Objective: To improve our understanding of EPEC, this study focused on analyzing and comparing the genomic characteristics of EPEC isolates from humans and companion animals in Korea. Methods: The whole genome of 26 EPEC isolates from patients with diarrhea and 20 EPEC isolates from companion animals in Korea were sequenced using the Illumina HiSeq X (Illumina, USA) and Oxford Nanopore MinION (Oxford Nanopore Technologies, UK) platforms. Results: Most isolates were atypical EPEC, and did not harbor the bfpA gene. The most prevalent virulence genes were found to be ompT (humans: 61.5%; companion animals:60.0%) followed by lpfA (humans: 46.2%; companion animals: 60.0%). Although pangenome analyses showed no apparent correlation among the origin of the strains, virulence profiles, and antimicrobial resistance profiles, isolates included in clade A obtained from both humans and companion animals exhibited high similarity. Additionally, all the isolates included in clade A encoded the ompT gene and did not encode the hlyE gene. The two isolates from companion animals harbored an incomplete bundle-forming pilus region encoding bfpA and bfpB. Moreover, the type IV secretion system-associated genes tra and trb were found in the bfpA-encoding isolates from humans. Conclusions and Relevance: Whole-genome sequencing enabled a more accurate analysis of the phylogenetic structure of EPEC and provided better insights into the understanding of EPEC epidemiology and pathogenicity.

Objective: To improve our understanding of EPEC, this study focused on analyzing and comparing the genomic characteristics of EPEC isolates from humans and companion animals in Korea. Methods: The whole genome of 26 EPEC isolates from patients with diarrhea and 20 EPEC isolates from companion animals in Korea were sequenced using the Illumina HiSeq X (Illumina, USA) and Oxford Nanopore MinION (Oxford Nanopore Technologies, UK) platforms. Results: Most isolates were atypical EPEC, and did not harbor the bfpA gene. The most prevalent virulence genes were found to be ompT (humans: 61.5%; companion animals:60.0%) followed by lpfA (humans: 46.2%; companion animals: 60.0%). Although pangenome analyses showed no apparent correlation among the origin of the strains, virulence profiles, and antimicrobial resistance profiles, isolates included in clade A obtained from both humans and companion animals exhibited high similarity. Additionally, all the isolates included in clade A encoded the ompT gene and did not encode the hlyE gene. The two isolates from companion animals harbored an incomplete bundle-forming pilus region encoding bfpA and bfpB. Moreover, the type IV secretion system-associated genes tra and trb were found in the bfpA-encoding isolates from humans. Conclusions and Relevance: Whole-genome sequencing enabled a more accurate analysis of the phylogenetic structure of EPEC and provided better insights into the understanding of EPEC epidemiology and pathogenicity.

Objective: To improve our understanding of EPEC, this study focused on analyzing and comparing the genomic characteristics of EPEC isolates from humans and companion animals in Korea. Methods: The whole genome of 26 EPEC isolates from patients with diarrhea and 20 EPEC isolates from companion animals in Korea were sequenced using the Illumina HiSeq X (Illumina, USA) and Oxford Nanopore MinION (Oxford Nanopore Technologies, UK) platforms. Results: Most isolates were atypical EPEC, and did not harbor the bfpA gene. The most prevalent virulence genes were found to be ompT (humans: 61.5%; companion animals:60.0%) followed by lpfA (humans: 46.2%; companion animals: 60.0%). Although pangenome analyses showed no apparent correlation among the origin of the strains, virulence profiles, and antimicrobial resistance profiles, isolates included in clade A obtained from both humans and companion animals exhibited high similarity. Additionally, all the isolates included in clade A encoded the ompT gene and did not encode the hlyE gene. The two isolates from companion animals harbored an incomplete bundle-forming pilus region encoding bfpA and bfpB. Moreover, the type IV secretion system-associated genes tra and trb were found in the bfpA-encoding isolates from humans. Conclusions and Relevance: Whole-genome sequencing enabled a more accurate analysis of the phylogenetic structure of EPEC and provided better insights into the understanding of EPEC epidemiology and pathogenicity.

