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Kikuchi-Ueda T, Maeno S, Gotoh Y, Ogura Y, Fujisaki R, Hayashi T. Complete genome sequences of 11 Streptococcus pneumoniae strains isolated from acute infectious purpura fulminans, sepsis, and pneumonia. Microbiol Resour Announc 2024; 13:e0077323. [PMID: 38132669 PMCID: PMC10868184 DOI: 10.1128/mra.00773-23] [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: 08/21/2023] [Accepted: 11/18/2023] [Indexed: 12/23/2023] Open
Abstract
The complete genome sequences of 11 Japanese Streptococcus pneumoniae isolates were determined by hybrid assembly of long and short reads, including two strains isolated from patients with acute infectious purpura fulminans, six strains from patients with sepsis, and three strains from patients with pneumonia.
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Affiliation(s)
- Takane Kikuchi-Ueda
- Department of Microbiology and Immunology, Teikyo University School of Medicine, Itabashi, Tokyo, Japan
| | - Shintaro Maeno
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshitoshi Ogura
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Fukuoka, Japan
| | - Ryuichi Fujisaki
- Department of Sport and Medical Science, Faculty of Medical Technology, Teikyo University, Tokyo, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
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Murata T, Gotoh Y, Hayashi T. A comprehensive list of genes required for the efficient conjugation of plasmid Rts1 was determined by systematic deletion analysis. DNA Res 2024; 31:dsae002. [PMID: 38300630 PMCID: PMC10838148 DOI: 10.1093/dnares/dsae002] [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] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/08/2024] [Accepted: 01/31/2024] [Indexed: 02/02/2024] Open
Abstract
While conjugation-related genes have been identified in many plasmids by genome sequencing, functional analyses have not yet been performed in most cases, and a full set of conjugation genes has been identified for only a few plasmids. Rts1, a prototype IncT plasmid, is a conjugative plasmid that was originally isolated from Proteus vulgaris. Here, we conducted a systematic deletion analysis of Rts1 to fully understand its conjugation system. Through this analysis along with complementation assays, we identified 32 genes that are required for the efficient conjugation of Rts1 from Escherichia coli to E. coli. In addition, the functions of the 28 genes were determined or predicted; 21 were involved in mating-pair formation, three were involved in DNA transfer and replication, including a relaxase gene belonging to the MOBH12 family, one was involved in coupling, and three were involved in transcriptional regulation. Among the functionally well-analysed conjugation systems, most of the 28 genes showed the highest similarity to those of the SXT element, which is an integrative conjugative element of Vibrio cholerae. The Rts1 conjugation gene set included all 23 genes required for the SXT system. Two groups of plasmids with conjugation systems nearly identical or very similar to that of Rts1 were also identified.
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Affiliation(s)
- Takahiro Murata
- Department of Pediatrics, Teikyo University School of Medicine, Mizonokuchi Hospital, Takatsu-ku, Kawasaki, Kanagawa 213-8507, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
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Mure A, Sugiura Y, Maeda R, Honda K, Sakurai N, Takahashi Y, Watada M, Katoh T, Gotoh A, Gotoh Y, Taniguchi I, Nakamura K, Hayashi T, Katayama T, Uemura T, Hattori Y. Identification of key yeast species and microbe-microbe interactions impacting larval growth of Drosophila in the wild. eLife 2023; 12:RP90148. [PMID: 38150375 PMCID: PMC10752588 DOI: 10.7554/elife.90148] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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] [Indexed: 12/29/2023] Open
Abstract
Microbiota consisting of various fungi and bacteria have a significant impact on the physiological functions of the host. However, it is unclear which species are essential to this impact and how they affect the host. This study analyzed and isolated microbes from natural food sources of Drosophila larvae, and investigated their functions. Hanseniaspora uvarum is the predominant yeast responsible for larval growth in the earlier stage of fermentation. As fermentation progresses, Acetobacter orientalis emerges as the key bacterium responsible for larval growth, although yeasts and lactic acid bacteria must coexist along with the bacterium to stabilize this host-bacterial association. By providing nutrients to the larvae in an accessible form, the microbiota contributes to the upregulation of various genes that function in larval cell growth and metabolism. Thus, this study elucidates the key microbial species that support animal growth under microbial transition.
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Affiliation(s)
- Ayumi Mure
- Graduate School of Biostudies, Kyoto UniversityKyotoJapan
| | - Yuki Sugiura
- Center for Cancer Immunotherapy and Immunobiology, Kyoto UniversityKyotoJapan
| | - Rae Maeda
- Center for Cancer Immunotherapy and Immunobiology, Kyoto UniversityKyotoJapan
| | - Kohei Honda
- Graduate School of Biostudies, Kyoto UniversityKyotoJapan
| | | | | | - Masayoshi Watada
- Graduate School of Science and Engineering, Ehime UniversityMatsuyamaJapan
| | | | - Aina Gotoh
- Graduate School of Biostudies, Kyoto UniversityKyotoJapan
| | - Yasuhiro Gotoh
- Graduate School of Medical Sciences, Kyushu UniversityFukuokaJapan
| | - Itsuki Taniguchi
- Graduate School of Medical Sciences, Kyushu UniversityFukuokaJapan
| | - Keiji Nakamura
- Graduate School of Medical Sciences, Kyushu UniversityFukuokaJapan
| | - Tetsuya Hayashi
- Graduate School of Medical Sciences, Kyushu UniversityFukuokaJapan
| | | | - Tadashi Uemura
- Graduate School of Biostudies, Kyoto UniversityKyotoJapan
- Center for Living Systems Information Science, Kyoto UniversityKyotoJapan
- AMED-CRESTTokyoJapan
| | - Yukako Hattori
- Graduate School of Biostudies, Kyoto UniversityKyotoJapan
- Center for Living Systems Information Science, Kyoto UniversityKyotoJapan
- JST FORESTTokyoJapan
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Nagano DS, Taniguchi I, Ono T, Nakamura K, Gotoh Y, Hayashi T. Systematic analysis of plasmids of the Serratia marcescens complex using 142 closed genomes. Microb Genom 2023; 9. [PMID: 37966169 DOI: 10.1099/mgen.0.001135] [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] [Subscribe] [Scholar Register] [Indexed: 11/16/2023] Open
Abstract
Plasmids play important roles in bacterial genome diversification. In the Serratia marcescens complex (SMC), a notable contribution of plasmids to genome diversification was also suggested by our recent analysis of >600 draft genomes. As accurate analyses of plasmids in draft genomes are difficult, in this study we analysed 142 closed genomes covering the entire complex, 67 of which were obtained in this study, and identified 132 plasmids (1.9-244.4 kb in length) in 77 strains. While the average numbers of plasmids in clinical and non-clinical strains showed no significant difference, strains belonging to clade 2 (one of the two hospital-adapted lineages) contained more plasmids than the others. Pangenome analysis revealed that of the 28 954 genes identified, 12.8 % were plasmid-specific, and 1.4 % were present in plasmids or chromosomes depending on the strain. In the latter group, while transposon-related genes were most prevalent (31.4 % of the function-predicted genes), genes related to antimicrobial resistance and heavy metal resistance accounted for a notable proportion (22.7 %). Mash distance-based clustering separated the 132 plasmids into 23 clusters and 50 singletons. Most clusters/singletons showed notably different GC contents compared to those of host chromosomes, suggesting their recent or relatively recent appearance in the SMC. Among the 23 clusters, 17 were found in only clinical or only non-clinical strains, suggesting the possible preference of their distribution on the environmental niches of host strains. Regarding the host strain phylogeny, 16 clusters were distributed in two or more clades, suggesting their interclade transmission. Moreover, for many plasmids, highly homologous plasmids were found in other species, indicating the broadness of their potential host ranges, beyond the genus, family, order, class or even phylum level. Importantly, highly homologous plasmids were most frequently found in Klebsiella pneumoniae and other species in the family Enterobacteriaceae, suggesting that this family, particularly K. pneumoniae, is the main source for plasmid exchanges with the SMC. These results highlight the power of closed genome-based analysis in the investigation of plasmids and provide important insights into the nature of plasmids distributed in the SMC.
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Affiliation(s)
- Debora Satie Nagano
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Itsuki Taniguchi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Tomoyuki Ono
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
- Department of Cardiovascular Surgery, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Keiji Nakamura
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
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Takano A, Yamauchi T, Takahashi M, Shimoda H, Gotoh Y, Mizuno J, Natsume M, Kontschán J, Kováts D, Tu VT, Hornok S. Description of three new bat-associated species of hard ticks (Acari, Ixodidae) from Japan. Zookeys 2023; 1180:1-26. [PMID: 37744948 PMCID: PMC10517414 DOI: 10.3897/zookeys.1180.108418] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 08/12/2023] [Indexed: 09/26/2023] Open
Abstract
In Eurasia, the geographically most widespread ixodid tick species of the bat families Rhinolophidae Gray, Vespertilionidae Gray, and Miniopteridae Dobson were considered to belong to four species, Ixodesvespertilionis Koch, I.collaris Hornok, I.ariadnae Hornok, and I.simplex Neumann. Previous data attest that bat-associated tick species from Eastern Asia show remarkable genetic difference from the above four tick species, but in the absence of detailed morphological comparison these were regarded as conspecific. In this study we compensate for this lack of data on three bat-associated tick species, reporting their morphological comparison, as well as molecular and phylogenetic relationships. According to the results we describe the females of three tick species new to science, i.e., I.nipponrhinolophi Hornok & Takano, sp. nov., I.fuliginosus Hornok & Takano, sp. nov., and I.fujitai Hornok & Takano, sp. nov. In case of all three new tick species the cytochrome c oxidase subunit (coxI) gene showed remarkably high sequence differences from the species that they previously were thought to belong to, well exceeding the average limit delineating ixodid tick species. This, as well as observed morphological differences fully justify their taxonomical status as new species.
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Affiliation(s)
- Ai Takano
- Department of Veterinary Medicine, Joint Faculty of Veterinary Medicine and The United Graduate School of Veterinary Science, Yamaguchi University, Yamaguchi, JapanYamaguchi UniversityYamaguchiJapan
| | - Takeo Yamauchi
- Laboratory of Entomology, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, JapanObihiro University of Agriculture and Veterinary MedicineObihiroJapan
| | - Mamoru Takahashi
- Department of Anesthesiology, Saitama Medical University, Saitama, JapanSaitama Medical UniversitySaitamaJapan
| | - Hiroshi Shimoda
- Department of Veterinary Medicine, Joint Faculty of Veterinary Medicine and The United Graduate School of Veterinary Science, Yamaguchi University, Yamaguchi, JapanYamaguchi UniversityYamaguchiJapan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, JapanKyushu UniversityFukuokaJapan
| | - Junko Mizuno
- Department of Veterinary Medicine, Joint Faculty of Veterinary Medicine and The United Graduate School of Veterinary Science, Yamaguchi University, Yamaguchi, JapanYamaguchi UniversityYamaguchiJapan
| | - Michio Natsume
- Natural Environmental Research Group, Gunma Prefecture, Gunma, JapanNatural Environmental Research GroupGunmaJapan
| | - Jenő Kontschán
- Department of Plant Sciences, Albert Kázmér Faculty of Mosonmagyaróvár, Széchenyi István University, Mosonmagyaróvár, HungarySzéchenyi István UniversityMosonmagyaróvárHungary
| | - Dávid Kováts
- Hungarian Biodiversity Research Society, Budapest, HungaryHungarian Biodiversity Research SocietyBudapestHungary
| | - Vuong Tan Tu
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Hanoi, VietnamInstitute of Ecology and Biological Resources, Vietnam Academy of Science and TechnologyHanoiVietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, VietnamGraduate University of Science and TechnologyHanoiVietnam
| | - Sándor Hornok
- Department of Parasitology and Zoology, University of Veterinary Medicine, Budapest, HungaryUniversity of Veterinary MedicineBudapestHungary
- HUN-REN–UVMB Climate Change: New Blood-sucking Parasites and Vector-borne Pathogens Research Group, Budapest, HungaryHUN-REN–UVMB Climate Change: New Blood-sucking Parasites and Vector-borne Pathogens Research GroupBudapestHungary
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Okuno M, Tsuru N, Yoshino S, Gotoh Y, Yamamoto T, Hayashi T, Ogura Y. Isolation and Genomic Characterization of a Heat-Labile Enterotoxin 1-Producing Escherichia fergusonii Strain from a Human. Microbiol Spectr 2023; 11:e0049123. [PMID: 37432125 PMCID: PMC10434266 DOI: 10.1128/spectrum.00491-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 02/02/2023] [Accepted: 06/23/2023] [Indexed: 07/12/2023] Open
Abstract
Escherichia fergusonii strains have been isolated from patients with diarrhea, but their virulence determinant has not been well elucidated. Here, we report the first isolation of a heat-labile enterotoxin 1 (LT1)-producing E. fergusonii strain (strain 30038) from a patient in Japan. The complete genome sequence of strain 30038 was determined and subjected to comparative genomics and phylogenetic analyses with 195 publicly available genomes of E. fergusonii. In addition to strain 30038, the elt1 gene was also identified in an E. fergusonii strain that is phylogenetically distinct and which was isolated from poultry in the United Kingdom. Fine genomic comparison revealed that these two strains share comparable elt1-bearing plasmids. However, an intriguing distinction arises in strain 30038, wherein the plasmid has integrated into the chromosome via a recombination process mediated by an insertion sequence. The production of active LT1 toxin by strain 30038 was verified through an in vitro assay using cultured cells. A large plasmid carrying 11 antimicrobial resistance genes was also identified in strain 30038. Our results indicate that extensive surveillance of elt1-positive E. fergusonii strains as diarrheagenic pathogens is needed. IMPORTANCE Escherichia fergusonii, a species closely related to Escherichia coli, is known to cause sporadic conditions in humans, including diarrhea. However, the critical virulence factors in E. fergusonii clinical isolates remain to be identified. This study shows the first isolation of an E. fergusonii strain carrying the elt1 gene, which encodes heat-labile enterotoxin 1, from a patient with diarrhea. Our analysis of public databases also revealed the presence of elt1-positive E. fergusonii strains isolated from poultry in the United Kingdom. Interestingly, while the elt1 gene in the poultry isolate was present on a large plasmid, in the human isolate it was integrated into the chromosome, which may confer stability on the elt1-carrying genetic element. Our findings highlight the need for extensive surveillance of elt1-positive E. fergusonii strains in livestock animals.
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Affiliation(s)
- Miki Okuno
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Japan
| | - Nami Tsuru
- Miyazaki Prefectural Institute for Public Health and Environment, Miyazaki, Japan
| | - Shuji Yoshino
- Miyazaki Prefectural Institute for Public Health and Environment, Miyazaki, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takeshi Yamamoto
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshitoshi Ogura
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Japan
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Okuno M, Arimizu Y, Miyahara S, Wakabayashi Y, Gotoh Y, Yoshino S, Harada T, Seto K, Yamamoto T, Nakamura K, Hayashi T, Ogura Y. Escherichia cryptic clade I is an emerging source of human intestinal pathogens. BMC Biol 2023; 21:81. [PMID: 37055811 PMCID: PMC10100065 DOI: 10.1186/s12915-023-01584-4] [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: 12/12/2022] [Accepted: 03/30/2023] [Indexed: 04/15/2023] Open
Abstract
BACKGROUND Within the genus Escherichia, several monophyletic clades other than the traditionally defined species have been identified. Of these, cryptic clade I (C-I) appears to represent a subspecies of E. coli, but due to the difficulty in distinguishing it from E. coli sensu stricto, the population structure and virulence potential of C-I are unclear. RESULTS We defined a set of true C-I strains (n = 465), including a Shiga toxin 2a (Stx2a)-producing isolate from a patient with bloody diarrhoea identified by the retrospective analyses using a C-I-specific detection system. Through genomic analysis of 804 isolates from the cryptic clades, including these C-I strains, we revealed their global population structures and the marked accumulation of virulence genes and antimicrobial resistance genes in C-I. In particular, half of the C-I strains contained hallmark virulence genes of Stx-producing E. coli (STEC) and/or enterotoxigenic E. coli (ETEC). We also found the host-specific distributions of virulence genes, which suggests bovines as the potential source of human infections caused by STEC- and STEC/ETEC hybrid-type C-I strains, as is known in STEC. CONCLUSIONS Our findings demonstrate the emergence of human intestinal pathogens in C-I lineage. To better understand the features of C-I strains and their infections, extensive surveillance and larger population studies of C-I strains are needed. The C-I-specific detection system developed in this study will be a powerful tool for screening and identifying C-I strains.
