Association of Microbial Dysbiosis with Gallbladder Diseases Identified by Bile Microbiome Profiling

Background@#Cholecystitis is an important risk factor for gallbladder cancer, but the bile microbiome and its association with gallbladder disease has not been investigated fully.We aimed to analyze the bile microbiome in normal conditions, chronic cholecystitis, and gallbladder cancer, and to identify candidate bacteria that play an important role in gallbladder carcinogenesis. @*Methods@#We performed metagenome sequencing on bile samples of 10 healthy individuals, 10 patients with chronic cholecystitis, and 5 patients with gallbladder cancer, and compared the clinical, radiological, and pathological characteristics of the participants. @*Results@#No significant bacterial signal was identified in the normal bile. The predominant dysbiotic bacteria in both chronic cholecystitis and gallbladder cancer were those belonging to the Enterobacteriaceae family. Klebsiella increased significantly in the order of normal, chronic cholecystitis, and gallbladder cancer. Patients with chronic cholecystitis and dysbiotic microbiome patterns had larger gallstones and showed marked epithelial atypia, which are considered as precancerous conditions. @*Conclusion@#We investigated the bile microbiome in normal, chronic cholecystitis, and gallbladder cancer. We suggest possible roles of Enterobacteriaceae, including Klebsiella, in gallbladder carcinogenesis. Our findings reveal a possible link between a dysbiotic bile microbiome and the development of chronic calculous cholecystitis and gallbladder cancer.

Association of Microbial Dysbiosis with Gallbladder Diseases Identified by Bile Microbiome Profiling

Background@#Cholecystitis is an important risk factor for gallbladder cancer, but the bile microbiome and its association with gallbladder disease has not been investigated fully.We aimed to analyze the bile microbiome in normal conditions, chronic cholecystitis, and gallbladder cancer, and to identify candidate bacteria that play an important role in gallbladder carcinogenesis. @*Methods@#We performed metagenome sequencing on bile samples of 10 healthy individuals, 10 patients with chronic cholecystitis, and 5 patients with gallbladder cancer, and compared the clinical, radiological, and pathological characteristics of the participants. @*Results@#No significant bacterial signal was identified in the normal bile. The predominant dysbiotic bacteria in both chronic cholecystitis and gallbladder cancer were those belonging to the Enterobacteriaceae family. Klebsiella increased significantly in the order of normal, chronic cholecystitis, and gallbladder cancer. Patients with chronic cholecystitis and dysbiotic microbiome patterns had larger gallstones and showed marked epithelial atypia, which are considered as precancerous conditions. @*Conclusion@#We investigated the bile microbiome in normal, chronic cholecystitis, and gallbladder cancer. We suggest possible roles of Enterobacteriaceae, including Klebsiella, in gallbladder carcinogenesis. Our findings reveal a possible link between a dysbiotic bile microbiome and the development of chronic calculous cholecystitis and gallbladder cancer.

A Case of Prosthetic Valve Endocarditis with Cerebral Hemorrhage Caused by Rothia mucilaginosa / 대한임상미생물학회지

Rothia spp. are aerobic, gram-positive cocci belonging to the family Micrococcaceae, and are a part of the normal microbial flora of the human oropharynx and upper respiratory tract. We present the first case of the prosthetic valve endocarditis with cerebral hemorrhage caused by Rothia mucilaginosa in South Korea. A 65-year-old man with a prosthetic aortic valve visited the outpatient clinic with a complaint of fever. R. mucilaginosa was identified in one among four sets of blood culture bottles obtained on the on day 30 of fever onset. Brain magnetic resonance imaging (MRI) showed multiple micro-hemorrhages suggesting septic emboli in both the hemispheres, corticomedullary junctions, and cerebellum. Rothia spp. should be considered as a possible pathogen in the cases of infective endocarditis with intracranial hemorrhage.

