Ruminococcoides bili gen. nov., sp. nov., a bile-resistant bacterium from human bile with autolytic behavior

A strictly anaerobic, resistant starch-degrading, bile-tolerant, autolytic strain, IPLA60002T, belonging to the family Ruminococcaceae , was isolated from a human bile sample of a liver donor without hepatobiliary disease. Cells were Gram-stain-positive cocci, and 16S rRNA gene and whole genome analyses showed that Ruminococcus bromii was the phylogenetically closest related species to the novel strain IPLA60002T, though with average nucleotide identity values below 90 %. Biochemically, the new isolate has metabolic features similar to those described previously for gut R. bromii strains, including the ability to degrade a range of different starches. The new isolate, however, produces lactate and shows distinct resistance to the presence of bile salts. Additionally, the novel bile isolate displays an autolytic phenotype after growing in different media. Strain IPLA60002T is phylogenetically distinct from other species within the genus Ruminococcus . Therefore, we propose on the basis of phylogenetic, genomic and metabolic data that the novel IPLA60002T strain isolated from human bile be given the name Ruminococcoides bili gen. nov., sp. nov., within the new proposed genus Ruminococcoides and the family Ruminococcaceae . Strain IPLA60002T (=DSM 110008T=LMG 31505T) is proposed as the type strain of Ruminococcoides bili.

ERCP-related adverse events: European Society of Gastrointestinal Endoscopy (ESGE) Guideline

Main Recommendations Prophylaxis 1 ESGE recommends routine rectal administration of 100 mg of diclofenac or indomethacin immediately before endoscopic retrograde cholangiopancreatography (ERCP) in all patients without contraindications to nonsteroidal anti-inflammatory drug administration.Strong recommendation, moderate quality evidence. 2 ESGE recommends prophylactic pancreatic stenting in selected patients at high risk for post-ERCP pancreatitis (inadvertent guidewire insertion/opacification of the pancreatic duct, double-guidewire cannulation).Strong recommendation, moderate quality evidence. 3 ESGE suggests against routine endoscopic biliary sphincterotomy before the insertion of a single plastic stent or an uncovered/partially covered self-expandable metal stent for relief of biliary obstruction.Weak recommendation, moderate quality evidence. 4 ESGE recommends against the routine use of antibiotic prophylaxis before ERCP.Strong recommendation, moderate quality evidence. 5 ESGE suggests antibiotic prophylaxis before ERCP in the case of anticipated incomplete biliary drainage, for severely immunocompromised patients, and when performing cholangioscopy.Weak recommendation, moderate quality evidence. 6 ESGE suggests tests of coagulation are not routinely required prior to ERCP for patients who are not on anticoagulants and not jaundiced.Weak recommendation, low quality evidence. Treatment 7 ESGE suggests against salvage pancreatic stenting in patients with post-ERCP pancreatitis.Weak recommendation, low quality evidence. 8 ESGE suggests temporary placement of a biliary fully covered self-expandable metal stent for post-sphincterotomy bleeding refractory to standard hemostatic modalities.Weak recommendation, low quality evidence. 9 ESGE suggests to evaluate patients with post-ERCP cholangitis by abdominal ultrasonography or computed tomography (CT) scan and, in the absence of improvement with conservative therapy, to consider repeat ERCP. A bile sample should be collected for microbiological examination during repeat ERCP.Weak recommendation, low quality evidence.