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Affiliation(s)
- Miki Okuno
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Fukuoka, 830-0011, Japan
| | - Yoko Arimizu
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
- Department of Infectious Disease, National Hospital Organization Kyushu Medical Center, Fukuoka, 810-0065, Japan
| | - Seina Miyahara
- Department of Microbiology, Miyazaki Prefectural Institute for Public Health and Environment, Miyazaki, 889-2155, Japan
| | - Yuki Wakabayashi
- Division of Microbiology, Osaka Institute of Public Health, Osaka, 537-0025, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Shuji Yoshino
- Department of Microbiology, Miyazaki Prefectural Institute for Public Health and Environment, Miyazaki, 889-2155, Japan
| | - Tetsuya Harada
- Division of Microbiology, Osaka Institute of Public Health, Osaka, 537-0025, Japan
| | - Kazuko Seto
- Division of Planning, Osaka Institute of Public Health, Osaka, 537-0025, Japan
| | - Takeshi Yamamoto
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Fukuoka, 830-0011, Japan
| | - Keiji Nakamura
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Yoshitoshi Ogura
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Fukuoka, 830-0011, Japan.
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Gotoh Y, Takano A, Andoh M, Kasama K, Nakamura K, Ando S, Hayashi T. Phylogenic position and low genomic diversity of 'Candidatus Rickettsia kotlanii' inferred by complete genome sequences of two Japanese isolates. Microbiol Immunol 2023. [PMID: 36994930 DOI: 10.1111/1348-0421.13065] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/03/2023] [Accepted: 03/18/2023] [Indexed: 03/31/2023]
Abstract
Many Rickettsia species of the spotted fever group (SFG) cause tick-borne diseases known as "spotted fever". One of the candidate SFG Rickettsia species is 'Candidatus Rickettsia kotlanii', which was first detected in Haemaphysalis concinna in Hungary in 2006. However, its precise phylogenetic position in the SFG is not clear because only single-gene sequence-based phylogenetic analyses were performed using very limited genes. Here, we present the complete genome sequences of two Japanese 'Ca. R. kotlanii' isolates, which differed only by a 135-bp insertion/deletion (InDel). Using these genomes and publicly available whole genome sequences of other Rickettsia species, the precise phylogenetic position of 'Ca. R. kotlanii' in Rickettsia was determined to be in a clade of the SFG. The phylogenetic relationships and average nucleotide identity of 'Ca. R. kotlanii' relative to the other species indicated that 'Ca. R. kotlanii' is an independent taxon in the SFG. Notably, although the genomes of the two isolates were almost identical, the isolates were obtained from different tick species in different regions and years, suggesting extremely low genomic diversity in 'Ca. R. kotlanii'. While the genome of 'Ca. R. kotlanii' is the smallest in the transitional group and SFG Rickettsia sequenced to date, we identified genes uniquely present or absent in 'Ca. R. kotlanii', but most were apparently degraded. Therefore, analyses of differences at the sequence (single nucleotide polymorphisms and small InDels) or gene expression level will be required to understand the functional or physiological features unique to 'Ca. R. kotlanii'. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Ai Takano
- Department of Veterinary Medicine, Joint Faculty of Veterinary Medicine, Yamaguchi University, 1677-1 Yoshida, Yamaguchi, 753-8515, Japan
| | - Masako Andoh
- Department of Pathogenetic and Preventive Veterinary Science, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, 1-21-24 Korimoto, Kagoshima, 890-0065, Japan
| | - Kentaro Kasama
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Keiji Nakamura
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Shuji Ando
- Department of Virology-1, National Institute of Infectious Diseases, Toyama 1-23-1, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
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Yano B, Taniguchi I, Gotoh Y, Hayashi T, Nakamura K. Dynamic changes in Shiga toxin (Stx) 1 transducing phage throughout the evolution of O26:H11 Stx-producing Escherichia coli. Sci Rep 2023; 13:4935. [PMID: 36973327 PMCID: PMC10042803 DOI: 10.1038/s41598-023-32111-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023] Open
Abstract
Shiga toxin (Stx) is the key virulence factor of Stx-producing Escherichia coli (STEC). All known Stxs (Stx1 and Stx2) are encoded by bacteriophages (Stx phages). Although the genetic diversity of Stx phages has frequently been described, systematic analyses of Stx phages in a single STEC lineage are limited. In this study, focusing on the O26:H11 STEC sequence type 21 (ST21) lineage, where the stx1a gene is highly conserved, we analysed the Stx1a phages in 39 strains representative of the entire ST21 lineage and found a high level of variation in Stx1a phage genomes caused by various mechanisms, including replacement by a different Stx1a phage at the same or different locus. The evolutionary timescale of events changing Stx1a phages in ST21 was also determined. Furthermore, by using an Stx1 quantification system developed in this study, we found notable variations in the efficiency of Stx1 production upon prophage induction, which sharply contrasted with the conserved iron regulated Stx1 production. These variations were associated with the Stx1a phage alteration in some cases but not in other cases; thus, Stx1 production in this STEC lineage was determined by differences not only in Stx1 phages but also in host-encoded factors.
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Affiliation(s)
- Bungo Yano
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 815-8582, Japan
| | - Itsuki Taniguchi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 815-8582, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 815-8582, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 815-8582, Japan
| | - Keiji Nakamura
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 815-8582, Japan.
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Kusumoto M, Tamamura-Andoh Y, Hikoda-Kogiku Y, Magome A, Okuhama E, Sato K, Mizuno Y, Arai N, Watanabe-Yanai A, Iwata T, Ogura Y, Gotoh Y, Nakamura K, Hayashi T, Akiba M. Nationwide analysis of antimicrobial resistance in pathogenic Escherichia coli strains isolated from diseased swine over 29 years in Japan. Front Microbiol 2023; 14:1107566. [PMID: 37007495 PMCID: PMC10065406 DOI: 10.3389/fmicb.2023.1107566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 03/06/2023] [Indexed: 03/19/2023] Open
Abstract
Pathogenic Escherichia coli strains are important causes of several swine diseases that result in significant economic losses worldwide. In Japan, the use of antimicrobials in swine is much higher than that in other farm animals every year. Antimicrobial resistance in pathogenic E. coli strains also heavily impacts the swine industry due to the limited treatment options and an increase in the potential risk of the One Health crisis. In 2016, we investigated 684 Japanese isolates of swine pathogenic E. coli belonging to four major serogroups and reported the emergence and increase in the highly multidrug-resistant serogroups O116 and OSB9 and the appearance of colistin-resistant strains. In the present study, by expanding our previous analysis, we determined the serotypes and antimicrobial resistance of 1,708 E. coli strains isolated from diseased swine between 1991 and 2019 in Japan and found recent increases in the prevalences of multidrug-resistant strains and minor serogroup strains. Among the antimicrobials examined in this study that have been approved for animal use, a third-generation cephalosporin was found to be effective against the most isolates (resistance rate: 1.2%) but not against highly multidrug-resistant strains. We also analyzed the susceptibilities of the 1,708 isolates to apramycin and bicozamycin, both which are available for treating swine in Japan, and found that the rates of resistance to apramycin and bicozamycin were low (6.7% and 5.8%, respectively), and both antimicrobials are more effective (resistance rates: 2.7% and 5.4%, respectively) than third-generation cephalosporins (resistance rate: 16.2%) against highly multidrug-resistant strains.
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Affiliation(s)
- Masahiro Kusumoto
- National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Japan
- Graduate School of Veterinary Science, Osaka Metropolitan University, Osaka, Japan
- *Correspondence: Masahiro Kusumoto,
| | - Yukino Tamamura-Andoh
- National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Japan
| | | | - Asami Magome
- Kagoshima Central Livestock Hygiene Service Center, Kagoshima, Japan
| | - Erina Okuhama
- Miyazaki Livestock Hygiene Service Center, Miyazaki, Japan
| | - Keisuke Sato
- Niigata Chuo Livestock Hygiene Service Center, Niigata, Japan
| | - Yoshino Mizuno
- Kumamoto Chuo Livestock Hygiene Service Center, Kumamoto, Japan
| | - Nobuo Arai
- National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Ayako Watanabe-Yanai
- National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Taketoshi Iwata
- National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Yoshitoshi Ogura
- Department of Infectious Medicine, Kurume University School of Medicine, Fukuoka, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Keiji Nakamura
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masato Akiba
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Japan
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11
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Nakamura K, Seto K, Lee K, Ooka T, Gotoh Y, Taniguchi I, Ogura Y, Mainil JG, Piérard D, Harada T, Etoh Y, Ueda S, Hamasaki M, Isobe J, Kimata K, Narimatsu H, Yatsuyanagi J, Ohnishi M, Iyoda S, Hayashi T. Global population structure, genomic diversity and carbohydrate fermentation characteristics of clonal complex 119 (CC119), an understudied Shiga toxin-producing E. coli (STEC) lineage including O165:H25 and O172:H25. Microb Genom 2023; 9. [PMID: 36951916 PMCID: PMC10132054 DOI: 10.1099/mgen.0.000959] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023] Open
Abstract
Among Shiga toxin (Stx)-producing Escherichia coli (STEC) strains of various serotypes, O157:H7 and five major non-O157 STEC (O26:H11, O111:H8, O103:H2, O121:H19 and O145:H28) can be selectively isolated by using tellurite-containing media. While human infections by O165:H25 STEC strains have been reported worldwide, their detection and isolation are not easy, as they are not resistant to tellurite. Systematic whole-genome sequencing (WGS) analyses have not yet been conducted. Here, we defined O165:H25 strains and their close relatives, including O172:H25 strains, as clonal complex 119 (CC119) and performed a global WGS analysis of the major lineage of CC119, called CC119 sensu stricto (CC119ss), by using 202 CC119ss strains, including 90 strains sequenced in this study. Detailed comparisons of 13 closed genomes, including 7 obtained in this study, and systematic analyses of Stx phage genomes in 50 strains covering the entire CC119ss lineage, were also conducted. These analyses revealed that the Stx2a phage, the locus of enterocyte effacement (LEE) encoding a type III secretion system (T3SS), many prophages encoding T3SS effectors, and the virulence plasmid were acquired by the common ancestor of CC119ss and have been stably maintained in this lineage, while unusual exchanges of Stx1a and Stx2c phages were found at a single integration site. Although the genome sequences of Stx2a phages were highly conserved, CC119ss strains exhibited notable variation in Stx2 production levels. Further analyses revealed the lack of SpLE1-like elements carrying the tellurite resistance genes in CC119ss and defects in rhamnose, sucrose, salicin and dulcitol fermentation. The genetic backgrounds underlying these defects were also clarified.
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Affiliation(s)
- Keiji Nakamura
- Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kazuko Seto
- Osaka Institute of Public Health, Osaka, Japan
| | - Kenichi Lee
- National Institute of Infectious Diseases, Tokyo, Japan
| | - Tadasuke Ooka
- Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Yasuhiro Gotoh
- Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Itsuki Taniguchi
- Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | | | | | - Denis Piérard
- Universitair Ziekenhuis Brussel (UZ Brussel), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | | | - Yoshiki Etoh
- Fukuoka Institute of Health and Environmental Sciences, Fukuoka, Japan
| | - Saori Ueda
- Fukuoka Institute of Health and Environmental Sciences, Fukuoka, Japan
| | | | | | | | | | | | - Makoto Ohnishi
- Present address: Chūbu Regional Public Health Center, Okinawa, Japan
- National Institute of Infectious Diseases, Tokyo, Japan
| | - Sunao Iyoda
- National Institute of Infectious Diseases, Tokyo, Japan
| | - Tetsuya Hayashi
- Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
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12
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Miyata T, Taniguchi I, Nakamura K, Gotoh Y, Yoshimura D, Itoh T, Hirai S, Yokoyama E, Ohnishi M, Iyoda S, Ogura Y, Hayashi T. Alteration of a Shiga toxin-encoding phage associated with a change in toxin production level and disease severity in Escherichia coli. Microb Genom 2023; 9:mgen000935. [PMID: 36821793 PMCID: PMC9997748 DOI: 10.1099/mgen.0.000935] [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: 02/25/2023] Open
Abstract
Among the nine clades of Shiga toxin (Stx)-producing Escherichia coli O157:H7, clade 8 is thought to be highly pathogenic, as it causes severe disease more often than other clades. Two subclades have been proposed, but there are conflicting reports on intersubclade differences in Stx2 levels, although Stx2 production is a risk factor for severe disease development. The global population structure of clade 8 has also yet to be fully elucidated. Here, we present genome analyses of a global clade 8 strain set (n=510), including 147 Japanese strains sequenced in this study. The complete genome sequences of 18 of the 147 strains were determined to perform detailed clade-wide genome analyses together with 17 publicly available closed genomes. Intraclade variations in Stx2 production level and disease severity were also re-evaluated within the phylogenetic context. Based on phylogenomic analysis, clade 8 was divided into four lineages corresponding to the previously proposed SNP genotypes (SGs): SG8_30, SG8_31A, SG8_31B and SG8_32. SG8_30 and the common ancestor of the other SGs were first separated, with SG8_31A and SG8_31B emerging from the latter and SG8_32 emerging from SG8_31B. Comparison of 35 closed genomes revealed the overall structure of chromosomes and pO157 virulence plasmids and the prophage contents to be well conserved. However, Stx2a phages exhibit notable genomic diversity, even though all are integrated into the argW locus, indicating that subtype changes in Stx2a phage occurred from the γ subtype to its variant (γ_v1) in SG8_31A and from γ to δ in SG8_31B and SG8_32 via replacement of parts or almost entire phage genomes, respectively. We further show that SG8_30 strains (all carrying γ Stx2a phages) produce significantly higher levels of Stx2 and cause severe disease more frequently than SG8_32 strains (all carrying δ Stx2a phages). Clear conclusions on SG8_31A and SG8_31B cannot be made due to the small number of strains available, but as SG8_31A (carrying γ_v1 Stx2a phages) contains strains that produce much more Stx2 than SG8_30 strains, attention should also be paid to this SG.
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Affiliation(s)
- Tatsuya Miyata
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan.,Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Itsuki Taniguchi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Keiji Nakamura
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Dai Yoshimura
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro, Tokyo 152-8550, Japan
| | - Takehiko Itoh
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro, Tokyo 152-8550, Japan
| | - Shinichiro Hirai
- Division of Bacteriology, Chiba Prefectural Institute of Public Health, Chiba 260-8715, Japan.,Center for Emergency Preparedness and Response, National Institute of Infectious Diseases, Musashi-Murayama, Tokyo 208-0011, Japan
| | - Eiji Yokoyama
- Division of Bacteriology, Chiba Prefectural Institute of Public Health, Chiba 260-8715, Japan
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases, Shinjuku, Tokyo 162-8640, Japan
| | - Sunao Iyoda
- Department of Bacteriology I, National Institute of Infectious Diseases, Shinjuku, Tokyo 162-8640, Japan
| | - Yoshitoshi Ogura
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan.,Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Fukuoka 830-0011, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
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13
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Ooka T, Gotoh Y, Hatanaka S, Yoshimori M, Nishitarumizu K, Kojo K, Kosakamoto H, Sameshima K, Kuroki Y, Chibana N, Doi Y, Yoshino S, Harada T, Seto K, Ikeda T, Miyanohara H, Nakayama K, Gokuden M, Imuta N, Kawamura H, Ogura Y, Hayashi T, Nishi J. A Salmonella enterica Serovar Oranienburg Clone Caused a Cluster of Bacteremia Cases in Persons With No Recognizable Underlying Diseases in Japan. Open Forum Infect Dis 2022; 10:ofac695. [PMID: 36686639 PMCID: PMC9846185 DOI: 10.1093/ofid/ofac695] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 12/26/2022] [Indexed: 12/29/2022] Open
Abstract
Background Salmonella enterica subspecies enterica serovar Oranienburg (SO) is a foodborne pathogen but rarely causes systemic infections such as bacteremia. Between July and September 2018, bacteremia cases caused by SO were identified in 12 persons without any underlying medical conditions in the southern Kyushu area of Japan. Methods Randomly amplified polymorphic DNA (RAPD) analysis was performed to investigate the genetic similarity of the 12 bacteremia-related strains and other Japanese isolates. Furthermore, a series of whole-genome sequence (WGS)-based phylogenetic analyses was performed with a global SO strain set (n = 1648). Results The resolution power of RAPD was insufficient to investigate the genetic similarity between the bacteremia-related strains and other strains. WGS-based phylogenetic analyses revealed that the bacteremia-related strains formed a tight cluster along with 2 strains isolated from asymptomatic carriers in 2018 in the same area, with a maximum within-cluster single-nucleotide polymorphism (SNP) distance of 11. While several strains isolated in the United States and the United Kingdom were found to be closely related to the bacteremia-related strains, 2 strains isolated in 2016 in the southern Kyushu area were most closely related, with SNP distances of 4-11 and 5-10, and had the same plasmids as the bacteremia-related strains. Conclusions The 12 bacteremia cases identified were caused by a single SO clone. As none of the bacteremia patients had any underlying diseases, this clone may be prone to cause bacteremia. Although further analyses are required to understand its virulence, particular attention should be given to this clone and its close relatives in the surveillance of nontyphoidal salmonellae.
