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Background@#Blastocystis is a genus of intestinal, anaerobic protozoan parasites that can be isolated from humans, animals, and the environment. We aimed to determine the distribution of Blastocystis and subtypes (STs) using stool samples obtained from healthy volunteers at collection centers in South Korea. @*Methods@#A total of 478 stool samples from volunteers were collected at five collection centers throughout South Korea. The presence of Blastocystis was determined using PCR based on the small subunit (SSU) rRNA gene, and Blastocystis STs were confirmed through sequencing of the SSU rRNA gene. @*Results@#Molecular analysis revealed the presence of Blastocystis in 27 (5.6%) of the enrolled participants. Two STs were identified: ST3 (66.7%) and ST1 (33.3%). The positive rates of Blastocystis varied by geographical region, ranging from 1.2%–12.0%. ST3 was the predominant subtype in all centers except one, where only ST1 was isolated. Phylogenic analysis showed clustering based on ST, but no significant differences were found among the regions. There was no association between Blastocystis colonization and either age or sex of the participants. @*Conclusions@#The results of this multicenter study demonstrated colonization by Blastocystis, mainly ST3, in the gastrointestinal tracts of asymptomatic individuals in South Korea.
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Primary amebic meningoencephalitis (PAM) is a rare, but almost always fatal, central nervous system infection caused by Naegleria fowleri, which are thermophilic free-living amoeba. Here, we report the first case of PAM detected in South Korea, probably imported from Thailand. Despite antimicrobial treatment for N. fowleri infection with a combination of intravenous liposomal amphotericin B, fluconazole, azithromycin, and oral rifampin, the patient died 13 days after the onset of symptoms. Clinicians in South Korea treating severe meningoencephalitis, especially in individuals returning from tropical areas, are encouraged to include PAM in the differential diagnoses, given the accelerated global warming and increased overseas trips.
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Background@#Rapid antimicrobial susceptibility testing (RAST) is important for the appropriate treatment of bloodstream infections. The QMAC-dRAST system (QuantaMatrix Inc., Korea) can directly perform RAST using positive blood culture samples with microscopic imaging. This study aimed to evaluate the performance of the QMAC-dRAST system for AmpCβ-lactamase-producing Enterobacterales. @*Methods@#Eighty isolates (20 Morganella morganii, 20 Serratia marcescens, 10 Klebsiella aerogenes, 10 Enterobacter cloacae, and 20 Citrobacter freundii) and 14 antimicrobial agents were included in the antimicrobial susceptibility testing (AST). The performance of the QMAC-dRAST system was evaluated by simulating the clinical blood culturing process. We conducted a comparative evaluation of the QMAC-dRAST and Vitek 2 systems (bioMérieux Inc., France). Broth microdilution tests were performed as the reference method to resolve any discrepancies in the AST results between the two systems. @*Results@#For 20 M. morganii and 20 S. marcescens, the categorical agreement (CA) between the QMAC-dRAST and Vitek 2 systems increased from 55.4% to 83.8% after AST algorithm optimization. Moreover, the discrepancy rates decreased as follows: from 19.1% to 5.4% very major errors (VME), from 38.3% to 4.3% major errors (ME), and from 14.6% to 12.1% minor errors (mE) for the QMAC-dRAST system compared to the Vitek 2 system. For all 80 tested isolates, the QMAC-dRAST system showed 93.0% CA, 1.7% VME, 2.3% ME, and 4.9% mE. @*Conclusion@#The QMAC-dRAST system was comparable to the Vitek 2 system after AST algorithm optimization for AmpC β-lactamase-producers, which are major pathogens and require time to express the enzyme. However, further modifications of the AST algorithm are still warranted.