A Case of Prosthetic Valve Endocarditis with Cerebral Hemorrhage Caused by Rothia mucilaginosa / 대한임상미생물학회지

Rothia spp. are aerobic, gram-positive cocci belonging to the family Micrococcaceae, and are a part of the normal microbial flora of the human oropharynx and upper respiratory tract. We present the first case of the prosthetic valve endocarditis with cerebral hemorrhage caused by Rothia mucilaginosa in South Korea. A 65-year-old man with a prosthetic aortic valve visited the outpatient clinic with a complaint of fever. R. mucilaginosa was identified in one among four sets of blood culture bottles obtained on the on day 30 of fever onset. Brain magnetic resonance imaging (MRI) showed multiple micro-hemorrhages suggesting septic emboli in both the hemispheres, corticomedullary junctions, and cerebellum. Rothia spp. should be considered as a possible pathogen in the cases of infective endocarditis with intracranial hemorrhage.

The First Case of Chronic Otitis Media due to Kerstersia gyiorum in Korea

No abstract available.

Is It Necessary to Repeat Fecal Occult Blood Tests with Borderline Results for Colorectal Cancer Screening?

The fecal immunochemical test (FIT) is the initial non-invasive investigation of choice for population-based colorectal cancer (CRC) screening. We evaluated the positivity rate in repeated tests using the same fecal specimen that showed borderline results in the FIT. A total of 6,465 patients were tested with the FIT in a tertiary-care hospital from July to December 2016. FIT was done using OC-Sensor PLEDIA (Eiken Chemical Co., Tokyo, Japan). Among 6,465 patients, 364 (5.6%) patients showed a positive FIT result of over 20 µg Hb/g feces. A total of 112 (1.7%) patients showed borderline scores of 10.2–20 µg Hb/g feces, and 5,989 (92.6%) patients showed negative results of less than 10 µg Hb/g feces. Among the 101 repeat-tested patients, 19 (18.8%) of the patients' scores converted to levels above the positive cut-off threshold. Repeated results of 19 patients showed score elevations from 20.2 to 68 µg Hb/g feces. These results suggest that it is most important to analyze properly prepared samples, even if only once. Therefore, the laboratory staff should ensure the proper preparation of stool specimens for FIT. Laboratory directors should choose the best cut-off value for detecting CRC at their respective institutions.

Prevalence of Escherichia coli Carrying pks Islands in Bacteremia Patients

Escherichia coli can harbor genomic pks islands that code for a polyketide-peptide genotoxin known as colibactin. E. coli strains carrying pks islands trigger genetic instability. pks islands have been significantly associated with bacteremia. We investigated the molecular epidemiology of bacteremic E. coli isolates and the prevalence of bacteremia-causing E. coli carrying pks islands. A total of 146 E. coli isolates were collected at a tertiary-care hospital from January 2015 to December 2016. The phylogenetic groups were determined by multiplex PCR. All isolates were screened by PCR for sequence type 131 (ST131)-associated single-nucleotide polymorphisms (SNPs) in mdh and gyrB. For detection of pks islands, we performed PCR for the clbB and clbN genes as colibactin system markers. Phylogenetic group B2 was the most common, accounting for 54.1% (N=79) of the isolates, followed by group D with 29.5% (N=43), group A with 11.6% (N=17), and group B1 with 4.8%. Of the group B2 isolates, 40.5% were ST131 strains and 32.9% carried pks islands. Only three ST131 isolates in group B2 carried the clbB and clbN genes, while the other 23 ST131 isolates did not. The pks gene might not be associated with ST131 strains.

Surveillance Culture of Carbapenemase-Producing Enterobacteriaceae in a Tertiary-Care Hospital / 대한임상미생물학회지

