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The population divergence process of deep-sea vent invertebrates is driven by both biotic (e.g., dispersal during the larval stage) and abiotic factors such as deep-ocean currents, depth, and the geological setting of vents. However, little is known regarding the divergence of hydrothermal vent microorganisms. Therefore, our study sought to investigate the influence of geological and geographic factors on the divergence of symbiotic bacteria of Bathymodiolus vent mussels. The genetic differentiation patterns of symbionts were examined using next-generation sequencing DNA data in two ocean basins with distinct geological features: the slow-spreading Central Indian Ridge (CIR) and the fast- or superfast-spreading eastern Pacific Ridges. Our findings showed that the degree of differentiation of symbiont populations was geographically hierarchical: the highest between ocean basins, followed by inter-ridge sites between the East Pacific Rise and the Pacific Antarctic Ridge. The Easter Microplate intervening these two ridges acted as a biogeographic physical barrier for both symbionts and their host mussels. On a scale of intra-ridge, symbionts showed isolation by distance in the CIR but not in the eastern Pacific ridges. These contrasting genetic patterns relate to different ridge spreading rates determining most of the geological characteristics of mid-ocean ridges that affect the connectivity of vent habitats in space and time. At the intra-ridge geographic scale of the CIR, population divergence processes of both symbionts and hosts from separate three ridge segments were analyzed in detail using a genetic model of isolation with migration (IM). The phylogenetic topology of symbiont populations was congruent with the host populations, indicating the influence of common historical and physical constraints for habitats and dispersal between vents in the Central Indian Ridge. Collectively, our findings provide key insights into the dynamics of microbial population divergence in deep-sea vents.

The mytilid mussel Bathymodiolus thermophilus lives in the deep-sea hydrothermal vent regions due to its symbiotic relationship with chemosynthetic Gammaproteobacteria species which reside inside specialized gill cells. The symbionts in the gill bacteriocytes oxidize the reduced sulfur amply available in the vent environment. Here we sequenced and assembled the complete genome of a gill symbiont sampled from an individual mussel from the East Pacific Rise (EPR9N), using PacBio sequencing technology. The final symbiont assembly consists of a single contig size of 2.83 Mb, with a GC content of 38.6% and encodes for 2,133 protein-coding genes. CRISPR diversity analysis confirmed this genome originated from a single symbiont strain. Comparative analysis revealed 2,554 core gene clusters were shared with other B. thermophilus thiotrophic gill symbiont genomes, whereas 125 were unique to this EPR9N strain. In addition, we found that EPR9N strain has a unique hydrogenase operon among Bathymodiolus mussels consisting of additional H2-sensing hydrogenase subunits and a histidine kinase gene. Also, we found methylated regions sparsely distributed throughout the EPR9N genome, mainly in the transposases regions and densely present in the rRNA gene regions. Variation in genome size, gene content and genome re-arrangements across individual hosts suggest multiple symbiont strains can associate with B. thermophilus. This complete mussel symbiont genome will be invaluable for further comparative genomic analyses studying structural genome evolution, symbiont population diversity, and symbiont ecology in deep-sea chemosynthetic environments.

The emergence of multidrug-resistant Acinetobacter baumanniias a nosocomial pathogen is one of the major public health problems. The aim of this study was to evaluate the role of an efflux pump gene adeJ for the multidrug resistance of A. baumanniiclinical isolates. Two groups (MDRAB and SAB) of A. baumanniiclinical isolates were studied. The SAB group consisted of strains that did not meet the criteria of MDRAB and were susceptible to more categories of antibiotics than MDRAB. Antimicrobial susceptibility results obtained by VITEKⅡ system were used in data analysis and bacterial group allocation. We performed real-time reverse transcription PCR to determine relative expression of adeJ. We compared relative expression of adeJ in comparison groups by considering two viewpoints: i) MDRAB and SAB groups and ii) susceptible and non-susceptible groups for each antibiotic used in this study.The mean value of relative expression of adeJ of MDRAB and SAB groups was 1.4 and 0.92, respectively, and showed significant difference (P=0.002). The mean values of relative expression of adeJ of susceptible and non-susceptible groups to the antibiotics cefepime, ceftazidime, ciprofloxacin, imipenem, meropenem, tigecycline, piperacillin/tazobactam, ticarcillin/clavulanic acid, trimethoprim/sulfamethoxazole, piperacillin, and gentamicin showed statistically significant differences. The overexpression of adeIJK might contribute to the multi-drug resistance in A. baumanniiclinical isolates. Further, the overexpression of adeIJK might be one of the factors contributing to the resistance to numerous antibiotics.

