiotherapy, Adjuvant , Chemotherapy, Adjuvant , Drug Resistance, Bacterial , Enterococcus/isolation & purification , Female , Humans , Klebsiella/isolation & purification , Male , Middle Aged , Pancreatectomy , Pancreaticoduodenectomy , Retrospective Studies , Stents , Surgical Wound Infection/epidemiologyABSTRACT
A 63-year-old patient was admitted to intensive treatment unit with biliary sepsis due to a small distal common bile duct stone. Endoscopic retrograde cholangiopancreatography was initially attempted for insertion of a biliary stent but failed due to the presence of a periampullary diverticulum. Referral to interventional radiology for percutaneous drainage was considered the next alternative even though there was no dilatation of intrahepatic ducts. Due to complete absence of intrahepatic duct dilatation, the traditional percutaneous transhepatic route was considered rather challenging. An alternative percutaneous approach via the gallbladder and subsequent catheterisation of the duodenum via the distal common bile duct was successfully performed instead without complication. We would like to describe this technique as an alternative option for drainage of the non-dilated biliary system in patients with sepsis.
Subject(s)
Biliary Tract/microbiology , Catheterization/instrumentation , Common Bile Duct Diseases/pathology , Constriction, Pathologic/surgery , Gallbladder/surgery , Biliary Tract/pathology , Catheterization/methods , Cholangiopancreatography, Endoscopic Retrograde/methods , Common Bile Duct/pathology , Common Bile Duct/surgery , Drainage/standards , Drainage/statistics & numerical data , Duodenum/surgery , Gallbladder/diagnostic imaging , Humans , Male , Middle Aged , Sepsis/etiology , Treatment Outcome , Ultrasonography/methodsABSTRACT
PURPOSE: Bile is a hepatobiliary lipid-rich sterile solution, and its colonization by microorganisms defines the condition of bactibilia. In this study, we aimed to assess the bile microbiological flora and its potential link with comorbidity in women. METHODOLOGY: We performed a microbiologic investigation on 53 female patients with biliopancreatic diseases who granted consent, and we analysed the data using a MATLAB platform. RESULTS: We found that the most frequent disease associated with bactibilia was pancreas head carcinoma (PHC) (P=0.0015), while the least frequent disease was gall bladder carcinoma (GBC) (P=0.0002). The most common microorganisms were Pseudomonas spp. (P<0.0001) and Escherichia coli (P<0.0001). In particular Pseudomonas spp. and E. coli were negatively correlated to PHC presence and positively correlated to CCA by both univariate and multivariate analysis. CONCLUSIONS: Gram-negative bacteria have been linked to a tumour-associated inflammatory status. In the last 30 years, the analysis of mortality rate in Italy for PHC and GBC shows an increasing and a decreasing trend, respectively. Although this study targeted only 53 patients and does not reflect the frequency of diagnosis in a Southern Italian population, the decrease in GBC may raise the suggestion ofnon-adherence to a Mediterranean diet that may have become more prevalent in Southern Italy since the 1990s.
Subject(s)
Bile/microbiology , Biliary Tract Neoplasms/microbiology , Biliary Tract/microbiology , Gram-Negative Bacteria/classification , Gram-Negative Bacteria/isolation & purification , Pancreatic Neoplasms/microbiology , Aged , Aged, 80 and over , Cross-Sectional Studies , Female , Humans , Italy , Middle AgedABSTRACT
Diseases of the liver and biliary tree have been described with significant frequency among patients with human immunodeficiency virus (HIV), and its advanced state, acquired immunodeficiency syndrome (AIDS). Through a variety of mechanisms, HIV/AIDS has been shown to affect the hepatic parenchyma and biliary tree, leading to liver inflammation and biliary strictures. One of the potential hepatobiliary complications of this viral infection is AIDS cholangiopathy, a syndrome of biliary obstruction and liver damage due to infection-related strictures of the biliary tract. AIDS cholangiopathy is highly associated with opportunistic infections and advanced immunosuppression in AIDS patients, and due to the increased availability of highly active antiretroviral therapy, is now primarily seen in instances of poor access to anti-retroviral therapy and medication non-compliance. While current published literature describes well the clinical, biochemical, and endoscopic management of AIDS-related cholangiopathy, information on its epidemiology, natural history, and pathology are not as well defined. The objective of this review is to summarize the available literature on AIDS cholangiopathy, emphasizing its epidemiology, course of disease, and determinants, while also revealing an updated approach for its evaluation and management.