Prevalence of Fascioliasis and Dicrocoeliasis in Cattle Slaughtered in Some Abattoirs in Akure Metropolis, Ondo State, Nigeria

The study was carried out in March-May 2019 to investigate the prevalence of fascioliasis and dicrocoeliasis in cattle slaughtered in parts of Akure abattoir, Ondo State, Nigeria. Two hundred (200) bile samples from cattle were collected from both male and female cattle. The parasitological analysis of the bile sample was carried out by sedimentation technique. Prevalence of Fasciola gigantica was (50.5%) for Dicrocoelium hospes was 16.0% and double infections accounted for (5.5%). Prevalence of Fasciola gigantica infections was high in female cattle (57.7%) compared to their male counterparts (38.9%). For Dicrocoelium hospes, the infection was higher in male (18.2%) than in the female (14.6%) while the prevalence of double infections was higher in males (7.8%) than in the females (4.07). The high infection rate for Fasciola gigantica (84.0%) and Dicrocoelium hospes (62.0%) was found to be high at Busa abattoir. Double infection was observed to be high at Oke-Odu abattoir (10%) than in other abattoirs while no infection was observed at Bola meat abattoir. Overall age prevalence of fascioliasis and dicrocoeliasis (82.8%) was within the age bracket of 9-10yrs while the least infection (54.2%) fall within the age bracket of 7-8yrs. Prevalence of fascioliasis and dicrocoeliasis in Sannia breed was 90.2% followed by the Ambala breed (84.0%) while the least was 31.2% in the White Fulani breed. This study which revealed a high prevalence of fascioliasis and dicrocoeliasis among cattle slaughtered in the studied abattoir possesses a threat to healthy livestock productions and it is significant public health importance. Adequate measures to improving the veterinary services are needed to put in place to reduce the economic losses accruing to these infections.

Az antibiotikumrezisztencia változása cholangitisben. Klinikai tapasztalataink

Introduction: Due to the inappropriate use of antibiotics (AB), more pathogens become multiresistant. One of the most severe sources of sepsis is cholangitis. To avoid fatal outcome, an effective AB policy plays a key role. Aim: To investigate the AB resistance of bacteria causing cholangitis and the efficacy of AB treatment. Patients and method: Microbiological tests of bile samples collected during cholangitis-indicated endoscopic retrograde cholangiopancreatographies were analysed at the First Department of Medicine, University of Szeged, in 2006 and in 2016. Results: 29 and 111 patients had bile sample collection in 2006 and in 2016, respectively. Of that, 22 (75%) and 106 (95%) were positive. Mean age: 61 ± 14 vs. 71 ± 14 years, no difference between men/women ratio. In 2006, 10 cases empirical AB (ciprofloxacine with metronidazole or imipenem) were used. In 9 cases (90%), the AB was adequate based on the microbiological results. In 2016, in 88 cases empirical AB was applied (ciprofloxacine and metronidazole, ceftriaxone with metronidazole or imipenem with metronidazole). In 29 cases, the empirical AB was ineffective. The efficacy of ciprofloxacine decreased to 64% in 2016. The profile of the most frequent cholangitis-causing pathogens (Escherichia coli, Enterococcus faecalis, Klebsiella pneumoniae) was the same, but their resistency against ciprofloxacine increased. The rates of polymicrobal infections were 73% and 63%, respectively. Conclusion: The rates of positive bile samples were significantly higher in 2016. The profile of the most frequent pathogens was the same. The efficacy of the first-choice empirical AB ciprofloxacine decreased in 2016. The types of the most frequent cholangitis-causing bacteria are in line with the ones included in the Tokyo Guideline. Orv Hetil. 2019; 160(36): 1437–1442.

Phylogenetic Analysis and Characterization of the Complete Hepatitis E Virus Genome (Zoonotic Genotype 3) in Swine Samples from Mexico

Hepatitis E virus (HEV) is an emerging public health problem with an estimated 20 million infections each year. In Mexico, Orthohepevirus A, genotype 2, has been reported in humans, but genotype 3 has only been reported in swine (zoonotic). No diagnostic tests are publicly available in Mexico, and only partial sequences have been reported from swine samples. Hence, research is necessary to determine circulating strains, understand the features and dynamics of infection on pig farms, determine how to implement surveillance programs, and to assess public health risks. In this study, a next-generation sequencing (NGS) approach was applied to obtain a complete genome of swine HEV. Liver, feces, and bile samples were taken at slaughterhouses and a farm in Mexico. RT-PCR was used to determine positive samples and confirmed by Sanger sequencing. Of the 64 slaughterhouse samples, one bile sample was positive (B1r) (1.56%). Of 21 sample pools from farm animals, 14 were positive (66.66%), representing all stages of production. A complete sequence strain MXCDg3_B1c|_2016 was obtained from the bile of a domestic swine in the fattening stage. In addition, two partial sequences—MXCDg3_H2cons|_2016 (1473 nt) and MXCDg3_C3Acons|_2016 (4777 nt)—were obtained from sampled farm animals. Comparison with all reported genome HEV sequences showed similarity to genotype 3 subgenotype a (G3a), which has been previously reported in acute cases of human hepatitis in the US, Colombia, China, and Japan.