Background Several factors contribute to differences in Streptococcus pneumoniae serotype distribution. We investigated the serotype distribution and antimicrobial resistance of S. pneumoniae isolated between 2014 and 2016 in Korea. Methods We collected a total of 1,855 S. pneumoniae isolates from 44 hospitals between May 2014 and May 2016, and analyzed the serotypes by sequential multiplex PCR. We investigated the distribution of each serotype by patient age, source of the clinical specimen, and antimicrobial resistance pattern. Results The most common serotypes were 11A (10.1%), followed by 19A (8.8%), 3 (8.5%), 34 (8.1%), 23A (7.3%), and 35B (6.2%). The major invasive serotypes were 3 (12.6%), 19A (7.8%), 34 (7.8%), 10A (6.8%), and 11A (6.8%). Serotypes 10A, 15B, 19A, and 12F were more common in patients ≤5 years old, while serotype 3 was more common in patients ≥65 years old compared with the other age groups. The coverage rates of pneumococcal conjugate vaccine (PCV)7, PCV10, PCV13, and pneumococcal polysaccharide vaccine 23 were 11.8%, 12.12%, 33.3%, and 53.6%, respectively. Of the 1,855 isolates, 857 (46.2%) were multi-drug resistant (MDR), with serotypes 11A and 19A predominant among the MDR strains. The resistance rates against penicillin, cefotaxime, and levofloxacin were 22.8%, 12.5%, and 9.4%, respectively. Conclusions There were significant changes in the major S. pneumoniae serotypes in the community. Non-PCV13 serotypes increased in patients ≤5 years old following the introduction of national immunization programs with the 10- and 13-polyvalent vaccines.

Background: Salmonella is an important pathogen that causes gastroenteritis and sepsis in humans. Recently, changes in serotype prevalence and an increase in antimicrobial resistance have been reported. This study investigated the distribution of Salmonella serotypes and determined the antimicrobial susceptibility of various strains. Methods: We collected 113 Salmonella isolates other than Salmonella serotype Typhi from 18 university hospitals in 2015. The serotypes were identified by Salmonella antisera O and H according to the Kauffman White scheme. Antimicrobial susceptibility tests for 12 antibiotics were performed using the disk diffusion method or E-test. Results: We identified 22 serotypes. Serotype group B (44.2%) was the most common, followed by groups C (34.5%) and D (21.2%). Salmonella I 4,[5],12:i:- (23.0%), S. Enteritidis (16.8%), and S. Typhimurium (12.4%) were the most common species. Resistance rates for ampicillin, chloramphenicol, ceftriaxone, and trimethoprim/sulfamethoxazole were 46.9%, 18.5%, 8.8%, and 5.3%, respectively. The intermediate resistance rate to ciprofloxacin was 29.2%. Six isolates were extended-spectrum β-lactamase (ESBL) producers, including 5 blaCTX-M-15 and 1 blaCTX-M-55. Conclusion: There have been changes in the serotype prevalence and antimicrobial resistance of Salmonella in Korea, with a high prevalence of CTX-M 15-positive strains. Continuous monitoring of Salmonella serotypes and antimicrobial resistance is warranted. (Ann Clin Microbiol 2019;22:55-60)

This study compared the accuracy of a new MALDI-TOF mass spectrometry system, ASTA MicroIDSys system, with that of MALDI Biotyper system for the identification of reference and clinical bacterial and yeast strains. The identification accuracy of the 2 systems was compared using a total of 406 strains comprising 142 aerobic and 180 anaerobic bacterial strains and 84 yeast strains. The genus and species identification rates were 98.0% and 89.4% using MicroIDSys and 96.1% and 89.4% using Biotyper, respectively. The species identification rates of MicroIDSys and Biotyper for aerobic bacteria were 93.0% and 97.2%, respectively, and those for anaerobic bacteria were 85.6% and 81.7%, respectively. The accuracy of yeast identification at the species level was 91.7% using MicroIDSys and 92.9% using Biotyper. These findings indicate that MicroIDSys could be useful for the accurate identification of bacteria and yeast in clinical microbiology laboratories.

Various mechanisms underlying antimicrobial resistance in Acinetobacter baumannii have been reported. There exists controversy regarding the relationships between efflux pump activity, biofilm formation, and antimicrobial resistance in A. baumannii. In this study, we investigated the relative expression of RND efflux pump genes, H33342 efflux activity, and biofilm-forming activity in 120 A. baumannii clinical isolates, examined their potential relationships with one another, and then statistically analyzed their effects on antibiotic resistance. High adeB expression and high H33342 efflux activity were correlated with low biofilm-forming activity. High adeB expression was significantly correlated with resistance to tigecycline and cefotaxime, but not with the multidrug resistance (MDR) phenotype. Importantly, only high adeJ expression was significantly correlated with the MDR phenotype, and was observed to be correlated with resistance to various antibiotics. However, we found no significant correlation between adeJ expression and biofilm-forming activity. Further, adeG expression was found to not be correlated with antibiotic resistance and biofilm-forming activity. The results of multivariate analysis showed that adeB overexpression and high H33342 efflux activity are related to biofilm-forming activity, and only adeJ overexpression is significantly associated with the MDR phenotype, highlighting the importance of adeJ overexpression.

This article contains supplementary data from the research paper entitled "A newly discovered Gigantidas bivalve mussel from the Onnuri Vent Field on the northern Central Indian Ridge" [1], describes a new mussel species within the subfamily Bathymodiolinae named Gigantidas vrijenhoeki. Data are comprised of two parts: 1) shell image and molecular analyses of G. vrijenhoeki and 2) metagenomic community analyses of gill-associated symbiotic bacteria on G. vrijenhoeki. G. vrijenhoeki data were obtained from type specimens described in Jang et al. 2020 [1]. The molecular analysis was conducted by calculating genetic distance at intra- and inter-specific level within genus Gigantidas based on the sequence data of two mitochondrial genes (COI and ND4). The metagenomic dataset of gill-associated symbionts were generated by Illumina Miseq sequencing of the V3-V4 region of 16S rRNA from 12 specimens of G. vrijenhoeki collected from the same vent site, Onnuri Vent Field.