BACKGROUND: Carbapenem-resistant Enterobacteriaceae (CRE) are increasingly being reported throughout the world, which is a significant problem for patient treatment and infection control. Carbapenem-resistance in Enterobacteriaceae is mainly due to carbapenem-hydrolyzing β-lactamase, which tends to spread through genetic mobile elements. Therefore, the detection of carbapenemase-producing Enterobacteriaceae (CPE) carriers is particularly important for the prevention and epidemiological monitoring of these infections. In this study, we performed surveillance cultures for CPE in patients admitted to the hospital and evaluated the prevalence of CPE. METHODS: Stool cultures were obtained from a total of 228 patients at our tertiary-care hospital between March and May 2017. Stool specimens were inoculated on ChromID CARBA agar (bioMérieux, France) and incubated for 18-24 hours. Suspicious colonies with pink or bluish-green color were screened for CPE by the modified Hodge test (MHT) and carbapenemase inhibition test (CIT). We performed PCR to detect five carbapenemase genes, bla(KPC), bla(IMP), bla(VIM), bla(NDM), and bla(OXA-48). RESULTS: Among 228 isolates, seven were suspicious for CPE: four Klebsiella pneumoniae, one Escherichia coli, one Enterobacter aerogenes, and one Serratia marcescens. Two K. pneumoniae isolates showed positive reactions in both the modified Hodge test and inhibition test with phenylboronic acid. By PCR, bla(KPC) was identified in these two K. pneumoniae isolates. CONCLUSION: Our results showed a very low prevalence (2/228, 0.9%) of CPE in our tertiary-care hospital based on surveillance culture in a recent three month period.

Campylobacter fetus Peritonitis in a Patient with Continuous Ambulatory Peritoneal Dialysis: A First Case Report in Korea / 대한임상미생물학회지

Campylobacter fetus may cause infections such as septicemia, peritonitis, meningitis, endocarditis, septic arthritis, and cellulitis, increasing the risk of spontaneous abortion but decreasing the likelihood of gastroenteritis. We identified C. fetus from continuous ambulatory peritoneal dialysis (CAPD) fluid using 16S rRNA gene sequencing. It is significant that this is the first case report in Korea of CAPD peritonitis caused by C. fetus, which is known to be rare.

Comparison of a New Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry Platform, ASTA MicroIDSys, With Bruker Biotyper for Species Identification

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, with its accuracy and speed, is widely used for bacterial identification. The ASTA MicroIDSys system (ASTA, Korea) was recently developed for species identification. We compared its performance with that of Bruker Biotyper (Bruker Daltonics, Germany). Microbes were recovered from sputum, urine, and pus samples from patients admitted to a tertiary care hospital in Korea from January to April 2016. Matrix solution (α-cyano-4-hydroxycinnamic acid) was used, and the peptide profiles acquired from the Microflex LT (Bruker Daltonics) and Tinkerbell LT (ASTA) were analyzed by using their respective software. From 5,322 isolates, Bruker Biotyper identified 163 species; fifty species from 4,919 isolates were identified more than 10 times, including Klebsiella pneumoniae (n=571), Acinetobacter baumannii (n=436), Pseudomonas aeruginosa (n=358), Escherichia coli (n=372), Staphylococcus aureus (n=511), S. epidermidis (n=444), Enterococcus faecium (n=262), E. faecalis (n=220), and Candida albicans (n=248). Identical results, confidence scores (≥ 2.0 for Bruker Biotyper), and acceptable scores (≥140 for ASTA MicroIDSys) were obtained for 86.1% of isolates. Of 4,267 isolates, 99.2% showed acceptable scores in both systems. Results from the ASTA MicroIDSys showed good agreement with those from the Bruker Biotyper. The ASTA MicroIDSys could reliably identify clinically important microorganisms.

Biofilm Formation and Antimicrobial Resistance in Enterococcus

No abstract available.

Prediction of Putative Resistance Islands in a Carbapenem-Resistant Acinetobacter baumannii Global Clone 2 Clinical Isolate