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Background@#Although urine culture is considered a reference standard for the diagnosis of urinary tract infection (UTI), it is time-consuming, labor-intensive, and expensive. Here, we evaluated the performance of five recent automated urine analyzers for UTI diagnosis. @*Methods@#For the 510 specimens analyzed, the criterion for ‘significant bacteriuria’ was defined as ≥ 104 CFU/mL in the inoculated plate for all specimens or ≥ 103 CFU/mL for specimens from patients using a Foley catheter or with urinary symptoms. Sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of UTI were analyzed using indicators individually, in different combinations, or with various cut-off values. @*Results@#Seventy-one specimens (13.9%) exhibited ‘significant bacteriuria’. In the eceiver operating characteristics curve analysis, UF-5000 (Sysmex Corp., Japan) showed the highest area under the curve values for both males and females (0.876 and 0.846, respectively). The PPVs for specimens from males with all indicators positive increased up to 100% after adjusting the cut-off values. NPVs for specimens with all indicators negative were 94.3%– 98.2% in males and 78.1%–93.8% in females after adjusting the cut-off values. @*Conclusion@#As a rapid and accurate diagnostic tool, urine sediment analyzers can be valuable for UTI diagnosis by reducing unnecessary culture and can help clinicians determine a treatment plan.
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Background@#Although urine culture is considered a reference standard for the diagnosis of urinary tract infection (UTI), it is time-consuming, labor-intensive, and expensive. Here, we evaluated the performance of five recent automated urine analyzers for UTI diagnosis. @*Methods@#For the 510 specimens analyzed, the criterion for ‘significant bacteriuria’ was defined as ≥ 104 CFU/mL in the inoculated plate for all specimens or ≥ 103 CFU/mL for specimens from patients using a Foley catheter or with urinary symptoms. Sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of UTI were analyzed using indicators individually, in different combinations, or with various cut-off values. @*Results@#Seventy-one specimens (13.9%) exhibited ‘significant bacteriuria’. In the eceiver operating characteristics curve analysis, UF-5000 (Sysmex Corp., Japan) showed the highest area under the curve values for both males and females (0.876 and 0.846, respectively). The PPVs for specimens from males with all indicators positive increased up to 100% after adjusting the cut-off values. NPVs for specimens with all indicators negative were 94.3%– 98.2% in males and 78.1%–93.8% in females after adjusting the cut-off values. @*Conclusion@#As a rapid and accurate diagnostic tool, urine sediment analyzers can be valuable for UTI diagnosis by reducing unnecessary culture and can help clinicians determine a treatment plan.
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Purpose@#Here, we report a case of a fungal corneal ulcer caused by Talaromyces allahabadensis (T. allahabadensis).Case summary: A 69-year-old male was admitted to our hospital with pain and hyperemia in his left eye after 2 months of treatmentat a local clinic for herpetic keratitis. The patient had a previous history of trauma to his left eye caused by a persimmon treebranch. He had a peripheral epithelial defect, stromal infiltration, and severe corneal edema in his left eye. Gram staining, a KOHsmear, and a culture were performed using corneal specimens; the results were all negative. With the assumption of herpetickeratitis, antiviral and empirical antibiotic treatments were started. After 2 weeks, the stromal infiltrations on his left eye increased,so we again conducted staining and culture studies. T. allahabadensis was isolated from a specimen, so treatment wasstarted using antifungal agents, and a conjunctival flap graft was performed due to the risk of a corneal perforation. @*Conclusions@#A case of corneal ulcer caused by T. allahabadensis in a patient with posttraumatic herpetic keratitis was successfullytreated with antifungal agents and conjunctival flap surgery.
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BACKGROUND: The existing modified carbapenem inactivation methods (mCIMs) recommended by the CLSI for detecting carbapenemase production have not been applicable for Acinetobacter baumannii. We evaluated the influence of matrices used in mCIMs and CIMTris on the stability of the disks for detecting carbapenemase producers and suggested optimal mCIM conditions for detecting carbapenemase-producing A. baumannii. METHODS: Seventy-three A. baumannii isolates characterized for antimicrobial susceptibility and carbapenemase encoding genes were tested for carbapenemase production using mCIM and CIMTris. The influence of the matrices (Tryptic soy broth [TSB] and Tris-HCl) used in these methods on the stability of the meropenem (MEM) disk was also evaluated. The mCIM conditions were adjusted to enhance screening sensitivity and specificity for detecting carbapenemase-producing A. baumannii. RESULTS: The matrices had an impact on the stability of the MEM disk after the incubation period (two or four hrs). TSB nutrient broth is an appropriate matrix for mCIM compared with Tris-HCl pH 7.6, which leads to the loss of MEM activity in CIMTris. The sensitivity and the specificity of the optimal mCIM were both 100%. CONCLUSIONS: We established optimal mCIM conditions for simple, accurate, and reproducible detection of carbapenemase-producing A. baumannii.