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Affiliation(s)
- Tadasuke Ooka
- Correspondence: Tadasuke Ooka, PhD, Department of Microbiology, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima-shi, Kagoshima 890-8544, Japan ()
| | - Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Shigeki Hatanaka
- Department of Emergency and General Internal Medicine, Imamura General Hospital, Kagoshima, Japan
| | - Miyuki Yoshimori
- Department of Infection Control and Prevention, Imamura General Hospital, Kagoshima, Japan
| | - Kazutaka Nishitarumizu
- Department of Emergency and General Internal Medicine, Imamura General Hospital, Kagoshima, Japan
| | - Kanami Kojo
- Department of Pediatrics, Kagoshima Children's Hospital, Kagoshima, Japan
| | - Hiroki Kosakamoto
- Department of Internal Medicine, Kokubu Seikyo Hospital, Kagoshima, Japan
| | - Koji Sameshima
- Department of Pediatrics, Kagoshima City Hospital, Kagoshima, Japan
| | - Yoichi Kuroki
- Department of Internal Medicine, Koga General Hospital, Miyazaki, Japan
| | - Naomi Chibana
- Department of General Internal Medicine, Naha City Hospital, Okinawa, Japan
| | - Yuriko Doi
- Kagoshima City Public Health Center, Kagoshima, Japan
| | - Shuji Yoshino
- Clinical Microbiology Section, Miyazaki Prefectural Institute for Public Health and Environment, Miyazaki, Japan
| | - Tetsuya Harada
- Division of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | - Kazuko Seto
- Division of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | - Tetsuya Ikeda
- Department of Infectious Diseases, Hokkaido Institute of Public Health, Hokkaido, Japan
| | - Hiroaki Miyanohara
- Department of Clinical Laboratory, Kagoshima Prefectural Comprehensive Health Center, Kagoshima, Japan
| | - Koichiro Nakayama
- Microorganism Section, Kagoshima Prefectural Institute for Environmental Research and Public Health, Kagoshima, Japan
| | - Mutsuyo Gokuden
- Microorganism Section, Kagoshima Prefectural Institute for Environmental Research and Public Health, Kagoshima, Japan
| | - Naoko Imuta
- Department of Microbiology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Hideki Kawamura
- Department of Infection Control and Prevention, Kagoshima University Hospital, Kagoshima, Japan
| | - Yoshitoshi Ogura
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan,Division of Microbiology, Department of Infectious Medicine, Kurume University, Fukuoka, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
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14
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Hori K, Taniguchi T, Elpita T, Khemgaew R, Sasaki S, Gotoh Y, Yasutomi I, Misawa N. Comprehensive Analyses of the Bacterial Population in Non-Healing Claw Lesions of Dairy Cattle. Animals (Basel) 2022; 12:ani12243584. [PMID: 36552504 PMCID: PMC9774328 DOI: 10.3390/ani12243584] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/07/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022] Open
Abstract
Non-healing claw lesions (NHCLs) are a newly characterized disorder affecting the deep dermis of the hoof in dairy cattle. Although NHCLs are thought to be associated with bovine digital dermatitis (BDD), their precise etiology is not yet understood. To investigate the bacterial populations present in each type of NHCL (toe necrosis: TN, non-healing white line disease: nhWLD, and a non-healing sole ulcer: nhSU), and the newly added entity non-healing verrucous-like lesions (nhVLL), 16S rRNA-based metagenomic analysis with next-generation sequencing (NGS) was employed. Twelve cases of NHCLs (3 TN, 3 nhWLD, 4 nhSU, and 2 nhVLL) were collected from five dairy farms in two prefectures in Japan. Three samples of healthy hoof dermis collected from two farms and a slaughterhouse were used as controls. Furthermore, culture-dependent and -independent approaches were conducted for detecting Treponema species and Fusobacterium necrophorum. As reported in BDD, Treponema species and F. necrophorum were detected frequently from NHCLs by PCR and immunohistochemistry, but NGS showed that these bacterial genera were not predominant in NHCLs. The predominant bacterial genera in NHCLs differed among the lesions examined, suggesting that Treponema species present predominantly in BDD were not predominant in NHCLs and that the bacterial population in NHCLs may vary among individual cattle and/or farms.
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Affiliation(s)
- Kaoru Hori
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, 5200 Kihara-kiyotake-cho, Miyazaki 889-1692, Japan
- Fuchu Veterinary Clinical Center, Hiroshima Agricultural Mutual Aid Association, 396-1 Fukae, Jyoge-cho, Fuchu, Hiroshima 729-3421, Japan
| | - Takako Taniguchi
- Center for Animal Disease Control, University of Miyazaki, 1-1 Gakuenkibanadai-nishi, Miyazaki 889-2192, Japan
| | - Trigan Elpita
- Center for Animal Disease Control, University of Miyazaki, 1-1 Gakuenkibanadai-nishi, Miyazaki 889-2192, Japan
| | - Rathanon Khemgaew
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, 5200 Kihara-kiyotake-cho, Miyazaki 889-1692, Japan
| | - Satomi Sasaki
- Center for Animal Disease Control, University of Miyazaki, 1-1 Gakuenkibanadai-nishi, Miyazaki 889-2192, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Ichiro Yasutomi
- Yubetsu Herd Management Service Ltd., 450-3 Baro, Mombetsu-gun, Yubetsu-cho 093-0731, Hokkaido, Japan
| | - Naoaki Misawa
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, 5200 Kihara-kiyotake-cho, Miyazaki 889-1692, Japan
- Center for Animal Disease Control, University of Miyazaki, 1-1 Gakuenkibanadai-nishi, Miyazaki 889-2192, Japan
- Correspondence: ; Tel./Fax: +81-985-58-7284
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15
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Koga R, Moriyama M, Onodera-Tanifuji N, Ishii Y, Takai H, Mizutani M, Oguchi K, Okura R, Suzuki S, Gotoh Y, Hayashi T, Seki M, Suzuki Y, Nishide Y, Hosokawa T, Wakamoto Y, Furusawa C, Fukatsu T. Single mutation makes Escherichia coli an insect mutualist. Nat Microbiol 2022; 7:1141-1150. [PMID: 35927448 PMCID: PMC9352592 DOI: 10.1038/s41564-022-01179-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [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: 02/20/2022] [Accepted: 06/21/2022] [Indexed: 02/07/2023]
Abstract
Microorganisms often live in symbiosis with their hosts, and some are considered mutualists, where all species involved benefit from the interaction. How free-living microorganisms have evolved to become mutualists is unclear. Here we report an experimental system in which non-symbiotic Escherichia coli evolves into an insect mutualist. The stinkbug Plautia stali is typically associated with its essential gut symbiont, Pantoea sp., which colonizes a specialized symbiotic organ. When sterilized newborn nymphs were infected with E. coli rather than Pantoea sp., only a few insects survived, in which E. coli exhibited specific localization to the symbiotic organ and vertical transmission to the offspring. Through transgenerational maintenance with P. stali, several hypermutating E. coli lines independently evolved to support the host's high adult emergence and improved body colour; these were called 'mutualistic' E. coli. These mutants exhibited slower bacterial growth, smaller size, loss of flagellar motility and lack of an extracellular matrix. Transcriptomic and genomic analyses of 'mutualistic' E. coli lines revealed independent mutations that disrupted the carbon catabolite repression global transcriptional regulator system. Each mutation reproduced the mutualistic phenotypes when introduced into wild-type E. coli, confirming that single carbon catabolite repression mutations can make E. coli an insect mutualist. These findings provide an experimental system for future work on host-microbe symbioses and may explain why microbial mutualisms are omnipresent in nature.
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Affiliation(s)
- Ryuichi Koga
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan.
| | - Minoru Moriyama
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Naoko Onodera-Tanifuji
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Yoshiko Ishii
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Hiroki Takai
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Masaki Mizutani
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Kohei Oguchi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Reiko Okura
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Shingo Suzuki
- Center for Biosystem Dynamics Research, RIKEN, Osaka, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masahide Seki
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Yutaka Suzuki
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Yudai Nishide
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan.,National Agriculture and Food Research Organization, Institute of Agrobiological Sciences, Tsukuba, Japan
| | - Takahiro Hosokawa
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka, Japan
| | - Yuichi Wakamoto
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan.,Universal Biology Institute, The University of Tokyo, Tokyo, Japan
| | - Chikara Furusawa
- Center for Biosystem Dynamics Research, RIKEN, Osaka, Japan.,Universal Biology Institute, The University of Tokyo, Tokyo, Japan
| | - Takema Fukatsu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan. .,Department of Biological Sciences, The University of Tokyo, Tokyo, Japan. .,Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan.
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16
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Gotoh Y, Atsuta Y, Taniguchi T, Nishida R, Nakamura K, Ogura Y, Misawa N, Hayashi T. Helicobacter cinaedi is a human-adapted lineage in the Helicobacter cinaedi/canicola/'magdeburgensis' complex. Microb Genom 2022; 8. [PMID: 35536747 PMCID: PMC9465070 DOI: 10.1099/mgen.0.000830] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Helicobacter cinaedi is an enterohepatic Helicobacter that causes bacteremia and other diseases in humans. While H. cinaedi-like strains are isolated from animals, including dog isolates belonging to a recently proposed H. canicola, little is known about the genetic differences between H. cinaedi and these animal isolates. Here, we sequenced 43 H. cinaedi- or H. canicola-like strains isolated from humans, hamsters, rats and dogs and collected 81 genome sequences of H. cinaedi, H. canicola and other enterohepatic Helicobacter strains from public databases. Genomic comparison of these strains identified four distinct clades (clades I–IV) in H. cinaedi/canicola/‘magderbugensis’ (HCCM) complex. Among these, clade I corresponds to H. cinaedi sensu stricto and represents a human-adapted lineage in the complex. We identified several genomic features unique to clade I. They include the accumulation of antimicrobial resistance-related mutations that reflects the human association of clade I and the larger genome size and the presence of a CRISPR-Cas system and multiple toxin-antitoxin and restriction-modification systems, both of which indicate the contribution of horizontal gene transfer to the evolution of clade I. In addition, nearly all clade I strains but only a few strains belonging to one minor clade contained a highly variable genomic region encoding a type VI secretion system (T6SS), which could play important roles in gut colonization by killing competitors or inhibiting their growth. We also developed a method to systematically search for H. cinaedi sequences in large metagenome data sets based on the results of genome comparison. Using this method, we successfully identified multiple HCCM complex-containing human faecal metagenome samples and obtained the sequence information covering almost the entire genome of each strain. Importantly, all were clade I strains, supporting our conclusion that H. cinaedi sensu stricto is a human-adapted lineage in the HCCM complex.
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Affiliation(s)
- Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yuya Atsuta
- Department of Hematology, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan
| | - Takako Taniguchi
- Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
| | - Ruriko Nishida
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Keiji Nakamura
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshitoshi Ogura
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Fukuoka, Japan
| | - Naoaki Misawa
- Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
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17
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Ono T, Taniguchi I, Nakamura K, Nagano DS, Nishida R, Gotoh Y, Ogura Y, Sato MP, Iguchi A, Murase K, Yoshimura D, Itoh T, Shima A, Dubois D, Oswald E, Shiose A, Gotoh N, Hayashi T. Global population structure of the Serratia marcescens complex and identification of hospital-adapted lineages in the complex. Microb Genom 2022; 8:000793. [PMID: 35315751 PMCID: PMC9176281 DOI: 10.1099/mgen.0.000793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Serratia marcescens is an important nosocomial pathogen causing various opportunistic infections, such as urinary tract infections, bacteremia and sometimes even hospital outbreaks. The recent emergence and spread of multidrug-resistant (MDR) strains further pose serious threats to global public health. This bacterium is also ubiquitously found in natural environments, but the genomic differences between clinical and environmental isolates are not clear, including those between S. marcescens and its close relatives. In this study, we performed a large-scale genome analysis of S. marcescens and closely related species (referred to as the 'S. marcescens complex'), including more than 200 clinical and environmental strains newly sequenced here. Our analysis revealed their phylogenetic relationships and complex global population structure, comprising 14 clades, which were defined based on whole-genome average nucleotide identity. Clades 10, 11, 12 and 13 corresponded to S. nematodiphila, S. marcescens sensu stricto, S. ureilytica and S. surfactantfaciens, respectively. Several clades exhibited distinct genome sizes and GC contents and a negative correlation of these genomic parameters was observed in each clade, which was associated with the acquisition of mobile genetic elements (MGEs), but different types of MGEs, plasmids or prophages (and other integrative elements), were found to contribute to the generation of these genomic variations. Importantly, clades 1 and 2 mostly comprised clinical or hospital environment isolates and accumulated a wide range of antimicrobial resistance genes, including various extended-spectrum β-lactamase and carbapenemase genes, and fluoroquinolone target site mutations, leading to a high proportion of MDR strains. This finding suggests that clades 1 and 2 represent hospital-adapted lineages in the S. marcescens complex although their potential virulence is currently unknown. These data provide an important genomic basis for reconsidering the classification of this group of bacteria and reveal novel insights into their evolution, biology and differential importance in clinical settings.
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Affiliation(s)
- Tomoyuki Ono
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
- Department of Cardiovascular Surgery, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Itsuki Taniguchi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Keiji Nakamura
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Debora Satie Nagano
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Ruriko Nishida
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Yoshitoshi Ogura
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Asahi-machi, Kurume, Fukuoka, 830-0011, Japan
| | - Mitsuhiko P. Sato
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
- Present address: Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
| | - Atsushi Iguchi
- Faculty of Agriculture, University of Miyazaki, Miyazaki, Miyazaki, 889-8192, Japan
| | - Kazunori Murase
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Sakyou-ku, Kyoto, 6060-8501, Japan
| | - Dai Yoshimura
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
| | - Takehiko Itoh
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
| | - Ayaka Shima
- IRSD, INSERM, ENVT, INRAE, Université de Toulouse, UPS, Toulouse, France
- Present address: Anicon Insurance, Inc., 8-17-1 Nishi-shinjuku, Shinjuku, Tokyo, 160-0023, Japan
| | - Damien Dubois
- IRSD, INSERM, ENVT, INRAE, Université de Toulouse, UPS, Toulouse, France
- CHU Toulouse, Hôpital Purpan, Service de Bactériologie-Hygiène, Toulouse, France
| | - Eric Oswald
- IRSD, INSERM, ENVT, INRAE, Université de Toulouse, UPS, Toulouse, France
- CHU Toulouse, Hôpital Purpan, Service de Bactériologie-Hygiène, Toulouse, France
| | - Akira Shiose
- Department of Cardiovascular Surgery, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Naomasa Gotoh
- Kyoto Pharmaceutical University, Yamashiro, Kyoto, 607-8414, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
- *Correspondence: Tetsuya Hayashi,
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18
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Miyakoshi M, Morita T, Kobayashi A, Berger A, Takahashi H, Gotoh Y, Hayashi T, Tanaka K. Glutamine synthetase mRNA releases sRNA from its 3'UTR to regulate carbon/nitrogen metabolic balance in Enterobacteriaceae. eLife 2022; 11:82411. [PMID: 36440827 PMCID: PMC9731577 DOI: 10.7554/elife.82411] [Citation(s) in RCA: 1] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 11/27/2022] [Indexed: 11/29/2022] Open
Abstract
Glutamine synthetase (GS) is the key enzyme of nitrogen assimilation induced under nitrogen limiting conditions. The carbon skeleton of glutamate and glutamine, 2-oxoglutarate, is supplied from the TCA cycle, but how this metabolic flow is controlled in response to nitrogen availability remains unknown. We show that the expression of the E1o component of 2-oxoglutarate dehydrogenase, SucA, is repressed under nitrogen limitation in Salmonella enterica and Escherichia coli. The repression is exerted at the post-transcriptional level by an Hfq-dependent sRNA GlnZ generated from the 3'UTR of the GS-encoding glnA mRNA. Enterobacterial GlnZ variants contain a conserved seed sequence and primarily regulate sucA through base-pairing far upstream of the translation initiation region. During growth on glutamine as the nitrogen source, the glnA 3'UTR deletion mutants expressed SucA at higher levels than the S. enterica and E. coli wild-type strains, respectively. In E. coli, the transcriptional regulator Nac also participates in the repression of sucA. Lastly, this study clarifies that the release of GlnZ from the glnA mRNA by RNase E is essential for the post-transcriptional regulation of sucA. Thus, the mRNA coordinates the two independent functions to balance the supply and demand of the fundamental metabolites.