BACKGROUND: We investigated the whole genome sequence (WGS) of a carbapenem-resistant Acinetobacter baumannii isolate belonging to the global clone 2 (GC2) and predicted resistance islands using a software tool. METHODS: A. baumannii strain YU-R612 was isolated from the sputum of a 61-yr-old man with sepsis. The WGS of the YU-R612 strain was obtained by using the PacBio RS II Sequencing System (Pacific Biosciences Inc., USA). Antimicrobial resistance genes and resistance islands were analyzed by using ResFinder and Genomic Island Prediction software (GIPSy), respectively. RESULTS: The YU-R612 genome consisted of a circular chromosome (ca. 4,075 kb) and two plasmids (ca. 74 kb and 5 kb). Its sequence type (ST) under the Oxford scheme was ST191, consistent with assignment to GC2. ResFinder analysis showed that YU-R612 possessed the following resistance genes: four β-lactamase genes bla(ADC-30), bla(OXA-66), bla(OXA-23), and bla(TEM-1); armA, aadA1, and aacA4 as aminoglycoside resistance-encoding genes; aac(6')Ib-cr for fluoroquinolone resistance; msr(E) for macrolide, lincosamide, and streptogramin B resistance; catB8 for phenicol resistance; and sul1 for sulfonamide resistance. By GIPSy analysis, six putative resistant islands (PRIs) were determined on the YU-R612 chromosome. Among them, PRI1 possessed two copies of Tn2009 carrying bla(OXA-23), and PRI5 carried two copies of a class I integron carrying sul1 and armA genes. CONCLUSIONS: By prediction of resistance islands in the carbapenem-resistant A. baumannii YU-R612 GC2 strain isolated in Korea, PRIs were detected on the chromosome that possessed Tn2009 and class I integrons. The prediction of resistance islands using software tools was useful for analysis of the WGS.

Fusobacterium Isolates Recovered From Colonic Biopsies of Inflammatory Bowel Disease Patients in Korea

No abstract available.

Bacteroides nordii and Bacteroides salyersiae Isolated from Post-operative Peritonitis Patients

In this study, we report three cases in which two species of the Bacteroides fragilis group, 'Bacteroides nordii' and 'Bacteroides salyersiae', were isolated from peritoneal fluid cultures from post-operative peritonitis patients. The two species of the B. fragilis group were initially misidentified as B. fragilis/Bacteroides stercoris and Bacteroides ovatus by Rapid ID 32A (bioMérieux, France), and finally confirmed as B. nordii and B. salyersiae using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and 16s rRNA sequencing. For the identification of anaerobes, particularly B. fragilis group organisms, MALDI-TOF MS is a useful method not only because of its concordance with 16S rRNA sequencing results, but also because of its rapidity and simple procedure.

Anaerobic Bacteremia: Impact of Inappropriate Therapy on Mortality

BACKGROUND: Investigation on incidence and mortality of anaerobic bacteremia (AB) is clinically relevant in spite of its infrequent occurrence and not often explored, which report varies according to period and institutions. Therefore, it is necessary to analyze the incidence and risk factors related to mortality and assess clinical outcomes of AB in current aspect. MATERIALS AND METHODS: Characteristics of AB patients and anaerobic bacteria from blood culture at a university hospital in 2012 were reviewed retrospectively. The correlation between risk factors and 28-day patient mortality was analyzed. RESULTS: A total of 70 non-duplicated anaerobic bacteria were isolated from blood of 70 bacteremia patients in 2012. The history of cardiovascular disease as host's risk factor was statistically significant (P = 0.0344) in univariate and multivariate analysis. Although the inappropriate therapy was not statistically significant in univariate and multivariate analysis, the survival rate of bacteremia was significantly worse in patients who had inappropriate therapy compared with those underwent appropriate therapy (hazard ratio, 5.4; 95% confidence interval, 1.7-6.9; P = 0.004). The most frequently isolated organism was Bacteroides fragilis (32 isolates, 46%), followed by Bacteroides thetaiotaomicron (10, 14%), and non-perfringens Clostridium (7, 10%). CONCLUSION: The incidence of AB in 2012 was 2.3% (number of AB patients per 100 positive blood culture patients) and the mortality rate in patients with clinically significant AB was 21.4%. In addition, AB was frequently noted in patients having malignancy and the survival rate of AB was significantly worse in patients who received inappropriate therapy compared with those underwent appropriate therapy.

Identification of Pasteurella canis in a Soft Tissue Infection Caused by a Dog Bite: The First Report in Korea

No abstract available.

Antimicrobial Susceptibility of Clinical Isolates of Bacteroides fragilis Group Organisms Recovered from 2009 to 2012 in a Korean Hospital

BACKGROUND: Periodic monitoring of antimicrobial resistance trends of clinically important anaerobic bacteria such as Bacteroides fragilis group organisms is required. We determined the antimicrobial susceptibilities of clinical isolates of B. fragilis group organisms recovered from 2009 to 2012 in a tertiary-care hospital in Korea. METHODS: A total of 180 nonduplicate clinical isolates of B. fragilis group organisms were collected in a tertiary care hospital. The species were identified by conventional methods: the ATB 32A rapid identification system (bioMerieux, France) and the Vitek MS matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (bioMerieux). Antimicrobial susceptibility was determined by the CLSI agar dilution method. RESULTS: Imipenem and meropenem resistance rates were 0-6% for B. fragilis group isolates. The rate of resistance to piperacillin-tazobactam was 2% for B. fragilis and 0% for other Bacteroides species, but 17% for B. thetaiotaomicron isolates. High resistance rates to piperacillin (72% and 69%), cefotetan (89% and 58%), and clindamycin (83% and 69%) were observed for B. thetaiotaomicron and other Bacteroides spp. The moxifloxacin resistance rate was 27% for other Bacteroides spp. The MIC50 and MIC90 of tigecycline were 2-4 microg/mL and 8-16 microg/mL, respectively. No isolates were resistant to chloramphenicol or metronidazole. CONCLUSIONS: Imipenem, meropenem, chloramphenicol, and metronidazole remain active against B. fragilis group isolates. Moxifloxacin and tigecycline resistance rates are 2-27% and 8-15% for B. fragilis group isolates, respectively.

Comparison of MALDI-TOF MS, Housekeeping Gene Sequencing, and 16S rRNA Gene Sequencing for Identification of Aeromonas Clinical Isolates

PURPOSE: The genus Aeromonas is a pathogen that is well known to cause severe clinical illnesses, ranging from gastroenteritis to sepsis. Accurate identification of A. hydrophila, A. caviae, and A. veronii is important for the care of patients. However, species identification remains difficult using conventional methods. The aim of this study was to compare the accuracy of different methods of identifying Aeromonas at the species level: a biochemical method, matrix-assisted laser desorption ionization mass spectrometry-time of flight (MALDI-TOF MS), 16S rRNA sequencing, and housekeeping gene sequencing (gyrB, rpoB). MATERIALS AND METHODS: We analyzed 65 Aeromonas isolates recovered from patients at a university hospital in Korea between 1996 and 2012. The isolates were recovered from frozen states and tested using the following four methods: a conventional biochemical method, 16S rRNA sequencing, housekeeping gene sequencing with phylogenetic analysis, and MALDI-TOF MS. RESULTS: The conventional biochemical method and 16S rRNA sequencing identified Aeromonas at the genus level very accurately, although species level identification was unsatisfactory. MALDI-TOF MS system correctly identified 60 (92.3%) isolates at the species level and an additional four (6.2%) at the genus level. Overall, housekeeping gene sequencing with phylogenetic analysis was found to be the most accurate in identifying Aeromonas at the species level. CONCLUSION: The most accurate method of identification of Aeromonas to species level is by housekeeping gene sequencing, although high cost and technical difficulty hinder its usage in clinical settings. An easy-to-use identification method is needed for clinical laboratories, for which MALDI-TOF MS could be a strong candidate.

Increasing Carbapenem-Resistant Gram-Negative Bacilli and Decreasing Metallo-beta-Lactamase Producers over Eight Years from Korea

The trends and types of carbapenemase-producing Gram-negative bacilli were analyzed from clinical specimens collected between 2005 and 2012 at a Korean teaching hospital. The proportions of carbapenem-resistant Acinetobacter spp. increased markedly to 66%. Metallo-beta-lactamase producers significantly decreased and the majority shifted from the bla(VIM-2) type to the bla(IMP-1) type.

Bacteroides faecis and Bacteroides intestinalis Recovered from Clinical Specimens of Human Intestinal Origin

We report three cases of recently named Bacteroides spp. isolates, two B. faecis isolates and one B. intestinalis isolate from clinical specimens of inpatients at a Korean tertiary-care hospital in 2011. All isolates were susceptible to piperacillin-tazobactam, imipenem, meropenem, chloramphenicol, and metronidazole.