Subject(s)
Acinetobacter baumannii , Acinetobacter , Hydrogen-Ion Concentration , Mass Screening , Methods , Sensitivity and SpecificityABSTRACT
BACKGROUND: As the spread of carbapenemase-producing Enterobacteriaceae poses a critical threat to public health, rapid detection of carbapenemase genes is urgently required for prompt initiation of appropriate antimicrobial therapy and infection control. We evaluated the performance of Xpert Carba-R v.2 (Cepheid, USA) compared with that of culture-based conventional PCR.METHODS: Using the results of 5,479 consecutive clinical rectal swabs, discrepant analysis (enriched culture followed by PCR) was performed for all discordant samples (N=100), which were Carba-R v.2-positive and culture-negative.RESULTS: Among the samples, 206 carbapenemase genes (3.6%) were detected by Carba-R v.2. The sensitivity and specificity were 95.0% and 98.1%, respectively. The positive predictive value (PPV) and negative predictive value (NPV) were 49.0% and 99.9%, respectively. Following discrepant analysis, the PPV increased to 73.5% and the low PPV (8.1%) of the 86 non-KPC improved to 48.8%. Among the 105 discrepancies, NDM was the most frequently observed (N=56), followed by KPC (N=26), VIM (N=10), IMP (N=8), OXA-48 (N=5). The threshold cycle values between discordant vs. concordant and resolved groups were significantly different (P<0.001).CONCLUSIONS: Carba-R v.2 is a rapid and sensitive method for detecting carbapenemase-encoding genes compared with culture-based conventional PCR. Most of our discrepant results were non-KPC genes. Thus, the clinical significance of the non-KPC positive cases detected by Carba-R v.2 should be investigated. This assay would be useful for deciding whether to isolate pre-exposed patients in hospital settings, based on the high specificity and NPV.
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Humans , Enterobacteriaceae , Infection Control , Korea , Methods , Polymerase Chain Reaction , Public Health , Sensitivity and SpecificityABSTRACT
BACKGROUND: Colistin has become a last-resort antibiotic for the management of multidrug-resistant gram-negative bacteria. The disk diffusion test is cheap and easy to perform but may be unreliable for colistin susceptibility testing due to poor diffusion of the large colistin molecule. An improved agar diffusion test would increase the reliability of colistin susceptibility testing. This study aimed to modify Muller-Hinton agar (MHA) to improve colistin diffusion in agar.METHODS: MHA was modified by reducing the agar concentration from 100% to 30% and supplementing with protamine. We tested 60 gram-negative clinical isolates of Pseudomonas aeruginosa (N=27) and Acinetobacter calcoaceticus-baumannii complex (N=33). Disk diffusion test results were interpreted based on minimum inhibitory concentrations determined by broth microdilution.RESULTS: The modified MHA yielded the best performance metrics, including 94.7% sensitivity, 100% specificity, and an area under the curve of 0.995 (95% confidence interval, 0.982–1.000), P<0.001, at a cut-off point of 13 mm.CONCLUSIONS: A reduction of the agar concentration from 100% to 30% and the addition of protamine improved colistin diffusion in agar and allowed routine colistin susceptibility testing in a clinical microbiology laboratory, but should be handled with caution.
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No abstract available.
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BACKGROUND: The weather has well-documented effects on infectious disease and reports suggest that summer peaks in the incidences of gram-negative bacterial infections among hospitalized patients. We evaluated how season and temperature changes affect bloodstream infection (BSI) incidences of major pathogens to understand BSI trends with an emphasis on acquisition sites.METHODS: Incidence rates of BSIs by Staphylococcus aureus, Enterococcus spp., Escherichia coli, Klebsiella pneumoniae, Acinetobacter spp., and Pseudomonas aeruginosa were retrospectively analyzed from blood cultures during 2008–2016 at a university hospital in Seoul, Korea according to the acquisition sites. Warm months (June–September) had an average temperature of ≥20℃ and cold months (December–February) had an average temperature of ≤5℃.RESULTS: We analyzed 18,047 cases, where 43% were with community-onset BSI. E. coli (N = 5,365) was the most common pathogen, followed by Enterococcus spp. (N = 3,980), S. aureus (N = 3,075), K. pneumoniae (N = 3,043), Acinetobacter spp. (N = 1,657), and P. aeruginosa (N = 927). The incidence of hospital-acquired BSI by Enterococcus spp. was weakly correlated with temperature, and the median incidence was higher during cold months. The incidence of community-onset BSI by E. coli was higher in warm months and was weakly correlated with temperature.CONCLUSION: We found seasonal or temperature-associated variation in some species-associated BSIs. This could be a useful information for enhancing infection control and public health policies by taking season or climate into consideration.