Hepatitis E virus infection in North Italy: high seroprevalence in swine herds and increased risk for swine workers

SUMMARYWe determined the hepatitis E virus (HEV) seroprevalence and detection rate in commercial swine herds in Italy's utmost pig-rich area, and assessed HEV seropositivity risk in humans as a function of occupational exposure to pigs, diet, foreign travel, medical history and hunting activities. During 2011–2014, 2700 sera from 300 swine herds were tested for anti-HEV IgG. HEV RNA was searched in 959 faecal pools from HEV-seropositive herds and in liver/bile/muscle samples from 179 pigs from HEV-positive herds. A cohort study of HEV seropositivity in swine workers (n = 149) was also performed using two comparison groups of people unexposed to swine: omnivores (n = 121) and vegetarians/vegans (n = 115). Herd-level seroprevalence was 75·6% and was highest in farrow-to-feeder herds (81·6%). Twenty-six out of 105 (24·8%) herds had HEV-positive faecal samples (25 HEV-3, one HEV-4). Only one bile sample tested positive. HEV seropositivity was 12·3% in swine workers, 0·9% in omnivores and 3·0% in vegetarians/vegans. Factors significantly associated with HEV seropositivity were occupational exposure to pigs, travel to Africa and increased swine workers’ age. We concluded that HEV is widespread in Italian swine herds and HEV-4 circulation is alarming given its pathogenicity, with those occupationally exposed to pigs being at increased risk of HEV seropositivity.

CTX-M-15-Producing Shewanella Species Clinical Isolate Expressing OXA-535, a Chromosome-Encoded OXA-48 Variant, Putative Progenitor of the Plasmid-Encoded OXA-436

ABSTRACT Shewanella spp. constitute a reservoir of antibiotic resistance determinants. In a bile sample, we identified three extended-spectrum-β-lactamase (ESBL)-producing bacteria (Escherichia coli, Klebsiella pneumoniae, and Shewanella sp. strain JAB-1) isolated from a child suffering from cholangitis. Our objectives were to characterize the genome and the resistome of the first ESBL-producing isolate of the genus Shewanella and determine whether plasmidic exchange occurred between the three bacterial species. Bacterial isolates were characterized using matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS), standard biochemical tools, and antimicrobial susceptibility testing. Shewanella sp. JAB-1 and ESBL gene-encoding plasmids were characterized using PacBio and Illumina whole-genome sequencing, respectively. The Shewanella sp. JAB-1 chromosome-encoded OXA-48 variant was cloned and functionally characterized. Whole-genome sequencing (WGS) of the Shewanella sp. clinical isolate JAB-1 revealed the presence of a 193-kb plasmid belonging to the IncA/C incompatibility group and harboring two ESBL genes, bla CTX-M-15 and bla SHV-2a. bla CTX-M-15 gene-carrying plasmids belonging to the IncY and IncR incompatibility groups were also found in the E. coli and K. pneumoniae isolates from the same patient, respectively. A comparison of the bla CTX-M-15 genetic environment indicated the independent origin of these plasmids and dismissed in vivo transfers. Furthermore, characterization of the resistome of Shewanella sp. JAB-1 revealed the presence of a chromosome-carried bla OXA-535 gene, likely the progenitor of the plasmid-carried bla OXA-436 gene, a novel bla OXA-48-like gene. The expression of bla OXA-535 in E. coli showed the carbapenem-hydrolyzing activity of OXA-535. The production of OXA-535 in Shewanella sp. JAB-1 could be evidenced using molecular and immunoenzymatic tests, but not with biochemical tests that monitor carbapenem hydrolysis. In this study, we have identified a CTX-M-15-producing Shewanella species that was responsible for a hepatobiliary infection and that is likely the progenitor of OXA-436, a novel plasmid-encoded OXA-48-like class D carbapenemase.

