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Segawa T, Masuda K, Hisatsune J, Ishida-Kuroki K, Sugawara Y, Kuwabara M, Nishikawa H, Hiratsuka T, Aota T, Tao Y, Iwahashi Y, Ueda K, Mae K, Masumoto K, Kitagawa H, Komatsuzawa H, Ohge H, Sugai M. Genomic analysis of inter-hospital transmission of vancomycin-resistant Enterococcus faecium sequence type 80 isolated during an outbreak in Hiroshima, Japan. Antimicrob Agents Chemother 2024; 68:e0171623. [PMID: 38506550 PMCID: PMC11064488 DOI: 10.1128/aac.01716-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 03/01/2024] [Indexed: 03/21/2024] Open
Abstract
Outbreaks caused by vancomycin-resistant enterococci that transcend jurisdictional boundaries are occurring worldwide. This study focused on a vancomycin-resistant enterococcus outbreak that occurred between 2018 and 2021 across two cities in Hiroshima, Japan. The study involved genetic and phylogenetic analyses using whole-genome sequencing of 103 isolates of vancomycin-resistant enterococci to identify the source and transmission routes of the outbreak. Phylogenetic analysis was performed using core genome multilocus sequence typing and core single-nucleotide polymorphisms; infection routes between hospitals were inferred using BadTrIP. The outbreak was caused by Enterococcus faecium sequence type (ST) 80 carrying the vanA plasmid, which was derived from strain A10290 isolated in India. Of the 103 isolates, 93 were E. faecium ST80 transmitted across hospitals. The circular vanA plasmid of the Hiroshima isolates was similar to the vanA plasmid of strain A10290 and transferred from E. faecium ST80 to other STs of E. faecium and other Enterococcus species by conjugation. The inferred transmission routes across hospitals suggest the existence of a central hospital serving as a hub, propagating vancomycin-resistant enterococci to multiple hospitals. Our study highlights the importance of early intervention at the key central hospital to prevent the spread of the infection to small medical facilities, such as nursing homes, with limited medical resources and a high number of vulnerable individuals.
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Ishida-Kuroki K, Hisatsune J, Segawa T, Sugawara Y, Masuda K, Tadera K, Kashiyama S, Yokozaki M, Le MNT, Kawada-Matsuo M, Ohge H, Komatsuzawa H, Sugai M. Complete genome sequence of cfr(B)-carrying Enterococcus raffinosus isolated from bile in a patient in Japan. J Glob Antimicrob Resist 2023; 34:43-45. [PMID: 37356664 DOI: 10.1016/j.jgar.2023.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/05/2023] [Accepted: 06/15/2023] [Indexed: 06/27/2023] Open
Abstract
OBJECTIVES Linezolid is an antibiotic used to treat infectious diseases caused by vancomycin-resistant enterococci and methicillin-resistant Staphylococcus aureus. Recently, Enterococcus Spp.-carrying mobile linezolid resistance genes were reported. Herein, we report the complete genome sequence of Enterococcus raffinosus JARB-HU0741, which was isolated from a bile sample of a patient in Japan on May 5, 2021, and carries a linezolid resistance gene, cfr(B). Nevertheless, this isolate was susceptible to linezolid. METHODS Whole-genome sequencing was performed using HiSeq X FIVE (Illumina) and GridION (Oxford Nanopore Technologies). The sequence reads were assembled using Unicycler v0.4.8, and the complete genome was annotated using DFAST v1.2.18. Antimicrobial resistance genes were detected with Abricate v1.0.1, using the ResFinder database. The minimum inhibitory concentrations (MICs) were determined using broth microdilution and interpreted according to the guidelines of the Clinical and Laboratory Standards Institute. RESULTS E. raffinosus JARB-HU0741 contained a 3 248 808-bp chromosome and a 1 156 277-bp megaplasmid. cfr(B) was present in the Tn6218-like transposon, which was inserted into a gene encoding a PRD domain-containing protein present in the megaplasmid, but the isolate was susceptible to linezolid (MIC, 0.5 µg/mL). The Tn6218-like transposon was similar to the Tn6218 of Clostridioides difficile Ox3196 and the Tn6218-like transposon of Enterococcus faecium UW11733; however, three genes encoding a topoisomerase, an S-adenosylmethionine-dependent methyltransferase, and a TetR family transcriptional regulator were present in the previous Tn6218- or Tn6218-like transposon. CONCLUSION This is the first report of the complete genome sequence of E. raffinosus carrying cfr(B). E. raffinosus carrying cfr(B) without linezolid resistance poses a threat, as it could serve as a reservoir for mobile linezolid resistance genes.
