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Tsukada M, Miyazaki T, Aoki K, Yoshizawa S, Kondo Y, Sawa T, Murakami H, Sato E, Tomida M, Otani M, Kumade E, Takamori E, Kambe M, Ishii Y, Tateda K. The outbreak of multispecies carbapenemase-producing Enterobacterales associated with pediatric ward sinks: IncM1 plasmids act as vehicles for cross-species transmission. Am J Infect Control 2024; 52:801-806. [PMID: 38613526 DOI: 10.1016/j.ajic.2024.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 04/15/2024]
Abstract
BACKGROUND This study describes an outbreak caused by multispecies carbapenemase-producing Enterobacterales (CPE) occurring in a pediatric ward at an academic medical center in Tokyo. METHODS The index case involved a 1-year-old boy with Klebsiella variicola (CPE) detected in anal swabs in June 2016. The second case was Klebsiella quasipneumoniae (CPE) occurred in March 2017 followed by further spread, leading to the declaration of an outbreak in April 2017. Extensive environmental and patient microbiological sampling was performed. The relatedness of the isolates was determined using draft-whole-genome sequencing. RESULTS CPE surveillance cultures of patients and environments were positive in 19 patients and 9 sinks in the ward. The sinks in hospital rooms uninhabited by CPE patients exhibited no positive CPE-positive specimen during the outbreak. All CPE strains analyzed using draft-whole-genome sequencing harbored blaIMP-1, except for one harboring blaIMP-11; these strains harbored identical blaIMP-1-carrying IncM1 plasmids. CPE was detected even after sink replacement; infection-control measures focused on sinks were implemented and the CPE outbreak ended after 7 months. CONCLUSIONS Multiple bacterial species can become CPE via blaIMP-1-carrying IncM1 plasmids of the same origin and spread through sinks in a hospital ward. Thorough infection-control measures implemented as a bundle might be crucial.
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Affiliation(s)
- Mayumi Tsukada
- Department of Infection Prevention and Control, Toho University Omori Medical Center, Tokyo, Japan
| | - Taito Miyazaki
- Department of Infection Prevention and Control, Toho University Omori Medical Center, Tokyo, Japan; Department of General Medicine and Emergency Care, Toho University School of Medicine, Tokyo, Japan
| | - Kotaro Aoki
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
| | - Sadako Yoshizawa
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan; Department of Clinical Laboratory, Toho University Omori Medical Center, Tokyo, Japan.
| | - Yoko Kondo
- Department of Infection Prevention and Control, Toho University Omori Medical Center, Tokyo, Japan
| | - Tomoka Sawa
- Department of Infection Prevention and Control, Toho University Omori Medical Center, Tokyo, Japan; Department of Pediatrics, Toho University School of Medicine, Tokyo, Japan
| | - Hinako Murakami
- Department of Infection Prevention and Control, Toho University Omori Medical Center, Tokyo, Japan; Department of Clinical Laboratory, Toho University Omori Medical Center, Tokyo, Japan
| | - Emi Sato
- Department of Infection Prevention and Control, Toho University Omori Medical Center, Tokyo, Japan
| | - Manabu Tomida
- Department of Infection Prevention and Control, Toho University Omori Medical Center, Tokyo, Japan
| | - Mariko Otani
- Department of Infection Prevention and Control, Toho University Omori Medical Center, Tokyo, Japan
| | - Eri Kumade
- Department of Infection Prevention and Control, Toho University Omori Medical Center, Tokyo, Japan; Department of General Medicine and Emergency Care, Toho University School of Medicine, Tokyo, Japan
| | - Emi Takamori
- Department of Infection Prevention and Control, Toho University Omori Medical Center, Tokyo, Japan
| | - Masako Kambe
- Department of Infection Prevention and Control, Toho University Omori Medical Center, Tokyo, Japan
| | - Yoshikazu Ishii
- Department of Infection Prevention and Control, Toho University Omori Medical Center, Tokyo, Japan; Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
| | - Kazuhiro Tateda
- Department of Infection Prevention and Control, Toho University Omori Medical Center, Tokyo, Japan; Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan; Department of Clinical Laboratory, Toho University Omori Medical Center, Tokyo, Japan
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2
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Sato Y, Mino S, Thompson F, Sawabe T. Core Transcriptome of Hydrogen Producing Marine Vibrios Reveals Contribution of Glycolysis in Their Efficient Hydrogen Production. Curr Microbiol 2024; 81:230. [PMID: 38896159 DOI: 10.1007/s00284-024-03764-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024]