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Affiliation(s)
- Masatoshi Miyakoshi
- Department of Infection Biology, Faculty of Medicine, University of TsukubaTsukubaJapan,Transborder Medical Research Center, University of TsukubaTsukubaJapan,International Joint Degree Master’s Program in Agro-Biomedical Science in Food and Health (GIP-TRIAD), University of TsukubaTsukubaJapan
| | - Teppei Morita
- Institute for Advanced Biosciences, Keio UniversityTsuruokaJapan,Graduate School of Media and Governance, Keio UniversityFujisawaJapan
| | - Asaki Kobayashi
- Transborder Medical Research Center, University of TsukubaTsukubaJapan
| | - Anna Berger
- International Joint Degree Master’s Program in Agro-Biomedical Science in Food and Health (GIP-TRIAD), University of TsukubaTsukubaJapan
| | | | - Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu UniversityFukuokaJapan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu UniversityFukuokaJapan
| | - Kan Tanaka
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of TechnologyYokohamaJapan
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19
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Tanaka Y, Yamashita R, Kawashima J, Mori H, Kurokawa K, Fukuda S, Gotoh Y, Nakamura K, Hayashi T, Kasahara Y, Sato Y, Fukudo S. Omics profiles of fecal and oral microbiota change in irritable bowel syndrome patients with diarrhea and symptom exacerbation. J Gastroenterol 2022; 57:748-760. [PMID: 35908139 PMCID: PMC9522833 DOI: 10.1007/s00535-022-01888-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/27/2022] [Indexed: 02/04/2023]
Abstract
BACKGROUND Irritable bowel syndrome (IBS) is a disorder of gut-brain interaction, including dysregulation of the hypothalamic-pituitary-adrenal axis with salivary cortisol changes. However, the role of gastrointestinal microbiota during IBS symptom exacerbation remains unclear. We tested the hypothesis that the microbial species, gene transcripts, and chemical composition of fecal and oral samples are altered during the exacerbation of IBS symptoms. METHODS Fecal, salivary, and dental plaque samples were collected at baseline from 43 men with IBS with diarrhea (IBS-D) and 40 healthy control (HC) men. Samples in the IBS-D patients were also collected during symptom exacerbation. The composition of the fecal microbiota was determined by analyzing the 16S rRNA gene, RNA-based metatranscriptome, and metabolites in samples from HC and IBS patients with and without symptom exacerbation. Oral samples were also analyzed using omics approaches. RESULTS The fecal microbiota during IBS symptom exacerbation exhibited significant differences in the phylogenic pattern and short-chain fatty acid compared with fecal samples during defecation when symptoms were not exacerbated. Although there were no significant differences in the phylogenic pattern of fecal microbiota abundance between HCs and IBS-D patients, significant differences were detected in the expression patterns of bacterial transcriptomes related to butyrate production and neuroendocrine hormones, including tryptophan-serotonin-melatonin synthesis and glutamine/GABA. The composition of plaque microbiota was different between HC and IBS-D patients during normal defecation. CONCLUSIONS Our findings suggest that colonic host-microbial interactions are altered in IBS-D patients during exacerbation of symptoms. There were no overlaps between feces and oral microbiomes.
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Affiliation(s)
- Yukari Tanaka
- grid.415501.4Department of Gastroenterology, Sendai Kousei Hospital, Sendai, Japan ,grid.69566.3a0000 0001 2248 6943Department of Behavioral Medicine, Tohoku University Graduate School of Medicine, 2-1 Seiryo, Aoba, Sendai 980-8575 Japan
| | - Riu Yamashita
- grid.272242.30000 0001 2168 5385Division of Translational Informatics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan
| | - Junko Kawashima
- grid.69566.3a0000 0001 2248 6943Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Hiroshi Mori
- grid.288127.60000 0004 0466 9350Advanced Genomics Center, National Institute of Genetics, Shizuoka, Japan
| | - Ken Kurokawa
- grid.288127.60000 0004 0466 9350Advanced Genomics Center, National Institute of Genetics, Shizuoka, Japan
| | - Shinji Fukuda
- grid.26091.3c0000 0004 1936 9959Institute for Advanced Biosciences, Keio University, Yamagata, Japan ,grid.26999.3d0000 0001 2151 536XGut Environmental Design Group, Kanagawa Institute of Industrial Science and Technology, Kanagawa, Japan ,grid.20515.330000 0001 2369 4728Transborder Medical Research Center, University of Tsukuba, Ibaraki, Japan
| | - Yasuhiro Gotoh
- grid.177174.30000 0001 2242 4849Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Keiji Nakamura
- grid.177174.30000 0001 2242 4849Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tetsuya Hayashi
- grid.177174.30000 0001 2242 4849Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshiyuki Kasahara
- grid.69566.3a0000 0001 2248 6943Department of Fetal and Maternal Therapeutics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yukuto Sato
- grid.267625.20000 0001 0685 5104Research Laboratory Center, Faculty of Medicine, University of the Ryukyus, Nishihara, Okinawa Japan
| | - Shin Fukudo
- grid.69566.3a0000 0001 2248 6943Department of Behavioral Medicine, Tohoku University Graduate School of Medicine, 2-1 Seiryo, Aoba, Sendai 980-8575 Japan
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20
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Prodinger F, Endo H, Takano Y, Li Y, Tominaga K, Isozaki T, Blanc-Mathieu R, Gotoh Y, Hayashi T, Taniguchi E, Nagasaki K, Yoshida T, Ogata H. Year-round dynamics of amplicon sequence variant communities differ among eukaryotes, Imitervirales, and prokaryotes in a coastal ecosystem. FEMS Microbiol Ecol 2021; 97:6486443. [PMID: 34962982 DOI: 10.1093/femsec/fiab167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 02/21/2021] [Accepted: 12/25/2021] [Indexed: 11/13/2022] Open
Abstract
Coastal microbial communities are affected by seasonal environmental change, biotic interactions, and fluctuating nutrient availability. We investigated the seasonal dynamics of communities of eukaryotes, a major group of double-stranded DNA viruses that infect eukaryotes (order Imitervirales; phylum Nucleocytoviricota), and prokaryotes in the Uranouchi Inlet, Kochi, Japan. We performed metabarcoding using ribosomal RNA genes and viral polB genes as markers in 43 seawater samples collected over 20 months. Eukaryotes, prokaryotes, and Imitervirales communities characterized by the compositions of amplicon sequence variants (ASVs) showed synchronic seasonal cycles. However, the community dynamics showed intriguing differences in several aspects, such as the recovery rate after a year. We also showed that the differences in community dynamics were at least partially explained by differences in recurrence/persistence levels of individual ASVs among eukaryotes, prokaryotes, and Imitervirales. Prokaryotic ASVs were the most persistent, followed by eukaryotic ASVs and Imitervirales ASVs, which were the least persistent. We argue that the differences in the specificity of interactions (virus-eukaryote vs. prokaryote-eukaryote) as well as the niche breadth of community members were at the origin of the distinct community dynamics among eukaryotes, their viruses, and prokaryotes.
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Affiliation(s)
- Florian Prodinger
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Japan
| | - Hisashi Endo
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Japan
| | - Yoshihito Takano
- Faculty of Science and Technology, Kochi University, Nankoku, Kochi, Japan
| | - Yanze Li
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Japan
| | - Kento Tominaga
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, Japan
| | - Tatsuhiro Isozaki
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, Japan
| | - Romain Blanc-Mathieu
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Japan.,Laboratoire de Physiologie Cellulaire & Végétale, CEA, Univ. Grenoble Alpes, CNRS, INRA, IRIG, Grenoble, France
| | - Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, Japan
| | | | - Keizo Nagasaki
- Faculty of Science and Technology, Kochi University, Nankoku, Kochi, Japan
| | - Takashi Yoshida
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, Japan
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Japan
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21
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Hayashi T, Yamashita T, Takahashi T, Tabata T, Watanabe H, Gotoh Y, Shinohara M, Kami K, Tanaka H, Matsumoto K, Hayashi T, Yamada T, Hirata KI. Uncovering the Role of Gut Microbiota in Amino Acid Metabolic Disturbances in Heart Failure Through Metagenomic Analysis. Front Cardiovasc Med 2021; 8:789325. [PMID: 34912870 PMCID: PMC8667331 DOI: 10.3389/fcvm.2021.789325] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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: 10/04/2021] [Accepted: 11/08/2021] [Indexed: 11/13/2022] Open
Abstract
Aims: Circulating amino acid (AA) abnormalities serve as predictors of adverse outcomes in patients with heart failure (HF). However, the role of the gut microbiota in AA disturbances remains unknown. Thus, we investigated gut microbial functions and their associations with AA metabolic alterations in patients with HF. Methods and Results: We performed whole-genome shotgun sequencing of fecal samples and mass spectrometry-based profiling of AAs in patients with compensated HF. Plasma levels of total essential AAs (EAAs) and histidine were significantly lower in patients with HF than in control subjects. HF patients also displayed increased and decreased abundance of gut microbial genes involved in the degradation and biosynthesis, respectively, of EAAs, including branched-chain AAs (BCAAs) and histidine. Importantly, a significant positive correlation was observed between the abundance of microbial genes involved in BCAA biosynthesis and plasma BCAA levels in patients with HF, but not in controls. Moreover, network analysis revealed that the depletion of Eubacterium and Prevotella, which harbor genes for BCAA and histidine biosynthesis, contributed to decreased abundance of microbial genes involved in the biosynthesis of those EAAs in patients with HF. Conclusions: The present study demonstrated the relationship between gut microbiota and AA metabolic disturbances in patients with HF.
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Affiliation(s)
- Tomohiro Hayashi
- Division of Cardiovascular Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan.,Cardiovascular Division, Department of Medicine, Center for Cardiovascular Research, Washington University School of Medicine, St. Louis, MO, United States
| | - Tomoya Yamashita
- Division of Cardiovascular Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Tomoya Takahashi
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Tokiko Tabata
- Division of Cardiovascular Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Hikaru Watanabe
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masakazu Shinohara
- Division of Epidemiology, Kobe University Graduate School of Medicine, Kobe, Japan.,The Integrated Center for Mass Spectrometry, Kobe University Graduate School of Medicine, Kobe, Japan
| | | | - Hidekazu Tanaka
- Division of Cardiovascular Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Kensuke Matsumoto
- Division of Cardiovascular Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takuji Yamada
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Ken-Ichi Hirata
- Division of Cardiovascular Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
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22
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Kajitani R, Noguchi H, Gotoh Y, Ogura Y, Yoshimura D, Okuno M, Toyoda A, Kuwahara T, Hayashi T, Itoh T. MetaPlatanus: a metagenome assembler that combines long-range sequence links and species-specific features. Nucleic Acids Res 2021; 49:e130. [PMID: 34570223 PMCID: PMC8682757 DOI: 10.1093/nar/gkab831] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/05/2021] [Accepted: 09/09/2021] [Indexed: 12/27/2022] Open
Abstract
De novo metagenome assembly is effective in assembling multiple draft genomes, including those of uncultured organisms. However, heterogeneity in the metagenome hinders assembly and introduces interspecies misassembly deleterious for downstream analysis. For this purpose, we developed a hybrid metagenome assembler, MetaPlatanus. First, as a characteristic function, it assembles the basic contigs from accurate short reads and then iteratively utilizes long-range sequence links, species-specific sequence compositions, and coverage depth. The binning information was also used to improve contiguity. Benchmarking using mock datasets consisting of known bacteria with long reads or mate pairs revealed the high contiguity MetaPlatanus with a few interspecies misassemblies. For published human gut data with nanopore reads from potable sequencers, MetaPlatanus assembled many biologically important elements, such as coding genes, gene clusters, viral sequences, and over-half bacterial genomes. In the benchmark with published human saliva data with high-throughput nanopore reads, the superiority of MetaPlatanus was considerably more evident. We found that some high-abundance bacterial genomes were assembled only by MetaPlatanus as near-complete. Furthermore, MetaPlatanus can circumvent the limitations of highly fragmented assemblies and frequent interspecies misassembles obtained by the other tools. Overall, the study demonstrates that MetaPlatanus could be an effective approach for exploring large-scale structures in metagenomes.
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Affiliation(s)
- Rei Kajitani
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Hideki Noguchi
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yoshitoshi Ogura
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Asahi-machi, Kurume, Fukuoka 830-0011, Japan
| | - Dai Yoshimura
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Miki Okuno
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Asahi-machi, Kurume, Fukuoka 830-0011, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.,Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Tomomi Kuwahara
- Department of Molecular Microbiology, Faculty of Medicine, Kagawa University, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Takehiko Itoh
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
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23
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Nishida R, Nakamura K, Taniguchi I, Murase K, Ooka T, Ogura Y, Gotoh Y, Itoh T, Toyoda A, Mainil JG, Piérard D, Seto K, Harada T, Isobe J, Kimata K, Etoh Y, Hamasaki M, Narimatsu H, Yatsuyanagi J, Kameyama M, Matsumoto Y, Nagai Y, Kawase J, Yokoyama E, Ishikawa K, Shiomoto T, Lee K, Kang D, Akashi K, Ohnishi M, Iyoda S, Hayashi T. The global population structure and evolutionary history of the acquisition of major virulence factor-encoding genetic elements in Shiga toxin-producing Escherichia coli O121:H19. Microb Genom 2021; 7. [PMID: 34878971 PMCID: PMC8767318 DOI: 10.1099/mgen.0.000716] [Citation(s) in RCA: 1] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Shiga toxin (Stx)-producing Escherichia coli (STEC) are foodborne pathogens causing serious diseases, such as haemorrhagic colitis and haemolytic uraemic syndrome. Although O157:H7 STEC strains have been the most prevalent, incidences of STEC infections by several other serotypes have recently increased. O121:H19 STEC is one of these major non-O157 STECs, but systematic whole genome sequence (WGS) analyses have not yet been conducted on this STEC. Here, we performed a global WGS analysis of 638 O121:H19 strains, including 143 sequenced in this study, and a detailed comparison of 11 complete genomes, including four obtained in this study. By serotype-wide WGS analysis, we found that O121:H19 strains were divided into four lineages, including major and second major lineages (named L1 and L3, respectively), and that the locus of enterocyte effacement (LEE) encoding a type III secretion system (T3SS) was acquired by the common ancestor of O121:H19. Analyses of 11 complete genomes belonging to L1 or L3 revealed remarkable interlineage differences in the prophage pool and prophage-encoded T3SS effector repertoire, independent acquisition of virulence plasmids by the two lineages, and high conservation in the prophage repertoire, including that for Stx2a phages in lineage L1. Further sequence determination of complete Stx2a phage genomes of 49 strains confirmed that Stx2a phages in lineage L1 are highly conserved short-tailed phages, while those in lineage L3 are long-tailed lambda-like phages with notable genomic diversity, suggesting that an Stx2a phage was acquired by the common ancestor of L1 and has been stably maintained. Consistent with these genomic features of Stx2a phages, most lineage L1 strains produced much higher levels of Stx2a than lineage L3 strains. Altogether, this study provides a global phylogenetic overview of O121:H19 STEC and shows the interlineage genomic differences and the highly conserved genomic features of the major lineage within this serotype of STEC.
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Affiliation(s)
- Ruriko Nishida
- Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Keiji Nakamura
- Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Itsuki Taniguchi
- Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | | | - Tadasuke Ooka
- Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | | | - Yasuhiro Gotoh
- Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takehiko Itoh
- Graduate School of Bioscience of Biotechnology, Tokyo Institute of Technology, Tokyo, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Shizuoka, Japan
| | | | - Denis Piérard
- Universitair Ziekenhuis Brussel (UZ Brussel), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Kazuko Seto
- Osaka Institute of Public Health, Osaka, Japan
| | | | | | | | - Yoshiki Etoh
- Fukuoka Institute of Health and Environmental Sciences, Fukuoka, Japan
| | | | | | | | - Mitsuhiro Kameyama
- Yamaguchi Prefectural Institute of Public Health and Environment, Yamaguchi, Japan
| | - Yuko Matsumoto
- Yokohama City Institute of Public Health, Kanagawa, Japan
| | - Yuhki Nagai
- Mie Prefectural Institute of Public Health and Environmental Sciences, Mie, Japan
| | - Jun Kawase
- Shimane Prefectural Institute of Public Health and Environmental Science, Shimane, Japan
| | - Eiji Yokoyama
- Chiba Prefectural Institute of Public Health, Chiba, Japan
| | | | - Takayuki Shiomoto
- Ishikawa Prefectural Institute of Public Health and Environmental Science, Ishikawa, Japan
| | - Kenichi Lee
- National Institute of Infectious Diseases, Tokyo, Japan
| | - Dongchon Kang
- Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Koichi Akashi
- Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | | | - Sunao Iyoda
- National Institute of Infectious Diseases, Tokyo, Japan
| | - Tetsuya Hayashi
- Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- *Correspondence: Tetsuya Hayashi,
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24
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Nakae K, Ooka T, Murakami K, Hara-Kudo Y, Imuta N, Gotoh Y, Ogura Y, Hayashi T, Okamoto Y, Nishi J. Diversification of Escherichia albertii H-Antigens and Development of H-Genotyping PCR. Front Microbiol 2021; 12:737979. [PMID: 34790177 PMCID: PMC8591213 DOI: 10.3389/fmicb.2021.737979] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 07/08/2021] [Accepted: 10/07/2021] [Indexed: 11/24/2022] Open
Abstract
Escherichia albertii is a recently recognized human enteropathogen that is closely related to Escherichia coli. As E. albertii sometimes causes outbreaks of gastroenteritis, rapid strain typing systems, such as the O- and H-serotyping systems widely used for E. coli, will be useful for outbreak investigation and surveillance. Although an O-genotyping system has recently been developed, the diversity of E. albertii H-antigens (flagellins) encoded by fliC genes remains to be systematically investigated, and no H-serotyping or genotyping system is currently available. Here, we analyzed the fliC genes of 243 genome-sequenced E. albertii strains and identified 73 sequence types, which were grouped into four clearly distinguishable types designated E. albertii H-genotypes 1–4 (EAHg1–EAHg4). Although there was a clear sign of intraspecies transfer of fliC genes in E. albertii, none of the four E. albertii H-genotypes (EAHgs) were closely related to any of the 53 known E. coli H-antigens, indicating the absence or rare occurrence of interspecies transfer of fliC genes between the two species. Although the analysis of more E. albertii strains will be required to confirm the low level of variation in their fliC genes, this finding suggests that E. albertii may exist in limited natural hosts or environments and/or that the flagella of E. albertii may function in a limited stage(s) in their life cycle. Based on the fliC sequences of the four EAHgs, we developed a multiplex PCR-based H-genotyping system for E. albertii (EAH-genotyping PCR), which will be useful for epidemiological studies of E. albertii infections.