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Segawa T, Hisatsune J, Ishida-Kuroki K, Sugawara Y, Masuda K, Tadera K, Kashiyama S, Yokozaki M, Le MNT, Kawada-Matsuo M, Ohge H, Komatsuzawa H, Sugai M. Complete genome sequence of optrA-carrying Enterococcus faecalis isolated from open pus in a Japanese patient. J Glob Antimicrob Resist 2023; 33:276-278. [PMID: 37127133 DOI: 10.1016/j.jgar.2023.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/13/2023] [Accepted: 04/13/2023] [Indexed: 05/03/2023] Open
Abstract
OBJECTIVES The occurrence of linezolid resistance in enterococci has recently increased. Here, we report the genomic characterization of Enterococcus faecalis strain JARB-HU0796-isolated from the open pus of a patient in Hiroshima, Japan-which shows non-susceptibility to linezolid (MIC of 4 μg/mL). METHODS JARB-HU0796 whole-genome sequencing was performed using short-read sequencing with Illumina Hiseq X Five and long-read sequencing using GridION. These reads were collected using the assembly pipeline Unicycler and annotated with DFAST. Antimicrobial resistance genes were detected using the Abricate and ResFinder databases, and the sequence type identified using PubMLST. The antimicrobial susceptibility of JARB-HU0796 was determined with the Eiken dry-plate QH02 System. RESULTS The JARB-HU0796 complete genome contained a circular chromosome (2 722 585-bp) and two circular plasmids (85 996-bp and 58 872-bp). The chromosome harbors the optrA gene, which confers resistance to oxazolidinones and phenicols. JARB-HU0796 showed non-susceptibility to linezolid and multidrug resistance to other antibiotics. MLST analysis identified JARB-HU0796 as ST476, similar to the optrA-positive E. faecalis ST476 isolates from swine (South Korea, 2020) and pet food (Switzerland, 2022). The optrA region of JARB-HU0796 is nearly identical to that of ST476 E. faecalis strain TZ2, isolated from humans (China, 2013). CONCLUSIONS To the best of our knowledge, this is the first report of the complete genome sequence of E. faecalis ST476 carrying optrA on a chromosome isolated from a patient in Japan. The strain may have originated in animals, suggesting that the organisms acquired resistance to linezolid because the optrA gene may be closely spread between animals and humans.
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Segawa T, Manias DA, Dunny GM. Structural Differences in Complexes between the Master Regulator PrgX, Peptide Pheromones, and Operator Binding Sites Determine the Induction State for Conjugative Transfer of pCF10. J Bacteriol 2022; 204:e0029822. [PMID: 36354318 PMCID: PMC9764970 DOI: 10.1128/jb.00298-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 10/13/2022] [Indexed: 11/12/2022] Open
Abstract
Pheromone-inducible conjugation in the Enterococcus faecalis pCF10 system is regulated by the PrgX transcription factor through binding interactions at two operator binding sites (XBS1 and XBS2) upstream of the transcription start site of the prgQ operon encoding the conjugation machinery. Repression of transcription requires the interaction of a PrgX tetramer with both XBSs via formation of a DNA loop. The ability of PrgX to regulate prgQ transcription is modulated by its interaction with two antagonistic regulatory peptides, ICF10 (I) and cCF10 (C); the former peptide inhibits prgQ transcription, while the latter peptide enhances prgQ transcription. In this report, we used electrophoretic mobility shift assays (EMSAs) and DNase footprinting to examine binding interactions between the XBS operator sites and various forms of PrgX (Apo-X, PrgX/I, and PrgX/C). Whereas a previous model based on high-resolution structures of PrgX proposed that the functional differences between PrgX/C and PrgX/I resulted from differences in PrgX oligomerization state, the current results show that specific differences in XBS2 occupancy by bound tetramers account for the differential regulatory properties of the two peptide/PrgX complexes and for the effects of XBS mutations on regulation. The results also confirmed a DNA looping model of PrgX function. IMPORTANCE Peptide pheromones regulate antibiotic resistance transfer in Enterococcus faecalis. Here, we present new data showing that pheromone-dependent regulation of transfer genes is mediated via effects on the structures of complexes between peptides, the intracellular peptide receptor, and operator sites on the target DNA.
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Fukuta Y, Arizono S, Tanaka S, Kawaguchi T, Fuseya T, Tsugita N, Magata J, Tawara Y, Segawa T. Effect of real-time remote-based cardiac rehabilitation on subjective satisfaction and objective performance during the coronavirus disease 2019 pandemic. Eur Heart J 2022. [PMCID: PMC9619548 DOI: 10.1093/eurheartj/ehac544.990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Background Real-time remote-based cardiac rehabilitation (CR) programmes improve exercise capacity. However, satisfaction and performance improvements after remote-based CR remain unclear. In addition to physical function, subjective satisfaction and objective performance may be adversely affected during the coronavirus disease 2019 pandemic. Purpose This study aimed to compare the effectiveness of real-time remote-based CR versus hospital-based CR in improving physical function, subjective satisfaction, and objective performance (i.e., activity limitations and participation restrictions). Methods We conducted a quasi-randomised controlled trial and recruited 38 patients with cardiovascular disease (CVD). The patients participated in 4 weeks of hospital-based CR, followed by 12 weeks of remote or hospital-based CR based on quasi-randomised allocation. We assessed the participants at baseline and after 12 weeks of remote or hospital-based CR using the shortened version of the World Health Organization Quality of Life scale (WHOQOL-BREF) for subjective satisfaction, the World Health Organization Disability Assessment Schedule (WHODAS 2.0) for objective performance, and peak oxygen uptake (peak VO2) using the cardiopulmonary exercise test, for physical function. We evaluated individual results by measuring baseline to post-CR changes (i.e., delta [Δ]) (paired t-test) and then compared the remote and hospital-based CR programmes (unpaired t-test). Results Sixteen patients (72.2±10.4 years) completed remote-based CR and fifteen patients (77.3±4.8 years) completed hospital-based CR. Seven patients were excluded owing to other health complications (n=2) and inability to attend hospital based-CR (n=5). In the remote-based CR group, the peak VO2 (before: 12.0±2.7 mL min–1 kg–1; after: 14.9±3.9 mL min–1 kg–1; p<0.05) and the WHOQOL-BREF score (before: 77.4±12.8 points; after: 93.9±12.9 points; p<0.001) were significantly higher, whereas the WHODAS 2.0 score was significantly lower (before: 19.9±13.2 points; after: 11.3±6.8 points; p<0.05) after rehabilitation than at baseline. The post-CR physical function differed significantly between the two groups (Δpeak VO2, remote: 2.8±3.0 mL min–1 kg–1; hospital: 0.84±1.8 mL min–1 kg–1; p<0.05). The post-CR change in the WHOQOL-BREF score was not significantly different between the groups. The post-CR change in the WHODAS 2.0 score was significantly lower in the remote-based CR group than in the hospital-based CR group. (ΔWHODAS 2.0 score, remote: –8.56±14.2 points; hospital: 2.14±7.6 points; p<0.01). Conclusions Remote-based CR significantly improved physical function and objective performance in patients with CVD. Remote-based CR could be an effective treatment for stable patients who are unable to visit the hospital during the coronavirus disease 2019 pandemic. In the future, risk stratification according to severity of illness is needed. Funding Acknowledgement Type of funding sources: Private company. Main funding source(s): Sanei Medicis company.
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Segawa T, Johnson CM, Berntsson RPA, Dunny GM. Two ABC transport systems carry out peptide uptake in Enterococcus faecalis: Their roles in growth and in uptake of sex pheromones. Mol Microbiol 2021; 116:459-469. [PMID: 33817866 DOI: 10.1111/mmi.14725] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 04/01/2021] [Accepted: 04/01/2021] [Indexed: 11/29/2022]
Abstract
Enterococcal pheromone-inducible plasmids encode a predicted OppA-family secreted lipoprotein. In the case of plasmid pCF10, the protein is PrgZ, which enhances the mating response to cCF10 pheromone. OppA proteins generally function with associated OppBCDF ABC transporters to import peptides. In this study, we analyzed the potential interactions of PrgZ with two host-encoded Opp transporters using two pheromone-inducible fluorescent reporter constructs. Based on our results, we propose renaming these loci opp1 (OG1RF_10634-10639) and opp2 (OG1RF_12366-12370). We also examined the ability of the Opp1 and Opp2 systems to mediate import in the absence of PrgZ. Cells expressing PrgZ were able to import pheromone if either opp1 or opp2 was functional, but not if both opp loci were disrupted. In the absence of PrgZ, pheromone import was dependent on a functional opp2 system, including opp2A. Comparative structural analysis of the peptide-binding pockets of PrgZ, Opp1A, Opp2A, and the related Lactococcus lactis OppA protein, suggested that the robust pheromone-binding ability of PrgZ relates to a nearly optimal fit of the hydrophobic peptide, whereas binding ability of Opp2A likely results from a more open, promiscuous peptide-binding pocket similar to L. lactis OppA.
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Hayashi M, Matsui M, Sekizuka T, Shima A, Segawa T, Kuroda M, Kawamura K, Suzuki S. Dissemination of IncF group F1:A2:B20 plasmid-harbouring multidrug-resistant Escherichia coli ST131 before the acquisition of bla CTX-M in Japan. J Glob Antimicrob Resist 2020; 23:456-465. [PMID: 33212283 DOI: 10.1016/j.jgar.2020.10.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/24/2020] [Accepted: 10/27/2020] [Indexed: 10/23/2022] Open
Abstract
OBJECTIVES The Escherichia coli O25-ST131 clone is responsible for global dissemination of the blaCTX-M gene. However, the prevalence of this clone in the digestive tract, devoid of antimicrobial selection, and its molecular epidemiology remain unclear. In this study, we examined the origin of blaCTX-M-positive E. coli O25-ST131 and its distribution. METHODS We separately sequenced the chromosomal and plasmid genomes of 50 E. coli O25 isolates obtained from faecal samples of patients with diarrhoea in Japan. RESULTS Although 36 (72%) of 50 E. coli O25 isolates were ST131, only 6 harboured blaCTX-M. According to the fimH and ybbW sequences and fluoroquinolone susceptibility, H30R1 isolates were dominant (27/36; 75%) and possessed IncFII-FIA-FIB with FAB formula subtype F1:A2:B20 plasmids at a high frequency (24/27; 89%). The F1:A2:B20 plasmids possessed more resistance genes such as blaTEM-1, aminoglycoside resistance genes and trimethoprim/sulfamethoxazole resistance genes compared with non-F1:A2:B20 plasmids. In contrast, only one blaCTX-M-14 gene was located on the F1:A2:B20 plasmids, whereas the other three were located on IncFII (F4:A-:B-) (n = 1) and IncZ (n = 2) plasmids. Two H30Rx-ST131 isolates harboured blaCTX-M-15: one was on the chromosome and the other on the IncFIA-R plasmid. The stability and conjugation ability of the F1:A2:B20 plasmids were compared with those of non-F1:A2:B20 plasmids, which revealed higher stability but lower conjugative ability. CONCLUSIONS These results suggest that E. coli H30R1-ST131 is a multidrug-resistant clone containing several resistance genes in the F1:A2:B20 plasmid, which were widely distributed before the acquisition of blaCTX-M.
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Sekizuka T, Inamine Y, Segawa T, Hashino M, Yatsu K, Kuroda M. Potential KPC-2 carbapenemase reservoir of environmental Aeromonas hydrophila and Aeromonas caviae isolates from the effluent of an urban wastewater treatment plant in Japan. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:589-597. [PMID: 31106978 PMCID: PMC6851574 DOI: 10.1111/1758-2229.12772] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 05/16/2019] [Indexed: 06/09/2023]
Abstract
Aeromonas hydrophila and Aeromonas caviae adapt to saline water environments and are the most predominant Aeromonas species isolated from estuaries. Here, we isolated antimicrobial-resistant (AMR) Aeromonas strains (A. hydrophila GSH8-2 and A. caviae GSH8M-1) carrying the carabapenemase blaKPC-2 gene from a wastewater treatment plant (WWTP) effluent in Tokyo Bay (Japan) and determined their complete genome sequences. GSH8-2 and GSH8M-1 were classified as newly assigned sequence types ST558 and ST13, suggesting no supportive evidence of clonal dissemination. The strains appear to have acquired blaKPC-2 -positive IncP-6-relative plasmids (pGSH8-2 and pGSH8M-1-2) that share a common backbone with plasmids in Aeromonas sp. ASNIH3 isolated from hospital wastewater in the United States, A. hydrophila WCHAH045096 isolated from sewage in China, other clinical isolates (Klebsiella, Enterobacter and Escherichia coli), and wastewater isolates (Citrobacter, Pseudomonas and other Aeromonas spp.). In addition to blaKPC-2 , pGSH8M-1-2 carries an IS26-mediated composite transposon including a macrolide resistance gene, mph(A). Although Aeromonas species are opportunistic pathogens, they could serve as potential environmental reservoir bacteria for carbapenemase and AMR genes. AMR monitoring from WWTP effluents will contribute to the detection of ongoing AMR dissemination in the environment and might provide an early warning of potential dissemination in clinical settings and communities.
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Sekizuka T, Inamine Y, Segawa T, Kuroda M. Characterization of NDM-5- and CTX-M-55-coproducing Escherichia coli GSH8M-2 isolated from the effluent of a wastewater treatment plant in Tokyo Bay. Infect Drug Resist 2019; 12:2243-2249. [PMID: 31413601 PMCID: PMC6662510 DOI: 10.2147/idr.s215273] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 06/17/2019] [Indexed: 12/29/2022] Open
Abstract
Purpose New Delhi metallo-β-lactamase (NDM)-5-producing Enterobacteriaceae have been detected in rivers, sewage, and effluents from wastewater treatment plants (WWTPs). Environmental contamination due to discharged effluents is of particular concern as NDM variants may be released into waterways, thereby posing a risk to humans. In this study, we collected effluent samples from a WWTP discharged into a canal in Tokyo Bay, Japan. Methods Testing included the complete genome sequencing of Escherichia coli GSH8M-2 isolated from the effluent as well as a gene network analysis. Results The complete genome sequencing of GSH8M-2 revealed that it was an NDM-5-producing E. coli strain sequence type ST542, which carries multiple antimicrobial resistance genes for β-lactams, quinolone, tetracycline, trimethoprim-sulfamethoxazole, florfenicol/chloramphenicol, kanamycin, and fosfomycin. The bla NDM-5 gene was found in the IncX3 replicon plasmid pGSH8M-2-4. Gene network analysis using 142 IncX3 plasmid sequences suggested that pGSH8M-2-4 is related to both clinical isolates of E. coli and Klebsiella species in Eastern Asia. GSH8M-2 also carries the bla CTX-M-55 gene in IncX1 plasmid pGSH8M-2-3. Conclusion This is the first report of environmental NDM-5-producing E. coli isolated from a WWTP in Japan. NDM-5 detection is markedly increasing in veterinary and clinical settings, suggesting that dual β-lactamases, such as NDM-5 and CTX-M-55, might be acquired through multiple steps in environment settings. Environmental contamination through WWTP effluents that contain producers of NDM variants could be an emerging potential health hazard. Thus, regular monitoring of WWTP effluents is important for the detection of antimicrobial-resistant bacteria that may be released into the waterways and nearby communities.
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Angelopoulos V, Cruce P, Drozdov A, Grimes EW, Hatzigeorgiu N, King DA, Larson D, Lewis JW, McTiernan JM, Roberts DA, Russell CL, Hori T, Kasahara Y, Kumamoto A, Matsuoka A, Miyashita Y, Miyoshi Y, Shinohara I, Teramoto M, Faden JB, Halford AJ, McCarthy M, Millan RM, Sample JG, Smith DM, Woodger LA, Masson A, Narock AA, Asamura K, Chang TF, Chiang CY, Kazama Y, Keika K, Matsuda S, Segawa T, Seki K, Shoji M, Tam SWY, Umemura N, Wang BJ, Wang SY, Redmon R, Rodriguez JV, Singer HJ, Vandegriff J, Abe S, Nose M, Shinbori A, Tanaka YM, UeNo S, Andersson L, Dunn P, Fowler C, Halekas JS, Hara T, Harada Y, Lee CO, Lillis R, Mitchell DL, Argall MR, Bromund K, Burch JL, Cohen IJ, Galloy M, Giles B, Jaynes AN, Le Contel O, Oka M, Phan TD, Walsh BM, Westlake J, Wilder FD, Bale SD, Livi R, Pulupa M, Whittlesey P, DeWolfe A, Harter B, Lucas E, Auster U, Bonnell JW, Cully CM, Donovan E, Ergun RE, Frey HU, Jackel B, Keiling A, Korth H, McFadden JP, Nishimura Y, Plaschke F, Robert P, Turner DL, Weygand JM, Candey RM, Johnson RC, Kovalick T, Liu MH, McGuire RE, Breneman A, Kersten K, Schroeder P. The Space Physics Environment Data Analysis System (SPEDAS). SPACE SCIENCE REVIEWS 2019; 215:9. [PMID: 30880847 PMCID: PMC6380193 DOI: 10.1007/s11214-018-0576-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 12/29/2018] [Indexed: 05/31/2023]
Abstract
With the advent of the Heliophysics/Geospace System Observatory (H/GSO), a complement of multi-spacecraft missions and ground-based observatories to study the space environment, data retrieval, analysis, and visualization of space physics data can be daunting. The Space Physics Environment Data Analysis System (SPEDAS), a grass-roots software development platform (www.spedas.org), is now officially supported by NASA Heliophysics as part of its data environment infrastructure. It serves more than a dozen space missions and ground observatories and can integrate the full complement of past and upcoming space physics missions with minimal resources, following clear, simple, and well-proven guidelines. Free, modular and configurable to the needs of individual missions, it works in both command-line (ideal for experienced users) and Graphical User Interface (GUI) mode (reducing the learning curve for first-time users). Both options have "crib-sheets," user-command sequences in ASCII format that can facilitate record-and-repeat actions, especially for complex operations and plotting. Crib-sheets enhance scientific interactions, as users can move rapidly and accurately from exchanges of technical information on data processing to efficient discussions regarding data interpretation and science. SPEDAS can readily query and ingest all International Solar Terrestrial Physics (ISTP)-compatible products from the Space Physics Data Facility (SPDF), enabling access to a vast collection of historic and current mission data. The planned incorporation of Heliophysics Application Programmer's Interface (HAPI) standards will facilitate data ingestion from distributed datasets that adhere to these standards. Although SPEDAS is currently Interactive Data Language (IDL)-based (and interfaces to Java-based tools such as Autoplot), efforts are under-way to expand it further to work with python (first as an interface tool and potentially even receiving an under-the-hood replacement). We review the SPEDAS development history, goals, and current implementation. We explain its "modes of use" with examples geared for users and outline its technical implementation and requirements with software developers in mind. We also describe SPEDAS personnel and software management, interfaces with other organizations, resources and support structure available to the community, and future development plans. ELECTRONIC SUPPLEMENTARY MATERIAL The online version of this article (10.1007/s11214-018-0576-4) contains supplementary material, which is available to authorized users.
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Tsuchie H, Miyakoshi N, Iba K, Kasukawa Y, Nozaka K, Dohke T, Kosukegawa I, Aizawa T, Maekawa S, Abe H, Takeshima M, Tomite T, Segawa T, Ouchi K, Kinoshita H, Suzuki M, Yamashita T, Shimada Y. The effects of teriparatide on acceleration of bone healing following atypical femoral fracture: comparison between daily and weekly administration. Osteoporos Int 2018; 29:2659-2665. [PMID: 30105400 DOI: 10.1007/s00198-018-4658-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 08/06/2018] [Indexed: 12/17/2022]
Abstract
UNLABELLED We compared the effectiveness of promoting bone healing between two teriparatide preparations for atypical femoral fracture (AFF). A total of 45 AFFs were included in this study, and we compared the duration of bone union. Teriparatide administered by daily injection enhanced bone union more than weekly administration in complete AFFs. INTRODUCTION The efficacy of teriparatide for atypical femoral fracture (AFF) has been recently reported. Although two different teriparatide preparations can be used to treat osteoporosis in Japan, daily or weekly injection, all previous reports on the effectiveness of teriparatide for AFF only examined daily injection formulations. Therefore, we compared the promotion of bone healing between the two teriparatide preparations for AFF. METHODS A total of 45 consecutive AFFs in 43 Japanese patients were included in this study. They received either a daily 20-μg teriparatide injection (daily group; n = 32) or a once-a-week 56.5-μg teriparatide injection (weekly group; n = 13). We compared the clinical background and duration of bone union between these two groups. RESULTS When all patents were included, the fracture healing time was not significantly different between the two groups. Only patients with complete AFFs had significantly fewer daily bisphosphonate or denosumab injections than the weekly group (P < 0.05). The fracture healing time in the daily group (6.1 ± 4.1 months) was significantly shorter than that in the weekly group (10.1 ± 4.2 months) (P < 0.05). Even if the influence of bisphosphonate or denosumab usage was excluded, a similar significant difference was observed in the fracture healing time (P < 0.05). There was no significant difference between the two groups among patients with incomplete AFFs. CONCLUSIONS Daily teriparatide injections enhance bone union more than weekly injections in complete AFF patients.
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Harada S, Segawa T, Sato T, Ehara S, Sera K, Goto S. Imaging of Primary and Metastatic Tumors and Their Treatment through Abscopal Effects and Cancer Immunotherapy Using Encapsulated, Radiation Therapy Directed Antigen-Capturing Nanoparticles. Int J Radiat Oncol Biol Phys 2018. [DOI: 10.1016/j.ijrobp.2018.06.375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Suzuki A, Segawa T, Sawa S, Nishitani C, Ueda K, Itou T, Asahina K, Suzuki M. Comparison of the gut microbiota of captive common bottlenose dolphins Tursiops truncatus
in three aquaria. J Appl Microbiol 2018; 126:31-39. [DOI: 10.1111/jam.14109] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 09/06/2018] [Accepted: 09/11/2018] [Indexed: 01/21/2023]
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Sekizuka T, Yatsu K, Inamine Y, Segawa T, Nishio M, Kishi N, Kuroda M. Complete Genome Sequence of a blaKPC-2-Positive Klebsiella pneumoniae Strain Isolated from the Effluent of an Urban Sewage Treatment Plant in Japan. mSphere 2018; 3:e00314-18. [PMID: 30232165 PMCID: PMC6147131 DOI: 10.1128/msphere.00314-18] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 08/16/2018] [Indexed: 02/06/2023] Open
Abstract
Antimicrobial resistance genes (ARGs) and the bacteria that harbor them are widely distributed in the environment, especially in surface water, sewage treatment plant effluent, soil, and animal waste. In this study, we isolated a KPC-2-producing Klebsiella pneumoniae strain (GSU10-3) from a sampling site in Tokyo Bay, Japan, near a wastewater treatment plant (WWTP) and determined its complete genome sequence. Strain GSU10-3 is resistant to most β-lactam antibiotics and other antimicrobial agents (quinolones and aminoglycosides). This strain is classified as sequence type 11 (ST11), and a core genome phylogenetic analysis indicated that strain GSU10-3 is closely related to KPC-2-positive Chinese clinical isolates from 2011 to 2017 and is clearly distinct from strains isolated from the European Union (EU), United States, and other Asian countries. Strain GSU10-3 harbors four plasmids, including a blaKPC-2-positive plasmid, pGSU10-3-3 (66.2 kb), which is smaller than other blaKPC-2-positive plasmids and notably carries dual replicons (IncFII [pHN7A8] and IncN). Such downsizing and the presence of dual replicons may promote its maintenance and stable replication, contributing to its broad host range with low fitness costs. A second plasmid, pGSU10-3-1 (159.0 kb), an IncA/C2 replicon, carries a class 1 integron (containing intI1, dfrA12, aadA2, qacEΔ1, and sul1) with a high degree of similarity to a broad-host-range plasmid present in the family Enterobacteriaceae The plasmid pGSU10-3-2 (134.8 kb), an IncFII(K) replicon, carries the IS26-mediated ARGs [aac(6')Ib-cr,blaOXA-1, catB4 (truncated), and aac(3)-IId], tet(A), and a copper/arsenate resistance locus. GSU10-3 is the first nonclinical KPC-2-producing environmental Enterobacteriaceae isolate from Japan for which the whole genome has been sequenced.IMPORTANCE We isolated and determined the complete genome sequence of a KPC-2-producing K. pneumoniae strain from a sampling site in Tokyo Bay, Japan, near a wastewater treatment plant (WWTP). In Japan, the KPC type has been very rarely detected, while IMP is the most predominant type of carbapenemase in clinical carbapenemase-producing Enterobacteriaceae (CPE) isolates. Although laboratory testing thus far suggested that Japan may be virtually free of KPC-producing Enterobacteriaceae, we have detected it from effluent from a WWTP. Antimicrobial resistance (AMR) monitoring of WWTP effluent may contribute to the early detection of future AMR bacterial dissemination in clinical settings and communities; indeed, it will help illuminate the whole picture in which environmental contamination through WWTP effluent plays a part.
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Ariga H, Kikuchi K, Iwaya T, Oikawa H, Kakuhara H, Segawa T, Yamaguchi S, Nakamura R. PO-0776: Induction chemotherapy with TPF followed by chemoradiotherapy for esophageal squamous cell carcinoma. Radiother Oncol 2018. [DOI: 10.1016/s0167-8140(18)31086-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Kikuchi K, Nakamura R, Segawa T, Kakuhara H, Oikawa H, Ariga H. PO-0831: Modified Glasgow prognostic score can predict survival in elderly patients with bladder cancer. Radiother Oncol 2018. [DOI: 10.1016/s0167-8140(18)31141-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Harada S, Segawa T, Ehara S, Sato T, Sera K, Goto S. Imaging and Treatment of Primary Tumors and Metastases by Targeted Macrophage Therapy, Using Radiation Therapy-Directed Encapsulated Nanoparticles. Int J Radiat Oncol Biol Phys 2017. [DOI: 10.1016/j.ijrobp.2017.06.507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Ozawa M, Tanaka F, Segawa T, Takahashi T, Matsuura Y, Sakai T, Nishiyama O, Onoda T, Nakamura M. P6255Temporal trends of incidence and clinical features of acute myocardial infarction in a Japanese rural area from 2006 to 2014. Eur Heart J 2017. [DOI: 10.1093/eurheartj/ehx493.p6255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Tachimoto H, Mezawa H, Segawa T, Akiyama N, Ida H, Urashima M. Improved control of childhood asthma with low-dose, short-term vitamin D supplementation: a randomized, double-blind, placebo-controlled trial. Allergy 2016; 71:1001-9. [PMID: 26841365 DOI: 10.1111/all.12856] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2016] [Indexed: 02/06/2023]
Abstract
BACKGROUND In our prior randomized trial on preventing influenza, asthma attacks as a secondary outcome occurred less often in the vitamin D group than in the placebo group. We aimed to clarify whether low-dose, short-term vitamin D supplementation, in addition to standard treatments, improves control of childhood asthma. METHODS We conducted a randomized, double-blind, placebo-controlled trial comparing vitamin D3 supplements (800 IU/day) with placebo for 2 months in schoolchildren with asthma. The primary outcomes were frequency and severity of asthma judging from changes in asthma control levels defined by the Global Initiative for Asthma (GINA) by collaborating doctors at 2 and 6 months. RESULTS Japanese schoolchildren with asthma (n = 89) were randomly assigned to receive vitamin D (n = 54) or placebo (n = 35). At 2 months, GINA asthma control was significantly more improved in the vitamin D group compared with the placebo group (P = 0.015). Childhood asthma control test (CACT) scores, a secondary outcome, were also significantly (P = 0.004) improved in the vitamin D group compared with the placebo group at 2 months, and differences remained significant (P = 0.012) at 6 months. The proportion of patients with a peak expiratory flow rate <80% predicted was significantly less in the vitamin D group (8/54: 15%) than in the placebo group (12/35: 34%) at 6 months (P = 0.032). CONCLUSIONS Low-dose, short-term vitamin D supplementation in addition to standard treatment may improve levels of asthma control in schoolchildren.
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Miyauchi O, Ueno T, Okubo T, Hayashi T, Kuroda M, Omi K, Watanabe Y, Segawa T, Osada H, Teramoto S. Comparison of oocytes derived from non-dominant small follicles collected 24 and 48 hours after triggering the luteinizing hormone surge in natural cycle in-vitro fertilization. Fertil Steril 2015. [DOI: 10.1016/j.fertnstert.2015.07.646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Oouchi M, Hasebe A, Hata H, Segawa T, Yamazaki Y, Yoshida Y, Kitagawa Y, Shibata KI. Age-related alteration of expression and function of TLRs and NK activity in oral candidiasis. Oral Dis 2015; 21:645-51. [PMID: 25704085 DOI: 10.1111/odi.12329] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 02/09/2015] [Accepted: 02/14/2015] [Indexed: 12/17/2022]
Abstract
OBJECTIVE Roles of aging or immune responses mediated by Toll-like receptors and natural killer cell in the onset or progression of human candidiasis remain unclear. This study was designed to elucidate the roles using peripheral blood mononuclear cells from healthy donors and patients with oral candidiasis. SUBJECTS AND METHODS Subjects tested were healthy volunteers and patients who visited Dental Clinical Division of Hokkaido University Hospital. The patients with oral candidiasis included 39 individuals (25-89 years of age) with major complaints on pain in oral mucosa and/or dysgeusia. Healthy volunteers include students (25-35 years of age) and teaching staffs (50-65 years of age) of Hokkaido University Graduate School of Dental Medicine. RESULTS Functions of Toll-like receptors 2 and 4 were downregulated significantly and the natural killer activity was slightly, but not significantly downregulated in aged healthy volunteers compared with healthy young volunteers. Functions of Toll-like receptors 2 and 4 and the natural killer activity were significantly downregulated in patients with oral candidiasis compared with healthy volunteers. CONCLUSION Downregulation of functions of Toll-like receptors 2 and 4 as well as natural killer activity is suggested to be associated with the onset or progression of oral candidiasis in human.
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Kanno K, Matsuda M, Segawa T, Tamura R, Kawamoto T. Pioglitazone treatment may lead to anti-atherogenic alterations of lipoproteins through increasing serum adiponectin in statin-treated diabetes patients. Atherosclerosis 2014. [DOI: 10.1016/j.atherosclerosis.2014.05.601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Villanueva SYAM, Saito M, Baterna RA, Estrada CAM, Rivera AKB, Dato MC, Zamora PRFC, Segawa T, Cavinta LL, Fukui T, Masuzawa T, Yanagihara Y, Gloriani NG, Yoshida SI. Leptospira-rat-human relationship in Luzon, Philippines. Microbes Infect 2014; 16:902-10. [PMID: 25048015 DOI: 10.1016/j.micinf.2014.07.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 06/11/2014] [Accepted: 07/06/2014] [Indexed: 12/24/2022]
Abstract
Leptospirosis is a zoonotic infection that is caused by the pathogenic species of Leptospira. Rats are the most important reservoirs of these organisms. Our study aimed to characterize Leptospira isolates from humans and rats and elucidate the Leptospira-rat-human relationship in Luzon, Philippines. Forty strains were isolated from humans and rats. The isolates were confirmed to be Leptospira and pathogenic through rrl- and flaB-PCR, respectively. Around 73% of the isolates were found to be lethal to hamsters. Serotyping showed that there were mainly three predominant leptospiral serogroups in the study areas namely Pyrogenes, Bataviae, and Grippotyphosa. Gyrase B gene sequence analysis showed that all the isolates belonged to Leptospira interrogans. Most had 100% similarity with serovar Manilae (15/40), serovar Losbanos (8/40), and serogroup Grippotyphosa (8/40). Strains from each group had highly identical pulsed-field gel electrophoresis patterns and were further grouped as A (Pyrogenes, 14), B (Bataviae, 8), and C (Grippotyphosa, 10). Results further revealed that similar serotypes were isolated from both humans and rats in the same areas. It is suggested that these three predominant groups with highly similar intra-group PFGE patterns may have been primarily transmitted by rats and persistently caused leptospirosis in humans particularly in the Luzon islands.
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Segawa T, Nomura KH, Villanueva SYAM, Saito M, Nomura K, Gloriani NG, Yoshida SI. Identification of leptospiral 3-hydroxyacyl-CoA dehydrogenase released in the urine of infected hamsters. BMC Microbiol 2014; 14:132. [PMID: 24884439 PMCID: PMC4036750 DOI: 10.1186/1471-2180-14-132] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Accepted: 05/07/2014] [Indexed: 01/03/2023] Open
Abstract
Background Leptospirosis is a global zoonosis caused by pathogenic Leptospira. The non-specific clinical signs and symptoms of leptospirosis lead to its misdiagnosis. To date, there is still no reliable rapid test kit that can accurately diagnose leptospirosis at bedside or in field. In this research, with the ultimate goal of formulating a rapid and accurate diagnostic tool for leptospirosis, we aimed to identify leptospiral proteins excreted in urine of infected hamsters, which are thought to mimic Weil’s disease. Results Hamsters were subcutaneously infected with leptospires, and the general attributes of urine as well as the proteins excreted in it were examined. Some leptospiral proteins were found to be excreted in the urine from the early phase of infection. The most important finding of this study was the detection of the lipid-metabolizing enzyme, 3-hydroxyacyl-CoA dehydrogenase (HADH), before the onset of illness, when leptospires were not yet detected in the urine of infected hamsters. Conclusions This is the first report on the detection of leptospiral HADH in the host urine, which may be a possible candidate leptospiral antigen that can be used in the early diagnosis of human and animal leptospirosis.
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Villanueva SYAM, Saito M, Tsutsumi Y, Segawa T, Baterna RA, Chakraborty A, Asoh T, Miyahara S, Yanagihara Y, Cavinta LL, Gloriani NG, Yoshida SI. High virulence in hamsters of four dominant Leptospira serovars isolated from rats in the Philippines. MICROBIOLOGY-SGM 2013; 160:418-428. [PMID: 24257815 DOI: 10.1099/mic.0.072439-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Leptospirosis is caused by pathogenic species of Leptospira. The aim of this study was to determine and characterize the pathogenicity of four dominant Leptospira isolates prevailing among rats in the Philippines. The isolates were Leptospira interrogans serovar Manilae strain K64, L. interrogans serovar Losbanos strain K37, L. interrogans serovar Ratnapura strain K5 and Leptospira borgpetersenii serovar Javanica strain K6. Pathogenicities were studied using hamsters, which reproduce severe human leptospirosis. The minimum lethal doses were 10(0) ( = 1) leptospires for K64, K37 and K5, and 10(1) leptospires for K6. Weight loss amongst the Leptospira-infected hamsters was observed from 1 day before death (K64-, K37- and K5-infected hamsters) to as much as 1 week before death for K6-infected hamsters. Similar and varied gross and microscopic lesions were observed amongst infected hamsters, even for strains belonging to the same species (i.e. L. interrogans). The most significant and common histopathological findings were congestion of the glomerulus, disarrangement of hepatic cords and erythrophagocytosis. Other findings were foamy splenic macrophages for K6, severe petechial pulmonary haemorrhage for K64, and hematuria and severe pulmonary congestion for K37. Immunostaining and culture revealed the presence of leptospires in different organs of the infected hamsters. Based on these results, Leptospira isolates from rats in the Philippines were shown to be highly virulent, causing pulmonary haemorrhage, severe hepato-renal damage and death in hamsters even at lower doses. The present findings on experimental leptospirosis support clinical data showing that patients with severe manifestations of leptospirosis, such as pulmonary haemorrhage, are increasing in the Philippines. These findings may serve as a basis to strengthen the early diagnosis and treatment of human leptospirosis.
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