Abstract
Pyruvate (Pyr) is the end product of the glycolysis pathway. Pyr is also renewable and is further metabolized to produce formate, which is the precursor of H2, via pyruvate formate lyase (PFL) under anaerobic conditions. The formate is excluded and re-imported via the formate channel and is then converted to H2 via the formate hydrogenlyase (FHL) complex. In H2 producing marine vibrios, such as Vibrio tritonius and Vibrio porteresiae in the Porteresiae clade of the family Vibrionaceae, apparent but inefficient H2 production from Pyr has been observed. To elucidate the molecular mechanism of why this inefficient H2 production is observed in Pry-metabolized marine vibrio cells and how glycolysis affects those H2 productions of marine vibrios, the "Core Transcriptome" approach to find common gene expressions of those two major H2 producing Vibrio species in Pyr metabolism was first applied. In the Pyr-metabolized vibrio cells, genes for the "Phosphoenolpyruvate (PEP)-Pyruvate-Oxalate (PPO)" node, due to energy saving, and PhoB-, RhaR-, and DeoR-regulons were regulated. Interestingly, a gene responsible for oxalate/formate family antiporter was up-regulated in Pyr-metabolized cells compared to those of Glc-metabolized cells, which provides new insights into the uses of alternative formate exclusion mechanics due to energy deficiencies in Pyr-metabolized marine vibrios cells. We further discuss the contribution of the Embden-Meyerhof-Parnas (EMP) pathway to efficient H2 production in marine vibrios.
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Affiliation(s)
- Yoshihiro Sato
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Sayaka Mino
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan.
| | - Fabiano Thompson
- Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Tomoo Sawabe
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan.
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Sutriswati Rahayu E, Suroto DA, Mariyatun M, Pramesi PC. Complete genome sequence of Indonesian probiotic strain Lactiplantibacillus plantarum subsp. plantarum Dad-13. Microbiol Resour Announc 2024:e0011824. [PMID: 38864610 DOI: 10.1128/mra.00118-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 05/16/2024] [Indexed: 06/13/2024] Open
Abstract
Previous studies have investigated the probiotic properties of L. plantarum subsp. plantarum Dad-13. Nevertheless, genomic sequence data from previous studies were not yet available to support each probiotic characteristic. This study focused on the complete genome sequence of the strain to validate its role in specific probiotic properties.
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Affiliation(s)
- Endang Sutriswati Rahayu
- University Center of Excellence for Integrated Probiotic Research and Application for Industry, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Center for Food and Nutrition Studies, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Faculty of Agricultural Technology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Dian Anggraini Suroto
- University Center of Excellence for Integrated Probiotic Research and Application for Industry, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Center for Food and Nutrition Studies, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Faculty of Agricultural Technology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Mariyatun Mariyatun
- University Center of Excellence for Integrated Probiotic Research and Application for Industry, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Center for Food and Nutrition Studies, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Putrika Citta Pramesi
- University Center of Excellence for Integrated Probiotic Research and Application for Industry, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Center for Food and Nutrition Studies, Universitas Gadjah Mada, Yogyakarta, Indonesia
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4
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Kondo R, Kataoka T. Whole-genome sequence of the strictly anaerobic bacterial strain SANA belonging to the family Gottschalkiaceae, isolated from a xenic culture of an anaerobic protist. Microbiol Resour Announc 2024; 13:e0017424. [PMID: 38767373 DOI: 10.1128/mra.00174-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 04/25/2024] [Indexed: 05/22/2024] Open
Abstract
An anaerobic bacterial strain SANA was isolated from a xenic culture of an anaerobic heterolobosean protist which was obtained from a saline lake in Japan. Its draft genome comprises 1 circular chromosome (3,490,293 bp), harboring 3,275 predicted protein-coding and 73 tRNA-encoding genes and 8 rRNA operons.
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Affiliation(s)
- Ryuji Kondo
- Department of Marine Science and Technology, Fukui Prefectural University, Obama, Fukui, Japan
| | - Takafumi Kataoka
- Department of Marine Science and Technology, Fukui Prefectural University, Obama, Fukui, Japan
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Machii Y, Tsukamoto M, Kataoka T, Kondo R. Whole-genome sequence of a marine bacterial strain, FRT2, belonging to the genus Leeuwenhoekiella, isolated from the seawater of the Obama Bay in Fukui, Japan. Microbiol Resour Announc 2024; 13:e0027724. [PMID: 38695583 DOI: 10.1128/mra.00277-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 04/20/2024] [Indexed: 06/12/2024] Open
Abstract
A marine bacterial strain, FRT2, was isolated from the surface water of the Obama Bay in Fukui, Japan. Its complete genome comprises one circular chromosome (3,806,097 bp), harboring 3,269 predicted protein- and 44-tRNA-encoding genes and 3 rRNA operons.
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Affiliation(s)
- Yuka Machii
- Department of Marine Science and Technology, Fukui Prefectural University, Obama, Fukui, Japan
| | - Mao Tsukamoto
- Department of Marine Science and Technology, Fukui Prefectural University, Obama, Fukui, Japan
| | - Takafumi Kataoka
- Department of Marine Science and Technology, Fukui Prefectural University, Obama, Fukui, Japan
| | - Ryuji Kondo
- Department of Marine Science and Technology, Fukui Prefectural University, Obama, Fukui, Japan
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Ichikawa Y, Borjigin L, Enkhtuul B, Khurtsbaatar O, Aoshima K, Kobayashi A, Batbaatar V, Kimura T. First molecular characterization of Burkholderia mallei strains isolated from horses in Mongolia. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 123:105616. [PMID: 38852916 DOI: 10.1016/j.meegid.2024.105616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/17/2024] [Accepted: 06/05/2024] [Indexed: 06/11/2024]
Abstract
Glanders, a highly contagious and often fatal disease affecting equids, is caused by Burkholderia mallei. Although sporadic cases of equine glanders have recently been documented in Mongolia, genome sequencing and molecular studies of the bacteria within this region are lacking. This study provided the first molecular characterization of B. mallei isolated from four native Mongolian horses from two different provinces in 2019 and 2022 by applying whole-genome sequencing with two SNP types (previously developed genotyping with 15 SNP markers that provide global coverage of the B. mallei population and the core genome coding SNP typing developed in this study). The Mongolian isolates were located within the L3B1 cluster, which was previously associated with the V-120 strain from Russia. Within the L3B1 cluster shared by neighboring countries, they were in a unique subbranch. In this study, specific SNP markers unique to the Mongolian strains were identified to track these strains using a high-resolution melting analysis (HRMA). This study revealed the unique phylogenetic background of Mongolian strains isolated from the eastern part of Mongolia. HRMA specific to the Mongolian subbranch may contribute to the molecular epidemiological monitoring of glanders in Mongolia and surrounding countries.
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Affiliation(s)
- Yoshiki Ichikawa
- Laboratory of Comparative Pathology, Department of Clinical Sciences, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Liushiqi Borjigin
- Faculty of Veterinary Medicine, Okayama University of Science, Imabari, Japan
| | - Batchuluun Enkhtuul
- Laboratory of Infectious Disease and Immunology, Institute of Veterinary Medicine, Mongolian University of Life Sciences, Khan-Uul district, Zaisan, 17024 Ulaanbaatar, Mongolia
| | - Ochirbat Khurtsbaatar
- Laboratory of Infectious Disease and Immunology, Institute of Veterinary Medicine, Mongolian University of Life Sciences, Khan-Uul district, