1
|
Horiba K, Aso S, Oda R, Tateishi Y, Ura K, Kuroda M. Complete genome sequence of Selenomonas species strain TAMA-11512, isolated from blood culture of a septic patient. Microbiol Resour Announc 2024:e0007024. [PMID: 38466101 DOI: 10.1128/mra.00070-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 02/29/2024] [Indexed: 03/12/2024] Open
Abstract
We report the complete sequence of Selenomonas species strain TAMA-11512, isolated from the blood culture of a septic patient. The phylogeny and average nucleotide identity show that the strain TAMA-11512 is considered a novel bacterial species in Selenomonas genus.
Collapse
Affiliation(s)
- Kazuhiro Horiba
- Laboratory of Bacterial Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Sakura Aso
- Department of Clinical Laboratory, Tokyo Metropolitan Tama Medical Center, Tokyo, Japan
| | - Rentaro Oda
- Department of Infectious Diseases, Tokyo Metropolitan Tama Medical Center, Tokyo, Japan
| | - Yoshinori Tateishi
- Department of Infectious Diseases, Tokyo Metropolitan Tama Medical Center, Tokyo, Japan
| | - Kuniko Ura
- Department of Clinical Laboratory, Tokyo Metropolitan Tama Medical Center, Tokyo, Japan
| | - Makoto Kuroda
- Laboratory of Bacterial Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| |
Collapse
|
2
|
Torii Y, Suzuki T, Fukuda Y, Haruta K, Yamaguchi M, Horiba K, Kawada JI, Ito Y. MicroRNA expression profiling of urine exosomes in children with congenital cytomegalovirus infection. Sci Rep 2024; 14:5475. [PMID: 38443656 PMCID: PMC10914720 DOI: 10.1038/s41598-024-56106-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 03/01/2024] [Indexed: 03/07/2024] Open
Abstract
Congenital cytomegalovirus (cCMV) infection can damage the central nervous system in infants; however, its prognosis cannot be predicted from clinical evaluations at the time of birth. Urinary exosomes can be used to analyze neuronal damage in neuronal diseases. To investigate the extent of neuronal damage in patients with cCMV, exosomal miRNA expression in the urine was investigated in cCMV-infected infants and controls. Microarray analysis of miRNA was performed in a cohort of 30 infants, including 11 symptomatic cCMV (ScCMV), 7 asymptomatic cCMV (AScCMV), and one late-onset ScCMV cases, and 11 healthy controls (HC). Hierarchical clustering analysis revealed the distinct expression profile of ScCMV. The patient with late-onset ScCMV was grouped into the ScCMV cluster. Pathway enrichment analysis of the target mRNAs differed significantly between the ScCMV and HC groups; this analysis also revealed that pathways related to brain development were linked to upregulated pathways. Six miRNAs that significantly different between groups (ScCMV vs. HC and ScCMV vs. AScCMV) were selected for digital PCR in another cohort for further validation. Although these six miRNAs seemed insufficient for predicting ScCMV, expression profiles of urine exosomal miRNAs can reveal neurological damage in patients with ScCMV compared to those with AcCMV or healthy infants.
Collapse
Affiliation(s)
- Yuka Torii
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
| | - Takako Suzuki
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
| | - Yuto Fukuda
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
| | - Kazunori Haruta
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
| | - Makoto Yamaguchi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
| | - Kazuhiro Horiba
- Pathogen Genomics Center, National Institute of Infectious Diseases, Toyama 1-23-1, Shinjuku-Ku, Tokyo, 162-8640, Japan
| | - Jun-Ichi Kawada
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
| | - Yoshinori Ito
- Department of Pediatrics, Aichi Medical University, 1-1 Yazakokarimata, Nagakute, 480-1195, Japan.
| |
Collapse
|
3
|
Go K, Horiba K, Yamamoto H, Morimoto Y, Fukasawa Y, Ohashi N, Yasuda K, Ishikawa Y, Kuraishi K, Suzuki K, Ito Y, Takahashi Y, Kato T. Dysbiosis of gut microbiota in patients with protein-losing enteropathy after the Fontan procedure. Int J Cardiol 2024; 396:131554. [PMID: 37875211 DOI: 10.1016/j.ijcard.2023.131554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/22/2023] [Accepted: 10/19/2023] [Indexed: 10/26/2023]
Abstract
BACKGROUND There is a lack of predictive biomarkers for the onset or activity of protein-losing enteropathy (PLE), a Fontan procedure-associated complication. Here, we aimed to identify the gut microbiota composition of patients with active PLE and investigate its relationship with PLE activity. METHODS This multicenter case-control study involved patients who developed PLE (n = 16) after the Fontan procedure and those who did not (non-PLE; n = 20). Patients with PLE who maintained a serum albumin level of ≥3 g/dL for >1 year were included in the remissive-stage-PLE group (n = 9) and those who did not maintain this level were included in the active-PLE group (n = 7). 16S rRNA gene sequencing analysis of fecal samples was performed using QIIME2 pipeline. Alpha (Shannon and Faith's phylogenetic diversity indices) and beta diversity was assessed using principal coordinate analysis based on unweighted UniFrac distances. RESULTS Shannon and Faith's phylogenetic diversity indices were lower in the active-PLE group than in the remissive-stage- (q = 0.028 and 0.025, respectively) and non-PLE (q = 0.028 and 0.017, respectively) groups. Analysis of beta diversity revealed a difference in the microbiota composition between the active-PLE and the other two groups. Linear discriminant effect size analysis demonstrated differences in the relative abundance of Bifidobacterium and Granulicatella spp., and Ruminococcus torques between patients with active- and those with remissive-stage-PLE. CONCLUSIONS Gut microbiota dysbiosis was observed in patients with active PLE. Changes in the bacterial composition of the gut microbiota and decreased diversity may be associated with the severity of PLE.
Collapse
Affiliation(s)
- Kiyotaka Go
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kazuhiro Horiba
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Hidenori Yamamoto
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshihito Morimoto
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshie Fukasawa
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Naoki Ohashi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan; Department of Pediatric Cardiology, Japan Community Healthcare Organization Chukyo Hospital, Nagoya, Japan
| | - Kazushi Yasuda
- Department of Pediatric Cardiology, Aichi Children's Health and Medical Center, Obu, Japan
| | - Yuichi Ishikawa
- Department of Pediatric Cardiology, Fukuoka Children's Hospital, Fukuoka, Japan
| | - Kenji Kuraishi
- Department of Pediatric Cardiology and Neonatology, Ogaki Municipal Hospital, Gifu, Japan
| | - Kazutaka Suzuki
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Yoshinori Ito
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, Japan
| | - Yoshiyuki Takahashi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Taichi Kato
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan.
| |
Collapse
|
4
|
Okumura T, Horiba K, Tetsuka N, Sato Y, Sugiyama Y, Haruta K, Yamaguchi M, Suzuki T, Torii Y, Kawada JI, Ogi T, Hayakawa M, Ito Y. Next-generation sequencing-based detection of Ureaplasma in the gastric fluid of neonates with respiratory distress and chorioamnionitis. J Matern Fetal Neonatal Med 2023; 36:2207113. [PMID: 37150592 DOI: 10.1080/14767058.2023.2207113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
BACKGROUND Respiratory distress is common in neonates admitted to neonatal intensive care units. Additionally, infectious diseases such as intrauterine infections or vertical transmission are important underlying causes of respiratory failure. However, pathogens often cannot be identified in neonates, and there are many cases in which antibacterial drugs are empirically administered. Next-generation sequencing (NGS) is advantageous in that it can detect trace amounts of bacteria that cannot be detected by culturing or bacteria that are difficult to cultivate. However, there are few reports on the diagnosis of infectious diseases using NGS in the neonatal field, especially those targeting respiratory distress. OBJECTIVE The purpose of our study was to investigate the microorganisms associated with neonatal respiratory distress and to determine whether less invasive collection specimens such as plasma and gastric fluid are useful. METHODS Neonates were prospectively recruited between January and August 2020 from Nagoya University Hospital. The inclusion criteria were as follows: 1) admission to the neonatal intensive care unit; 2) respiratory distress presentation within 48 h of birth; and 3) suspected infection, collection of blood culture, and administration of antibiotics. Plasma samples and blood cultures were simultaneously collected. Gastric fluid samples were also collected if the patient was not started on enteral nutrition. Information on the patients and their mothers were collected from the medical records. DNA was extracted from 140 µL of plasma and gastric fluid samples. DNA sequencing libraries were prepared, and their quality was analyzed. DNA libraries were sequenced using high-throughput NGS. The NGS data of plasma and gastric fluid samples were analyzed using the metagenomic pipeline PATHDET, which calculated the number of reads assigned to microorganisms and their relative abundance. Putative pathogens were listed. RESULTS Overall, 30 plasma samples and 25 gastric fluid samples from 30 neonates were analyzed. Microorganism-derived reads of gastric fluid samples were significantly higher than those of plasma samples. Transient tachypnea of the newborn was the most common cause of respiratory distress with 13 cases (43%), followed by respiratory distress syndrome with 7 cases (23%). There were 8 cases (29%) of chorioamnionitis and 7 cases (25%) of funisitis pathologically diagnosed. All blood cultures were negative, and only two gastric fluid cultures were positive for group B Streptococcus (Patient 15) and Candida albicans (Patient 24). Putative pathogens that met the positive criteria for PATHET were detected in four gastric fluid samples, one of which was group B Streptococcus from Patient 15. In the gastric fluid sample of Patient 24, Candida albicans were detected by NGS but did not meet the positive criteria for PATHDET. Cluster analysis of the plasma samples divided them into two study groups, and the indicator genera of each cluster (Phormidium or Toxoplasma) are shown in Figure 1. Clinical findings did not show any significant differences between the two groups. Cluster analysis of the gastric fluid samples divided them into three study groups, and the indicator genera of each cluster (Ureaplasma, Nostoc, and Streptococcus) are shown in Figure 2. The incidence rate of chorioamnionitis was significantly higher in Ureaplasma group than in the other two groups. CONCLUSION Gastric fluid may be useful for assessing neonatal patients with respiratory distress. To the best of our knowledge, this was the first study to reveal that the presence of Ureaplasma in the gastric fluid of neonates with respiratory distress was associated with chorioamnionitis. The early diagnosis of intra-amniotic infections using gastric fluid and its treatment may change the treatment strategy for neonatal respiratory distress. Screening for Ureaplasma in neonates with respiratory distress may reduce the need for empirical antibiotic administration. Further research is required to confirm these findings.
Collapse
Affiliation(s)
- Toshihiko Okumura
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kazuhiro Horiba
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Department of Genetics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
- Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Nobuyuki Tetsuka
- Department of Infection Control, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Yoshiaki Sato
- Division of Neonatology, Center for Maternal-Neonatal Care, Nagoya University Hospital, Nagoya, Japan
| | - Yuichiro Sugiyama
- Department of Pediatrics, Japanese Red Cross Aichi Medical Center Nagoya Daiichi Hospital, Nagoya, Japan
| | - Kazunori Haruta
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Makoto Yamaguchi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takako Suzuki
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuka Torii
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Jun-Ichi Kawada
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
- Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Masahiro Hayakawa
- Division of Neonatology, Center for Maternal-Neonatal Care, Nagoya University Hospital, Nagoya, Japan
| | - Yoshinori Ito
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, Japan
| |
Collapse
|
5
|
Honma A, Takane D, Souma S, Yamauchi K, Wang Y, Nakayama K, Sugawara K, Kitamura M, Horiba K, Kumigashira H, Tanaka K, Kim TK, Cacho C, Oguchi T, Takahashi T, Ando Y, Sato T. Antiferromagnetic topological insulator with selectively gapped Dirac cones. Nat Commun 2023; 14:7396. [PMID: 37978297 PMCID: PMC10656484 DOI: 10.1038/s41467-023-42782-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 10/20/2023] [Indexed: 11/19/2023] Open
Abstract
Antiferromagnetic (AF) topological materials offer a fertile ground to explore a variety of quantum phenomena such as axion magnetoelectric dynamics and chiral Majorana fermions. To realize such intriguing states, it is essential to establish a direct link between electronic states and topology in the AF phase, whereas this has been challenging because of the lack of a suitable materials platform. Here we report the experimental realization of the AF topological-insulator phase in NdBi. By using micro-focused angle-resolved photoemission spectroscopy, we discovered contrasting surface electronic states for two types of AF domains; the surface having the out-of-plane component in the AF-ordering vector displays Dirac-cone states with a gigantic energy gap, whereas the surface parallel to the AF-ordering vector hosts gapless Dirac states despite the time-reversal-symmetry breaking. The present results establish an essential role of combined symmetry to protect massless Dirac fermions under the presence of AF order and widen opportunities to realize exotic phenomena utilizing AF topological materials.
Collapse
Affiliation(s)
- A Honma
- Department of Physics, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan
| | - D Takane
- Department of Physics, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan
| | - S Souma
- Center for Science and Innovation in Spintronics (CSIS), Tohoku University, Sendai, 980-8577, Japan.
- Advanced Institute for Materials Research (WPI-AIMR), Tohoku University, Sendai, 980-8577, Japan.
| | - K Yamauchi
- Center for Spintronics Research Network (CSRN), Osaka University, Toyonaka, Osaka, 560-8531, Japan
| | - Y Wang
- Institute of Physics II, University of Cologne, Köln, 50937, Germany
| | - K Nakayama
- Department of Physics, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), Tokyo, 102-0076, Japan
| | - K Sugawara
- Department of Physics, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan
- Advanced Institute for Materials Research (WPI-AIMR), Tohoku University, Sendai, 980-8577, Japan
| | - M Kitamura
- Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, 305-0801, Japan
- National Institutes for Quantum Science and Technology (QST), Sendai, 980-8579, Japan
| | - K Horiba
- National Institutes for Quantum Science and Technology (QST), Sendai, 980-8579, Japan
| | - H Kumigashira
- Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University, Sendai, 980-8577, Japan
| | - K Tanaka
- UVSOR Synchrotron Facility, Institute for Molecular Science, Okazaki, 444-8585, Japan
| | - T K Kim
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0QX, UK
| | - C Cacho
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0QX, UK
| | - T Oguchi
- Center for Spintronics Research Network (CSRN), Osaka University, Toyonaka, Osaka, 560-8531, Japan
| | - T Takahashi
- Department of Physics, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan
- Advanced Institute for Materials Research (WPI-AIMR), Tohoku University, Sendai, 980-8577, Japan
| | - Yoichi Ando
- Institute of Physics II, University of Cologne, Köln, 50937, Germany
| | - T Sato
- Department of Physics, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan.
- Center for Science and Innovation in Spintronics (CSIS), Tohoku University, Sendai, 980-8577, Japan.
- Advanced Institute for Materials Research (WPI-AIMR), Tohoku University, Sendai, 980-8577, Japan.
- International Center for Synchrotron Radiation Innov1ation Smart (SRIS), Tohoku University, Sendai, 980-8577, Japan.
| |
Collapse
|
6
|
Haruta K, Takeuchi S, Yamaguchi M, Horiba K, Suzuki T, Torii Y, Narita A, Muramatsu H, Takahashi Y, Ito Y, Kawada JI. Droplet digital PCR development for adenovirus load monitoring in children after hematopoietic stem cell transplantation. J Mol Diagn 2023; 25:403-409. [PMID: 36965664 DOI: 10.1016/j.jmoldx.2023.03.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/03/2023] [Accepted: 03/13/2023] [Indexed: 03/27/2023] Open
Abstract
Human adenovirus (AdV) reactivation after hematopoietic stem cell transplantation (HSCT) is associated with life-threatening clinical manifestations. Real-time quantitative PCR (qPCR) has been widely used to measure AdV loads. However, qPCR has not been standardized for AdV. Droplet digital polymerase chain reaction (ddPCR) enables the absolute quantification of viral loads that is a novel pathogen detection technology. DdPCR would enable a more accurate AdV DNA detection compared to qPCR. In this study, ddPCR was developed for AdV DNA and compared its performance characteristics with qPCR. Then, AdV DNAemia incidence during the first 12 weeks after allogenic HSCT was retrospectively examined by qPCR and ddPCR in 97 HSCT episodes using the preserved 545 DNA samples. DdPCR showed better reproducibility and sensitivity, as well as equivalent quantifiability compared to qPCR. AdV DNA among HSCT patients was detected in 11 (2.0%) and 49 (9.0%) of 545 samples by qPCR and ddPCR, respectively. AdV DNA levels of >1000 copies/mL were observed in five cases by qPCR and/or ddPCR. However, two developed fulminant hepatitis and died, while other patients remained asymptomatic with subsequently undetectable AdV DNA. In conclusion, ddPCR was more sensitive and reproducible in detecting AdV DNA among pediatric HSCT recipients than qPCR. DdPCR represents the potential to provide a more accurate DNAemia detection, determine cutoff values for treatment initiation, and antiviral efficacy assessment.
Collapse
Affiliation(s)
- Kazunori Haruta
- Department of Pediatrics, Nagoya University Graduate school of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Suguru Takeuchi
- Department of Pediatrics, Nagoya University Graduate school of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Makoto Yamaguchi
- Department of Pediatrics, Nagoya University Graduate school of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Kazuhiro Horiba
- Department of Genetics, Research Institute of Environmental Medicine, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan; Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
| | - Takako Suzuki
- Department of Pediatrics, Nagoya University Graduate school of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Yuka Torii
- Department of Pediatrics, Nagoya University Graduate school of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Atsushi Narita
- Department of Pediatrics, Nagoya University Graduate school of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Hideki Muramatsu
- Department of Pediatrics, Nagoya University Graduate school of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Yoshiyuki Takahashi
- Department of Pediatrics, Nagoya University Graduate school of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Yoshinori Ito
- Department of Pediatrics, Nagoya University Graduate school of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan; Department of Pediatrics and Child Health, Nihon University School of Medicine, 30-1 Oyaguchi, Kami-cho, Itabashi-ku, Tokyo 173-8610, Japan
| | - Jun-Ichi Kawada
- Department of Pediatrics, Nagoya University Graduate school of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan.
| |
Collapse
|
7
|
Horiba K, Torii Y, Yamaguchi M, Haruta K, Okumura T, Suzuki T, Kawano Y, Kawada JI, Hara S, Giske C, Ogi T, Ito Y. 542. Nanopore and Illumina sequencing for pathogen metagenomics and host transcriptomics of cerebrospinal fluid in infantile central nervous system infections. Open Forum Infect Dis 2022. [DOI: 10.1093/ofid/ofac492.595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Abstract
Background
Infantile central nervous system infections (CNSIs) can be life-threatening and severe sequelae can be observed in encephalitis and bacterial meningitis. The causative microorganism is unknown in > 40% of patients with aseptic infections. This study aimed to analyze metagenome for detection of pathogen, and transcriptome for host reaction of infection in a single cerebrospinal fluid (CSF) sample using two different next-generation sequencing (NGS) platforms, Illumina and Nanopore.
Methods
Twenty-eight CNSIs patients (< 12 months), treated between June 2012 and April 2020, were enrolled. A total of 49 clinical samples (28 CSF and 21 blood) from 28 patients were collected. Extracted RNA, which was obtained from 23 CSF in sufficient quantities, was sequenced using both Nanopore and Illumina platforms to compare their performances in the detection of pathogens. Human-derived reads subtracted during pathogen detection were used for host transcriptomic analysis from both Nanopore and Illumina sequencing. All the extracted DNA from 28 CSF and 21 blood, was sequenced using Illumina sequencer for the detection of pathogens. Data analysis was performed on the in-house PATHDET pipeline.
A flowchart for pathogen detection and transcriptome analysis
Pathogen detection was performed on the in-house PATHDET pipeline and transcriptome analysis was performed by using the secondary outputs.
Results
RNA sequencing of CSF samples in 23 cases revealed potential viral pathogens in 10 cases: coxsackievirus B5 (4 cases), coxsackievirus B4 (3 cases), coxsackievirus B2 (1 case), echovirus E7 (1 case), and human parechovirus 3 (1 case). DNA sequencing was performed in 28 cases using Illumina sequencing, and Proteus mirabilis (1 case, consistent with the culture test) and human parvovirus B19 (1 case) were detected. The results of Nanopore sequencing and Illumina sequencing were consistent. However, the mapping coverage and depth to the detected pathogen genome of Nanopore sequencing was superior to that of Illumina sequencing. MX1, ISG15, and OAS1 were differentially expressed genes in patients with identified pathogens via metagenomic NGS, both the Nanopore and Illumina sequencing, and were associated with antiviral roles in innate immunity.
A pie chart for patients with central nervous system infections (CNSIs)
Results of next-generation sequencing (NGS) and the detected pathogen candidates using DNA/RNA workflows.
Performance of Nanopore and Illumina sequencing for pathogen genome mapping
The sequencing output, which is 100,000 reads randomly extracted from original sequencing reads, was mapped to the pathogen reference genome to determine (A) mapping coverage and (B) mapping depth.
Volcano plot of all genes analyzed in Nanopore and Illumina sequencing
Volcano plots showing differentially expressed genes in the cerebrospinal fluid between identified-pathogen and unidentified-pathogen samples from (A) Nanopore sequencing and (B) Illumina RNA sequencing.
Conclusion
The use of Nanopore sequencing for metagenomic diagnostics of CSF samples should help to understand both pathogens and host immune responses of CNSI and could shed light on the pathogenesis of these infections.
Disclosures
All Authors: No reported disclosures.
Collapse
Affiliation(s)
| | - Yuka Torii
- Nagoya University Graduate School of Medicine , Nagoya, Aichi , Japan
| | - Makoto Yamaguchi
- Nagoya University Graduate School of Medicine , Nagoya, Aichi , Japan
| | - Kazunori Haruta
- Nagoya University Graduate School of Medicine , Nagoya, Aichi , Japan
| | | | - Takako Suzuki
- Nagoya University Graduate School of Medicine , Nagoya, Aichi , Japan
| | | | - Jun-ichi Kawada
- Nagoya University Graduate School of Medicine , Nagoya, Aichi , Japan
| | - Shinya Hara
- Department of Pediatrics , Toyota, Aichi , Japan
| | - Christian Giske
- Karolinska Institute and Karolinska University Hospital , Stockholm, Stockholms Lan , Sweden
| | - Tomoo Ogi
- Research Institute of Environmental Medicine, Nagoya University , Nagoya, Aichi , Japan
| | - Yoshinori Ito
- Nihon University School of Medicine , Itabashi-ku, Tokyo , Japan
| |
Collapse
|
8
|
Horiba K, Torii Y, Aizawa Y, Yamaguchi M, Haruta K, Okumura T, Suzuki T, Kawano Y, Kawada JI, Hara S, Saitoh A, Giske CG, Ogi T, Ito Y. Performance of Nanopore and Illumina metagenomic sequencing for pathogen detection and transcriptome analysis in infantile central nervous system infections. Open Forum Infect Dis 2022; 9:ofac504. [PMID: 36299531 PMCID: PMC9587384 DOI: 10.1093/ofid/ofac504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 09/28/2022] [Indexed: 12/04/2022] Open
Abstract
Background Infantile central nervous system infections (CNSIs) can be life-threatening and cause severe sequelae. However, the causative microorganism remains unknown in >40% of patients with aseptic infections. This study aimed to analyze the metagenome for detection of pathogens and the transcriptome for host immune responses during infection in a single cerebrospinal fluid (CSF) sample using 2 different next-generation sequencing (NGS) platforms, Nanopore and Illumina. Methods Twenty-eight CNSIs patients (<12 months) were enrolled, and 49 clinical samples (28 CSF and 21 blood) were collected. The DNA extracted from all 49 samples was sequenced using the Illumina sequencer for the detection of pathogens. Extracted RNA was obtained in sufficient quantities from 23 CSF samples and subjected to sequencing on both Nanopore and Illumina platforms. Human-derived reads subtracted during pathogen detection were used for host transcriptomic analysis from both Nanopore and Illumina sequencing. Results RNA metagenomic sequencing using both sequencing platforms revealed putative viral pathogens in 10 cases. DNA sequencing using the Illumina sequencer detected 2 pathogens. The results of Nanopore and Illumina RNA sequencing were consistent; however, the mapping coverage and depth to the detected pathogen genome of Nanopore RNA sequencing were greater than those of Illumina. Host transcriptomic analysis of Nanopore sequencing revealed highly expressed genes related to the antiviral roles of innate immunity from pathogen-identified cases. Conclusions The use of Nanopore RNA sequencing for metagenomic diagnostics of CSF samples should help to elucidate both pathogens and host immune responses of CNSI and could shed light on the pathogenesis of these infections.
Collapse
Affiliation(s)
- Kazuhiro Horiba
- Department of Genetics, Research Institute of Environmental Medicine, Nagoya University , Nagoya , Japan
- Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine , Nagoya , Japan
- Department of Pediatrics, Nagoya University Graduate School of Medicine , Nagoya , Japan
- Department of Pediatrics, TOYOTA Memorial Hospital , Toyota , Japan
| | - Yuka Torii
- Department of Pediatrics, Nagoya University Graduate School of Medicine , Nagoya , Japan
| | - Yuta Aizawa
- Department of Pediatrics, Niigata University Graduate School of Medical and Dental Sciences , Niigata , Japan
| | - Makoto Yamaguchi
- Department of Pediatrics, Nagoya University Graduate School of Medicine , Nagoya , Japan
| | - Kazunori Haruta
- Department of Pediatrics, Nagoya University Graduate School of Medicine , Nagoya , Japan
| | - Toshihiko Okumura
- Department of Pediatrics, Nagoya University Graduate School of Medicine , Nagoya , Japan
| | - Takako Suzuki
- Department of Pediatrics, Nagoya University Graduate School of Medicine , Nagoya , Japan
| | - Yoshihiko Kawano
- Department of Pediatrics, TOYOTA Memorial Hospital , Toyota , Japan
| | - Jun ichi Kawada
- Department of Pediatrics, Nagoya University Graduate School of Medicine , Nagoya , Japan
| | - Shinya Hara
- Department of Pediatrics, TOYOTA Memorial Hospital , Toyota , Japan
| | - Akihiko Saitoh
- Department of Pediatrics, Niigata University Graduate School of Medical and Dental Sciences , Niigata , Japan
| | - Christian G Giske
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute and Karolinska University Hospital , Stockholm , Sweden
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine, Nagoya University , Nagoya , Japan
- Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine , Nagoya , Japan
| | - Yoshinori Ito
- Department of Pediatrics, Nagoya University Graduate School of Medicine , Nagoya , Japan
- Department of Pediatrics and Child Health, Nihon University School of Medicine , Tokyo , Japan
| |
Collapse
|
9
|
Torii Y, Horiba K, Kawada JI, Haruta K, Yamaguchi M, Suzuki T, Uryu H, Kashiwa N, Goishi K, Ogi T, Ito Y. Detection of antiviral drug resistance in patients with congenital cytomegalovirus infection using long-read sequencing: a retrospective observational study. BMC Infect Dis 2022; 22:568. [PMID: 35733089 PMCID: PMC9219161 DOI: 10.1186/s12879-022-07537-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 06/08/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Congenital human cytomegalovirus (cCMV) infection can cause sensorineural hearing loss and neurodevelopmental disabilities in children. Ganciclovir and valganciclovir (GCV/VGCV) improve long-term audiologic and neurodevelopmental outcomes for patients with cCMV infection; however, antiviral drug resistance has been documented in some cases. Long-read sequencing can be used for the detection of drug resistance mutations. The objective of this study was to develop full-length analysis of UL97 and UL54, target genes with mutations that confer GCV/VGCV resistance using long-read sequencing, and investigate drug resistance mutation in patients with cCMV infection. METHODS Drug resistance mutation analysis was retrospectively performed in 11 patients with cCMV infection treated with GCV/VGCV. UL97 and UL54 genes were amplified using blood DNA. The amplicons were sequenced using a long-read sequencer and aligned with the reference gene. Single nucleotide variants were detected and replaced with the reference sequence. The replaced sequence was submitted to a mutation resistance analyzer, which is an open platform for drug resistance mutations. RESULTS Two drug resistance mutations (UL54 V823A and UL97 A594V) were found in one patient. Both mutations emerged after 6 months of therapy, where viral load increased. Mutation rates subsided after cessation of GCV/VGCV treatment. CONCLUSIONS Antiviral drug resistance can emerge in patients with cCMV receiving long-term therapy. Full-length analysis of UL97 and UL54 via long-read sequencing enabled the rapid and comprehensive detection of drug resistance mutations.
Collapse
Affiliation(s)
- Yuka Torii
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, 466-8550, Nagoya, Japan
| | - Kazuhiro Horiba
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, 466-8550, Nagoya, Japan.,Department of Genetics, Research Institute of Environmental Medicine Nagoya University, Furo-cho, Chikusa-ku, 464-8601, Nagoya, Japan.,Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, 466-8550, Nagoya, Japan
| | - Jun-Ichi Kawada
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, 466-8550, Nagoya, Japan
| | - Kazunori Haruta
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, 466-8550, Nagoya, Japan
| | - Makoto Yamaguchi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, 466-8550, Nagoya, Japan
| | - Takako Suzuki
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, 466-8550, Nagoya, Japan
| | - Hideko Uryu
- Department of Pediatrics, National Center for Global Health and Medicine, 1-21-1 Toyama Shinjuku-ku, Tokyo, Japan
| | - Naoyuki Kashiwa
- Department of Pediatrics, National Center for Global Health and Medicine, 1-21-1 Toyama Shinjuku-ku, Tokyo, Japan
| | - Keiji Goishi
- Department of Pediatrics, National Center for Global Health and Medicine, 1-21-1 Toyama Shinjuku-ku, Tokyo, Japan
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine Nagoya University, Furo-cho, Chikusa-ku, 464-8601, Nagoya, Japan.,Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, 466-8550, Nagoya, Japan
| | - Yoshinori Ito
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, 466-8550, Nagoya, Japan. .,Department of Pediatrics and Child Health, Nihon University School of Medicine, 30-1 Oyaguchi, Kami-cho, Itabashi-ku, 173-8610, Tokyo, Japan.
| |
Collapse
|
10
|
Yamaguchi M, Kawada J, Torii Y, Haruta K, Suzuki T, Horiba K, Takahashi Y, Ito Y. Quantitative assessment of viral load in the blood and urine of patients with congenital cytomegalovirus infection using droplet digital PCR. J Med Virol 2022; 94:4559-4564. [DOI: 10.1002/jmv.27844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 04/20/2022] [Accepted: 05/06/2022] [Indexed: 11/05/2022]
Affiliation(s)
- Makoto Yamaguchi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai‐cho, Showa‐kuNagoyaAichi466‐8550Japan
| | - Jun‐ichi Kawada
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai‐cho, Showa‐kuNagoyaAichi466‐8550Japan
| | - Yuka Torii
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai‐cho, Showa‐kuNagoyaAichi466‐8550Japan
| | - Kazunori Haruta
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai‐cho, Showa‐kuNagoyaAichi466‐8550Japan
| | - Takako Suzuki
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai‐cho, Showa‐kuNagoyaAichi466‐8550Japan
| | - Kazuhiro Horiba
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai‐cho, Showa‐kuNagoyaAichi466‐8550Japan
| | - Yoshiyuki Takahashi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai‐cho, Showa‐kuNagoyaAichi466‐8550Japan
| | - Yoshinori Ito
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai‐cho, Showa‐kuNagoyaAichi466‐8550Japan
| |
Collapse
|
11
|
Torii Y, Kawada JI, Horiba K, Okumura T, Suzuki T, Ito Y. MicroRNA expression profiling of cerebrospinal fluid/serum exosomes in children with human herpesvirus 6-associated encephalitis/encephalopathy by high-throughput sequencing. J Neurovirol 2022; 28:151-157. [PMID: 35212942 DOI: 10.1007/s13365-022-01058-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 05/13/2021] [Accepted: 02/01/2022] [Indexed: 11/25/2022]
Abstract
Primary human herpesvirus 6 (HHV-6) infection is sometimes accompanied by acute encephalopathy with reduced subcortical diffusion (AED) in immunocompetent children. We investigated exosomal microRNA (miRNA) expression profiles in cerebrospinal fluid (CSF) and sera of patients with HHV-6-associated AED (n = 5) and febrile seizure (FS) (n = 5) using high-throughput sequencing. A total of 176 and 663 miRNAs were identified in CSF and serum exosomes, respectively. Comparative analysis determined that some miRNAs (miR-381-3p, miR-155) were exclusively expressed in the CSF exosomes of AED but not of FS patients, suggesting their potential application as novel diagnostic biomarkers for AED.
Collapse
Affiliation(s)
- Yuka Torii
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Jun-Ichi Kawada
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan.
| | - Kazuhiro Horiba
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Toshihiko Okumura
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Takako Suzuki
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Yoshinori Ito
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| |
Collapse
|
12
|
Horiba K, Torii Y, Okumura T, Takeuchi S, Suzuki T, Kawada JI, Muramatsu H, Takahashi Y, Ogi T, Ito Y. Next-Generation Sequencing to Detect Pathogens in Pediatric Febrile Neutropenia: A Single-Center Retrospective Study of 112 Cases. Open Forum Infect Dis 2021; 8:ofab223. [PMID: 34859110 PMCID: PMC8634086 DOI: 10.1093/ofid/ofab223] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/27/2021] [Indexed: 12/22/2022] Open
Abstract
Background Febrile neutropenia (FN) is a frequent complication in immunocompromised patients. However, causative microorganisms are detected in only 10% of patients. This study aimed to detect the microorganisms that cause FN using next-generation sequencing (NGS) to identify the genome derived from pathogenic microorganisms in the bloodstream. Here, we implemented a metagenomic approach to comprehensively analyze microorganisms present in clinical samples from patients with FN. Methods FN is defined as a neutrophil count <500 cells/µL and fever ≥37.5°C. Plasma/serum samples of 112 pediatric patients with FN and 10 patients with neutropenia without fever (NE) were sequenced by NGS and analyzed by a metagenomic pipeline, PATHDET. Results The putative pathogens were detected by NGS in 5 of 10 FN patients with positive blood culture results, 15 of 87 FN patients (17%) with negative blood culture results, and 3 of 8 NE patients. Several bacteria that were common in the oral, skin, and gut flora were commonly detected in blood samples, suggesting translocation of the human microbiota to the bloodstream in the setting of neutropenia. The cluster analysis of the microbiota in blood samples using NGS demonstrated that the representative bacteria of each cluster were mostly consistent with the pathogens in each patient. Conclusions NGS technique has great potential for detecting causative pathogens in patients with FN. Cluster analysis, which extracts characteristic microorganisms from a complex microbial population, may be effective to detect pathogens in minute quantities of microbiota, such as those from the bloodstream.
Collapse
Affiliation(s)
- Kazuhiro Horiba
- Department of Genetics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
- Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuka Torii
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Toshihiko Okumura
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Suguru Takeuchi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takako Suzuki
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Jun-ichi Kawada
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hideki Muramatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshiyuki Takahashi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
- Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshinori Ito
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Correspondence: Yoshinori Ito, MD, PhD, Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466–8550, Japan ()
| |
Collapse
|
13
|
Okumura T, Horiba K, Kamei H, Takeuchi S, Suzuki T, Torii Y, Kawada JI, Takahashi Y, Ogura Y, Ogi T, Ito Y. Temporal dynamics of the plasma microbiome in recipients at early post-liver transplantation: a retrospective study. BMC Microbiol 2021; 21:104. [PMID: 33823791 PMCID: PMC8025517 DOI: 10.1186/s12866-021-02154-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 03/16/2021] [Indexed: 01/07/2023] Open
Abstract
Background Immunosuppression during liver transplantation (LT) enables the prevention and treatment of organ rejection but poses a risk for severe infectious diseases. Immune modulation and antimicrobials affect the plasma microbiome. Thus, determining the impact of immunosuppression on the microbiome may be important to understand immunocompetence, elucidate the source of infection, and predict the risk of infection in LT recipients. We characterized the plasma microbiome of LT recipients at early post-LT and assessed the association between the microbiome and clinical events. Results In this study, 51 patients who received LT at Nagoya University Hospital from 2016 to 2018 were enrolled. Plasma samples were retrospectively collected at the following time points: 1) within a week after LT; 2) 4 ± 1 weeks after LT; 3) 8 ± 1 weeks after LT; and 4) within 2 days after a positive blood culture. A total of 111 plasma samples were analyzed using shotgun next-generation sequencing (NGS) with the PATHDET pipeline. Relative abundance of Anelloviridae, Nocardiaceae, Microbacteriaceae, and Enterobacteriaceae significantly changed during the postoperative period. Microbiome diversity was higher within a week after LT than that at 8 weeks after LT. Antimicrobials were significantly associated with the microbiome of LT recipients. In addition, the proportion of Enterobacteriaceae was significantly increased and the plasma microbiome diversity was significantly lower in patients with acute cellular rejection (ACR) than non-ACR patients. Sequencing reads of bacteria isolated from blood cultures were predominantly identified by NGS in 8 of 16 samples, and human herpesvirus 6 was detected as a causative pathogen in one recipient with severe clinical condition. Conclusions The metagenomic NGS technique has great potential in revealing the plasma microbiome and is useful as a comprehensive diagnostic procedure in clinical settings. Temporal dynamics of specific microorganisms may be used as indirect markers for the determination of immunocompetence and ACR in LT recipients. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02154-w.
Collapse
Affiliation(s)
- Toshihiko Okumura
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Kazuhiro Horiba
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan.,Department of Genetics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan.,Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hideya Kamei
- Department of Transplantation Surgery, Nagoya University Hospital, Nagoya, Japan
| | - Suguru Takeuchi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Takako Suzuki
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Yuka Torii
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Jun-Ichi Kawada
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Yoshiyuki Takahashi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Yasuhiro Ogura
- Department of Transplantation Surgery, Nagoya University Hospital, Nagoya, Japan
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan.,Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshinori Ito
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan.
| |
Collapse
|
14
|
Takeuchi S, Kawada JI, Horiba K, yamaguchi M, Okumura T, Suzuki T, Torii Y, Kawabe S, Wada S, Ikeyama T, Ito Y. 1224. Investigation of Infectious Etiologies in the Lower Respiratory Tract from Pediatric Patients with Unexpected Cardiopulmonary Deterioration using Next-Generation Sequencing. Open Forum Infect Dis 2020. [PMCID: PMC7776594 DOI: 10.1093/ofid/ofaa439.1409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Background In pediatric patients, unexpected cardiopulmonary deterioration with or without following cardiopulmonary arrest (CPA) are rare events, but can be caused by any of several etiologies, including infectious diseases. The most common cause of out-of-hospital CPA in children ≤12 years old was sudden infant death syndrome (SIDS), whereas infectious diseases were responsible for approximately 10% of the CPA cases. However, the role of infection may have been underestimated as triggers of SIDS or CPA. This study aimed to investigate the infectious etiologies in pediatric patients with unexpected cardiopulmonary deterioration using next-generation sequencing (NGS). Methods A total of 16 pediatric patients who were admitted to the pediatric intensive care unit with unexpected cardiopulmonary deterioration with or without following CPA were enrolled. Ten bronchoalveolar fluid (BALF) and six transtracheal aspirates (TTA) samples obtained in the acute phase were used to prepare NGS libraries. The libraries were sequenced on HiSeq and analyzed using metagenome analysis tools. Results In ten of 16 patients, one or more bacterial/viral pathogens were detected in the BALF or TTA specimens using NGS. Compared to the conventional culture and viral antigen test results, an additional 6 bacterial (e.g., Chlamydia trachomatis) and 4 viral pathogens (e.g., coxsackievirus A6 and human coronavirus NL63) were identified by NGS in four of ten patients in whom no causative pathogen had been identified by conventional culture and viral antigen tests. A summary of the detected pathogens is listed in Table 1. Notably, sequencing results allowed us to define genotypes for all of the detected viruses in a single NGS assay per patient. Furthermore, based on phylogenetic analysis of the VP1 region, the coxsackievirus A6 strain detected in this study belongs to lineage E2 and harbors an amino acid change (T283A), a substitution that has potential to cause severe illness. Table 1 ![]()
Conclusion Our results suggest that viral and bacterial infection are common triggers in unexpected cardiopulmonary deterioration in pediatric patients. NGS has the potential to contribute to the clarification of the etiology of pediatric critical illness. Disclosures All Authors: No reported disclosures
Collapse
Affiliation(s)
- Suguru Takeuchi
- Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Jun-ichi Kawada
- Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Kazuhiro Horiba
- Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Aichi, Japan
| | - Makoto yamaguchi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | | | - Takako Suzuki
- Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Yuka Torii
- Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Shinji Kawabe
- Aichi Children’s Health and Medical Center, Obu, Aichi, Japan
| | - Sho Wada
- Aichi Children’s Health and Medical Center, Obu, Aichi, Japan
| | | | - Yoshinori Ito
- Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| |
Collapse
|
15
|
Okumura T, Horiba K, Kamei H, Takeuchi S, Suzuki T, Torii Y, Kawada JI, Takahashi Y, Ogura Y, Ogi T, Ito Y. 1212. Temporal Dynamics of the Plasma Microbiome in Recipients at Early Post-liver Transplantation. Open Forum Infect Dis 2020. [PMCID: PMC7776645 DOI: 10.1093/ofid/ofaa439.1397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
Immunosuppression during liver transplantation (LT) enables the prevention and treatment of organ rejection, but poses a risk for severe infectious diseases. Antimicrobials are often required for patients after LT. Recently, the genomes of multiple microorganisms have been detected in blood, which is essentially sterile. Immune modulation and antimicrobials affect the blood microbiome. Thus, determining the impact of immunosuppression and antimicrobials on the microbiome may be important to understand immunocompetence, predict clinical adverse events after LT such as acute cellular rejection (ACR), and treat infectious diseases.
Methods
Fifty-one patients who received LT at Nagoya University Hospital from 2016 to 2018 were enrolled. Plasma samples were retrospectively collected within a week after LT, 4±1 weeks after LT, 8±1 weeks after LT, and within 2 days after a positive blood culture. A total of 111 plasma samples were analyzed using shotgun next-generation sequencing (NGS). Sequence data were imported into the custom-made analysis pipeline PATHDET.
Results
The relative abundance of Anelloviridae, Nocardiaceae, Microbacteriaceae, and Enterobacteriaceae significantly changed during the postoperative period (figure 1). Microbiome diversity was higher within a week after LT than at 8 weeks after LT. Antimicrobials were significantly associated with the microbiome of LT recipients. In addition, the proportion of Enterobacteriaceae was significantly decreased (figure 2) and the plasma microbiome diversity was significantly higher in patients with ACR than in non-ACR patients. Finally, sequencing reads of bacteria isolated from blood cultures were predominantly identified by NGS in 8 of 16 samples (figure 3), and human herpesvirus 6 was detected as a causative pathogen in one recipient with severe infectious diseases.
Change in the relative abundance of each microorganism at the family level of taxonomic hierarchy in plasma samples after liver transplantation
Comparison of the plasma microbiome at the family level in patients with and without acute cellular rejection
Relative abundance of microorganisms at the species level in plasma from patients with positive blood cultures
Conclusion
The metagenomic NGS technique has great potential in revealing the plasma microbiome and is useful as a comprehensive diagnostic procedure in clinical settings. Temporal dynamics of specific microorganisms may be used as indirect markers for the determination of immunocompetence and ACR in LT recipients.
Disclosures
All Authors: No reported disclosures
Collapse
Affiliation(s)
| | - Kazuhiro Horiba
- Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Aichi, Japan
| | - Hideya Kamei
- Department of Transplantation Surgery, Nagoya University Hospital, nagoya, Aichi, Japan
| | - Suguru Takeuchi
- Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Takako Suzuki
- Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Yuka Torii
- Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Jun-ichi Kawada
- Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Yoshiyuki Takahashi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Yasuhiro Ogura
- Department of Transplantation Surgery, Nagoya University Hospital, nagoya, Aichi, Japan
| | - Tomoo Ogi
- Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Aichi, Japan
| | - Yoshinori Ito
- Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| |
Collapse
|
16
|
Torii Y, Horiba K, Hayano S, Kato T, Suzuki T, Kawada JI, Takahashi Y, Kojima S, Okuno Y, Ogi T, Ito Y. Comprehensive pathogen detection in sera of Kawasaki disease patients by high-throughput sequencing: a retrospective exploratory study. BMC Pediatr 2020; 20:482. [PMID: 33059644 PMCID: PMC7557310 DOI: 10.1186/s12887-020-02380-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/08/2020] [Indexed: 12/11/2022] Open
Abstract
Background Kawasaki disease (KD) is an idiopathic systemic vasculitis that predominantly damages coronary arteries in children. Various pathogens have been investigated as triggers for KD, but no definitive causative pathogen has been determined. As KD is diagnosed by symptoms, several days are needed for diagnosis. Therefore, at the time of diagnosis of KD, the pathogen of the trigger may already be diminished. The aim of this study was to explore comprehensive pathogens in the sera at the acute stage of KD using high-throughput sequencing (HTS). Methods Sera of 12 patients at an extremely early stage of KD and 12 controls were investigated. DNA and RNA sequences were read separately using HTS. Sequence data were imported into the home-brew meta-genomic analysis pipeline, PATHDET, to identify the pathogen sequences. Results No RNA virus reads were detected in any KD case except for that of equine infectious anemia, which is known as a contaminant of commercial reverse transcriptase. Concerning DNA viruses, human herpesvirus 6B (HHV-6B, two cases) and Anelloviridae (eight cases) were detected among KD cases as well as controls. Multiple bacterial reads were obtained from KD and controls. Bacteria of the genera Acinetobacter, Pseudomonas, Delfita, Roseomonas, and Rhodocyclaceae appeared to be more common in KD sera than in the controls. Conclusion No single pathogen was identified in serum samples of patients at the acute phase of KD. With multiple bacteria detected in the serum samples, it is difficult to exclude the possibility of contamination; however, it is possible that these bacteria might stimulate the immune system and induce KD.
Collapse
Affiliation(s)
- Yuka Torii
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Kazuhiro Horiba
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan.,Department of Genetics, Research Institute of Environmental Medicine Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan.,Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Satoshi Hayano
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Taichi Kato
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Takako Suzuki
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Jun-Ichi Kawada
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Yoshiyuki Takahashi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Seiji Kojima
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Yusuke Okuno
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan.,Center for Advanced Medicine and Clinical Research, Nagoya University Hospital, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan.,Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Yoshinori Ito
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan.
| |
Collapse
|
17
|
Kawada JI, Takeuchi S, Imai H, Okumura T, Horiba K, Suzuki T, Torii Y, Yasuda K, Imanaka-Yoshida K, Ito Y. Immune cell infiltration landscapes in pediatric acute myocarditis analyzed by CIBERSORT. J Cardiol 2020; 77:174-178. [PMID: 32891480 DOI: 10.1016/j.jjcc.2020.08.004] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/14/2020] [Accepted: 08/03/2020] [Indexed: 12/23/2022]
Abstract
BACKGROUND Myocarditis is an inflammatory disease of the myocardium, which leads to cardiac dysfunction and heart failure. Previous studies have suggested that complex cross-talk between innate and adaptive immune responses is involved in the pathogenesis of acute myocarditis. Immunohistochemistry is the current standard method for the evaluation of infiltrating immune cells, however, it is difficult to investigate and quantify many immune cell populations using this technique. METHODS Endomyocardial biopsy samples of five pediatric patients with myocarditis were analyzed by cell-type identification by estimating relative subsets of RNA transcript (CIBERSORT), a computational method for quantifying cell fractions from tissue gene expression profiles. CIBERSORT results were then compared with immunohistochemistry analyses. RESULTS Significant results of immune infiltrate deconvolution were obtained in four patients with fulminant myocarditis by CIBERSORT analysis. Among 22 immune cell types, 19 cell types were detected in one or more patients. Activated NK cells were the most prevalent population in two patients, whereas activated memory CD4+ T cells and M2 macrophages were the most prevalent population in one patient each. Overall CIBERSORT results were consistent with those of immunohistochemistry, although some discrepancies were observed. CONCLUSIONS Infiltrating immune cell subsets detected by CIBERSORT analysis can reflect the time course of innate and adaptive immune responses in acute myocarditis. CIBERSORT may have the potential to characterize the detail of infiltrating immune cells in myocardial tissues and provide novel insights into the pathogenesis of acute myocarditis.
Collapse
Affiliation(s)
- Jun-Ichi Kawada
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan.
| | - Suguru Takeuchi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hiroshi Imai
- Pathology Division, Mie University Hospital, Mie, Japan
| | - Toshihiko Okumura
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kazuhiro Horiba
- Department of Genetics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan; Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takako Suzuki
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuka Torii
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kazushi Yasuda
- Department of Pediatric Cardiology, Aichi Children's Health and Medical Center, Obu, Japan
| | - Kyoko Imanaka-Yoshida
- Department of Pathology and Matrix Biology, Mie University Graduate School of Medicine, Mie, Japan
| | - Yoshinori Ito
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| |
Collapse
|
18
|
Nishioka D, Tsuchiya T, Namiki W, Takayanagi M, Kawamura K, Fujita T, Yukawa R, Horiba K, Kumigashira H, Higuchi T. Surface Proton Conduction of Sm-Doped CeO 2-δ Thin Film Preferentially Grown on Al 2O 3 (0001). Nanoscale Res Lett 2020; 15:42. [PMID: 32065313 PMCID: PMC7026374 DOI: 10.1186/s11671-020-3267-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 01/22/2020] [Indexed: 06/10/2023]
Abstract
Sm-doped CeO2-δ (Ce0.9Sm0.1O2-δ; SDC) thin films were prepared on Al2O3 (0001) substrates by radio frequency magnetron sputtering. The prepared thin films were preferentially grown along the [111] direction, with the spacing of the (111) plane (d111) expanded by 2.6% to compensate for a lattice mismatch against the substrate. The wet-annealed SDC thin film, with the reduced d111 value, exhibited surface protonic conduction in the low-temperature region below 100 °C. The O1s photoemission spectrum exhibits H2O and OH- peaks on the SDC surface. These results indicate the presence of physisorbed water layers and the generation of protons on the SDC (111) surface with oxygen vacancies. The protons generated on the SDC surface were conducted through a physisorbed water layer by the Grotthuss mechanism.
Collapse
Affiliation(s)
- D Nishioka
- Department of Applied Physics, Tokyo University of Science, Katsushika, Tokyo, 125-8585, Japan.
| | - T Tsuchiya
- International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science (NIMS), Tsukuba, Ibaraki, 305-0044, Japan
| | - W Namiki
- Department of Applied Physics, Tokyo University of Science, Katsushika, Tokyo, 125-8585, Japan
| | - M Takayanagi
- Department of Applied Physics, Tokyo University of Science, Katsushika, Tokyo, 125-8585, Japan
| | - K Kawamura
- Department of Applied Physics, Tokyo University of Science, Katsushika, Tokyo, 125-8585, Japan
| | - T Fujita
- Department of Applied Physics, Tokyo University of Science, Katsushika, Tokyo, 125-8585, Japan
| | - R Yukawa
- Photon Factory, High Energy Accelerator Organization (KEK), Tsukuba, Ibaraki, 305-0801, Japan
| | - K Horiba
- Photon Factory, High Energy Accelerator Organization (KEK), Tsukuba, Ibaraki, 305-0801, Japan
| | - H Kumigashira
- Photon Factory, High Energy Accelerator Organization (KEK), Tsukuba, Ibaraki, 305-0801, Japan
- Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University, Sendai, 980-8577, Japan
| | - T Higuchi
- Department of Applied Physics, Tokyo University of Science, Katsushika, Tokyo, 125-8585, Japan
| |
Collapse
|
19
|
Kriener M, Sakano M, Kamitani M, Bahramy MS, Yukawa R, Horiba K, Kumigashira H, Ishizaka K, Tokura Y, Taguchi Y. Evolution of Electronic States and Emergence of Superconductivity in the Polar Semiconductor GeTe by Doping Valence-Skipping Indium. Phys Rev Lett 2020; 124:047002. [PMID: 32058775 DOI: 10.1103/physrevlett.124.047002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Indexed: 06/10/2023]
Abstract
GeTe is a chemically simple IV-VI semiconductor which bears a rich plethora of different physical properties induced by doping and external stimuli. Here, we report a superconductor-semiconductor-superconductor transition controlled by finely-tuned In doping. Our results reveal the existence of a critical doping concentration x_{c}=0.12 in Ge_{1-x}In_{x}Te, where various properties, including structure, resistivity, charge carrier type, and the density of states, take either an extremum or change their character. At the same time, we find indications of a change in the In-valence state from In^{3+} to In^{1+} with increasing x by core-level photoemission spectroscopy, suggesting that this system is a new promising playground to probe valence fluctuations and their possible impact on structural, electronic, and thermodynamic properties of their host.
Collapse
Affiliation(s)
- M Kriener
- RIKEN Center for Emergent Matter Science (CEMS), Wako 351-0198, Japan
| | - M Sakano
- Department of Applied Physics and Quantum-Phase Electronics Center (QPEC), University of Tokyo, Tokyo 113-8656, Japan
| | - M Kamitani
- RIKEN Center for Emergent Matter Science (CEMS), Wako 351-0198, Japan
| | - M S Bahramy
- RIKEN Center for Emergent Matter Science (CEMS), Wako 351-0198, Japan
- Department of Applied Physics and Quantum-Phase Electronics Center (QPEC), University of Tokyo, Tokyo 113-8656, Japan
| | - R Yukawa
- Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan
| | - K Horiba
- Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan
| | - H Kumigashira
- Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan
- Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University, Sendai 980-8577, Japan
| | - K Ishizaka
- RIKEN Center for Emergent Matter Science (CEMS), Wako 351-0198, Japan
- Department of Applied Physics and Quantum-Phase Electronics Center (QPEC), University of Tokyo, Tokyo 113-8656, Japan
| | - Y Tokura
- RIKEN Center for Emergent Matter Science (CEMS), Wako 351-0198, Japan
- Department of Applied Physics and Quantum-Phase Electronics Center (QPEC), University of Tokyo, Tokyo 113-8656, Japan
- Tokyo College, University of Tokyo, Tokyo 113-8656, Japan
| | - Y Taguchi
- RIKEN Center for Emergent Matter Science (CEMS), Wako 351-0198, Japan
| |
Collapse
|
20
|
Horiba K, Torii Y, Hara Y, Shimada M, Suzuki T, Takeuchi S, Okumura T, Kawada JI, Muramatsu H, Takahashi Y, Ogi T, Ito Y. 242. Comprehensive Pathogen Detection for Pediatric Febrile Neutropenia by Metagenomic Next-Generation Sequencing. Open Forum Infect Dis 2019. [PMCID: PMC6810412 DOI: 10.1093/ofid/ofz360.317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Background Febrile neutropenia (FN) is a common complication in patients with solid tumors and hematologic malignancies. Identification of the causative microorganisms would contribute to optimization of antimicrobial treatment and thus improve the outcome of FN. However, causative microorganisms are detected in only 10% to 20% of FN patients. Next-generation sequencing (NGS) allows us to comprehensively analyze all microorganisms present in a clinical sample. In this study, we aimed to utilize NGS for the detection of microbial pathogens in infectious diseases and elucidate the infection source in FN. Methods FN is defined by two characteristics: (1) neutrophils count < 500/µL, and (2) fever ≥38.0°C. From 2016 to 2018, 112 plasma/serum samples of pediatric FN patients (11 positive blood cultures) were analyzed. Serum samples from 10 neutropenic patients without fever were also analyzed as controls. Shotgun sequencing method was applied for these samples. The metagenomic analyses were performed through the pipeline PATHDET, which has been newly established in our laboratory. Diagnosis based on NGS results was made based on the following criteria: (1) number of reads from all pathogens per million reads (PR) >650, (2) a specific pathogen’s reads per million reads (RPM) >200, and (3) diversity index >3.0. The NGS results were compared with those from blood culture. Results Sequencing reads of bacteria isolated through blood culture were identified by NGS in all 11 plasma/serum samples leading to the diagnosis of FN. The causative pathogens were diagnosed by NGS using the above criteria in 11 patients. However, the results were consistent with those of blood culture in only 4 samples. Of 101 cases with negative blood culture results, the causative pathogens were detected in 17 cases: Acinetobacter soli (2 cases), Burkholderia cepacian (1 case), Klebsiella variicola (1 case), and Roseomonas sp. (1 case) were identified at the species level. In addition, 7 cases (e.g., Acinetobacter) were identified at the genus level, and 5 cases (e.g., Enterobacteriaceae) were identified at the family level. Conclusion Metagenomic NGS technique has great potential for detecting causative pathogens with greater efficiency than the conventional methods. ![]()
Disclosures All authors: No reported disclosures.
Collapse
Affiliation(s)
- Kazuhiro Horiba
- Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Aichi, Japan
| | - Yuka Torii
- Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Yuichiro Hara
- Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Aichi, Japan
| | - Mayuko Shimada
- Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Aichi, Japan
| | - Takako Suzuki
- Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Suguru Takeuchi
- Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | | | - Jun-ichi Kawada
- Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Hideki Muramatsu
- Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Yoshiyuki Takahashi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Tomoo Ogi
- Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Aichi, Japan
| | - Yoshinori Ito
- Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| |
Collapse
|
21
|
Takeuchi S, Kawada JI, Horiba K, Okuno Y, Okumura T, Suzuki T, Torii Y, Kawabe S, Wada S, Ikeyama T, Ito Y. Metagenomic analysis using next-generation sequencing of pathogens in bronchoalveolar lavage fluid from pediatric patients with respiratory failure. Sci Rep 2019; 9:12909. [PMID: 31501513 PMCID: PMC6733840 DOI: 10.1038/s41598-019-49372-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 08/23/2019] [Indexed: 01/29/2023] Open
Abstract
Next-generation sequencing (NGS) has been applied in the field of infectious diseases. Bronchoalveolar lavage fluid (BALF) is considered a sterile type of specimen that is suitable for detecting pathogens of respiratory infections. The aim of this study was to comprehensively identify causative pathogens using NGS in BALF samples from immunocompetent pediatric patients with respiratory failure. Ten patients hospitalized with respiratory failure were included. BALF samples obtained in the acute phase were used to prepare DNA- and RNA-sequencing libraries. The libraries were sequenced on MiSeq, and the sequence data were analyzed using metagenome analysis tools. A mean of 2,041,216 total reads were sequenced for each library. Significant bacterial or viral sequencing reads were detected in eight of the 10 patients. Furthermore, candidate pathogens were detected in three patients in whom etiologic agents were not identified by conventional methods. The complete genome of enterovirus D68 was identified in two patients, and phylogenetic analysis suggested that both strains belong to subclade B3, which is an epidemic strain that has spread worldwide in recent years. Our results suggest that NGS can be applied for comprehensive molecular diagnostics as well as surveillance of pathogens in BALF from patients with respiratory infection.
Collapse
Affiliation(s)
- Suguru Takeuchi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Jun-Ichi Kawada
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan.
| | - Kazuhiro Horiba
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Yusuke Okuno
- Center for Advanced Medicine and Clinical Research, Nagoya University Hospital, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Toshihiko Okumura
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Takako Suzuki
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Yuka Torii
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Shinji Kawabe
- Departments of Infection and Immunity, Aichi Children's Health and Medical Center, 7-426 Morioka-machi, Obu, 474-8710, Japan
| | - Sho Wada
- Division of Pediatric Critical Care Medicine, Aichi Children's Health and Medical Center, 7-426 Morioka-machi, Obu, 474-8710, Japan
| | - Takanari Ikeyama
- Division of Pediatric Critical Care Medicine, Aichi Children's Health and Medical Center, 7-426 Morioka-machi, Obu, 474-8710, Japan
| | - Yoshinori Ito
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| |
Collapse
|
22
|
Torii Y, Yoshida S, Yanase Y, Mitsui T, Horiba K, Okumura T, Takeuchi S, Suzuki T, Kawada JI, Kotani T, Yamashita M, Ito Y. Serological screening of immunoglobulin M and immunoglobulin G during pregnancy for predicting congenital cytomegalovirus infection. BMC Pregnancy Childbirth 2019; 19:205. [PMID: 31221131 PMCID: PMC6585127 DOI: 10.1186/s12884-019-2360-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 06/12/2019] [Indexed: 11/16/2022] Open
Abstract
Background Cytomegalovirus (CMV) is one of the most frequent pathogens for congenital infections. Most cases of congenital CMV infection (cCMV) are asymptomatic at birth, but sensorineural hearing loss (SNHL) or neurodevelopmental delay can appear later in childhood. This prospective study examined the practicability of serological screening for anti-CMV immunoglobulin (Ig) G and anti-CMV IgM in pregnant women. Methods A total of 11,753 pregnant women were examined for CMV IgG and CMV IgM during the first or second trimester. When IgM was positive, IgG was reevaluated more than two weeks later. When IgG was negative, IgG was reevaluated in the second or third trimester. All neonates from mothers with positive/borderline IgM or IgG seroconversion underwent polymerase chain reaction assay for CMV using urine samples to diagnose cCMV. Levels of IgG and IgM were compared between mothers with and without cCMV. Receiver operating characteristic (ROC) curves for IgM titers were analyzed. Results Eight of 500 neonates (1.6%) born from mothers with positive IgG and positive IgM, and 3 of 13 neonates (23.1%) born from mothers with IgG seroconversion were diagnosed with cCMV. Neither IgM titers nor IgG titers differed significantly between cCMV and non-cCMV groups. The area under the ROC curve was 0.716 and the optimal cut-off for IgM was 7.28 index (sensitivity = 0.625, specificity = 0.965, positive predictive value = 0.238, negative predictive value = 0.993). Titers of IgG were not frequently elevated in pregnant women with positive IgM during the observation period, including in those with cCMV. All 11 cCMV cases were asymptomatic at birth and none had shown SNHL or developmental delay as of the last regular visit (mean age, 40 months). Conclusions Seroconversion of CMV IgG and high-titer IgM during early pregnancy are predictors of cCMV. High IgM titer (> 7.28 index) is a predictor despite relatively low sensitivity. Levels of IgG had already plateaued at first evaluation in mothers with cCMV. Maternal screening offered insufficient positive predictive value for diagnosing cCMV, but allowed identifying asymptomatic cCMV cases in an early stage.
Collapse
Affiliation(s)
- Yuka Torii
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Shigeru Yoshida
- Department of Pediatrics, Kishokai Medical Corporation, 4-122 Koike, Inazawa, 492-8144, Japan
| | - Yoichiro Yanase
- Department of Pediatrics, Kishokai Medical Corporation, 4-122 Koike, Inazawa, 492-8144, Japan
| | - Takashi Mitsui
- Department of Obstetrics and Gynecology, Kishokai Medical Corporation, 4-122 Koike, Inazawa, 492-8144, Japan
| | - Kazuhiro Horiba
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Toshihiko Okumura
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Suguru Takeuchi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Takako Suzuki
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Jun-Ichi Kawada
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Tomomi Kotani
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Mamoru Yamashita
- Department of Obstetrics and Gynecology, Kishokai Medical Corporation, 4-122 Koike, Inazawa, 492-8144, Japan
| | - Yoshinori Ito
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan.
| |
Collapse
|
23
|
Takeuchi S, Kawada JI, Okuno Y, Horiba K, Suzuki T, Torii Y, Yasuda K, Numaguchi A, Kato T, Ito Y. 2513. The Utility of Next-Generation Sequencing for Detection of Causative Viruses in Sera of Patients With Acute Myocarditis. Open Forum Infect Dis 2018. [PMCID: PMC6253800 DOI: 10.1093/ofid/ofy210.2165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background Myocarditis is an inflammatory disease of the myocardium with a wide range of clinical presentations, occasionally leading to cardiac dysfunction and heart failure. Although viral infections are considered to be the most common etiology of myocarditis, identification of the causative virus is still challenging. Recently, next-generation sequencing (NGS) has been applied in the diagnosis of infectious diseases. The aim of this study was to evaluate the utility of NGS for detection of causative viruses in sera of patients with acute myocarditis. Methods Twelve pediatric and five adult patients hospitalized for acute myocarditis were included in this study. Serum samples before initiation of treatment were collected in the acute phase and analyzed with NGS-based approach. To detect pathogen-derived sequencing reads, we performed DNA and RNA sequencing for each sample. Results An average of 20,062,443 and 19,506,189 total reads were obtained in DNA and RNA sequencing libraries, respectively. Viral sequence reads were detected in 7 (41%) of the 17 myocarditis patients. Substantial sequence reads of GB virus C (GBV-C) reads were detected from one patient by RNA sequencing; however, its pathogenicity to human is unknown. Detection of Epstein–Barr virus, human parvovirus B19, and respiratory syncytial virus reads by NGS was consistent with PCR or antigen test results. Conversely, the number of detected virus-derived reads was small in most cases. No significant bacterial or fungal reads other than normal bacterial flora was detected. Conclusion NGS-based approach may have potential to detect the causative viruses and contribute to clarification of the etiology of acute myocarditis. Disclosures All authors: No reported disclosures.
Collapse
Affiliation(s)
- Suguru Takeuchi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Jun-Ichi Kawada
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yusuke Okuno
- Center for Advanced Medicine and Clinical Research, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kazuhiro Horiba
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takako Suzuki
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuka Torii
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kazushi Yasuda
- Department of Pediatric Cardiology, Aichi Children’s Health and Medical Center, Obu, Japan
| | - Atsushi Numaguchi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Taichi Kato
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshinori Ito
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| |
Collapse
|
24
|
Takeuchi S, Kawada JI, Okuno Y, Horiba K, Suzuki T, Torii Y, Yasuda K, Numaguchi A, Kato T, Takahashi Y, Ito Y. Identification of potential pathogenic viruses in patients with acute myocarditis using next-generation sequencing. J Med Virol 2018; 90:1814-1821. [PMID: 30011073 DOI: 10.1002/jmv.25263] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 06/30/2018] [Indexed: 12/18/2022]
Abstract
Myocarditis is an inflammatory disease of the myocardium and leads to cardiac dysfunction and heart failure. Although viral infections are considered to be the most common etiology of myocarditis, the identification of the causative virus is still challenging. Recently, next-generation sequencing (NGS) has been applied in the diagnosis of infectious diseases. The aim of the current study was to comprehensively analyze potential pathogenic microorganisms using NGS in the sera of patients with myocarditis. Twelve pediatric and five adult patients hospitalized for acute myocarditis were included. Serum samples in the acute phase were obtained and analyzed using NGS to detect pathogen-derived DNA and RNA. Viral sequence reads were detected in 7 (41%) of the 17 myocarditis patients by NGS. Among these patients, detection of Epstein-Barr virus, human parvovirus B19, torque teno virus, and respiratory syncytial virus reads by NGS was consistent with polymerase chain reaction or antigen test results in one patient each. A large number of human pegivirus reads were detected from one patient by RNA sequencing; however, its pathogenicity to human is unknown. Conversely, the number of detected virus-derived reads was small in most cases, and the pathophysiological role of these viruses remains to be clarified. No significant bacterial or fungal reads other than normal bacterial flora was detected. These data indicate that comprehensive detection of virus-derived DNA and RNA using NGS can be useful for the identification of potential pathogenic viruses in myocarditis.
Collapse
Affiliation(s)
- Suguru Takeuchi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Jun-Ichi Kawada
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yusuke Okuno
- Center for Advanced Medicine and Clinical Research, Nagoya University Hospital, Nagoya, Japan
| | - Kazuhiro Horiba
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takako Suzuki
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuka Torii
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kazushi Yasuda
- Department of Pediatric Cardiology, Aichi Children's Health and Medical Center, Obu, Japan
| | - Atsushi Numaguchi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Taichi Kato
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshiyuki Takahashi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshinori Ito
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| |
Collapse
|
25
|
Yamamoto S, Omi T, Akai H, Kubota Y, Takahashi Y, Suzuki Y, Hirata Y, Yamamoto K, Yukawa R, Horiba K, Yumoto H, Koyama T, Ohashi H, Owada S, Tono K, Yabashi M, Shigemasa E, Yamamoto S, Kotsugi M, Wadati H, Kumigashira H, Arima T, Shin S, Matsuda I. Element Selectivity in Second-Harmonic Generation of GaFeO_{3} by a Soft-X-Ray Free-Electron Laser. Phys Rev Lett 2018; 120:223902. [PMID: 29906133 DOI: 10.1103/physrevlett.120.223902] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Indexed: 05/27/2023]
Abstract
Nonlinear optical frequency conversion has been challenged to move down to the extreme ultraviolet and x-ray region. However, the extremely low signals have allowed researchers to only perform transmission experiments of the gas phase or ultrathin films. Here, we report second harmonic generation (SHG) of the reflected beam of a soft x-ray free-electron laser from a solid, which is enhanced by the resonant effect. The observation revealed that the double resonance condition can be met by absorption edges for transition metal oxides in the soft x-ray range, and this suggests that the resonant SHG technique can be applicable to a wide range of materials. We discuss the possibility of element-selective SHG spectroscopy measurements in the soft x-ray range.
Collapse
Affiliation(s)
- Sh Yamamoto
- Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan
| | - T Omi
- Department of Advanced Materials Science, The University of Tokyo, Kashiwa 277-8561, Japan
| | - H Akai
- Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan
| | - Y Kubota
- Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan
| | - Y Takahashi
- Tokyo University of Science, Katsushika 125-8585, Japan
| | - Y Suzuki
- Tokyo University of Science, Katsushika 125-8585, Japan
| | - Y Hirata
- Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan
| | - K Yamamoto
- Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan
| | - R Yukawa
- Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba 305-0801, Japan
| | - K Horiba
- Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba 305-0801, Japan
| | - H Yumoto
- Japan Synchrotron Radiation Research Institute, Sayo, Hyogo 679-5198, Japan
| | - T Koyama
- Japan Synchrotron Radiation Research Institute, Sayo, Hyogo 679-5198, Japan
| | - H Ohashi
- Japan Synchrotron Radiation Research Institute, Sayo, Hyogo 679-5198, Japan
| | - S Owada
- RIKEN SPring-8 Center, Sayo, Hyogo 679-5148, Japan
| | - K Tono
- Japan Synchrotron Radiation Research Institute, Sayo, Hyogo 679-5198, Japan
| | - M Yabashi
- RIKEN SPring-8 Center, Sayo, Hyogo 679-5148, Japan
| | - E Shigemasa
- UVSOR Facility, Institute for Molecular Science, Okazaki 444-8585, Japan
- Sokendai (the Graduate University for Advanced Studies), Okazaki 444- 8585, Japan
| | - S Yamamoto
- Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan
| | - M Kotsugi
- Tokyo University of Science, Katsushika 125-8585, Japan
| | - H Wadati
- Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan
| | - H Kumigashira
- Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba 305-0801, Japan
| | - T Arima
- Department of Advanced Materials Science, The University of Tokyo, Kashiwa 277-8561, Japan
- RIKEN Center for Emergent Matter Science (CEMS), Wako 351-0198, Japan
| | - S Shin
- Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan
| | - I Matsuda
- Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan
| |
Collapse
|
26
|
Horiba K, Kawada JI, Okuno Y, Tetsuka N, Suzuki T, Ando S, Kamiya Y, Torii Y, Yagi T, Takahashi Y, Ito Y. Comprehensive Detection of Pathogens in Immunocompromised Children with Bloodstream Infections by Next-generation Sequencing. Open Forum Infect Dis 2017. [PMCID: PMC5631451 DOI: 10.1093/ofid/ofx162.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background Bloodstream infection (BSI) is a severe complication in immunocompromised patients. Prompt identification of causative microorganisms would improve the outcome of BSI due to optimization of antimicrobial treatment. Next-generation sequencing (NGS) allows us to analyze comprehensively and quantitatively all microorganisms present in a clinical sample in comparison with blood culture. However, there are currently no established methods to identify causative pathogens by NGS. Methods BSI was defined by the following criteria: (i) pathogen isolated from blood culture and (ii) fever ≥38.0°C or C-reactive protein >1.0mg/dl. Thirty-five pediatric patients (12 with BSI and 23 with suspected BSI/negative blood culture) were enrolled. Plasma/serum samples were used for sequencing and the results were compared with those from blood culture. The bacterial reads per million reads of the sequence depth (BR) and relative importance values of the dominant bacteria (P1) were applied to identify causative pathogens. Results Sequencing reads of bacteria isolated in blood culture were identified by NGS in all plasma/serum samples at the onset of BSI. Additionally, bacteria isolated in blood culture were identical to the dominant bacteria by NGS in 8 of 12 patients with BSI. Causative microorganisms were detected when the NGS results fulfilled the criteria of BR >200 and P1 >0.5. In two patients with catheter-related BSI, causative bacteria were detected in the plasma/serum at 7 days before disease onset. Causative pathogens (Tatlockia micdadei, Escherichia coli, and human adenovirus 2) were identified in three of 23 patients in the suspected BSI group. A total of 62 resistance genes were detected in nine patients with sequences covering 5–100% of references. Conclusion An NGS-based approach has great potential for analysis of causative microorganisms in BSI and may help to diagnose a disease before disease onset. Antimicrobial resistance genes can also be found through sequence data processing. Disclosures All authors: No reported disclosures.
Collapse
Affiliation(s)
- Kazuhiro Horiba
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Jun-Ichi Kawada
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yusuke Okuno
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Nobuyuki Tetsuka
- Department of Infectious Diseases, Nagoya University Hospital, Nagoya, Aichi, Japan
| | - Takako Suzuki
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shotaro Ando
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yasuko Kamiya
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuka Torii
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tetsuya Yagi
- Department of Infectious Diseases, Nagoya University Hospital, Nagoya, Aichi, Japan
| | - Yoshiyuki Takahashi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshinori Ito
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| |
Collapse
|
27
|
Kawada J, Okuno Y, Torii Y, Horiba K, Suzuki T, Ando S, Kamiya Y, Ito Y. Next-Generation Sequencing for the Identification of Viruses in Pediatric Acute Encephalitis and Encephalopathy. Open Forum Infect Dis 2016. [DOI: 10.1093/ofid/ofw172.875] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Junichi Kawada
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yusuke Okuno
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuka Torii
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kazuhiro Horiba
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takako Suzuki
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shotaro Ando
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yasuko Kamiya
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshinori Ito
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| |
Collapse
|
28
|
Watarai K, Yoshimatsu K, Horiba K, Kumigashira H, Sakata O, Ohtomo A. Epitaxial synthesis and physical properties of double-perovskite oxide Sr2CoRuO6 thin films. J Phys Condens Matter 2016; 28:436005. [PMID: 27603328 DOI: 10.1088/0953-8984/28/43/436005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We report epitaxial structures and physical properties of double-perovskite Sr2CoRuO6 films grown using pulsed-laser deposition. Samples with a degree of Co/Ru order of 2-73% were obtained by changing growth temperature. X-ray absorption spectroscopy (XAS) on the highest ordered sample revealed that Co ions were trivalent with a high-spin configuration and Ru ions were pentavalent. We found large differences in magnetization and resistivity between the highest and lowest ordered samples as well as the absence of strong magnetism and metallicity, which are common characteristics of SrCoO3 and SrRuO3. Using resonant photoemission spectroscopy and XAS, dominant d-orbital components at the top of the occupied state (the bottom of the unoccupied state) were identified to be Ru 4d t 2g (Co 3d and Ru 4d t 2g ). These results suggest that the ground state of double-perovskite Sr2CoRuO6 is a ferrimagnetic insulator.
Collapse
Affiliation(s)
- K Watarai
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8552, Japan
| | | | | | | | | | | |
Collapse
|
29
|
Kamiya Y, Hasegawa T, Takegami Y, Horiba K, Ando S, Torii Y, Kidokoro H, Kato T, Natsume J, Kawada JI, Ito Y. Primary psoas abscess caused by group A streptococcus in a child: Case report with microbiologic findings. J Infect Chemother 2016; 22:811-814. [PMID: 27692341 DOI: 10.1016/j.jiac.2016.06.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Revised: 05/14/2016] [Accepted: 06/20/2016] [Indexed: 11/18/2022]
Abstract
Primary abscess of the iliopsoas muscle in children is uncommon, especially due to Streptococcus pyogenes (group A streptococcus: GAS), which causes a variety of diseases ranging from pharyngitis to invasive life-threatening infection. We present primary iliopsoas abscess in a nine-year-old boy presenting with fever, mild disturbance of consciousness, limp, and pain in the right loin. Magnetic resonance imaging and isolation of GAS from both blood and abscess samples led us to the confirmative diagnosis. The patient recovered after treatment comprising drainage and intravenous antibiotics. The CovRS system is one of the best-characterized systems with two-component signal transduction in the GAS, and mutations in covRS induce overproduction of various virulence factors that play a crucial role in invasive GAS infection. RopB, also known as a GAS regulator, influences the expression of multiple regulatory networks to coregulate virulence factor expression in GAS. In the present case, sequence analysis revealed the isolated GAS as emm type 6 with alterations in covS, whereas the covR and ropB genes were intact. The covS alterations might have influenced the virulence of the strain causing this severe GAS infection.
Collapse
Affiliation(s)
- Yasuko Kamiya
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tadao Hasegawa
- Department of Bacteriology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Yasuhiko Takegami
- Orthopaedic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kazuhiro Horiba
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shotaro Ando
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuka Torii
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hiroyuki Kidokoro
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Taichi Kato
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Jun Natsume
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Jun-Ich Kawada
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshinori Ito
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan.
| |
Collapse
|
30
|
Horiba K, Gotoh K, Hattori F, Takeuchi S, Nishimura N, Ozaki T, Shiraki K. [Analysis of 23S rRNA of Mycoplasma pneumoniae detected from pediatric inpatients with community-acquired pneumonia in a regional hospital in Japan]. ACTA ACUST UNITED AC 2015; 88:715-6. [PMID: 25672146 DOI: 10.11150/kansenshogakuzasshi.88.715] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
31
|
Ozaki T, Nishimura N, Gotoh K, Horiba K, Hattori F, Takeuchi S, Funahashi K, Yoshii H, Okuno Y. [Usefulness of phase 3 and 4 immunization with MR vaccine]. Kansenshogaku Zasshi 2015; 88:711-2. [PMID: 25672144 DOI: 10.11150/kansenshogakuzasshi.88.711] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
32
|
Gotoh K, Nishimura N, Takeuchi S, Hattori F, Horiba K, Isaji M, Okai Y, Ohshima Y, Hosono H, Takemoto K, Iwata Y, Nakane K, Funahashi K, Ozaki T. Assessment of the loop-mediated isothermal amplification assay for rapid diagnosis of Mycoplasma pneumoniae in pediatric community-acquired pneumonia. Jpn J Infect Dis 2014; 66:539-42. [PMID: 24270147 DOI: 10.7883/yoken.66.539] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Rapid diagnosis of Mycoplasma pneumoniae pneumonia is required for timely treatment with effective antibiotics; however, PCR-based methods are often too expensive and technologically intensive for general use in clinical practice. In this study, the efficacy of the loop-mediated isothermal amplification (LAMP) assay for diagnosis of M. pneumoniae pneumonia in clinical practice was prospectively evaluated. From July 2011 to March 2012, 531 children hospitalized for community-acquired pneumonia were enrolled. In all patients, throat swabs were obtained on admission for the detection of M. pneumoniae DNA, and paired serum samples were obtained to assay M. pneumoniae particle agglutination (PA) antibody titers. M. pneumoniae pneumonia was diagnosed by either a positive LAMP assay or an increase of 4-fold or greater in the PA titer. Overall, 271 children (51.0% of the patients with pneumonia) were diagnosed with M. pneumoniae pneumonia. Among these, 258 (95.2%) and 248 (91.5%) were identified by the LAMP assay and serological tests, respectively. When the results of serological tests were considered as standard, the sensitivity, specificity, and positive and negative predictive values of the LAMP assay were 94.8%, 91.9%, and 91.1% and 95.2%, respectively. The median duration of pharyngeal carriage, as measured by the LAMP assay, was 9.5 days. Thus, the LAMP assay is useful in the rapid diagnosis of M. pneumoniae pneumonia.
Collapse
|
33
|
Horiba K, Nishimura N, Gotoh K, Kawaguchi M, Takeuchi S, Hattori F, Isaji M, Okai Y, Hosono H, Takemoto K, Ozaki T. Clinical Manifestations of Children with Microbiologically Confirmed Pertussis Infection and Antimicrobial Susceptibility of Isolated Strains in a Regional Hospital in Japan, 2008^|^ndash;2012. Jpn J Infect Dis 2014. [DOI: 10.7883/yoken.67.345] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
34
|
Horiba K, Nishimura N, Gotoh K, Kawaguchi M, Takeuchi S, Hattori F, Isaji M, Okai Y, Hosono H, Takemoto K, Ozaki T. Clinical manifestations of children with microbiologically confirmed pertussis infection and antimicrobial susceptibility of isolated strains in a regional hospital in Japan, 2008-2012. Jpn J Infect Dis 2014; 67:345-348. [PMID: 25241683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We conducted a retrospective study in 57 children (median age, 3.5 years; range, 1 month-14.5 years) with microbiologically confirmed pertussis infection over a recent 4-year period in a regional hospital in Japan. We obtained nasal swabs from all patients for Bordetella pertussis isolation as well as performed B. pertussis DNA detection using loop-mediated isothermal amplification (LAMP). Of the 57 cases, 34 (60%) were culture-positive and 57 (100%) were LAMP-positive. The frequency of each symptom was as follows: typical paroxysmal cough for over 14 days, 96% (55/57); paroxysms, 86% (49/57); posttussive vomiting, 33% (19/57); inspiratory whoop, 25% (14/57); and apnea, 12% (7/57). Hospitalization was required in 14 cases (25%), 93% (13/14) of which were aged <1 year. The proportion of patients previously immunized against diphtheria-tetanus-acellular pertussis vaccine (DTaP) was 19% (4/21) in children aged <1 year and 92% (11/12) in children aged ≥ 10 years. Minimum inhibitory concentrations for 6 antimicrobials (erythromycin, clarithromycin, azithromycin, minocycline, amoxicillin, and sulfamethoxazole/trimethoprim) were measured for 30 isolated strains, and all strains were susceptible to all aforementioned antimicrobials. Thus, an additional pertussis vaccination in older children is necessary, and the current macrolides-based treatment strategy is considered reasonable.
Collapse
|
35
|
Daikoku T, Horiba K, Kawana T, Hirano M, Shiraki K. Novel deletion in glycoprotein G forms a cluster and causes epidemiologic spread of herpes simplex virus type 2 infection. J Med Virol 2013; 85:1818-28. [PMID: 23861013 DOI: 10.1002/jmv.23668] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2013] [Indexed: 11/07/2022]
Abstract
The herpes simplex virus type 2 (HSV-2) glycoprotein G (gG-2) gene of 106 clinical isolates was analyzed and six isolates were identified with 63 nucleotides comprising 21 amino acids (aa) deleted in the immunodominant region. Compared with strain HG52, variations in the gG-2 gene were found at 276 and 27 sites in nucleotide and aa sequences, respectively, in the 106 strains. Significant variations in both nucleotides and aa were accumulated in the immunodominant region rather than in the other regions (P < 0.001), indicating that the immunodominant region might be indispensable in vivo and a hot spot for variation. The frequency of 21 aa-deleted strains (HSVΔ21/gG-2) among clinical isolates was 5%, indicating the advantage of this deletion of gG-2 for epidemiological expansion. Phylogenetic analysis of the 106 strains indicated that the HSVΔ21/gG-2 strains formed a cluster among the various variations but that their genomes showed different endonuclease digestion patterns. The antibody titers to total HSV antigens of patients infected with wild HSV-2 and HSVΔ21/gG-2 were similar, but patients with HSVΔ21/gG-2 had a lower antibody titer to gG-2 than those with wild HSV-2 (P < 0.001). HSVΔ21/gG-2 might be less immnunogenic and reduce antibody production to gG-2, while its pathogenicity in humans was not distinguished in its clinical manifestations. Thus, infection with HSVΔ21/gG-2 caused genital lesions similar to wild HSV-2 infection, but evaded the immune response to gG-2 to allow epidemiological spread, indicating the importance of this deletion in the immunodominant region of gG-2 in the pathogenesis and transmission of genital herpes.
Collapse
Affiliation(s)
- Tohru Daikoku
- Department of Virology, University of Toyama, Toyama, Japan.
| | | | | | | | | |
Collapse
|
36
|
Aizaki S, Yoshida T, Yoshimatsu K, Takizawa M, Minohara M, Ideta S, Fujimori A, Gupta K, Mahadevan P, Horiba K, Kumigashira H, Oshima M. Self-energy on the low- to high-energy electronic structure of correlated metal SrVO3. Phys Rev Lett 2012; 109:056401. [PMID: 23006190 DOI: 10.1103/physrevlett.109.056401] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Indexed: 06/01/2023]
Abstract
The correlated electronic structure of SrVO(3) has been investigated by angle-resolved photoemission spectroscopy using in situ prepared thin films. Pronounced features of band renormalization have been observed: a sharp kink ∼60 meV below the Fermi level (E(F)) and a broad so-called "high-energy kink" ∼0.3 eV below E(F) as in the high-T(c) cuprates, although SrVO(3) does not show magnetic fluctuations. We have deduced the self-energy in a wide energy range by applying the Kramers-Kronig relation to the observed spectra. The obtained self-energy clearly shows a large energy scale of ∼0.7 eV, which is attributed to electron-electron interaction and gives rise to the ∼0.3 eV kink in the band dispersion as well as the incoherent peak ∼1.5 eV below E(F). The present analysis enables us to obtain a consistent picture for both the incoherent spectra and the band renormalization.
Collapse
Affiliation(s)
- S Aizaki
- Department of Physics, The University of Tokyo, Japan
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Horiba K, Nakamura Y, Nagamura N, Toyoda S, Kumigashira H, Oshima M, Amemiya K, Senba Y, Ohashi H. Scanning photoelectron microscope for nanoscale three-dimensional spatial-resolved electron spectroscopy for chemical analysis. Rev Sci Instrum 2011; 82:113701. [PMID: 22128978 DOI: 10.1063/1.3657156] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
In order to achieve nondestructive observation of the three-dimensional spatially resolved electronic structure of solids, we have developed a scanning photoelectron microscope system with the capability of depth profiling in electron spectroscopy for chemical analysis (ESCA). We call this system 3D nano-ESCA. For focusing the x-ray, a Fresnel zone plate with a diameter of 200 μm and an outermost zone width of 35 nm is used. In order to obtain the angular dependence of the photoelectron spectra for the depth-profile analysis without rotating the sample, we adopted a modified VG Scienta R3000 analyzer with an acceptance angle of 60° as a high-resolution angle-resolved electron spectrometer. The system has been installed at the University-of-Tokyo Materials Science Outstation beamline, BL07LSU, at SPring-8. From the results of the line-scan profiles of the poly-Si/high-k gate patterns, we achieved a total spatial resolution better than 70 nm. The capability of our system for pinpoint depth-profile analysis and high-resolution chemical state analysis is demonstrated.
Collapse
Affiliation(s)
- K Horiba
- Department of Applied Chemistry, The University of Tokyo, Tokyo 113-8656, Japan.
| | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Yoshimatsu K, Horiba K, Kumigashira H, Yoshida T, Fujimori A, Oshima M. Metallic Quantum Well States in Artificial Structures of Strongly Correlated Oxide. Science 2011; 333:319-22. [DOI: 10.1126/science.1205771] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
|
39
|
Takizawa M, Hotta Y, Susaki T, Ishida Y, Wadati H, Takata Y, Horiba K, Matsunami M, Shin S, Yabashi M, Tamasaku K, Nishino Y, Ishikawa T, Fujimori A, Hwang HY. Spectroscopic evidence for competing reconstructions in polar multilayers LaAlO3/LaVO3/LaAlO3. Phys Rev Lett 2009; 102:236401. [PMID: 19658952 DOI: 10.1103/physrevlett.102.236401] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2008] [Indexed: 05/28/2023]
Abstract
We have studied the valence redistribution of V in LaAlO(3)/LaVO(3)/LaAlO(3) trilayers, which are composed of only polar layers grown on SrTiO3 (001) substrates, by core-level photoemission spectroscopy. We have found that the V valence is intermediate between V3+ and V4+ for thin LaAlO3 cap layers, decreases with increasing cap-layer thickness, and finally recovers the bulk value of V3+ at approximately 10 unit-cell thickness. In order to interpret these results, we propose that the atomic reconstruction of the polar LaAlO3 surface competes with the purely electronic V valence change so that the polar catastrophe is avoided at the cost of minimum energy.
Collapse
Affiliation(s)
- M Takizawa
- Department of Physics, University of Tokyo, 3-7-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Matsunami M, Eguchi R, Kiss T, Horiba K, Chainani A, Taguchi M, Yamamoto K, Togashi T, Watanabe S, Wang XY, Chen CT, Senba Y, Ohashi H, Sugawara H, Sato H, Harima H, Shin S. Anomalous duality of 4f electrons in filled skutterudite CeOs4Sb12. Phys Rev Lett 2009; 102:036403. [PMID: 19257374 DOI: 10.1103/physrevlett.102.036403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2008] [Indexed: 05/27/2023]
Abstract
We study the electronic structure of the filled skutterudite CeOs4Sb12 using photoemission spectroscopy (PES). Soft x-ray excited Ce 3d-4f resonant PES confirms the existence of Ce 4f states at the Fermi level (EF). Temperature dependent high-resolution laser-PES spectra reveal a pseudogap formation around EF, which can be explained in terms of the hybridization gap. Simultaneously, a sharp feature is formed just above EF with decreasing temperature. The heavy-fermion-like specific heat is attributed to the occupation of this feature. The results identify the origin of the anomalous coexistence of heavy-fermion and pseudogap behavior in terms of a symmetry dependent hybridization.
Collapse
Affiliation(s)
- M Matsunami
- RIKEN SPring-8 Center, Sayo-gun, Hyogo 679-5148, Japan.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Taguchi Y, Yamamoto K, Mimura K, Ichikawa K, Kitamoto K, Aita O, Ishibashi H, Takata Y, Horiba K, Shin S, Yabashi M, Tamasaku K, Nishino Y, Miwa D, Ishikawa T, Ikenaga E, Kobayashi K. Ir 4f hard X-ray photoemission spectrum of CuIr2S4. Radiat Phys Chem Oxf Engl 1993 2006. [DOI: 10.1016/j.radphyschem.2005.07.058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
42
|
Taguchi M, Chainani A, Horiba K, Takata Y, Yabashi M, Tamasaku K, Nishino Y, Miwa D, Ishikawa T, Takeuchi T, Yamamoto K, Matsunami M, Shin S, Yokoya T, Ikenaga E, Kobayashi K, Mochiku T, Hirata K, Hori J, Ishii K, Nakamura F, Suzuki T. Evidence for suppressed screening on the surface of high temperature La(2-x)SrxCuO4 and Nd2(2-x)CexCuO4 superconductors. Phys Rev Lett 2005; 95:177002. [PMID: 16383858 DOI: 10.1103/physrevlett.95.177002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2005] [Indexed: 05/05/2023]
Abstract
Hard x-ray photoemission spectroscopy (PES) of Cu core electronic states, with a probing depth of approximately 60 A, is used to show that the Zhang-Rice singlet feature is present in La2CuO4 but is absent in Nd2CuO4. Hole and electron doping in La(2-x)SrxCuO4 (LSCO) and Nd(2-x)CexCuO4 (NCCO) result in new well-screened features which are missing in soft x-ray PES. Impurity Anderson model calculations establish screening from doped states as its origin, which is strongly suppressed within 15 A of the surface. Complemented with x-ray absorption spectroscopy, the small chemical-potential shift in core levels (approximately 0.2 eV) are shown to be consistent with modifications of valence and conduction band states spanning the band gap (approximately 1 eV) upon hole and electron doping in LSCO and NCCO.
Collapse
Affiliation(s)
- M Taguchi
- Soft X-ray Spectroscopy Laboratory, RIKEN/SPring-8, Mikazuki, Hyogo 679-5148, Japan
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Horiba K, Taguchi M, Chainani A, Takata Y, Ikenaga E, Miwa D, Nishino Y, Tamasaku K, Awaji M, Takeuchi A, Yabashi M, Namatame H, Taniguchi M, Kumigashira H, Oshima M, Lippmaa M, Kawasaki M, Koinuma H, Kobayashi K, Ishikawa T, Shin S. Nature of the well screened state in hard X-ray Mn 2p core-level photoemission measurements of La1-xSrxMnO3 films. Phys Rev Lett 2004; 93:236401. [PMID: 15601180 DOI: 10.1103/physrevlett.93.236401] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2004] [Indexed: 05/24/2023]
Abstract
Using hard x-ray (HX; hnu=5.95 keV) synchrotron photoemission spectroscopy (PES), we study the intrinsic electronic structure of La(1-x)Sr(x)MnO(3) (LSMO) thin films. Comparison of Mn 2p core-levels with soft x-ray (SX; hnu approximately 1000 eV) PES shows a clear additional well-screened feature only in HX PES. Takeoff-angle dependent data indicate its bulk (> or =20 A) character. The doping and temperature dependence track the ferromagnetism and metallicity of the LSMO series. Cluster model calculations including charge transfer from doping-induced states show good agreement, confirming this picture of bulk properties reflected in Mn 2p core-levels using HX PES.
Collapse
Affiliation(s)
- K Horiba
- Soft X-Ray Spectroscopy Laboratory, RIKEN/SPring-8, Mikazuki-cho, Hyogo 679-5148, Japan.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Shundo Y, Neyatani H, Mochizuki T, Horiba K, Ishigami N. [Sudden death due to massive pulmonary thromboembolism after pneumonectomy; report of a case]. Kyobu Geka 2004; 57:897-9. [PMID: 15366579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
A 76-year-old woman underwent a left pneumonectomy for a primary adenocarcinoma. On the fourth postoperative day, when walking to the toilet, she suddenly developed syncope followed by dyspnea and cardiopulmonary arrest. Although we performed cardiopulmonary resusciation, she died 1 hour later. With her family's approval, we performed autopsy. We found massive pulmonary thromboembolism was identified in the right main artery. To prevent postoperative thromboembolic complications, we use postoperatively continuous intravenous heparin sodium infusion (5,000-6,000/24 h) for the patients underwent thoracotomy and examine the ultrasonography for deep vein thrombosis before they begin to walk.
Collapse
Affiliation(s)
- Yasumasa Shundo
- Department of Thoracic and Cardiovascular Surgery, Fujieda Municipal General Hospital, Fujieda, Japan
| | | | | | | | | |
Collapse
|
45
|
Banno K, Shiomi T, Sasanabe R, Hasegawa R, Otake K, Yamakawa H, Kobayashi T, Horiba K, Nishino S. Narcolepsy and other non-SAS hypersomnia in sleep breathing disorders clinic. Psychiatry Clin Neurosci 2001; 55:203-4. [PMID: 11422842 DOI: 10.1046/j.1440-1819.2001.00826.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Four of the 708 snorers (0.56%), referred to our sleep breathing disorders clinic for the past 2 years were diagnosed as having narcolepsy-cataplexy. Detecting HLA DRB1*1501/DQB1*0602 positive was informative for differentiating genuine narcolepsy from non-sleep apnea syndrome (non-SAS) hypersomnia in our clinic. A non-SAS obese boy, diagnosed as having essential hypersomnia syndrome, was found to be HLA DRB1*1502/DQB1*0601 positive. His hypocretin concentration was 206 pg/mL in the cerebrospinal fluid.
Collapse
Affiliation(s)
- K Banno
- The Third Department of Internal Medicine, Sleep Disorders Center, Aichi Medical University School of Medicine, Aichi, Japan.
| | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Zhang J, Kumar A, Stalker HJ, Virdi G, Ferrans VJ, Horiba K, Fricker FJ, Wallace MR. Clinical and molecular studies of a large family with desmin-associated restrictive cardiomyopathy. Clin Genet 2001; 59:248-56. [PMID: 11298680 DOI: 10.1034/j.1399-0004.2001.590406.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Patients with restrictive cardiomyopathy (RC) have impaired diastolic function, but intact systolic function until later stages of the disease, ultimately leading to heart failure. Primary RC is often sporadic, but also may be inherited in an autosomal dominant fashion, particularly the idiopathic forms. Recently there has been great interest in inherited cardiomyopathy associated with myocyte desmin deposition ('desminopathies'). In some such families, desmin or alpha-B crystallin gene mutation is the underlying cause, and the desmin accumulation affects skeletal muscle as well, usually causing skeletal myopathy. We describe a large family with apparent autosomal dominant inheritance of desmin-associated RC spanning four generations, with the age of onset and severity/rate of progression being highly variable. This family is relatively unique in that there is no symptom-based evidence of skeletal muscle involvement, and the known desminopathy and cardiomyopathy genes/loci have been ruled out. These data support literature suggesting that desmin deposition may be associated with different underlying gene defects, and that a novel desminopathy gene is responsible for the condition in this family.
Collapse
Affiliation(s)
- J Zhang
- Division of Genetics, Department of Pediatrics, University of Florida College of Medicine, Gainesville, FL 32610-0266, USA
| | | | | | | | | | | | | | | |
Collapse
|
47
|
Sparacino M, Cereda M, Frank A, Horiba K, Ferrans V, Kolobow T. Crit Care 2001; 1:P053. [DOI: 10.1186/cc3831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
48
|
Galateau-Salle FB, Luna RE, Horiba K, Sheppard MN, Hayashi T, Fleming MV, Colby TV, Bennett W, Harris CC, Stetler-Stevenson WG, Liotta L, Ferrans VJ, Travis WD. Matrix metalloproteinases and tissue inhibitors of metalloproteinases in bronchial squamous preinvasive lesions. Hum Pathol 2000; 31:296-305. [PMID: 10746671 DOI: 10.1016/s0046-8177(00)80242-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Metalloproteinases and their inhibitors are known to play an important role in the extracellular matrix remodeling associated with preinvasive lesions and invasive carcinomas; however, little is known about their role in early lung carcinoma. Immunohistochemical studies were made of the reactivity of bronchial squamous preneoplastic lesions from cigarette smokers, including basal cell hyperplasia, squamous metaplasia, dysplasia, carcinoma in situ, and invasive squamous cell carcinoma for matrix metalloproteinases (MMPs), their tissue inhibitors (TIMPs), and type IV collagen in 13 patients. Staining for type IV collagen disclosed discontinuities in basement membranes from basal cell hyperplasia to dysplasia, progressing to destruction in carcinoma in situ and invasive carcinoma. Reactivity for MMP-9 was mild in basal cell hyperplasia and squamous metaplasia, increasing in carcinoma in situ and invasive carcinoma. In contrast, reactivity for MMP-1 was strong in basal cell hyperplasia and squamous metaplasia, decreasing in carcinoma in situ and invasive carcinoma. Some neoplastic cells in carcinoma in situ and invasive carcinoma were MMP-3 positive. Staining for MMP-2 and TIMP-1 was moderate to strong in all squamous preinvasive lesions. Confocal microscopy showed MMP-9-positive cells passing through fragmented basement membranes in which type IV collagen and MMP-9 were colocalized. Type IV collagen colocalized with MMP-2 in all lesions and with TIMP-1 in basal cell hyperplasia and squamous metaplasia. The inverse relationships between the reactivity for MMP-1 and MMP-9 with progression of bronchial squamous preinvasive lesions suggest important roles for these MMPs in basement membrane remodeling in these lesions.
Collapse
Affiliation(s)
- F B Galateau-Salle
- Department of Pathology, Centre Hôpitalier Regional et Universitaire de Caen, France
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Matsumoto Y, Horiba K, Usuki J, Chu SC, Ferrans VJ, Moss J. Markers of cell proliferation and expression of melanosomal antigen in lymphangioleiomyomatosis. Am J Respir Cell Mol Biol 1999; 21:327-36. [PMID: 10460750 DOI: 10.1165/ajrcmb.21.3.3693] [Citation(s) in RCA: 101] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Pulmonary lymphangioleiomyomatosis (LAM), a disease of young women, is characterized by proliferation of immature-appearing smooth-muscle cells (LAM cells) in the lungs and abdomen. LAM cells react with monoclonal antibody HMB45, which recognizes a 100-kD glycoprotein (gp100) originally found in human melanoma cells. We investigated the expression and the subcellular localization of gp100 in lung tissue from patients with LAM and in human melanoma cell lines (Malme-3M, A2058, and CHL-1), and the relationship between this expression and cellular proliferation. Binding sites for HMB45 antibody in melanoma and LAM cells were located in cytoplasmic granules resembling immature melanosomes. LAM cells reactive for proliferating-cell nuclear antigen (PCNA), a marker of cellular proliferation, were spindle-shaped, in contrast to the large, epithelioid cells reacting with HMB45 antibody. In accord with this finding, we observed an inverse relationship between the immunostaining for HMB45 antibody and PCNA in LAM and melanoma cells. Thus, LAM and melanoma cells are heterogeneous with respect to their stages of proliferation and their expression of melanoma antigens. PCNA-positive cells, which are more likely to be negative for reactivity with HMB45 antibody, may be more relevant to the progression of LAM than are HMB45-positive cells, which are the hallmark of LAM.
Collapse
Affiliation(s)
- Y Matsumoto
- Pulmonary-Critical Care Medicine Branch and Pathology Section, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | | | | | | | | | | |
Collapse
|
50
|
Balducci E, Horiba K, Usuki J, Park M, Ferrans VJ, Moss J. Selective expression of RT6 superfamily in human bronchial epithelial cells. Am J Respir Cell Mol Biol 1999; 21:337-46. [PMID: 10460751 DOI: 10.1165/ajrcmb.21.3.3638] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
RT6 proteins are glycosylphosphatidylinositol (GPI)-linked alloantigens that are localized to cytotoxic T lymphocytes and that have nicotinamide adenine dinucleotide glycohydrolase and adenosine diphosphate (ADP)-ribosyltransferase activities. In view of the importance of GPI-linked surface proteins in mediating interactions of cells with their milieu, and the varied functions of airway cells in inflammation, we undertook the present study to determine whether human homologues of the RT6 superfamily of ADP-ribosyltransferases (ART) are expressed in pulmonary epithelial cells. We hypothesized that these surface proteins or related family members may be present in cells that interact with inflammatory cells, and that they may thereby be involved in intercellular signaling. Using in situ analysis and Northern blot analysis, we identified ART1 messenger RNA (mRNA) in airway epithelial cells. As expected for GPI-anchored proteins, the localization of ART1 at the apical surface of ciliated epithelial cells was demonstrated by staining with polyclonal anti-ART1 antibody, and was confirmed by loss of this immunoreactivity after treatment with phosphatidylinositol-specific phospholipase C (PI-PLC), which selectively cleaves GPI anchors and releases proteins from the plasma membrane. Using in situ hybridization with specific ART3 and ART4 oligonucleotides, we also identified two additional members of the RT6 superfamily in epithelial cells. In accord with these findings, we identified ART3 and ART4 mRNAs through reverse transcription- polymerase chain reaction of polyadenine-positive RNA from human trachea. Interestingly, these proteins appeared to be preferentially localized to the airway epithelium. The localized expression of these members of the RT6 superfamily in human pulmonary epithelial cells may reflect a role for them in cell-cell signaling during immune responses within the airway.
Collapse
Affiliation(s)
- E Balducci
- Pulmonary-Critical Care Medicine Branch and Pathology Section, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | | | | | | | | | | |
Collapse
|