This article contains supplementary data from the research paper entitled “A newly discovered Gigantidas bivalve mussel from the Onnuri Vent Field on the northern Central Indian Ridge” [1], describes a new mussel species within the subfamily Bathymodiolinae named Gigantidas vrijenhoeki. Data are comprised of two parts: 1) shell image and molecular analyses of G. vrijenhoeki and 2) metagenomic community analyses of gill-associated symbiotic bacteria on G. vrijenhoeki. G. vrijenhoeki data were obtained from type specimens described in Jang et al. 2020 [1]. The molecular analysis was conducted by calculating genetic distance at intra- and inter-specific level within genus Gigantidas based on the sequence data of two mitochondrial genes (COI and ND4). The metagenomic dataset of gill-associated symbionts were generated by Illumina Miseq sequencing of the V3-V4 region of 16S rRNA from 12 specimens of G. vrijenhoeki collected from the same vent site, Onnuri Vent Field.

Human granulocytic anaplasmosis (HGA) is a tick-borne infectious disease caused by Anaplasma phagocytophilum, an obligate intracellular bacterium. Until now, the utility of tick-bite site samples for HGA diagnosis has not been reported. Using a patient's buffy coat and tick-bite site crust samples, we performed polymerase chain reaction (PCR) testing using Ehrlichia- or Anaplasma-specific primers. PCR with buffy coat and crust samples obtained before doxycycline administration was positive. Six days after doxycycline administration, PCR with the buffy coat sample was negative but PCR with a crust tissue sample from the tick-bite site remained positive. This is the first case to suggest that crust tissue at the tick-bite site may be useful for early HGA diagnosis in patients who have already been treated with antibiotics such as doxycycline.

Background Understanding the contribution of efflux pumps to the resistance of antibiotics is useful when considering strategies for antimicrobial therapy. Objectives To assess the role of efflux activity on the resistance of antibiotics commonly used in hospitals. Methods We analyzed the efflux activity of 120 clinical isolates of Acinetobacter baumannii using an Hoechst 33342 (H33342) dye-accumulation assay. We compared the indicators for efflux activity of susceptible and non-susceptible groups of each of 16 tested antibiotics. To determine the role of efflux activity on resistance to an antibiotic, we used 3 criteria based on the results of the H33342-accumulation assay. Results The evaluation suggests that efflux activity contributed to resistance to the following 11 antibiotics: cefepime, cefotaxime, ceftazidime, ciprofloxacin, gentamicin, imipenem, meropenem, piperacillin, piperacillin/tazobactam, ticarcillin/ clavulanic acid, and tigecycline. However, ampicillin/sulbactam, minocycline, and trimethoprim/sulfamethoxazole did not meet the criteria, suggesting resistance may not be mediated by efflux activity. A significant difference in efflux activity was observed between bacteria belonging to the multidrug-resistant Acinetobacter baumannii (MDRAB) group and those belonging to the non-MDRAB group. Conclusions Efflux activity may contribute to multidrug resistance and particularly resistance to numerous antibiotics used in hospitals. These antibiotics would be good candidates for combination therapeutic regimens consisting of an antibiotic and an efflux pump inhibitor as an adjuvant to combat drug efflux.

Background Chemolithoautotrophic primary production sustains dense invertebrate communities at deep-sea hydrothermal vents and hydrocarbon seeps. Symbiotic bacteria that oxidize dissolved sulfur, methane, and hydrogen gases nourish bathymodiolin mussels that thrive in these environments worldwide. The mussel symbionts are newly acquired in each generation via infection by free-living forms. This study examined geographical subdivision of the thiotrophic endosymbionts hosted by Bathymodiolus mussels living along the eastern Pacific hydrothermal vents. High-throughput sequencing data of 16S ribosomal RNA encoding gene and fragments of six protein-coding genes of symbionts were examined in the samples collected from nine vent localities at the East Pacific Rise, Galápagos Rift, and Pacific-Antarctic Ridge. Results Both of the parapatric sister-species, B. thermophilus and B. antarcticus, hosted the same numerically dominant phylotype of thiotrophic Gammaproteobacteria. However, sequences from six protein-coding genes revealed highly divergent symbiont lineages living north and south of the Easter Microplate and hosted by these two Bathymodiolus mussel species. High heterogeneity of symbiont haplotypes among host individuals sampled from the same location suggested that stochasticity associated with initial infections was amplified as symbionts proliferated within the host individuals. The mussel species presently contact one another and hybridize along the Easter Microplate, but the northern and southern symbionts appear to be completely isolated. Vicariance associated with orogeny of the Easter Microplate region, 2.5–5.3 million years ago, may have initiated isolation of the symbiont and host populations. Estimates of synonymous substitution rates for the protein-coding bacterial genes examined in this study were 0.77–1.62%/nucleotide/million years. Conclusions Our present study reports the most comprehensive population genetic analyses of the chemosynthetic endosymbiotic bacteria based on high-throughput genetic data and extensive geographical sampling to date, and demonstrates the role of the geographical features, the Easter Microplate and geographical distance, in the intraspecific divergence of this bacterial species along the mid-ocean ridge axes in the eastern Pacific. Altogether, our results provide insights into extrinsic and intrinsic factors affecting the dispersal and evolution of chemosynthetic symbiotic partners in the hydrothermal vents along the eastern Pacific Ocean. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0966-3) contains supplementary material, which is available to authorized users.

We evaluated the ability of the Filamentous Fungi Library 1.0 of the MALDI-TOF MS Biotyper system to identify 345 clinical Aspergillus isolates from 11 Korean hospitals. Compared with results of the internal transcribed spacer region sequencing, the frequencies of correct identification at the species-complex level were 94.5% and 98.8% with cutoff values of 2.0 and 1.7, respectively. Compared with results of β-tubulin gene sequencing, the frequencies of correct identification at the species level were 96.0% (cutoff 2.0) and 100% (cutoff 1.7) for 303 Aspergillus isolates of five common, non-cryptic species, but only 4.8% (cutoff 1.7) and 0% (cutoff 2.0) for 42 Aspergillus isolates of six cryptic species (identifiable by β-tubulin or calmodulin sequencing). These results show that the MALDI Biotyper using the Filamentous Fungi Library version 1.0 enables reliable identification of the majority of common clinical Aspergillus isolates, although the database should be expanded to facilitate identification of cryptic species.

Background Several factors contribute to differences in Streptococcus pneumoniae serotype distribution. We investigated the serotype distribution and antimicrobial resistance of S. pneumoniae isolated between 2014 and 2016 in Korea. Methods We collected a total of 1,855 S. pneumoniae isolates from 44 hospitals between May 2014 and May 2016, and analyzed the serotypes by sequential multiplex PCR. We investigated the distribution of each serotype by patient age, source of the clinical specimen, and antimicrobial resistance pattern. Results The most common serotypes were 11A (10.1%), followed by 19A (8.8%), 3 (8.5%), 34 (8.1%), 23A (7.3%), and 35B (6.2%). The major invasive serotypes were 3 (12.6%), 19A (7.8%), 34 (7.8%), 10A (6.8%), and 11A (6.8%). Serotypes 10A, 15B, 19A, and 12F were more common in patients ≤5 years old, while serotype 3 was more common in patients ≥65 years old compared with the other age groups. The coverage rates of pneumococcal conjugate vaccine (PCV)7, PCV10, PCV13, and pneumococcal polysaccharide vaccine 23 were 11.8%, 12.12%, 33.3%, and 53.6%, respectively. Of the 1,855 isolates, 857 (46.2%) were multi-drug resistant (MDR), with serotypes 11A and 19A predominant among the MDR strains. The resistance rates against penicillin, cefotaxime, and levofloxacin were 22.8%, 12.5%, and 9.4%, respectively. Conclusions There were significant changes in the major S. pneumoniae serotypes in the community. Non-PCV13 serotypes increased in patients ≤5 years old following the introduction of national immunization programs with the 10- and 13-polyvalent vaccines.

Objective Aural irrigation using antiseptic solutions can be an effective medical treatment of chronic suppurative otitis media (CSOM) owing to the increasing prevalence of antibiotic-resistant CSOM infections. In the present study, we compared the antimicrobial activities of 100% Burow's solution, 50% Burow's solution, 2% acetic acid, vinegar with water (1:1), and 4% boric acid solution against methicillin-resistant Staphylococcus aureus (MRSA), methicillin-susceptible S. aureus (MSSA), quinolone-resistant Pseudomonas aeruginosa (QRPA), and quinolone-susceptible P. aeruginosa (QSPA) in vitro. Methods We examined the antimicrobial activities of five antiseptic solutions against MRSA, MSSA, QRPA, and QSPA. The antimicrobial activities of the solutions were calculated as a percentage of the surviving microorganisms by dividing the viable count in each antiseptic solution with that in control. The time (D10 value) required for each of the five solutions to inactivate 90% of the microorganism population was also investigated. Results Burow's solution exhibited the highest antimicrobial activity and the lowest D10 value against MRSA, MSSA, QRPA, and QSPA, followed by 2% acetic acid, vinegar with water (1:1), and 4% boric acid solution. Conclusion Our results indicate that Burow's solution has the most potent activity against bacteria including antibiotic-resistant strains. Twofold dilution of the solution is recommended to avoid ototoxicity.

Background Acinetobacter baumannii infections are difficult to treat owing to the emergence of various antibiotic resistant isolates. Because treatment options are limited for multidrug-resistant (MDR) A. baumannii infection, the discovery of new therapies, including combination therapy, is required. We evaluated the synergistic activity of colistin, doripenem, and tigecycline combinations against extensively drug-resistant (XDR) A. baumannii and MDR A. baumannii. Methods Time-kill assays were performed for 41 XDR and 28 MDR clinical isolates of A. baumannii by using colistin, doripenem, and tigecycline combinations. Concentrations representative of clinically achievable levels (colistin 2 µg/mL, doripenem 8 µg/mL) and achievable tissue levels (tigecycline 2 µg/mL) for each antibiotic were used in this study. Results The colistin-doripenem combination displayed the highest rate of synergy (53.6%) and bactericidal activity (75.4%) in 69 clinical isolates of A. baumannii. Among them, thedoripenem-tigecycline combination showed the lowest rate of synergy (14.5%) and bacteri-cidal activity (24.6%). The doripenem-tigecycline combination showed a higher antagonistic interaction (5.8%) compared with the colistin-tigecycline (1.4%) combination. No antagonism was observed for the colistin-doripenem combination. Conclusions The colistin-doripenem combination is supported in vitro by the high rate of synergy and bactericidal activity and lack of antagonistic reaction in XDR and MDR A. baumannii. It seems to be necessary to perform synergy tests to determine the appropri-ate combination therapy considering the antagonistic reaction found in several isolates against the doripenem-tigecycline and colistin-tigecycline combinations. These findings should be further examined in clinical studies.

We describe a new vent mussel species, Gigantidas vrijenhoeki n. sp., from material collected at a depth of 2022 m in the newly discovered Onnuri Vent Field (OVF) during the 2018 expedition to the Central Indian Ridge. This large modioliform mussel thrives around diffusive vents in aggregation with another dominant hydrothermal vent mussel, Bathymodiolus marisindicus. G. vrijenhoeki n. sp. was distinguished from its neighboring B. marisindicus by its distinct shell profile, which consists of an elongated shell with a short and low anterior region, high expanded posterior region, and deep ventral concavity. Visually, the new mussel species resembles G. securiformis; however, it is clearly distinguished by several shell and anatomical features. Genetically, the new species is closely related to two undescribed Gigantidas species found in the cold seeps of the western Pacific. Phylogenetic analysis of G. vrijenhoeki n. sp. supports the connectivity of vent fauna between the Indian Ocean and the western Pacific in the past. To the best of our knowledge, this is the first record of a Gigantidas species in the Indian Ocean. In addition, we found gill-associated sulfur-oxidizing and methane-oxidizing bacteria, Gammaproteobacteria and Epsilonproteobacteria, symbionts present on this new species. Their composition was clearly different from symbionts found on the co-occurring B. marisindicus at the OVF. Notably, the sulfurovum-related Epsilonproteobacteria on the G. vrijenhoeki n. sp. were phylogenetically distinct from the family of Bathymodiolinae-related Epsilonproteobacteria. Taken together, the co-occurrence of two mussel species at the new vent field and their distinct gill symbiotic communities provides a useful setting in which to study the genetic connectivity of vent mussels along the Central Indian Ridge and the evolutionary dynamics between host mussels and symbionts.

Acinetobacter baumannii infection is a significant health problem worldwide due to increased drug resistance. The limited antimicrobial alternatives for the treatment of severe infections by multidrug-resistant A. baumanniiA. baumannii A. baumannii(MDRAB) make the search for other therapeutic options more urgent. Linalool, the major oil compound in Coriandrum sativum, was recently found to have high antibacterial activity against A. baumannii. The purpose of this study was to investigate the synergistic effect of linalool and colistin combinations against MDRAB and extensively drug-resistant A. baumanniiA. baumannii A. baumannii(XDRAB). A total of 51 strains of A. baumanniiA. baumannii A. baumanniiclinical isolates, consisting of 10 MDRAB and 41 XDRAB were tested. We determined the minimum inhibitory concentration (MIC) of linalool for the test strains using the broth microdilution method and searched for interactions using the time-kill assay. The time-kill assay showed that the linalool and colistin combination displayed a high rate of synergy (92.1%) (by synergy criteria 2), low rate of indifference (7.8%), and a high rate of bactericidal activity (74.5%) in the 51 clinical isolates of A. baumannii. The synergy rates for the linalool and colistin combination against MDRAB and XDRAB were 96% and 92.1%, respectively. No antagonism was observed for the linalool and colistin combination. The combination of linalool and colistin showed a high synergy rate, which may be beneficial for controlling MDRAB infections. Therefore, this combination is a good candidate for in vivo studies to assess its efficacy in the treatment of MDRAB infections.

The four methods for assigning bacterial species are the Clinical and Laboratory Standards Institute (CLSI), modified CLSI (mCLSI), phylogenetic analysis (PA) and closest match (CM) methods, these are used to identify the genus and species using 16S rRNA gene sequence results. In this study, the results of identification by these four methods of 37 aerobic reference strains, 30 anaerobic reference strains, 15 Acinetobacter reference strains and 167 Acinetobacter clinical strains were compared. The rates of accurate identification to the species level using the CLSI, mCLSI, PA and CM methods were as follows: 24.3, 86.5, 86.5 and 89.2%, respectively, for the 37 aerobic reference strains; 73.3%, 96.7%, 90.0% and 93.3%, respectively, for the 30 anaerobic reference strains; 40.0%, 93.3%, 100% and 93.3%, respectively, for the 15 Acinetobacter reference strains; and 53.9%, 90.4%, 95.8% and 90.4%, respectively, for the 167 Acinetobacter clinical strains. The rates of accurate identification to the genus level using the CLSI, mCLSI, PA, and CM methods were as follows: 91.9%, 91.9%, 94.6% and 91.9%, respectively, for the 37 aerobic reference strains; 100%, 100%, 100% and 100%, respectively, for all of the 30 anaerobic reference strains, 15 Acinetobacter reference strains and the 167 Acinetobacter clinical strains. The mCLSI is the most practical and pragmatic method for identification of species based on 16S rRNA sequences for hospital, research or industry laboratories because it performs well and involves a simple procedure.

8p11 myeloproliferative syndrome (EMS) is a rare disease characterized by myeloproliferative neoplasm (MPN) associated with eosinophilia and T or B lymphoblastic lymphoma/leukemia. EMS is defined by molecular disruption of the FGFR1 gene at the 8p11-12 chromosome locus, and various partner genes are associated with FGFR1 gene translocation or insertion. The different partner-FGFR1 fusion genes are associated with slightly different disease phenotypes. The present patient showed T lymphoblastic lymphoma in a cervical lymph node, involvement of malignant lymphoma in the skin, and MPN bone marrow morphology with peripheral monocytosis. Chromosome analysis of the patient showed t(1;8)(q25;p11.2). To our knowledge, only 2 cases of EMS with translocation of t(1;8)(q25;p11.2) have been previously reported. Including this case, all 3 cases with EMS with t(1;8)(q25;p11.2) showed MPN bone marrow morphology and peripheral monocytosis. These findings support that t(1;8)(q25;p11.2) is associated with peripheral monocytosis in EMS patients. Of the 2 cases of EMS with t(1;8)(q25;p11.2) which were previously reported, FGFR1 rearrangement was not confirmed in 1 case. Similarly, FGFR1 rearrangement in the present case was not detected by fluorescence in situ hybridization or reverse transcription-polymerase chain reaction. Further study is needed to identify other techniques that could be used to demonstrate FGFR1 rearrangement.

Objective To assess whether this compound (ALH-L1005) is conceivably an effective agent in protecting against cochlear damage induced by LPS. Materials and methods Tube formation using human umbilical vein endothelial cell (HUVEC) and matrix metalloproteinase (MMP)-9 inhibition assay was performed. 24 guinea pigs were randomly divided into three groups. Intratympanic instillation of LPS ( n = 8) as negative control, instillation of oxytetracycline 1 h after LPS as positive control ( n = 8), and intratympanic instillation of ALH-L1005 ( n = 8) 1 h after LPS were considered experimental group. Evaluation by auditory brainstem response (ABR) measurement, cochlear blood flow, and blood–labyrinth barrier (BLB) permeability were performed. Cochlear hair cells were observed by field emission-scanning electron microscopy (FE-SEM). MMP-9 activation was measured by gelatin zymography. Results For HUVEC, the tube formation was suppressed in a dose dependant manner. ALH-L1005 inhibited the MMP-9 activity prominently. It also attenuated the elevation of LPS-induced hearing threshold shift and recovery of CBF. By FE-SEM, cochlear hair cells could be preserved in experimental group. ALH-L1005 significantly reduced the BLB opening compared to LPS group. Active MMP-9 expression could be detected in the LPS group. In contrast to ALH-L1005 group, active MMP-9 expression was not detected. Conclusion Our results conclude that ALH-L1005 showed a protective effect in the cochlear lateral wall damage induced by LPS.

A novel FLCN c.1489_1490delTG (p.Val497Glyfs*22) mutation at the genomic DNA and mRNA levels was identified in a 43-year-old woman with complaining of recurrent primary spontaneous pneumothorax. The aberrant FLCN mRNA escaped the nonsense-mediated decay system (NMD) because of a premature termination code located in an NMD-incompetent region. To the best of our knowledge, this is the first case report of an FLCN mutation escaping the NMD.

Enterobacter aerogenes is recognized as an important bacterial pathogen in hospital-acquired infections. This report describes two unusual cases of septicemia caused by E. aerogenes in immunocompetent healthcare workers. E. aerogenes was isolated from blood cultures of the two patients experiencing septicemia. The clinical isolates were initially identified as E. aerogenes using a VITEK II automated system and 16S rRNA sequence analysis, and; both isolates involved in the outbreak shared a common pulse-field gel electrophoresis pattern. The similarities between the two cases included the simultaneous development of gastroenteritis symptoms, severe sepsis and thrombocytopenia after taking intravenous injections of ketorolac tromethamine. A common source of normal saline, a 100 mL bottle, was used for diluting the analgesic in both cases. In addition to the general population, healthcare workers, especially those who are also intravenous drug abusers, should be considered subjects that could cause a transmission of Enterobacter infection.