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Affiliation(s)
- Koji Nakae
- Department of Pediatrics, Kagoshima University Hospital, Kagoshima, Japan
| | - Tadasuke Ooka
- Department of Microbiology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Koichi Murakami
- Center for Emergency Preparedness and Response, National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Naoko Imuta
- Department of Microbiology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshitoshi Ogura
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan.,Department of Infectious Medicine, Division of Microbiology, Kurume University School of Medicine, Kurume, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yasuhiro Okamoto
- Department of Pediatrics, Kagoshima University Hospital, Kagoshima, Japan
| | - Junichiro Nishi
- Department of Microbiology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
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25
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Song I, Gotoh Y, Ogura Y, Hayashi T, Fukiya S, Yokota A. Comparative Genomic and Physiological Analysis against Clostridium scindens Reveals Eubacterium sp. c-25 as an Atypical Deoxycholic Acid Producer of the Human Gut Microbiota. Microorganisms 2021; 9:microorganisms9112254. [PMID: 34835380 PMCID: PMC8623032 DOI: 10.3390/microorganisms9112254] [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: 09/24/2021] [Revised: 10/22/2021] [Accepted: 10/22/2021] [Indexed: 12/27/2022] Open
Abstract
The human gut houses bile acid 7α-dehydroxylating bacteria that produce secondary bile acids such as deoxycholic acid (DCA) from host-derived bile acids through enzymes encoded by the bai operon. While recent metagenomic studies suggest that these bacteria are highly diverse and abundant, very few DCA producers have been identified. Here, we investigated the physiology and determined the complete genome sequence of Eubacterium sp. c-25, a DCA producer that was isolated from human feces in the 1980s. Culture experiments showed a preference for neutral to slightly alkaline pH in both growth and DCA production. Genomic analyses revealed that c-25 is phylogenetically distinct from known DCA producers and possesses a multi-cluster arrangement of predicted bile-acid inducible (bai) genes that is considerably different from the typical bai operon structure. This arrangement is also found in other intestinal bacterial species, possibly indicative of unconfirmed 7α-dehydroxylation capabilities. Functionality of the predicted bai genes was supported by the induced expression of baiB, baiCD, and baiH in the presence of cholic acid substrate. Taken together, Eubacterium sp. c-25 is an atypical DCA producer with a novel bai gene cluster structure that may represent an unexplored genotype of DCA producers in the human gut.
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Affiliation(s)
- Isaiah Song
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan; (I.S.); (A.Y.)
| | - Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan; (Y.G.); (T.H.)
| | - Yoshitoshi Ogura
- Department of Infectious Medicine, Kurume University School of Medicine, Kurume 830-0011, Japan;
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan; (Y.G.); (T.H.)
| | - Satoru Fukiya
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan; (I.S.); (A.Y.)
- Correspondence: ; Tel.: +81-11-706-2501
| | - Atsushi Yokota
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan; (I.S.); (A.Y.)
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26
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Takano SI, Gotoh Y, Hayashi T. "Candidatus Mesenet longicola": Novel Endosymbionts of Brontispa longissima that Induce Cytoplasmic Incompatibility. Microb Ecol 2021; 82:512-522. [PMID: 33454808 DOI: 10.1007/s00248-021-01686-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 01/06/2021] [Indexed: 06/12/2023]
Abstract
Intracellular bacteria that are mainly transmitted maternally affect their arthropod hosts' biology in various ways. One such effect is known as cytoplasmic incompatibility (CI), and three bacterial species are known to induce CI: Wolbachia, Cardinium hertigii, and a recently found alphaproteobacterial symbiont. To clarify the taxonomic status and provide the foundation for future studies to reveal CI mechanisms and other phenotypes, we investigated genetic and morphological properties of the third CI inducer that we have previously reported inducing CI in the coconut beetle Brontispa longissima. The draft genome of the bacteria was obtained from the oocytes of two isofemale lines of B. longissima infected with the bacteria: one from Japan (GL2) and the other from Vietnam (L5). Genome features of the symbionts (sGL2 and sL5) were highly similar, showing 1.3 Mb in size, 32.1% GC content, and 99.83% average nucleotide sequence. A phylogenetic study based on 43 universal and single-copy phylogenetic marker genes indicates that they formed a distinct clade in the family Anaplasmataceae. 16S rRNA gene sequences indicate that they are different from the closest known relatives, at least at the genus level. Therefore, we propose a new genus and species, "Candidatus Mesenet longicola", for the symbionts of B. longissima. Morphological analyses showed that Ca. M. longicola is an intracellular bacterium that is ellipsoidal to rod-shaped and 0.94 ± 0.26 μm (mean ± SD) in length, and accumulated in the anterior part of the oocyte. Candidates for the Ca. M. longicola genes responsible for CI induction are also described.
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Affiliation(s)
- Shun-Ichiro Takano
- Faculty of Agriculture, Kyushu University, 744 Motooka, Fukuoka, 819-0395, Japan.
| | - Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
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27
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Nakamura K, Tokuda C, Arimitsu H, Etoh Y, Hamasaki M, Deguchi Y, Taniguchi I, Gotoh Y, Ogura Y, Hayashi T. Development of a homogeneous time-resolved FRET (HTRF) assay for the quantification of Shiga toxin 2 produced by E. coli. PeerJ 2021; 9:e11871. [PMID: 34395095 PMCID: PMC8325423 DOI: 10.7717/peerj.11871] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/06/2021] [Indexed: 11/20/2022] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) is a major intestinal pathogen and causes serious gastrointestinal illness, which includes diarrhea, hemorrhagic colitis, and life-threatening hemolytic uremic syndrome. The major virulence factors of STEC are Shiga toxins (Stx1 and Stx2), which belong to the AB-type toxin family. Among several subtypes of Stx1 and Stx2, the production of Stx2a is thought to be a risk factor for severe STEC infections, but Stx2a production levels vary markedly between STEC strains, even strains with the same serotype. Therefore, quantitative analyses of Stx2 production by STEC strains are important to understand the virulence potential of specific lineages or sublineages. In this study, we developed a novel Stx2 quantification method by utilizing homogeneous time-resolved fluorescence resonance energy transfer (HTRF) technology. To determine suitable “sandwich” assay conditions, we tested 6 combinations of fluorescence-labeled monoclonal antibodies (mAbs) specific to Stx2 and compared the HTRF signal intensities obtained at various incubation times. Through this analysis, we selected the most suitable mAb pair, one recognizing the A subunit and the other recognizing the B subunit, thus together detecting Stx holotoxins. The optimal incubation time was also determined (18 h). Then, we optimized the concentrations of the two mAbs based on the range for linearity. The established HTRF assay detected 0.5 ng/ml of the highly purified recombinant Stx2a and Stx2e proteins and the working range was 1–64 ng/ml for both Stx2a and Stx2e. Through the quantification analysis of Stx proteins in STEC cell lysates, we confirmed that other Stx2 subtypes (Stx2b, Stx2c, Stx2d and Stx2g) can also be quantified at a certain level of accuracy, while this assay system does not detect Stx2f, which is highly divergent in sequence from other Stx2 subtypes, and Stx1. As the HTRF protocol we established is simple, this assay system should prove useful for the quantitative analysis of Stx2 production levels of a large number of STEC strains.
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Affiliation(s)
- Keiji Nakamura
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | | | - Hideyuki Arimitsu
- School of Human Science and Environment, University of Hyogo, Himeji, Japan
| | - Yoshiki Etoh
- Fukuoka Institute of Health and Environmental Sciences, Dazaifu, Japan
| | | | - Yuichiro Deguchi
- Production Medicine Center, Agricultural Mutual Aid Association in Miyazaki Prefecture, Koyugun-Shintomicho, Japan
| | - Itsuki Taniguchi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshitoshi Ogura
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
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28
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Emoto T, Hayashi T, Tabata T, Yamashita T, Watanabe H, Takahashi T, Gotoh Y, Kami K, Yoshida N, Saito Y, Tanaka H, Matsumoto K, Hayashi T, Yamada T, Hirata KI. Metagenomic analysis of gut microbiota reveals its role in trimethylamine metabolism in heart failure. Int J Cardiol 2021; 338:138-142. [PMID: 34102245 DOI: 10.1016/j.ijcard.2021.06.003] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 04/13/2021] [Accepted: 06/02/2021] [Indexed: 02/08/2023]
Abstract
BACKGROUND We had previously reported an increase in trimethylamine N-oxide (TMAO) levels in patients with both compensated and decompensated heart failure (HF) and alteration in gut microbiota composition using 16S rRNA gene amplicon analysis. Although a metagenome-wide analysis showed that choline-TMA lyase levels increased in HF patients, which TMA generation pathway from choline, carnitine, or betaine contributes to the increase in TMAO levels in HF needs to be elucidated. METHODS We conducted a metagenome-wide shotgun sequencing analysis of gut microbiota and measured the TMAO levels in plasma of 22 HF patients during the compensated phase and 11 age-, sex-, and comorbidity-matched control subjects, whose gut microbiota compositions were reported in a previous 16S rRNA-based analysis. RESULTS The abundance of cntA/B was positively correlated with TMAO, especially in HF patients, whereas that of cutC/D or betaine reductase was not correlated either in controls or HF patients. The abundance of cntA/B was mainly derived from the genera Escherichia and Klebsiella either in controls or HF patients. CONCLUSION TMAO levels in plasma depend on the abundance of cntA/B in HF. Although it is difficult to exclude the involvement of confounding factors, microbial dysbiosis connecting the abundance of cntA/B in the gut and the increase of TMAO in plasma can be a therapeutic target for HF.
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Affiliation(s)
- Takuo Emoto
- Division of Cardiovascular Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Tomohiro Hayashi
- Division of Cardiovascular Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Tokiko Tabata
- Division of Cardiovascular Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Tomoya Yamashita
- Division of Cardiovascular Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan.
| | - Hikaru Watanabe
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Tomoya Takahashi
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | | | - Naofumi Yoshida
- Division of Cardiovascular Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Yoshihiro Saito
- Division of Cardiovascular Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Hidekazu Tanaka
- Division of Cardiovascular Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Kensuke Matsumoto
- Division of Cardiovascular Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takuji Yamada
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Ken-Ichi Hirata
- Division of Cardiovascular Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
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29
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Kajitani R, Yoshimura D, Ogura Y, Gotoh Y, Hayashi T, Itoh T. Platanus_B: an accurate de novo assembler for bacterial genomes using an iterative error-removal process. DNA Res 2021; 27:5870828. [PMID: 32658266 PMCID: PMC7433917 DOI: 10.1093/dnares/dsaa014] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [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: 04/06/2020] [Accepted: 07/07/2020] [Indexed: 11/14/2022] Open
Abstract
De novo assembly of short DNA reads remains an essential technology, especially for large-scale projects and high-resolution variant analyses in epidemiology. However, the existing tools often lack sufficient accuracy required to compare closely related strains. To facilitate such studies on bacterial genomes, we developed Platanus_B, a de novo assembler that employs iterations of multiple error-removal algorithms. The benchmarks demonstrated the superior accuracy and high contiguity of Platanus_B, in addition to its ability to enhance the hybrid assembly of both short and nanopore long reads. Although the hybrid strategies for short and long reads were effective in achieving near full-length genomes, we found that short-read-only assemblies generated with Platanus_B were sufficient to obtain ≥90% of exact coding sequences in most cases. In addition, while nanopore long-read-only assemblies lacked fine-scale accuracies, inclusion of short reads was effective in improving the accuracies. Platanus_B can, therefore, be used for comprehensive genomic surveillances of bacterial pathogens and high-resolution phylogenomic analyses of a wide range of bacteria.
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Affiliation(s)
- Rei Kajitani
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Dai Yoshimura
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Yoshitoshi Ogura
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Fukuoka 830-0011, Japan.,Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Takehiko Itoh
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo 152-8550, Japan
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30
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Nakamura K, Ogura Y, Gotoh Y, Hayashi T. Prophages integrating into prophages: A mechanism to accumulate type III secretion effector genes and duplicate Shiga toxin-encoding prophages in Escherichia coli. PLoS Pathog 2021; 17:e1009073. [PMID: 33914852 PMCID: PMC8112680 DOI: 10.1371/journal.ppat.1009073] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 05/11/2021] [Accepted: 04/14/2021] [Indexed: 11/20/2022] Open
Abstract
Bacteriophages (or phages) play major roles in the evolution of bacterial pathogens via horizontal gene transfer. Multiple phages are often integrated in a host chromosome as prophages, not only carrying various novel virulence-related genetic determinants into host bacteria but also providing various possibilities for prophage-prophage interactions in bacterial cells. In particular, Escherichia coli strains such as Shiga toxin (Stx)-producing E. coli (STEC) and enteropathogenic E. coli (EPEC) strains have acquired more than 10 prophages (up to 21 prophages), many of which encode type III secretion system (T3SS) effector gene clusters. In these strains, some prophages are present at a single locus in tandem, which is usually interpreted as the integration of phages that use the same attachment (att) sequence. Here, we present phages integrating into T3SS effector gene cluster-associated loci in prophages, which are widely distributed in STEC and EPEC. Some of the phages integrated into prophages are Stx-encoding phages (Stx phages) and have induced the duplication of Stx phages in a single cell. The identified attB sequences in prophage genomes are apparently derived from host chromosomes. In addition, two or three different attB sequences are present in some prophages, which results in the generation of prophage clusters in various complex configurations. These phages integrating into prophages represent a medically and biologically important type of inter-phage interaction that promotes the accumulation of T3SS effector genes in STEC and EPEC, the duplication of Stx phages in STEC, and the conversion of EPEC to STEC and that may be distributed in other types of E. coli strains as well as other prophage-rich bacterial species. Multiple prophages are often integrated in a bacterial host chromosome and some are present at a single locus in tandem. The most striking examples are Shiga toxin (Stx)-producing and enteropathogenic Escherichia coli (STEC and EPEC) strains, which usually contain more than 10 prophages (up to 21). Many of them encode a cluster of type III secretion system (T3SS) effector genes, contributing the acquisition of a large number of effectors (>30) by STEC and EPEC. Here, we describe prophages integrating into T3SS effector gene cluster-associated loci in prophages, which are widely distributed in STEC and EPEC. Two or three different attachment sequences derived from host chromosomes are present in some prophages, generating prophage clusters in various complex configurations. Of note, some of such phages integrating into prophages are Stx-encoding phages (Stx phages) and have induced the duplication of Stx phages. Thus, “prophage-in-prophage” represents an important inter-phage interaction as they can promote not only the accumulation of T3SS effectors in STEC and EPEC but also the duplication of Stx phages and the conversion of EPEC to STEC.
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Affiliation(s)
- Keiji Nakamura
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshitoshi Ogura
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- * E-mail:
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31
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Aihara M, Nishida R, Akimoto M, Gotoh Y, Kiyosuke M, Uchiumi T, Nishioka M, Matsushima Y, Hayashi T, Kang D. Within-host evolution of a Klebsiella pneumoniae clone: selected mutations associated with the alteration of outer membrane protein expression conferred multidrug resistance. J Antimicrob Chemother 2021; 76:362-369. [PMID: 33099622 DOI: 10.1093/jac/dkaa439] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 09/23/2020] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND A patient repeatedly developed bacteraemia despite the continuous use of antibiotics. We obtained two Klebsiella pneumoniae isolates from the patient's blood on Days 72 and 105 after hospitalization. Each of the two isolates belonged to ST45, but while the first isolate was susceptible to most antibiotics, the second one was resistant to multiple drugs including carbapenems. OBJECTIVES To identify the genetic differences between the two isolates and uncover alterations formed by the within-host bacterial evolution leading to the antimicrobial resistance. METHODS Whole-genome comparison of the two isolates was carried out to identify their genetic differences. We then profiled their outer membrane proteins related to membrane permeability to drugs. To characterize a ramR gene mutation found in the MDR isolate, its WT and mutant genes were cloned and expressed in the MDR isolate. RESULTS The two isolates showed only three genomic differences, located in mdoH, ramR and upstream of ompK36. In the MDR isolate, a single nucleotide substitution in the ompK36 upstream region attenuated OmpK36 expression. A single amino acid residue insertion in RamR in the MDR isolate impaired its function, leading to the down-regulation of OmpK35 and the subsequent up-regulation of the AcrAB-TolC transporter, which may contribute to the MDR. CONCLUSIONS We identified very limited genomic changes in the second K. pneumoniae clone during within-host evolution, but two of the three identified mutations conferred the MDR phenotype on the clone by modulating drug permeability.
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Affiliation(s)
- Masamune Aihara
- Department of Health Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan.,Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Ruriko Nishida
- Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Hospital, Fukuoka 812-8582, Japan.,Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan.,Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Masaru Akimoto
- Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Hospital, Fukuoka 812-8582, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Makiko Kiyosuke
- Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Hospital, Fukuoka 812-8582, Japan
| | - Takeshi Uchiumi
- Department of Health Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan.,Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Mitsuaki Nishioka
- Division of Laboratory, Yamaguchi University Hospital, Ube 755-8505, Japan
| | - Yuichi Matsushima
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Dongchon Kang
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan.,Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Hospital, Fukuoka 812-8582, Japan
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32
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Wada N, Yuasa H, Kajitani R, Gotoh Y, Ogura Y, Yoshimura D, Toyoda A, Tang SL, Higashimura Y, Sweatman H, Forsman Z, Bronstein O, Eyal G, Thongtham N, Itoh T, Hayashi T, Yasuda N. A ubiquitous subcuticular bacterial symbiont of a coral predator, the crown-of-thorns starfish, in the Indo-Pacific. Microbiome 2020; 8:123. [PMID: 32831146 PMCID: PMC7444263 DOI: 10.1186/s40168-020-00880-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Accepted: 06/08/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Population outbreaks of the crown-of-thorns starfish (Acanthaster planci sensu lato; COTS), a primary predator of reef-building corals in the Indo-Pacific Ocean, are a major threat to coral reefs. While biological and ecological knowledge of COTS has been accumulating since the 1960s, little is known about its associated bacteria. The aim of this study was to provide fundamental information on the dominant COTS-associated bacteria through a multifaceted molecular approach. METHODS A total of 205 COTS individuals from 17 locations throughout the Indo-Pacific Ocean were examined for the presence of COTS-associated bacteria. We conducted 16S rRNA metabarcoding of COTS to determine the bacterial profiles of different parts of the body and generated a full-length 16S rRNA gene sequence from a single dominant bacterium, which we designated COTS27. We performed phylogenetic analysis to determine the taxonomy, screening of COTS27 across the Indo-Pacific, FISH to visualize it within the COTS tissues, and reconstruction of the bacterial genome from the hologenome sequence data. RESULTS We discovered that a single bacterium exists at high densities in the subcuticular space in COTS forming a biofilm-like structure between the cuticle and the epidermis. COTS27 belongs to a clade that presumably represents a distinct order (so-called marine spirochetes) in the phylum Spirochaetes and is universally present in COTS throughout the Indo-Pacific Ocean. The reconstructed genome of COTS27 includes some genetic traits that are probably linked to adaptation to marine environments and evolution as an extracellular endosymbiont in subcuticular spaces. CONCLUSIONS COTS27 can be found in three allopatric COTS species, ranging from the northern Red Sea to the Pacific, implying that the symbiotic relationship arose before the speciation events (approximately 2 million years ago). The universal association of COTS27 with COTS and nearly mono-specific association at least with the Indo-Pacific COTS provides a useful model system for studying symbiont-host interactions in marine invertebrates and may have applications for coral reef conservation. Video Abstract.
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Affiliation(s)
- Naohisa Wada
- Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadai-Nishi, Miyazaki, Miyazaki, 889-2192, Japan
- Biodiversity Research Center, Academia Sinica, No.128, Sec 2, Academia Rd, Nangang, Taipei, 11529, Taiwan
| | - Hideaki Yuasa
- School of Life Science and Technology, Department of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Rei Kajitani
- School of Life Science and Technology, Department of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, 3-1-1 Maidashi Higashi-ku, Fukuoka, 812-8582, Japan
| | - Yoshitoshi Ogura
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, 3-1-1 Maidashi Higashi-ku, Fukuoka, 812-8582, Japan
| | - Dai Yoshimura
- School of Life Science and Technology, Department of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Atsushi Toyoda
- Center for Information Biology, National Institute of Genetics, Yata 1111, Mishima, Shizuoka, 411-8540, Japan
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, No.128, Sec 2, Academia Rd, Nangang, Taipei, 11529, Taiwan
| | - Yukihiro Higashimura
- Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadai-Nishi, Miyazaki, Miyazaki, 889-2192, Japan
| | - Hugh Sweatman
- Australian Institute of Marine Science, PMB No.3, Townsville, QLD, 4810, Australia
| | - Zac Forsman
- Hawai'i Institute of Marine Biology, School of Ocean & Earth Sciences & Technology, University of Hawai'i at Mānoa, Coconut Island, Kāne'ohe, HI, USA
| | - Omri Bronstein
- George S. Wise Faculty of Life Sciences, School of Zoology, Tel Aviv University, 6997801, Tel Aviv, Israel
- The Steinhardt Museum of Natural History, Israel National Center for Biodiversity Studies, Tel-Aviv University, Tel-Aviv, 6997801, Israel
| | - Gal Eyal
- ARC Centre of Excellence for Coral Reef Studies, School of Biological Sciences, The University of Queensland, St. Lucia, QLD, 4072, Australia
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, 5290002, Ramat Gan, Israel
| | | | - Takehiko Itoh
- School of Life Science and Technology, Department of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, 3-1-1 Maidashi Higashi-ku, Fukuoka, 812-8582, Japan.
| | - Nina Yasuda
- Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadai-Nishi, Miyazaki, Miyazaki, 889-2192, Japan.
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Ooka T, Seto K, Ogura Y, Nakamura K, Iguchi A, Gotoh Y, Honda M, Etoh Y, Ikeda T, Sugitani W, Konno T, Kawano K, Imuta N, Yoshiie K, Hara-Kudo Y, Murakami K, Hayashi T, Nishi J. O-antigen biosynthesis gene clusters of Escherichia albertii: their diversity and similarity to Escherichia coli gene clusters and the development of an O-genotyping method. Microb Genom 2020; 5. [PMID: 31738701 PMCID: PMC6927306 DOI: 10.1099/mgen.0.000314] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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] [Indexed: 12/31/2022] Open
Abstract
Escherichia albertii is a recently recognized human enteropathogen that is closely related to Escherichia coli. In many Gram-negative bacteria, including E. coli, O-antigen variation has long been used for the serotyping of strains. In E. albertii, while eight O-serotypes unique to this species have been identified, some strains have been shown to exhibit genetic or serological similarity to known E. coli/Shigella O-serotypes. However, the diversity of O-serotypes and O-antigen biosynthesis gene clusters (O-AGCs) of E. albertii remains to be systematically investigated. Here, we analysed the O-AGCs of 65 E. albertii strains and identified 40 E. albertii O-genotypes (EAOgs) (named EAOg1–EAOg40). Analyses of the 40 EAOgs revealed that as many as 20 EAOgs exhibited significant genetic and serological similarity to the O-AGCs of known E. coli/Shigella O-serotypes, and provided evidence for the inter-species horizontal gene transfer of O-AGCs between E. albertii and E. coli. Based on the sequence variation in the wzx gene among the 40 EAOgs, we developed a multiplex PCR-based O-genotyping system for E. albertii (EAO-genotyping PCR) and verified its usefulness by genotyping 278 E. albertii strains from various sources. Although 225 (80.9 %) of the 278 strains could be genotyped, 51 were not assigned to any of the 40 EAOgs, indicating that further analyses are required to better understand the diversity of O-AGCs in E. albertii and improve the EAO-genotyping PCR method. A phylogenetic view of E. albertii strains sequenced so far is also presented with the distribution of the 40 EAOgs, which provided multiple examples for the intra-species horizontal transfer of O-AGCs in E. albertii.
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Affiliation(s)
- Tadasuke Ooka
- Department of Microbiology, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan
| | - Kazuko Seto
- Osaka Institute of Public Health, 1-3-69 Nakamichi, Higasinari-ku, Osaka 537-0025, Japan
| | - Yoshitoshi Ogura
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Keiji Nakamura
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Atsushi Iguchi
- Department of Animal and Grassland Sciences, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuen-kibanadai-nishi, Miyazaki 889-2192, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Mikiko Honda
- Fukuoka City Institute of Hygiene and the Environment, 2-1-34 Jigyohama, Chuo-ku, Fukuoka 810-0065, Japan
| | - Yoshiki Etoh
- Fukuoka Institute of Health and Environmental Sciences, 39 Mukaizano, Dazaifu, Fukuoka 818-0135, Japan
| | - Tetsuya Ikeda
- Hokkaido Institute of Public Health, Kita-19, Nishi-12, Kita-ku, Sapporo 060-0819, Japan
| | - Wakana Sugitani
- Kumamoto City Environmental Research Institute, 404-1, Ezumachi Tokorojima, Higashi-ku, Kumamoto 862-0946, Japan
| | - Takayuki Konno
- Akita Prefectural Research Center for Public Health and Environment, 6-6 Senshu Kubota-machi, Akita 010-0874, Japan
| | - Kimiko Kawano
- Miyazaki Prefectural Institute for Public Health and Environment, 2-3-2 Gakuen-kibanadai-nishi, Miyazaki 889-2155, Japan
| | - Naoko Imuta
- Department of Microbiology, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan
| | - Kiyotaka Yoshiie
- Department of Microbiology, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan
| | - Yukiko Hara-Kudo
- National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki-ku, Kawasaki 210-9501, Japan
| | - Koichi Murakami
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashi-murayama, Tokyo 208-0011, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Junichiro Nishi
- Department of Microbiology, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan
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Gotoh Y, Chiba K, Sekiyama Y, Okada K, Hayashi T, Misawa N. 16S rRNA-based amplicon analysis of changes in the bacterial population in the lesions of papillomatous digital dermatitis in dairy cattle after topical treatment with allyl isothiocyanate. Microbiol Immunol 2020; 64:416-423. [PMID: 32190917 DOI: 10.1111/1348-0421.12786] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 01/28/2020] [Revised: 03/05/2020] [Accepted: 03/15/2020] [Indexed: 12/20/2022]
Abstract
Papillomatous digital dermatitis (PDD) is a foot disease causing lameness in dairy cattle. It is regarded as a polymicrobial infection, although its etiology is not fully understood. PDD is treated by the topical or systemic administration of antibiotics such as lincomycin (LCM); however, the milk of the cows cannot be marketed during the treatment and withdrawal period due to the residual antibiotics in milk. Allyl isothiocyanate (AITC), an extract of Wasabia japonica (known as wasabi or Japanese horseradish) widely employed as a food additive, can be used as an alternative antimicrobial agent that overcomes this problem. We previously showed that AITC is as effective as LCM in PDD treatment. Here, using the samples obtained in the previous clinical study, we analyzed changes in the bacterial population in the PDD-associated microbiota after AITC treatment and compared those with that following LCM treatment by 16S ribosomal RNA (rRNA)-based amplicon analysis. Both treatments induced major changes in the bacterial population, and Treponema species, which have been regarded as the major causative agents of PDD, were efficiently eliminated by both agents. However, the AITC-treated samples exhibited higher diversity compared with pretreatment samples, but this trend was not observed for LCM treatment, probably reflecting different antibacterial activities of the two agents. Importantly, this analysis detected population changes before morphological changes in PDD lesions (clinical signs of healing) became evident, indicating that 16S rRNA-based amplicon analysis represents an efficient strategy for analyzing and monitoring the treatment efficiency of PDD as well as other polymicrobial diseases.
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Affiliation(s)
- Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kanako Chiba
- Laboratory of Food Animal Clinical Science, Cooperative Department of Veterinary Medicine, Faculty of Agriculture, Iwate University, Iwate, Japan
| | - Yasushi Sekiyama
- Sales and Market Development Group Division Ⅱ, Mitsubishi-Chemical Foods Corporation, Tokyo, Chiyoda-ku, Japan.,University Research Administration Center, Osaka City University, Osaka, Japan
| | - Keiji Okada
- Laboratory of Food Animal Clinical Science, Cooperative Department of Veterinary Medicine, Faculty of Agriculture, Iwate University, Iwate, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Naoaki Misawa
- Laboratory of Veterinary Public Health, Department of Veterinary Medical Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
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35
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Sato MP, Ogura Y, Nakamura K, Nishida R, Gotoh Y, Hayashi M, Hisatsune J, Sugai M, Takehiko I, Hayashi T. Comparison of the sequencing bias of currently available library preparation kits for Illumina sequencing of bacterial genomes and metagenomes. DNA Res 2020; 26:391-398. [PMID: 31364694 PMCID: PMC6796507 DOI: 10.1093/dnares/dsz017] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [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: 04/05/2019] [Accepted: 07/17/2019] [Indexed: 01/23/2023] Open
Abstract
In bacterial genome and metagenome sequencing, Illumina sequencers are most frequently used due to their high throughput capacity, and multiple library preparation kits have been developed for Illumina platforms. Here, we systematically analysed and compared the sequencing bias generated by currently available library preparation kits for Illumina sequencing. Our analyses revealed that a strong sequencing bias is introduced in low-GC regions by the Nextera XT kit. The level of bias introduced is dependent on the level of GC content; stronger bias is generated as the GC content decreases. Other analysed kits did not introduce this strong sequencing bias. The GC content-associated sequencing bias introduced by Nextera XT was more remarkable in metagenome sequencing of a mock bacterial community and seriously affected estimation of the relative abundance of low-GC species. The results of our analyses highlight the importance of selecting proper library preparation kits according to the purposes and targets of sequencing, particularly in metagenome sequencing, where a wide range of microbial species with various degrees of GC content is present. Our data also indicate that special attention should be paid to which library preparation kit was used when analysing and interpreting publicly available metagenomic data.
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Affiliation(s)
- Mitsuhiko P Sato
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Fukuoka, Japan
| | - Yoshitoshi Ogura
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Fukuoka, Japan
| | - Keiji Nakamura
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Fukuoka, Japan
| | - Ruriko Nishida
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Fukuoka, Japan.,Department of Medicine and Biosystemic Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Fukuoka, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Fukuoka, Japan
| | - Masahiro Hayashi
- Division of Anaerobe Research, Life Science Research Center, Gifu University, Gifu, Gifu, Japan.,Center for Conservation of Microbial Genetic Resource, Gifu University, Gifu, Gifu, Japan
| | - Junzo Hisatsune
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Hiroshima, Japan.,Department of Bacteriology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Hiroshima, Japan.,Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Motoyuki Sugai
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Hiroshima, Japan.,Department of Bacteriology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Hiroshima, Japan.,Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Itoh Takehiko
- Department of Biological Information, Tokyo Institute of Technology, Tokyo, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Fukuoka, Japan
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Ikeda T, Shinagawa T, Ito T, Ohno Y, Kubo A, Nishi J, Gotoh Y, Ogura Y, Ooka T, Hayashi T. Hypoosmotic stress induces flagellar biosynthesis and swimming motility in Escherichia albertii. Commun Biol 2020; 3:87. [PMID: 32111956 PMCID: PMC7048735 DOI: 10.1038/s42003-020-0816-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [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: 09/24/2019] [Accepted: 02/10/2020] [Indexed: 11/17/2022] Open
Abstract
Bacteria use flagella as propellers to move to favorable environments. Escherichia albertii, a growing cause of foodborne illness and diarrhea, is reportedly non-motile and lacks flagella on its surface. Here, we report that 27 out of 59 E. albertii strains, collected mainly from humans and birds, showed swimming motility when cultured at low osmotic pressure. The biosynthesis of flagella in E. albertii cells was induced under ambient temperature and hypoosmotic pressure: conditions which resemble aquatic environments. Flagellar induction increased E. albertii survival in the intestinal epithelial cell culture containing gentamicin. Although genes involved in chemotaxis are not present in the E. albertii genome, the addition of glutamic acid, an amino acid known to regulate the internal cell osmolarity, augmented the proportion of swimming cells by 35-fold. These results suggest that flagellar biosynthesis and motility in E. albertii cells are controlled by their internal and external osmolarity. Ikeda et al. report that enteropathogen E. albertii, thought to be a non-motile microorganism, may form flagella and acquire swimming motility in a hypoosmotic environment and ambient temperatures. Further addition of glutamic acid, an amino acid known to regulate the internal cell osmolarity, augments the proportion of swimming cells.
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Affiliation(s)
- Tetsuya Ikeda
- Hokkaido Institute of Public Health, Kita-19, Nishi-12, Kita-ku, Sapporo, 060-0819, Japan.
| | - Toshie Shinagawa
- Regenerative Medicine Laboratory, Nozaki Tokushukai Hospital Research Institute, 2-10-50 Tanigawa, Daito, 574-0074, Japan
| | - Takuya Ito
- Hokkaido Institute of Public Health, Kita-19, Nishi-12, Kita-ku, Sapporo, 060-0819, Japan
| | - Yuta Ohno
- Hokkaido Institute of Public Health, Kita-19, Nishi-12, Kita-ku, Sapporo, 060-0819, Japan
| | - Akiko Kubo
- Hokkaido Institute of Public Health, Kita-19, Nishi-12, Kita-ku, Sapporo, 060-0819, Japan
| | - Junichiro Nishi
- Department of Microbiology, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima, 890-8544, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Yoshitoshi Ogura
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Tadasuke Ooka
- Department of Microbiology, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima, 890-8544, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
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37
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Ishimaru K, Sasaki M, Narimatsu H, Arimizu Y, Gotoh Y, Nakamura K, Hayashi T, Ogura Y. Escherichia coli O8:H8 Carrying a Novel Variant of the Heat-Labile Enterotoxin LT2 Gene Caused Outbreaks of Diarrhea. Open Forum Infect Dis 2020; 7:ofaa021. [PMID: 32016129 PMCID: PMC6988837 DOI: 10.1093/ofid/ofaa021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 09/25/2019] [Accepted: 01/11/2020] [Indexed: 01/20/2023] Open
Abstract
No outbreaks caused by Escherichia coli–producing heat-labile enterotoxin LT2 have been reported to date. Here, we revealed that the E. coli O8:H8 strains isolated from patients in 2 independent diarrhea outbreaks were negative for any known virulence determinants in routine microbiological tests, were very closely related, and carried a prophage-encoded gene for a novel LT2 variant (LT2d) and the genes for colonization factor antigen III. We also showed that LT2d has a cytotonic activity similar to LT1. These data indicate the importance of E. coli strains producing LT2d as a human pathogen.
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Affiliation(s)
- Kai Ishimaru
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Mari Sasaki
- Section in Charge of Microbiology, Oita Prefectural Institute of Health and the Environment, Oita, Japan
| | - Hiroshi Narimatsu
- Section in Charge of Microbiology, Oita Prefectural Institute of Health and the Environment, Oita, Japan
| | - Yoko Arimizu
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Keiji Nakamura
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshitoshi Ogura
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
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Nakamura K, Murase K, Sato MP, Toyoda A, Itoh T, Mainil JG, Piérard D, Yoshino S, Kimata K, Isobe J, Seto K, Etoh Y, Narimatsu H, Saito S, Yatsuyanagi J, Lee K, Iyoda S, Ohnishi M, Ooka T, Gotoh Y, Ogura Y, Hayashi T. Differential dynamics and impacts of prophages and plasmids on the pangenome and virulence factor repertoires of Shiga toxin-producing Escherichia coli O145:H28. Microb Genom 2020; 6:e000323. [PMID: 31935184 PMCID: PMC7067040 DOI: 10.1099/mgen.0.000323] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 12/09/2019] [Indexed: 12/20/2022] Open
Abstract
Phages and plasmids play important roles in bacterial evolution and diversification. Although many draft genomes have been generated, phage and plasmid genomes are usually fragmented, limiting our understanding of their dynamics. Here, we performed a systematic analysis of 239 draft genomes and 7 complete genomes of Shiga toxin (Stx)-producing Escherichia coli O145:H28, the major virulence factors of which are encoded by prophages (PPs) or plasmids. The results indicated that PPs are more stably maintained than plasmids. A set of ancestrally acquired PPs was well conserved, while various PPs, including Stx phages, were acquired by multiple sublineages. In contrast, gains and losses of a wide range of plasmids have frequently occurred across the O145:H28 lineage, and only the virulence plasmid was well conserved. The different dynamics of PPs and plasmids have differentially impacted the pangenome of O145:H28, with high proportions of PP- and plasmid-associated genes in the variably present and rare gene fractions, respectively. The dynamics of PPs and plasmids have also strongly impacted virulence gene repertoires, such as the highly variable distribution of stx genes and the high conservation of a set of type III secretion effectors, which probably represents the core effectors of O145:H28 and the genes on the virulence plasmid in the entire O145:H28 population. These results provide detailed insights into the dynamics of PPs and plasmids, and show the application of genomic analyses using a large set of draft genomes and appropriately selected complete genomes.
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Affiliation(s)
- Keiji Nakamura
- Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kazunori Murase
- Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Mitsuhiko P. Sato
- Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Atsushi Toyoda
- Center for Information Biology, National Institute of Genetics, Tokyo, Japan
| | - Takehiko Itoh
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Tokyo, Japan
| | | | | | - Shuji Yoshino
- Miyazaki Prefectural Institute for Public Health and Environment, Miyazaki, Japan
| | | | | | - Kazuko Seto
- Osaka Institute of Public Health, Osaka, Japan
| | - Yoshiki Etoh
- Fukuoka Institute of Health and Environmental Sciences, Fukuoka, Japan
| | | | - Shioko Saito
- Akita Research Center for Public Health and Environment, Akita, Japan
| | - Jun Yatsuyanagi
- Akita Research Center for Public Health and Environment, Akita, Japan
| | - Kenichi Lee
- National Institute of Infectious Diseases, Tokyo, Japan
| | - Sunao Iyoda
- National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Tadasuke Ooka
- Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Yasuhiro Gotoh
- Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshitoshi Ogura
- Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tetsuya Hayashi
- Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
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39
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Kasama K, Fujita H, Yamamoto S, Ooka T, Gotoh Y, Ogura Y, Ando S, Hayashi T. Genomic Features of Rickettsia heilongjiangensis Revealed by Intraspecies Comparison and Detailed Comparison With Rickettsia japonica. Front Microbiol 2019; 10:2787. [PMID: 31866968 PMCID: PMC6908463 DOI: 10.3389/fmicb.2019.02787] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 08/26/2019] [Accepted: 11/15/2019] [Indexed: 11/26/2022] Open
Abstract
Rickettsia heilongjiangensis is the causative agent of Far-Eastern spotted fever (FESF). In Japan, a human case of FESF was identified in Sendai in Miyagi Prefecture in 2008, and R. heilongjiangensis bacteria were isolated from Haemaphysalis concinna ticks collected in the suspected geographical area of infection. Although the intraspecies genome diversity of Rickettsia has been poorly investigated, our recent analysis revealed extremely low genomic diversity of R. japonica, the agent of Japanese spotted fever, which is a close relative of R. heilongjiangensis. In this study, to investigate the genomic diversity of R. heilongjiangensis and understand the genetic relationship between Japanese and Chinese isolates, we sequenced three isolates from H. concinna ticks collected in Sendai and one isolate from a H. concinna tick collected in Inner Mongolia, China, and performed genomic comparisons between these isolates and strain 054, the type strain isolated from a Dermacentor silvarum tick in Heilongjiang Province, China. Although the three Japanese strains were isolated in 2008, 2009, and 2012, their genome sequences were identical, indicating that H. concinna ticks carrying a single R. heilongjiangensis clone have been distributed in Sendai, Japan. Among the five R. heilongjiangensis isolates, only 81 SNPs and 13 insertion/deletion sites were identified, despite the significant differences in these isolates both geographically and temporally. A significant portion of the 81 SNPs (16/81) were found to be recombinogenic. These results indicate low genomic diversity of R. heilongjiangensis, as observed in R. japonica. We further performed a detailed genomic comparison of R. heilongjiangensis and R. japonica to accurately define conserved and species-specific genes. This analysis revealed that although notable variations were found in the genomic loci encoding RelA/SpoT family proteins and tandem repeats in major surface proteins, there was only a small difference in the gene repertoire between the two species, suggesting that SNPs and small InDels are responsible for the functional or physiological differences between the two species, if present. Through this analysis, several species-specific genomic regions that can serve as ideal PCR targets for distinguishing R. heilongjiangensis and R. japonica were also identified.
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Affiliation(s)
- Kentaro Kasama
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hiromi Fujita
- Mahara Institute of Medical Acarology, Tokushima, Japan
| | - Seigo Yamamoto
- Frontier Science Research Center, University of Miyazaki, Miyazaki, Japan
| | - Tadasuke Ooka
- Department of Microbiology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshitoshi Ogura
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Shuji Ando
- Department of Virology-I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
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Arimizu Y, Kirino Y, Sato MP, Uno K, Sato T, Gotoh Y, Auvray F, Brugere H, Oswald E, Mainil JG, Anklam KS, Döpfer D, Yoshino S, Ooka T, Tanizawa Y, Nakamura Y, Iguchi A, Morita-Ishihara T, Ohnishi M, Akashi K, Hayashi T, Ogura Y. Large-scale genome analysis of bovine commensal Escherichia coli reveals that bovine-adapted E. coli lineages are serving as evolutionary sources of the emergence of human intestinal pathogenic strains. Genome Res 2019; 29:1495-1505. [PMID: 31439690 PMCID: PMC6724679 DOI: 10.1101/gr.249268.119] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [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: 02/12/2019] [Accepted: 07/03/2019] [Indexed: 01/15/2023]
Abstract
How pathogens evolve their virulence to humans in nature is a scientific issue of great medical and biological importance. Shiga toxin (Stx)–producing Escherichia coli (STEC) and enteropathogenic E. coli (EPEC) are the major foodborne pathogens that can cause hemolytic uremic syndrome and infantile diarrhea, respectively. The locus of enterocyte effacement (LEE)–encoded type 3 secretion system (T3SS) is the major virulence determinant of EPEC and is also possessed by major STEC lineages. Cattle are thought to be the primary reservoir of STEC and EPEC. However, genome sequences of bovine commensal E. coli are limited, and the emerging process of STEC and EPEC is largely unknown. Here, we performed a large-scale genomic comparison of bovine commensal E. coli with human commensal and clinical strains, including EPEC and STEC, at a global level. The analyses identified two distinct lineages, in which bovine and human commensal strains are enriched, respectively, and revealed that STEC and EPEC strains have emerged in multiple sublineages of the bovine-associated lineage. In addition to the bovine-associated lineage-specific genes, including fimbriae, capsule, and nutrition utilization genes, specific virulence gene communities have been accumulated in stx- and LEE-positive strains, respectively, with notable overlaps of community members. Functional associations of these genes probably confer benefits to these E. coli strains in inhabiting and/or adapting to the bovine intestinal environment and drive their evolution to highly virulent human pathogens under the bovine-adapted genetic background. Our data highlight the importance of large-scale genome sequencing of animal strains in the studies of zoonotic pathogens.
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Affiliation(s)
- Yoko Arimizu
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan.,Department of Medicine and Biosystemic Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Yumi Kirino
- Laboratory of Veterinary Radiology, Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan
| | - Mitsuhiko P Sato
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Koichi Uno
- Japan Microbiological Laboratory, Sendai, Miyagi 983-0034, Japan
| | - Toshio Sato
- Japan Microbiological Laboratory, Sendai, Miyagi 983-0034, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Frédéric Auvray
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, 31300 Toulouse, France
| | - Hubert Brugere
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, 31300 Toulouse, France
| | - Eric Oswald
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, 31300 Toulouse, France.,CHU de Toulouse, Hôpital Purpan, 31300 Toulouse, France
| | - Jacques G Mainil
- Bacteriology, Department of Infectious Diseases, Faculty of Veterinary Medicine and Institute for Fundamental and Applied Research in Animal Health (FARAH), University of Liège, 4000 Liège, Belgium
| | - Kelly S Anklam
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, Wisconsin 53705, USA
| | - Dörte Döpfer
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, Wisconsin 53705, USA
| | - Shuji Yoshino
- Department of Microbiology, Miyazaki Prefectural Institute for Public Health and Environment, Miyazaki 889-2155, Japan
| | - Tadasuke Ooka
- Department of Microbiology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8520, Japan
| | - Yasuhiro Tanizawa
- Center for Information Biology, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka 411-8540, Japan
| | - Yasukazu Nakamura
- Center for Information Biology, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka 411-8540, Japan
| | - Atsushi Iguchi
- Department of Animal and Grassland Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan
| | - Tomoko Morita-Ishihara
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Koichi Akashi
- Department of Medicine and Biosystemic Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Yoshitoshi Ogura
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
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Gotoh Y, Taniguchi T, Yoshimura D, Katsura K, Saeki Y, Hirabara Y, Fukuda M, Takajo I, Tomida J, Kawamura Y, Ogura Y, Itoh T, Misawa N, Okayama A, Hayashi T. Multi-step genomic dissection of a suspected intra-hospital Helicobacter cinaedi outbreak. Microb Genom 2019; 4. [PMID: 30629483 PMCID: PMC6412056 DOI: 10.1099/mgen.0.000236] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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] [Indexed: 12/27/2022] Open
Abstract
Helicobacter cinaedi is an emerging pathogen causing bacteraemia and cellulitis. Nosocomial transmission of this microbe has been described, but detailed molecular-epidemiological analyses have not been performed. Here, we describe the results of a multi-step genome-wide phylogenetic analysis of a suspected intra-hospital outbreak of H. cinaedi that occurred in a hospital in Japan. The outbreak was recognized by the infectious control team (ICT) of the hospital as a sudden increase in H. cinaedi bacteraemia. ICT defined this outbreak case based on 16S rRNA sequence data and epidemiological information, but were unable to determine the source and route of the infections. We therefore re-investigated this case using whole-genome sequencing (WGS). We first performed a species-wide analysis using publicly available genome sequences to understand the level of genomic diversity of this under-studied species. The clusters identified were then separately analysed using the genome sequence of a representative strain in each cluster as a reference. These analyses provided a high-level phylogenetic resolution of each cluster, identified a confident set of outbreak isolates, and discriminated them from other closely related but distinct clones, which were locally circulating and invaded the hospital during the same period. By considering the epidemiological data, possible strain transmission chains were inferred, which highlighted the role of asymptomatic carriers or environmental contamination. The emergence of a subclone with increased resistance to fluoroquinolones in the outbreak was also recognized. Our results demonstrate the impact of the use of a closely related genome as a reference to maximize the power of WGS.
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Affiliation(s)
- Yasuhiro Gotoh
- 1Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan.,2Previous address: Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Takako Taniguchi
- 3Laboratory of Veterinary Public Health, Department of Veterinary Medical Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Dai Yoshimura
- 4Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Tokyo, Japan
| | - Keisuke Katsura
- 5Frontier Science Research Center, University of Miyazaki, Miyazaki, Japan
| | - Yuji Saeki
- 6Center for Infection Control, University of Miyazaki Hospital, Miyazaki, Japan
| | - Yasutoshi Hirabara
- 6Center for Infection Control, University of Miyazaki Hospital, Miyazaki, Japan
| | - Mayumi Fukuda
- 6Center for Infection Control, University of Miyazaki Hospital, Miyazaki, Japan
| | - Ichiro Takajo
- 6Center for Infection Control, University of Miyazaki Hospital, Miyazaki, Japan
| | - Junko Tomida
- 7Department of Microbiology, School of Pharmacy, Aichi Gakuin University, Nagoya, Japan
| | - Yoshiaki Kawamura
- 7Department of Microbiology, School of Pharmacy, Aichi Gakuin University, Nagoya, Japan
| | - Yoshitoshi Ogura
- 1Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan.,2Previous address: Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Takehiko Itoh
- 4Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Tokyo, Japan
| | - Naoaki Misawa
- 3Laboratory of Veterinary Public Health, Department of Veterinary Medical Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan.,8Faculty of Agriculture, University of Miyazaki Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
| | - Akihiko Okayama
- 6Center for Infection Control, University of Miyazaki Hospital, Miyazaki, Japan.,9Department of Rheumatology, Infectious Diseases and Laboratory Medicine, University of Miyazaki, Miyazaki, Japan
| | - Tetsuya Hayashi
- 1Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan.,2Previous address: Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
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42
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Li Y, Endo H, Gotoh Y, Watai H, Ogawa N, Blanc-Mathieu R, Yoshida T, Ogata H. The Earth Is Small for "Leviathans": Long Distance Dispersal of Giant Viruses across Aquatic Environments. Microbes Environ 2019; 34:334-339. [PMID: 31378760 PMCID: PMC6759346 DOI: 10.1264/jsme2.me19037] [Citation(s) in RCA: 10] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Giant viruses of ‘Megaviridae’ have the ability to widely disperse around the globe. We herein examined ‘Megaviridae’ communities in four distinct aquatic environments (coastal and offshore seawater, brackish water, and hot spring freshwater), which are distantly located from each other (between 74 and 1,765 km), using a meta-barcoding method. We identified between 593 and 3,627 OTUs in each sample. Some OTUs were detected in all five samples tested as well as in many of the Tara Oceans metagenomes, suggesting the existence of viruses of this family in a wide range of habitats and the ability to circulate on the planet.
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Affiliation(s)
- Yanze Li
- Institute for Chemical Research, Kyoto University
| | - Hisashi Endo
- Institute for Chemical Research, Kyoto University
| | - Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University
| | | | - Nana Ogawa
- Graduate School of Agriculture, Kyoto University
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Ogura Y, Seto K, Morimoto Y, Nakamura K, Sato MP, Gotoh Y, Itoh T, Toyoda A, Ohnishi M, Hayashi T. Genomic Characterization of β-Glucuronidase-Positive Escherichia coli O157:H7 Producing Stx2a. Emerg Infect Dis 2019; 24:2219-2227. [PMID: 30457544 PMCID: PMC6256406 DOI: 10.3201/eid2412.180404] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Among Shiga toxin (Stx)–producing Escherichia coli (STEC) O157:H7 strains, those producing Stx2a cause more severe diseases. Atypical STEC O157:H7 strains showing a β-glucuronidase–positive phenotype (GP STEC O157:H7) have rarely been isolated from humans, mostly from persons with asymptomatic or mild infections; Stx2a-producing strains have not been reported. We isolated, from a patient with bloody diarrhea, a GP STEC O157:H7 strain (PV15-279) that produces Stx2a in addition to Stx1a and Stx2c. Genomic comparison with other STEC O157 strains revealed that PV15-279 recently emerged from the stx1a/stx2c-positive GP STEC O157:H7 clone circulating in Japan. Major virulence genes are shared between typical (β-glucuronidase–negative) and GP STEC O157:H7 strains, and the Stx2-producing ability of PV15-279 is comparable to that of typical STEC O157:H7 strains; therefore, PV15-279 presents a virulence potential similar to that of typical STEC O157:H7. This study reveals the importance of GP O157:H7 as a source of highly pathogenic STEC clones.
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Yoshimura D, Kajitani R, Gotoh Y, Katahira K, Okuno M, Ogura Y, Hayashi T, Itoh T. Evaluation of SNP calling methods for closely related bacterial isolates and a novel high-accuracy pipeline: BactSNP. Microb Genom 2019; 5. [PMID: 31099741 PMCID: PMC6562250 DOI: 10.1099/mgen.0.000261] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [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] [Indexed: 12/30/2022] Open
Abstract
Bacteria are highly diverse, even within a species; thus, there have been many studies which classify a single species into multiple types and analyze the genetic differences between them. Recently, the use of whole-genome sequencing (WGS) has been popular for these analyses, and the identification of single-nucleotide polymorphisms (SNPs) between isolates is the most basic analysis performed following WGS. The performance of SNP-calling methods therefore has a significant effect on the accuracy of downstream analyses, such as phylogenetic tree inference. In particular, when closely related isolates are analyzed, e.g. in outbreak investigations, some SNP callers tend to detect a high number of false-positive SNPs compared with the limited number of true SNPs among isolates. However, the performances of various SNP callers in such a situation have not been validated sufficiently. Here, we show the results of realistic benchmarks of commonly used SNP callers, revealing that some of them exhibit markedly low accuracy when target isolates are closely related. As an alternative, we developed a novel pipeline BactSNP, which utilizes both assembly and mapping information and is capable of highly accurate and sensitive SNP calling in a single step. BactSNP is also able to call SNPs among isolates when the reference genome is a draft one or even when the user does not input the reference genome. BactSNP is available at https://github.com/IEkAdN/BactSNP.
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Affiliation(s)
- Dai Yoshimura
- 1School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Rei Kajitani
- 1School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Yasuhiro Gotoh
- 2Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Katsuyuki Katahira
- 2Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Miki Okuno
- 1School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Yoshitoshi Ogura
- 2Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tetsuya Hayashi
- 2Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takehiko Itoh
- 1School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
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Sawada O, Gotoh Y, Taniguchi T, Furukawa S, Yoshimura D, Sasaki S, Shida H, Kusunoki Y, Yamamura T, Furuya K, Itoh T, Horita T, Hayashi T, Misawa N. Genome Sequencing Verifies Relapsed Infection of Helicobacter cinaedi. Open Forum Infect Dis 2019; 6:ofz200. [PMID: 31139675 PMCID: PMC6527084 DOI: 10.1093/ofid/ofz200] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 02/18/2019] [Accepted: 04/22/2019] [Indexed: 11/14/2022] Open
Abstract
Background Recurrent infections of Helicobacter cinaedi are often reported, and long-term antimicrobial treatment is empirically recommended to prevent such infections. However, there have been no studies examining whether recurrent infections are relapses of former infections or reinfections with different clones. Methods A 69-year-old woman presented with recurrent H cinaedi bacteremia-associated cellulitis after a 51-day interval. We isolated 10 colonies from the blood cultures obtained during each of the 2 episodes and subjected them to whole-genome sequencing (WGS). High-confidence single-nucleotide polymorphisms (SNPs) were identified by an assembly based method. Heterogeneous SNP sites were identified by read mapping. The susceptibility of a representative isolate to 14 antimicrobials was also examined. Results Whole-genome sequence analysis revealed only 6 SNP sites among the 20 isolates at the whole-genome level. Based on the 6 SNPs, 5 within-host variants (referred to as genotypes) were identified. All 5 genotypes were detected in the first infection; however, only 2 genotypes were detected in the second infection. Although the H cinaedi clone showed a higher minimum inhibitory concentration to fluoroquinolones and macrolides and responsible mutations were identified, none of the 6 SNPs appeared related to additional resistance. Conclusions The second infection analyzed here was a relapse of the first infection. A certain level of within-host genomic heterogeneity of the H cinaedi clone was already present in the first infection. Our results suggest the importance of longer treatment courses to eradicate H cinaedi for preventing the relapse of its infection.
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Affiliation(s)
- Osamu Sawada
- Center of Nephrology and Connective Tissue Disease, Japan Community Health Care Organization Hokkaido Hospital, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Japan
| | - Takako Taniguchi
- Center for Animal Disease Control, University of Miyazaki, Japan
| | - Shota Furukawa
- Center of Nephrology and Connective Tissue Disease, Japan Community Health Care Organization Hokkaido Hospital, Japan
| | - Dai Yoshimura
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Japan
| | - Satomi Sasaki
- Center for Animal Disease Control, University of Miyazaki, Japan
| | - Haruki Shida
- Center of Nephrology and Connective Tissue Disease, Japan Community Health Care Organization Hokkaido Hospital, Japan
| | - Yoshihiro Kusunoki
- Center of Nephrology and Connective Tissue Disease, Japan Community Health Care Organization Hokkaido Hospital, Japan
| | - Tsuyoshi Yamamura
- Center of Nephrology and Connective Tissue Disease, Japan Community Health Care Organization Hokkaido Hospital, Japan
| | - Ken Furuya
- Center of Nephrology and Connective Tissue Disease, Japan Community Health Care Organization Hokkaido Hospital, Japan
| | - Takehiko Itoh
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Japan
| | - Tetsuya Horita
- Center of Nephrology and Connective Tissue Disease, Japan Community Health Care Organization Hokkaido Hospital, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Japan
| | - Naoaki Misawa
- Center for Animal Disease Control, University of Miyazaki, Japan
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Oogai Y, Gotoh Y, Ogura Y, Kawada-Matsuo M, Hayashi T, Komatsuzawa H. Small RNA repertoires and their intraspecies variation in Aggregatibacter actinomycetemcomitans. DNA Res 2018; 25:207-215. [PMID: 29211829 PMCID: PMC5909427 DOI: 10.1093/dnares/dsx050] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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: 04/06/2017] [Accepted: 11/15/2017] [Indexed: 11/13/2022] Open
Abstract
Aggregatibacter actinomycetemcomitans is a major periodontal pathogen that has several virulence factors such as leukotoxin and cytolethal distending toxin. Although the genes responsible for virulence have been identified, little is known about their regulatory mechanisms. Small RNA (sRNA) has been recognized as an important factor for gene regulation. To identify new regulatory mechanisms via sRNA in A. actinomycetemcomitans HK1651, we performed a systematic search for sRNAs by RNA-seq and identified 90 intergenic region sRNAs and 30 antisense sRNAs. Of the 85 analysable sRNAs, we successfully detected and quantified 70 sRNAs by developing an RT-PCR system, and we identified 17 sRNAs that were differentially expressed during different growth phases. In addition, we found notable intraspecies variation in the sRNA repertoire of A. actinomycetemcomitans, thus suggesting that frequent acquisition or deletion of sRNAs occurred during the evolution of this species. The predicted target genes of the intergenic region sRNAs indicated the possibility of sRNA interaction with several virulence genes including leukotoxin and cytolethal distending toxin. Our results should serve as an important genomic and genetic basis for future studies to fully understand the regulatory network in A. actinomycetemcomitans and provide new insights into the intraspecies variation of the bacterial sRNA repertoire in bacteria.
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Affiliation(s)
- Yuichi Oogai
- Department of Oral Microbiology, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1, Sakuragaoka, Kagoshima 890-8544, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yoshitoshi Ogura
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Miki Kawada-Matsuo
- Department of Oral Microbiology, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1, Sakuragaoka, Kagoshima 890-8544, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Hitoshi Komatsuzawa
- Department of Oral Microbiology, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1, Sakuragaoka, Kagoshima 890-8544, Japan
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47
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Kusumoto M, Ogura Y, Gotoh Y, Iwata T, Hayashi T, Akiba M. Colistin-Resistant mcr-1-Positive Pathogenic Escherichia coli in Swine, Japan, 2007-2014. Emerg Infect Dis 2018; 22:1315-7. [PMID: 27314277 PMCID: PMC4918142 DOI: 10.3201/eid2207.160234] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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48
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Ogura Y, Gotoh Y, Itoh T, Sato MP, Seto K, Yoshino S, Isobe J, Etoh Y, Kurogi M, Kimata K, Maeda E, Piérard D, Kusumoto M, Akiba M, Tominaga K, Kirino Y, Kato Y, Shirahige K, Ooka T, Ishijima N, Lee KI, Iyoda S, Mainil JG, Hayashi T. Population structure of Escherichia coli O26 : H11 with recent and repeated stx2 acquisition in multiple lineages. Microb Genom 2017; 3:e000141. [PMID: 29208163 PMCID: PMC5729918 DOI: 10.1099/mgen.0.000141] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 11/06/2017] [Indexed: 12/21/2022] Open
Abstract
A key virulence factor of enterohaemorrhagic Escherichia coli (EHEC) is the bacteriophage-encoded Shiga toxin (Stx). Stxs are classified into two types, Stx1 and Stx2, and Stx2-producing strains are thought to cause more severe infections than strains producing only Stx1. Although O26 : H11 is the second most prevalent EHEC following O157 : H7, the majority of O26 : H11 strains produce Stx1 alone. However, Stx2-producing O26 strains have increasingly been detected worldwide. Through a large-scale genome analysis, we present a global phylogenetic overview and evolutionary timescale for E. coli O26 : H11. The origin of O26 has been estimated to be 415 years ago. Sequence type 21C1 (ST21C1), one of the two sublineages of ST21, the most predominant O26 : H11 lineage worldwide, emerged 213 years ago from one of the three ST29 sublineages (ST29C2). The other ST21 lineage (ST21C2) emerged 95 years ago from ST21C1. Increases in population size occurred in the late 20th century for all of the O26 lineages, but most remarkably for ST21C2. Analysis of the distribution of stx2-positive strains revealed the recent and repeated acquisition of the stx2 gene in multiple lineages of O26, both in ST21 and ST29. Other major EHEC virulence genes, such as type III secretion system effector genes and plasmid-encoded virulence genes, were well conserved in ST21 compared to ST29. In addition, more antimicrobial-resistance genes have accumulated in the ST21C1 lineage. Although current attention is focused on several highly virulent ST29 clones that have acquired the stx2 gene, there is also a considerable risk that the ST21 lineage could yield highly virulent clones.
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Affiliation(s)
| | | | | | | | - Kazuko Seto
- Osaka Prefectural Institute of Public Health, Osaka, Japan
| | - Shyuji Yoshino
- Miyazaki Prefectural Institute for Public Health and Environment, Miyazaki, Japan
| | | | - Yoshiki Etoh
- Fukuoka Institute of Health and Environmental Sciences, Fukuoka, Japan
| | - Mariko Kurogi
- Miyazaki Prefectural Institute for Public Health and Environment, Miyazaki, Japan
| | | | - Eriko Maeda
- Fukuoka Institute of Health and Environmental Sciences, Fukuoka, Japan
| | | | - Masahiro Kusumoto
- National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan
| | - Masato Akiba
- National Institute of Animal Health, Ibaraki, Japan
| | - Kiyoshi Tominaga
- Yamaguchi Prefectural Institute of Public Health and Environment, Yamaguchi, Japan
| | | | | | | | | | | | - Ken-ichi Lee
- National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan
| | - Sunao Iyoda
- National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan
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Akter A, Ooka T, Gotoh Y, Yamamoto S, Fujita H, Terasoma F, Kida K, Taira M, Nakadouzono F, Gokuden M, Hirano M, Miyashiro M, Inari K, Shimazu Y, Tabara K, Toyoda A, Yoshimura D, Itoh T, Kitano T, Sato MP, Katsura K, Mondal SI, Ogura Y, Ando S, Hayashi T. Extremely Low Genomic Diversity of Rickettsia japonica Distributed in Japan. Genome Biol Evol 2017; 9:124-133. [PMID: 28057731 PMCID: PMC5381555 DOI: 10.1093/gbe/evw304] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [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] [Accepted: 12/27/2016] [Indexed: 12/25/2022] Open
Abstract
Rickettsiae are obligate intracellular bacteria that have small genomes as a result of reductive evolution. Many Rickettsia species of the spotted fever group (SFG) cause tick-borne diseases known as “spotted fevers”. The life cycle of SFG rickettsiae is closely associated with that of the tick, which is generally thought to act as a bacterial vector and reservoir that maintains the bacterium through transstadial and transovarial transmission. Each SFG member is thought to have adapted to a specific tick species, thus restricting the bacterial distribution to a relatively limited geographic region. These unique features of SFG rickettsiae allow investigation of how the genomes of such biologically and ecologically specialized bacteria evolve after genome reduction and the types of population structures that are generated. Here, we performed a nationwide, high-resolution phylogenetic analysis of Rickettsia japonica, an etiological agent of Japanese spotted fever that is distributed in Japan and Korea. The comparison of complete or nearly complete sequences obtained from 31 R. japonica strains isolated from various sources in Japan over the past 30 years demonstrated an extremely low level of genomic diversity. In particular, only 34 single nucleotide polymorphisms were identified among the 27 strains of the major lineage containing all clinical isolates and tick isolates from the three tick species. Our data provide novel insights into the biology and genome evolution of R. japonica, including the possibilities of recent clonal expansion and a long generation time in nature due to the long dormant phase associated with tick life cycles.
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Affiliation(s)
- Arzuba Akter
- Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Tadasuke Ooka
- Department of Microbiology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Seigo Yamamoto
- Frontier Science Research Center, University of Miyazaki, Miyazaki, Japan
| | - Hiromi Fujita
- Mahara Institute of Medical Acarology, Tokushima, Japan
| | - Fumio Terasoma
- Wakayama Prefectural Research Center of Environment and Public Health, Wakayama, Japan
| | - Kouji Kida
- Okayama Prefectural Institute for Environmental Science and Public Health, Okayama, Japan
| | | | - Fumiko Nakadouzono
- Kagoshima Prefectural Institute for Environmental Research and Public Health, Kagoshima, Japan
| | - Mutsuyo Gokuden
- Kagoshima Prefectural Institute for Environmental Research and Public Health, Kagoshima, Japan
| | - Manabu Hirano
- Seihi Public Health Center of Nagasaki Prefecture, Nagasaki, Japan
| | - Mamoru Miyashiro
- Fukuoka City Institute for Health and Environment, Fukuoka, Japan
| | - Kouichi Inari
- Mahara Institute of Medical Acarology, Tokushima, Japan
| | - Yukie Shimazu
- Hiroshima Prefectural Technology Research Institute, Public Health and Environment Center, Hiroshima, Japan
| | - Kenji Tabara
- Department of Health and Welfare, Shimane Prefectural Government, Shimane, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Dai Yoshimura
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Takehiko Itoh
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Tomokazu Kitano
- Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Mitsuhiko P Sato
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Keisuke Katsura
- Frontier Science Research Center, University of Miyazaki, Miyazaki, Japan
| | - Shakhinur Islam Mondal
- Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Yoshitoshi Ogura
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Shuji Ando
- Department of Virology-1, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
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Affiliation(s)
- Y. Gotoh
- Central Research Laboratory, Hitachi, Ltd. Kokubunji, Tokyo 185 Japan (0423) 23-1111
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