Objective: To improve our understanding of EPEC, this study focused on analyzing and comparing the genomic characteristics of EPEC isolates from humans and companion animals in Korea. Methods: The whole genome of 26 EPEC isolates from patients with diarrhea and 20 EPEC isolates from companion animals in Korea were sequenced using the Illumina HiSeq X (Illumina, USA) and Oxford Nanopore MinION (Oxford Nanopore Technologies, UK) platforms. Results: Most isolates were atypical EPEC, and did not harbor the bfpA gene. The most prevalent virulence genes were found to be ompT (humans: 61.5%; companion animals:60.0%) followed by lpfA (humans: 46.2%; companion animals: 60.0%). Although pangenome analyses showed no apparent correlation among the origin of the strains, virulence profiles, and antimicrobial resistance profiles, isolates included in clade A obtained from both humans and companion animals exhibited high similarity. Additionally, all the isolates included in clade A encoded the ompT gene and did not encode the hlyE gene. The two isolates from companion animals harbored an incomplete bundle-forming pilus region encoding bfpA and bfpB. Moreover, the type IV secretion system-associated genes tra and trb were found in the bfpA-encoding isolates from humans. Conclusions and Relevance: Whole-genome sequencing enabled a more accurate analysis of the phylogenetic structure of EPEC and provided better insights into the understanding of EPEC epidemiology and pathogenicity.

Background: Ensuring reference material (RM) commutability is crucial for evaluating measurement traceability in order to standardize laboratory tests. However, commutability assessment is not routinely performed. We assessed whether RMs prepared following CLSI C37-A guidelines could be used without assessing commutability by evaluating their commutability for four lipid measurements using the International Federation of Clinical Chemistry and Laboratory Medicine (IFCC) and CLSI EP14 protocols. Methods: We analyzed total cholesterol (TC), triglycerides (TGs), high-density lipoprotein cholesterol (HDL-C), and low-density lipoprotein cholesterol (LDL-C) in frozen sera from 20 individuals and 11 RMs, prepared by the Korea Disease Control and Prevention AgencyLaboratory Standardization Project (per CLSI C37-A), using six routine measurement procedures (MPs). Regression equations and 95% prediction intervals derived from single-donor sera were analyzed following CLSI EP14. The IFCC protocol was used to assess differences in inter-MP biases between RM and clinical samples. The effect of the TG concentration on commutability was evaluated by analyzing biases between MP results and reference procedure-assigned values. Results: RMs were commutable for most MP pairs for TC and TG. Commutability for HDL-C and LDL-C varied across RMs, with RM10 and RM11 showing higher TG levels (2.38 and 2.95 mmol/L, respectively) and lower commutability. Increased bias percentages from assigned values were observed for RMs with higher TG levels. Conclusions RMs prepared per CLSI C37-A were commutable with most MP pairs for TC and TG. Elevated TG levels affected HDL-C and LDL-C commutability, highlighting the need to consider TG concentrations during RM preparation and assess commutability to standardize laboratory tests.

Helicobacter cinaedi is an enterohepatic species. It can cause bacteremia, gastroenteritis, and cellulitis, particularly in immunocompromised individuals, such as those with acquired immunodeficiency syndrome, malignancy, or alcoholism. There are no previous reports of H. cinaedi infection in Korea. A 71-yr-old man was admitted to the emergency room because of dyspnea on November 9, 2011. He had undergone splenectomy 3 yr ago because of immune hemolytic anemia. Chest plain radiography revealed bilateral pleural effusion. He developed fever on hospital day (HD) 21. Three sets of blood cultures were taken, and gram-negative spiral bacilli were detected in all aerobic vials. The isolate grew in tiny colonies on chocolate agar after 3-day incubation under microaerophilic conditions. This organism tested positive for catalase and oxidase, and negative for urease. The 16S rRNA gene sequence of this isolate exhibited 99.8% homology with the published sequence of H. cinaedi CCUG 18818T (GenBank accession no. ABQT01000054) and 98.5% homology with the sequence of Helicobacter bilis Hb1T (GenBank accession no. U18766). The patient was empirically treated with piperacillin/tazobactam and levofloxacin, and discharged with improvement on HD 31. To our knowledge, this is the first report of H. cinaedi bacteremia in an asplenic patient. Asplenia appears to be a risk factor for H. cinaedi bacteremia.

BACKGROUND: In 2010, the Clinical and Laboratory Standards Institute (CLSI) revised the minimum inhibitory concentration (MIC) breakpoints of cephalosporins and aztreonam to exempt extended-spectrum beta-lactamase (ESBL) confirmatory tests for Enterobacteriaceae. However, the CLSI did not change the MIC breakpoint of cefepime. Here, a proficiency survey of a strain of ESBL-producing Klebsiella pneumoniae was analyzed for MIC distribution and interpretation of cephalosporins and aztreonam. METHODS: The survey strain, K. pneumoniae, which produced SHV-18, was distributed to 170 clinical laboratories as 1 of 5 presumptive clinical specimens through the proficiency survey of the clinical microbiology division of the Korean Association of Quality Assurance for Clinical Laboratories (KAQACL). MIC, zone diameter of inhibition (ZDI), and interpretation of tested antimicrobials, methods of antimicrobial susceptibility testing (AST), and ESBL confirmatory results were collected. RESULTS: According to the revised breakpoints of the 2010 CLSI guidelines, MIC results indicated resistance to aztreonam in 100%, cefepime in 5.5%, cefotaxime in 20%, ceftazidime in 100%, and ceftriaxone in 100% of samples by broth microdilution methods. ZDI results also indicated resistance to aztreonam in 75%, cefepime in 0%, cefotaxime in 66.7%, ceftazidime in 100%, and ceftriaxone in 80% of samples by disk diffusion method. Ninety (75.6%) participants performed an ESBL confirmatory test, and 89 (98.9%) reported ESBL-positive tests. Of the 55 laboratories that tested the susceptibility of cefepime, 50 (90.9%) self-reported to be "resistant" because of ESBL-positive results. CONCLUSIONS: In conclusion, susceptibility testing of ESBL producers against certain cephalosporins is not reliable enough to apply the revised breakpoints presented in the 2010 CLSI guidelines. It is therefore necessary to reach a consensus for interpretation of ASTs of ESBL producers in Korea. Ideally, clinicians should be provided two interpretations based on both the revised breakpoints and ESBL confirmatory testing.
Aztreonam ; beta-Lactamases ; Cefotaxime ; Ceftazidime ; Ceftriaxone ; Cephalosporins ; Consensus ; Diffusion ; Enterobacteriaceae ; Klebsiella ; Klebsiella pneumoniae ; Korea ; Microbial Sensitivity Tests ; Pneumonia ; Sprains and Strains

The HACEK group of microorganisms is responsible for approximately 3-6% of endocarditis cases and is a major cause of culture-negative endocarditis. Here, we report a case of Haemophilus parainfluenzae infective endocarditis that was diagnosed by direct PCR sequencing of 16S rRNA from resected vegetation. A healthy 26-yr-old man was admitted to the emergency room (ER) on March 27, 2011 because of intermittent high fever. The patient was prescribed cefpodoxime for 5 days at the ER. Six and 11 sets of blood cultures were performed at the ER and in a general ward, respectively, using BACTEC Plus Aerobic/F (Becton-Dickinson, USA) and Lytic Anaerobic/F Plus (BD) together. Echocardiography revealed a large vegetation at the posterior mitral valve leaflet. After performing mitral valvoplasty on hospital day (HD) 11, the vegetation tissue was cultured in thioglycolate broth, blood agar, Brucella agar, and MacConkey agar for 7 days, but no organism was grown. Direct PCR sequencing of 16S rRNA of the tissue revealed the presence of H. parainfluenzae. In the 17 sets of blood cultures, bacterial growth was detected in only 2 aerobic bottles of 5 sets taken at HD 9 after 10-day and 14-day incubation. The organism was identified as H. parainfluenzae by using the VITEK NHI card (bioMerieux, France). Direct PCR sequencing of vegetation could be useful in diagnosing bacterial pathogens in infective endocarditis patients, especially in culture-negative cases.
Agar ; Brucella ; Ceftizoxime ; Echocardiography ; Emergencies ; Endocarditis ; Fever ; Haemophilus ; Haemophilus parainfluenzae ; Humans ; Mitral Valve ; Paramyxoviridae Infections ; Patients' Rooms ; Polymerase Chain Reaction ; Sequence Analysis, RNA

BACKGROUND: Differentiation of atypical pathogens is important for community-acquired pneumonia (CAP). In this study, we compared sputum and nasopharyngeal swabs (NPS) for use in detection of Mycoplasma pneumoniae (MP), Chlamydophila pneumoniae (CP), and Legionella pneumophila (LP), using Seeplex PneumoBacter ACE Detection Assay (PneumoBacter; Seegene). METHODS: Sputum and NPS specimens were collected from patients in 15 hospitals. DNA was extracted from sputum using QIAamp DNA Stool Mini Kit (Qiagen) and from NPS using easyMAG (bioMerieux). Both types of specimens were evaluated by multiplex PCR using PneumoBacter. To determine the diagnostic performance of this assay, sputum samples were also tested using BD ProbeTec ET Atypical Pneumonia Assay (APA; Becton Dickinson). RESULTS: Among 217 sputum and NPS, 20 (9.2%), 2 (0.9%), and 0 sputum were positive for MP, LP, and CP, respectively, whereas 8 (3.7%) NPS were positive for MP. The sputum APA test yielded 186, 206, and 204 interpretable results for MP, LP, and CP, respectively. Of these, 21 (11.3%) were positive for MP, 2 (1.0%) were positive for LP, and 0 samples were positive for CP. Compared to APA, the sensitivity and specificity of the sputum assay for MP were 95.2% and 100.0%, respectively, whereas for the NPS assay, these were 38.1% and 93.9%. Sputum testing was more sensitive than NPS testing (P=0.002). For LP and CP diagnosis, PneumoBacter and APA tests agreed 100%. CONCLUSIONS: Specimen type is crucial and sputum is preferred over NPS for simultaneous detection of MP, LP, and CP using multiplex PCR in CAP.
Chlamydophila Infections/diagnosis ; Chlamydophila pneumoniae/*genetics/isolation & purification ; Community-Acquired Infections/*diagnosis ; DNA, Bacterial/analysis/isolation & purification ; Humans ; Legionella pneumophila/*genetics/isolation & purification ; Legionnaires' Disease/diagnosis ; Multiplex Polymerase Chain Reaction ; Mycoplasma pneumoniae/*genetics/isolation & purification ; Nasopharynx/*microbiology ; Pneumonia, Mycoplasma/diagnosis ; Reagent Kits, Diagnostic ; Sputum/*microbiology

Haemophilus influenzae has rarely been implicated as the causative agent of urinary tract infections (UTIs). However, cases of UTIs caused by H. influenza in patients with anatomical or functional urinary tract abnormalities have been steadily reported. We report a case of asymptomatic bacteriuria caused by H. influenzae in a kidney transplant recipient. The patient was a 61-yr-old woman who visited the hospital for a routine follow-up after receiving a kidney transplant from a living-related donor; the patient showed no symptoms. Urine microscopy revealed white blood cell (WBC) count of >30/high power field (HPF). Urine culture on blood agar showed non-hemolytic, tiny, translucent, grayish colonies with satellitism around beta-hemolytic colonies of Staphylococcus epidermidis. The organism in the satellite colonies was identified as H. influenzae by using VITEK Neisseria/Haemophilus Identification Card (bioMerieux, Marcy L'Etoile, France) and found to require both X and V factors for growth. The organism did not produce beta-lactamase. Urine culture performed 1 week later revealed H. influenza again. The patient was not treated with antimicrobials. Urine culture performed using chocolate agar 7 weeks later did not reveal H. influenzae. Since H. influenzae does not grow in the media commonly used for urine culture such as blood agar, the use of these media could lead to underestimation of the true frequency of H. influenzae. If UTI is suspected in a patient with anatomical or functional urinary tract abnormality, chocolate agar should be considered for urine culture.
Agar ; Bacteriuria ; beta-Lactamases ; Cacao ; Female ; Follow-Up Studies ; Haemophilus ; Haemophilus influenzae ; Humans ; Influenza, Human ; Kidney ; Kidney Transplantation ; Leukocytes ; Microscopy ; Staphylococcus epidermidis ; Transplants ; Urinary Tract ; Urinary Tract Infections