Prevalence of pancreaticobiliary reflux in symptomatic cholelithiasis and its significance

Aims: Pancreaticobiliary reflux (PBR) is reflux of pancreatic enzymes into the biliary tree which occurs as a result of an anamoly of pancreaticobiliary junction (PBJ) or functionally impaired sphincter. PBR is associated with changes in biliary epithelium and is known to cause benign and malignant biliary pathology. Various authors have reported prevalence of PBR in patients with normal PBJ ranging from 20 % to 83.5 %. With aim to detect the prevalence of PBR in patients with symptomatic cholelithiasis in Nepalese population we conducted this study. Materials and methods: Thirty patients undergoing elective laparoscopic cholecystectomy (LC) for symptomatic cholelithiasis were included in the study. History, physical findings and relevant investigations including liver function test, serum amylase and abdominal ultrasound were recorded. Bile sample for amylase was taken from gall bladder during LC percuatneously before manipulation of calot’s triangle and common bile duct. Bile amylase level above serum amylase level was considered positive for PBR. Results: Mean age of the patient was 37.27 (± 14.41) years. Out of 30, 6 (20 %) patients were male and 24 (80 %) were female. Mean BMI was 21.58 (± 3.2). PBR reflux was present in 66.7 % of patients out of which 2 were male and 18 were female that was not statistically significant (p = 1.41) when compared with patients without PBR. Conclusion: PBR occurs in patient with cholelithiasis and has role in pathogenesis of gallstones disease and gall bladder carcinoma. Long term surveillance would be required to ascertain the significance of detection of PBR after LC. Journal of College of Medical Sciences-Nepal, 2013, Vol-9, No-1, 1-6 DOI: http://dx.doi.org/10.3126/jcmsn.v9i1.9666

Retrograde intrabiliary injection of amphipathic materials causes phospholipid secretion into bile. Taurocholate causes phosphatidylcholine secretion, 3-[(3-cholamidopropyl)dimethylammonio]-propane-1-sulphonate (CHAPS) causes mixed phospholipid secretion

The control of biliary phospholipid and cholesterol secretions by bile acid was studied by using the technique of retrograde intrabiliary injection. Taurocholate (TC), a moderately hydrophobic bile acid, taurodehydrocholate (TDHC), a hydrophilic non-micelle-forming bile acid, and 3-[(3-cholamidopropyl)-dimethylammonio]propane-1-sulphonate (CHAPS), a detergent, were individually administered by retrograde intrabiliary injection (RII) into the biliary tree, and bile acids, phospholipids and cholesterol subsequently appearing in the bile were measured. TC (1.3 mumol; 45 microliters) injected retrogradely provoked a 3.5-fold increase in biliary phospholipid output for 40 min, as compared with the saline control. Injection of 2.7 mumol of TC (90 microliters) caused a 7.5-fold increase in phospholipid output, which reached a peak at 12 min after RII, and phospholipid output continued for 40 min. Cholesterol output was also elicited under these conditions, showing both dose-dependency and extended secretion. Injection of 1.8 mumol of TDHC caused very little increase in either biliary phospholipid or cholesterol. Injection of 0.9 mumol of CHAPS (45 microliters) provoked a single substantial peak of phospholipid output in the 3 min bile sample. T.l.c. analysis of the phospholipid extracts of the bile collected after each compound showed, for TC, a single compound which co-migrated with the phosphatidylcholine standard, whereas for CHAPS substantial amounts of other phospholipids were present.