Subject(s)
AIDS-Related Opportunistic Infections/epidemiology , Bile Duct Diseases/epidemiology , Cryptosporidium/physiology , HIV-1/physiology , AIDS-Related Opportunistic Infections/diagnosis , AIDS-Related Opportunistic Infections/microbiology , AIDS-Related Opportunistic Infections/therapy , Analgesics, Opioid/therapeutic use , Anti-HIV Agents/therapeutic use , Bile Duct Diseases/diagnosis , Bile Duct Diseases/microbiology , Bile Duct Diseases/therapy , Biliary Tract/diagnostic imaging , Biliary Tract/microbiology , Biliary Tract/pathology , Biliary Tract Surgical Procedures , Cryptosporidium/drug effects , Cryptosporidium/isolation & purification , Drug Resistance , HIV-1/drug effects , Humans , Liver/diagnostic imaging , Liver/pathology , Liver/virology , Nerve Block/methodsABSTRACT
The close relationship between primary sclerosing cholangitis (PSC) and inflammatory bowel disease has inspired hypothetical models in which gut bacteria or bacterial products are key players in PSC pathogenesis. Several studies using high-throughput sequencing technology to characterize the gut microbiota in PSC have been published over the past years. They all report reduced diversity and significant shifts in the overall composition of the gut microbiota. However, it remains unclear as to whether the observed changes are primary or secondary to PSC development and further studies are needed to assess the biological implications of the findings. In the present article, we review the published data in perspective of similar studies in other diseases. We discuss aspects of methodology and study design that are relevant to interpretation of the data. Furthermore, we propose that interpretation and further assessments of findings are structured into conceptual compartments, and elaborate three such possible concepts relating to immune function (the "immunobiome"), host metabolism (the "endobiome"), and dietary and xenobiotic factors (the "xenobiome") in PSC.
Subject(s)
Bacteria/growth & development , Biliary Tract/microbiology , Cholangitis, Sclerosing/microbiology , Gastrointestinal Microbiome , Intestines/microbiology , Liver/microbiology , Animals , Bacteria/immunology , Bacteria/metabolism , Biliary Tract/immunology , Biliary Tract/metabolism , Cholangitis, Sclerosing/diagnosis , Cholangitis, Sclerosing/immunology , Cholangitis, Sclerosing/metabolism , Disease Models, Animal , Dysbiosis , Gastrointestinal Microbiome/immunology , Host-Pathogen Interactions , Humans , Intestinal Mucosa/metabolism , Intestines/immunology , Liver/immunology , Liver/metabolismABSTRACT
OBJECTIVE: The etiopathogenesis and risk for development of biliary neoplasia in primary sclerosing cholangitis (PSC) are largely unknown. Microbes or their metabolites have been suggested to play a role. To explore this potential microbial involvement, we evaluated the differences in biliary microbiota in PSC patients at an early disease stage without previous endoscopic retrograde cholangiography (ERC) examinations, advanced disease stage, and with biliary dysplasia or cholangiocarcinoma. DESIGN: Bile samples from the common bile duct were collected from 46 controls and 80 patients with PSC during ERC (37 with early disease, 32 with advanced disease, and 11 with biliary dysplasia). DNA isolation, amplification, and Illumina MiSeq sequencing were performed for the V1-V3 regions of the bacterial 16S rRNA gene. RESULTS: The most common phyla found were Bacteroidetes, Firmicutes, Proteobacteria, Fusobacteria, and Actinobacteria. The most common families were Prevotellaceae, Streptococcaceae, Veillonellaceae, Fusobacteriaceae, and Pasteurellaceae, and the most common genera were Prevotella, Streptococcus, Veillonella, Fusobacterium, and Haemophilus. The bacterial communities of non-PSC subjects and early stage PSC patients were similar. Alpha diversity was lower in patients with biliary dysplasia/cholangiocarcinoma than in other groups. An increase in Streptococcus abundance was positively correlated with the number of ERC examinations. Streptococcus abundance was also positively correlated with an increase in disease severity, even after controlling for the number of ERC examinations. CONCLUSIONS: Our findings suggest that the aetiology of PSC is not associated with changes in bile microbial communities, but the genus Streptococcus may play a pathogenic role in the progression of the disease.