BACKGROUND National surveillance of antimicrobial resistance becomes more important for the control of antimicrobial resistance and determination of treatment guidelines. We analyzed Korean Antimicrobial Resistance Monitoring System (KARMS) data collected from 2013 to 2015. METHODS Of the KARMS participants, 16 secondary or tertiary hospitals consecutively reported antimicrobial resistance rates from 2013 to 2015. Data from duplicate isolates and institutions with fewer than 20 isolates were excluded. To determine the long-term trends, previous KARMS data from 2004 to 2012 were also considered. RESULTS The prevalence of methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus faecium from 2013 to 2015 was 66-72% and 29-31%, respectively. The resistance rates of Escherichia coli to cefotaxime and cefepime gradually increased to 35% and 31%, respectively, and fluoroquinolone resistance reached 48% in 2015. The resistance rates of Klebsiella pneumoniae to cefotaxime, cefepime, and carbapenem were 38-41%, 33-41%, and

Molecular methods have the potential to improve the speed and accuracy of Acinetobacter species identification in clinical settings. The goal of this study is to develop species-specific PCR assays based on differences in the RNA polymerase beta-subunit gene (rpoB) to detect nine commonly isolated Acinetobacter species including Acinetobacter baumannii, Acinetobacter calcoaceticus, Acinetobacter pittii, Acinetobacter nosocomialis, Acinetobacter lwoffii, Acinetobacter ursingii, Acinetobacter bereziniae, Acinetobacter haemolyticus, and Acinetobacter schindleri. The sensitivity and specificity of these nine assays were measured using genomic DNA templates from 55 reference strains and from 474 Acinetobacter clinical isolates. The sensitivity of A. baumannii-specific PCR assay was 98.9%, and the sensitivity of species-specific PCR assays for all other species was 100%. The specificities of A. lwoffii- and A. schindleri-specific PCR were 97.8 and 98.9%, respectively. The specificity of species-specific PCR for all other tested Acinetobacter species was 100%. The lower limit of detection for the nine species-specific PCR assays developed in this study was 20 or 200 pg of genomic DNA from type strains of each species. The Acinetobacter species-specific PCR assay would be useful to determine the correct species among suggested candidate Acinetobacter species when conventional methods including MALDI-TOF MS identify Acinetobacter only to the genus level. The species-specific assay can be used to screen large numbers of clinical and environmental samples obtained for epidemiologic study of Acinetobacter for the presence of target species.

Micro (mi)RNA dysregulation is implicated in the development of myelodysplastic syndrome (MDS). Chromosomal abnormalities on 1q are frequently detected in Korean patients with MDS; however, how these are related to disease development is unknown. The present study compared the expression profiles of miRNAs encoded by chromosome 1q between 65 MDS patients and 11 controls. We found that miR-205-5p levels were 12.5 fold higher in the former (P=0.001). miR-205-5p level was increased in 44.7% of patients when an arbitrary 2(-ΔCt) cut-off value of 1.25 was used. miR-205-5p expression data were used to generate a receiver operating characteristic (ROC) curve for miR-205-5p, for which the area under the curve (AUC) was 0.825 (95% confidence interval: 0.710-0.941; P=0.001). Moreover, transfection with a miR-205-5p mimic induced cell proliferation by inhibiting the expression of the tumor suppressor protein phosphatase and tensin homolog (PTEN). Our findings suggest that miR-205-5p upregulation contributes to MDS by suppressing PTEN and that miR-205-5p thus acts as an oncogene in hematopoietic cells.

Primer pairs for nested PCR of twelve genetic loci of Alvinella pompejana. (DOCX 21.3 kb)

Relationship between genetic differentiation (F ST) and geographical distance (km): F ST of nuclear genes (black) and F ST of mtCOI gene (white). Mantelâ s r and significance of correlation (P-value) is listed in a box. (DOCX 199Â kb)

Likelihood values of Structure. (DOCX 17.2Â kb)

Tajima’s D and Fu’s F S of each locus in each sample. Table S7: Tajima's D and Fu’s F S of each genetic locus across three geographical groups. Table S8. Isolation with Migration 2-population analyses. Estimated effects of Equatorial and Easter Microplate boundaries on demographic parameters. Maximum likelihood estimates (MLE) of six demographic quantities. Figure S2. Posterior probability estimates for population demographic quantities of the model parameters of IMa2 2-population analyses. Posterior probability curves of divergence time (t) (A), migration rates (2Nm) (B), and effective population sizes (N) (C) between NEPR and SEPR are illustrated on the upper panel, and same posterior curves for the quantities between SEPR and PAR are shown in (D), (E), and (F). The geographical groups of N in figures (C) and (F) are represented as subscripts: n, NEPR; s, SEPR; p, PAR; and a, ancestral population. (DOCX 309 kb)

Table S3. Isolation with Migration 3-population analyses (NEPR, SEPR and PAR). Table S4. Log-likelihood ratio tests for nested models of migration in Isolation with Migration 3-population analyses (NEPR, SEPR and PAR). Table S5. Log-likelihood ratio tests between a model of absence of gene flow and the other nested models of migration. (DOCX 39.5Â kb)

T was more resistant to UA and OA than that of the MRSA strains. The MBC values of UA and OA against MRSA had broad ranges; 4 to 32 µg/ml and 16 to >256 µg/ml, respectively. It was difficult to understand the different antimicrobial activities of UA and OA among the MRSA strains, because UA and OA antimicrobial mechanisms are unknown. These results indicate that the antimicrobial effects of UA and OA against MRSA are dependent on resistance to UA and OA in each strain.

To compare the identification accuracies of VITEK 2 (bioMérieux), MicroScan (Siemens Healthcare), and Phoenix (Becton Dickinson), microbial identification was performed on 160 clinical isolates and 50 reference strains on each of these 3 systems, using the appropriate identification kit provided by each system. Of the 142 clinical isolates that were identified at the species level, VITEK 2, MicroScan, and Phoenix correctly identified 93.7%, 82.4%, and 93.0%, and incorrectly identified 2.1%, 7.0%, and 0%, respectively. In the reference strain tests, VITEK 2, MicroScan, and Phoenix correctly identified 55.3%, 54.4%, and 78.0% of the reference strains at the species level and incorrectly identified 10.6%, 13.0%, and 6.0% of the reference strains, respectively. In conclusion, the identification rate of VITEK 2, Phoenix, and MicroScan was high or acceptable on clinical isolates. Phoenix showed a significantly higher performance than VITEK 2 or MicroScan in identifying the reference strains.

Background and objective β-Tricalcium phosphate (TCP) has good biodegradability and osteoconductivity as a scaffold material for bone tissue engineering. Both block and granular forms are available; however, it has been associated with risk of infection and exposure. To this end, the study evaluated the effect of piperacillin-tazobactam coated β-TCPs for mastoid obliteration in otitis media. Materials and methods Ten guinea pigs were divided into the experimental (piperacillin-tazobactam coated β-TCP granules, n = 5) and control groups (uncoated β-TCP granules, n = 5). After mastoid obliteration, transtympanic injection with a saline suspension of lipopolysaccharide established inflammation. The animals were sacrificed 5 weeks later. Tissue sections were stained with hematoxylin and eosin and examined. Results Encapsulation and formation of fibrous capsule by foreign material in the bulla were not evident. The histological evaluation did not reveal inflammatory cells and fibrosis in the piperacillin-tazobactam coated β-TCP group. In contrast, the control group showed numerous inflammatory cells around the implanted uncoated β-TCP granules and incomplete new bone formation. Conclusion β-TCP is an effective carrier material for piperacillin-tazobactam. The use of piperacillin-tazobactam coated β-TCP may be optimal for mastoid obliteration.

BACKGROUND JAK2 genetic variations have been described in a high proportion of patients with BCR/ABL1-negative myeloproliferative neoplasms (MPN). This study was designed to analyze the frequencies of JAK2 V617F and exon 12 variations, and their correlations with clinical characteristics of Korean patients with BCR/ABL1-negative MPN. METHODS We examined a total of 154 patients with BCR/ABL1-negative MPN that included 24, 26, 89, and 15 patients with polycythemia vera (PV), primary myelofibrosis (PMF), essential thrombocythemia (ET), and unclassified myeloproliferative neoplasms (MPNU), respectively. We performed allele-specific PCR to detect V617F in all BCR/ABL1-negative patients, and performed direct sequencing to detect exon 12 variations in 47 V617F-negative MPN patients. JAK2 c.1641+179_183del5 variation was detected by restriction fragment length polymorphism assay in 176 healthy subjects. RESULTS JAK2 V617F was detected in 91 patients (59.1%): PV (91.6%), PMF (46.2%), ET (52.8%), and MPNU (66.7%). In V617F-negative MPN patients, no mutations were found in exon 12. The c.1641+179_183del5 was detected in 68.1% of V617F-negative MPN patients and 45.4% of healthy subjects (P=0.008). JAK2 V617F was closely correlated with age and leukocytosis in BCR/ABL1-negative MPN patients (P

Background We developed a new disposable anaerobic culture system, namely, the Quick anaero-system, for easy culturing of obligate anaerobes. Methods Our system consists of 3 components: 1) new disposable anaerobic gas pack, 2) disposable culture-envelope and sealer, and 3) reusable stainless plate rack with mesh containing 10 g of palladium catalyst pellets. To evaluate the efficiency of our system, we used 12 anaerobic bacteria. We prepared 2 sets of ten-fold serial dilutions of the 12 anaerobes, and inoculated these samples on Luria-Bertani (LB) broth and LB blood agar plate (LB-BAP) (BD Diagnostic Systems, USA). Each set was incubated in the Quick anaero-system (DAS Tech, Korea) and BBL GasPak jar with BD GasPak EZ Anaerobe Container System (BD Diagnostic Systems) at 35-37 degrees C for 48 hr. The minimal inoculum size showing visible growth of 12 anaerobes when incubated in both the systems was compared. Results The minimal inoculum size showing visible growth for 2 out of the 12 anaerobes in the LB broth and 9 out of the 12 anaerobes on LB-BAP was lower for the Quick anaero-system than in the BD GasPak EZ Anaerobe Container System. The mean time (+/-SD) required to achieve absolute anaerobic conditions of the Quick anaero-system was 17 min and 56 sec (+/-3 min and 25 sec). Conclusions The Quick anaero-system is a simple and effective method of culturing obligate anaerobes, and its performance is superior to that of the BD GasPak EZ Anaerobe Container System.