Subject(s)
Humans , Acinetobacter , Climate , Climate Change , Communicable Diseases , Enterococcus , Escherichia coli , Gram-Negative Bacterial Infections , Incidence , Infection Control , Klebsiella pneumoniae , Korea , Pneumonia , Pseudomonas aeruginosa , Public Health , Retrospective Studies , Seasons , Seoul , Staphylococcus aureus , Tertiary Care Centers , WeatherABSTRACT
BACKGROUND: Next-generation sequencing is increasingly used for taxonomic identification of pathogenic bacterial isolates. We evaluated the performance of a newly introduced whole genome-based bacterial identification system, TrueBac ID (ChunLab Inc., Seoul, Korea), using clinical isolates that were not identified by three matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) systems and 16S rRNA gene sequencing. METHODS: Thirty-six bacterial isolates were selected from a university-affiliated hospital and a commercial clinical laboratory. Species was identified by three MALDI-TOF MS systems: Bruker Biotyper MS (Bruker Daltonics, Billerica, MA, USA), VITEK MS (bioMérieux, Marcy l'Étoile, France), and ASTA MicroIDSys (ASTA Inc., Suwon, Korea). Whole genome sequencing was conducted using the Illumina MiSeq system (Illumina, San Diego, CA, USA), and genome-based identification was performed using the TrueBac ID cloud system (www.truebacid.com). RESULTS: TrueBac ID assigned 94% (34/36) of the isolates to known (N=25) or novel (N=4) species, genomospecies (N=3), or species group (N=2). The remaining two were identified at the genus level. CONCLUSIONS: TrueBac ID successfully identified the majority of isolates that MALDI-TOF MS failed to identify. Genome-based identification can be a useful tool in clinical laboratories, with its superior accuracy and database-driven operations.
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Genes, rRNA , Genome , Mass Spectrometry , SeoulABSTRACT
BACKGROUND: Respiratory tract infections are major public health threats, and the identification of their causative microbes helps clinicians to initiate timely and appropriate antimicrobial therapy and prevent the secondary spread of infection. The main goal of this study was to compare two multiplex real-time polymerase chain reaction (PCR) assays used to detect respiratory viral pathogens in nasopharyngeal swab specimens. METHODS: Between September and October 2017, a total of 84 nasopharyngeal specimens were obtained consecutively from patients in a tertiary hospital using a flocked swab with 3 mL universal transport medium (COPAN Diagnostics, USA). A total of 64 positive and 20 negative sample results from the LG AdvanSure RV real-time RT-PCR kit (LG Life Sciences, Korea) were further retested using a new AdvanSure RV-plus a real-time RT-PCR kit to compare their performance. RESULTS: Statistical analysis of positive and negative agreement between the two different kits was conducted between the newly introduced AdvanSure RV-plus real-time RT-PCR kit and the AdvanSure RV real-time RT-PCR. The overall agreement was 96.4%, with positive agreement of 98.4% and negative agreement of 90%. The evaluated sensitivity and specificity of AdvanSure RV-plus real-time RT-PCR were 96.9% and 94.7%, respectively, with a kappa value of 0.9 (P<0.001). CONCLUSION: The performances of LG AdvanSure RV real-time RT-PCR and the new AdvanSure RV-plus real-time RT-PCR kit showed strong overall agreement. AdvanSure RV-plus real-time RT-PCR had a better detection rate and could detect coronavirus 229E and enterovirus, especially with a high detection rate in coinfection. AdvanSure RV-plus real-time RT-PCR can be considered a useful tool for respiratory virus diagnosis in clinical laboratories.
Subject(s)
Humans , Biological Science Disciplines , Coinfection , Coronavirus , Diagnosis , Enterovirus , Multiplex Polymerase Chain Reaction , Pneumonia , Public Health , Real-Time Polymerase Chain Reaction , Respiratory Tract Infections , Sensitivity and Specificity , Tertiary Care CentersABSTRACT
Chryseobacterium hominis is non-fermenting Gram-negative rod that was first identified as a novel species in 2007. Here, we report the first clinical case of C. hominis bacteremia, which was confirmed by MALDI-TOF MS and 16S rRNA gene sequencing. A 16-year-old boy diagnosed with acute lymphoblastic leukemia was hospitalized for three months. Two sets of blood culture test through a peripherally inserted central catheter (PICC), which was inserted a month ago, was performed when his white blood cell count declined and he had a high fever. Colonies of medium sizes that looked round, mucoid, sticky, and grayish on blood and chocolate agar plates were observed. Identification of bacteria using the VITEK MALDI-TOF MS system (BioMérieux, France) was not successful and the VITEK 2 system (BioMérieux, USA) indicated Sphingomonas paucimobilis, with a questionable level of confidence (92%). However, Microflex LT Biotyper (Bruker Daltonics, Germany) showed C. homins (log score: 1.81) and sequence of 16S rRNA showed a 100% identity with C. hominis. Piperacillin-tazobactam was administered since the isolate was susceptible to piperacillin-tazobactam but C. hominis showed growth in the next four follow-up culture of blood drawn through PICC. The fever subsided only after PICC was changed. The clinical prognosis and antimicrobial susceptibility test of C. hominis should be further studied.
Subject(s)
Adolescent , Humans , Male , Agar , Bacteremia , Bacteria , Cacao , Catheters , Chryseobacterium , Fever , Follow-Up Studies , Genes, rRNA , Leukocyte Count , Precursor Cell Lymphoblastic Leukemia-Lymphoma , Prognosis , SphingomonasABSTRACT
BACKGROUND: Fast identification of Candida glabrata is important, because empirical antifungal therapy for fungemia with C. glabrata and non-C. glabrata varies. We proposed an algorithm for rapid presumptive diagnosis to identify fungemia with C. glabrata using earlier or only growth from anaerobic bottles and longer time to positivity (TTP) in blood cultures. METHODS: Positivity and TTP using the BacT/Alert 3D system (bioMerieux Inc, USA) with resin bottles (FA Plus and FN Plus) were analyzed in 215 candidemia patients from June 2014 to June 2016 in a university-affiliated hospital in Korea. RESULTS: A higher proportion of earlier or only growth from anaerobic bottles was observed in C. glabrata (38.8%, 7/18) than in C. albicans (7.6%, 8/105), C. parapsilosis (10.5%, 4/138), and C. tropicalis (9.2%, 5/54) (P=0.006). The mean (±standard deviation) TTP for C. glabrata was 41.7 h (±16.3 h) compared with 26.7 h (±15.9 h) for C. albicans, 33.4 h (±8.4 h) for C. parapsilosis, and 23.1 h (±17.3 h) for C. tropicalis (P 31.4 h. CONCLUSION: This two-step algorithm in the BacT/Alert 3D system could be the basis for an initial empirical antifungal therapy for fungemia with C. glabrata prior to final identification.
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Humans , Candida glabrata , Candida , Candidemia , Diagnosis , Fungemia , Korea , Sensitivity and SpecificityABSTRACT
BACKGROUND: The molecular characterization of Streptococcus dysgalactiae subsp. equisimilis (SDSE) has not yet been performed in Korea. This study aimed to find the differences or similarities in the clinical features, molecular epidemiological findings, and antimicrobial resistance patterns of SDSE from two countries (Korea and Japan). METHODS: SDSE isolates were collected from Korea (N=69) from 2012–2016 and Japan (N=71) from 2014–2016. Clinical characteristics, emm genotypes, and sequence types (STs) were compared. Microdilution tests were performed using different antimicrobials, and their resistance determinants were screened. RESULTS: Median ages were 69 years in Korea and 76 years in Japan. The most common underlying diseases were diabetes and malignancy. Blood-derived isolates comprised 36.2% and 50.7% of Korean and Japanese isolates, respectively; mortality was not different between the two groups (5.8% vs 9.9%, P=0.53). Among Korean isolates with 20 different combined ST-emm types, ST127-stG245 (N=16), ST128-stG485 (N=10), and ST138-stG652 (N=8) were prevalent. Among Japanese isolates with 29 different combined types, ST17-stG6792 (N=11), ST29-stG485 (N=7), and ST205-stG6792 (N=6) were prevalent. Resistance rates to erythromycin, clindamycin, and minocycline were 34.8%, 17.4%, and 30.4% in Korea and 28.2%, 14.1%, and 21.4% in Japan, respectively. CONCLUSIONS: SDSE infections commonly occurred in elderly persons with underlying diseases. There was a significant difference in the distribution of ST-emm types between the two countries. Antimicrobial resistance rates were comparable with different frequencies of resistance determinants in each country.
Subject(s)
Aged , Humans , Asian People , Clindamycin , Erythromycin , Genotype , Japan , Korea , Minocycline , Mortality , Multilocus Sequence Typing , StreptococcusABSTRACT
BACKGROUND: Stool cultures are essential for diagnosing bacterial gastrointestinal infections. Laboratory procedures and target organisms for stool culture testing can vary by institute. Therefore, a nationwide survey was conducted to determine the stool culture procedures performed in clinical laboratories of Korea. METHODS: Questionnaires were delivered by electronic mail to 98 clinical microbiologists and by Google survey to the 301 institutes participating in the Korean External Quality Control Program of Bacterial Cultures. RESULTS: Of the 68 institutes sent complete responses, Gram staining and wet smears were performed in 73.5% and 64.7%, respectively. A molecular test was conducted in 32.4% of laboratories, and blood agar plates were used in 23.5%. Staphylococcus aureus , Pseudomonas aeruginosa , and Candida species were reported for predominant growth by 17.6%, 8.8%, and 7.4% of the respondents, respectively. Campylobacter culture was available only in 25.0% of laboratories, whereas Clostridium difficile could be cultivated in 38.2%. Susceptibility testing results of Salmonella-Shigella were reported for all tested antibiotics in 22.1% of laboratories, whereas 69.1% reported results for antibiotics specified by the Clinical and Laboratory Standard Institute guidelines. CONCLUSIONS: Methods and results of gram staining, wet smears, use of stool culture media, target microorganisms, and antibiotic susceptibility differed among the institutes. Further discussion is needed to develop a standardized protocol for stool culture to maximize isolation of bacterial pathogens that cause gastroenteritis.
Subject(s)
Academies and Institutes , Agar , Anti-Bacterial Agents , Campylobacter , Candida , Clostridioides difficile , Culture Media , Diagnosis , Diarrhea , Electronic Mail , Gastroenteritis , Korea , Methods , Pseudomonas aeruginosa , Quality Control , Staphylococcus aureus , Surveys and QuestionnairesABSTRACT
BACKGROUND: Prolonged transport or poor accessibility of blood culture equipment during night time may cause delayed entry of blood culture bottles. The effect of prestorage conditions on time to detection (TTD) for the blood culture was evaluated for the important gram-negative lactose nonfermentative bacteria. METHODS: Three different clinical isolates of Pseudomonas aeruginosa, Acinetobacter baumannii, Stenotrophomonas maltophilia, and Burkholdera cepacia were diluted to 150 CFU/mL and 15 CFU/mL and inoculated into standard aerobic bottles. These were stored at 25℃ and at 37℃ for 0, 6, 12, 18, and 24 h. They were entered to BacT/Alert 3D Systems (bio-Mérieux Inc.) and TTD was monitored for each condition. RESULTS: At the 150 CFU/mL concentration, P. aeruginosa and A. baumannii showed false-negative for the bottles prestored at 37℃ for 18 h and 24 h, respectively. However, there was no false-negative for S. maltophilia or B. cepacia at any prestorage conditions. There was a significant decrease of TTD for all experimental microorganisms except P. aeruginosa prestored for 24 h either at 25℃ or at 37℃ (P< 0.05). CONCLUSION: Delayed entry may cause false-negative, especially for the high level of bacteremia of P. aeruginosa or A. baumannii when the bottles are stored at 37℃ for ≥18 h. TTD could be reduced by prestorage of the bottles at 37℃ until 12 h without false-negative for nonfermentative bacteria.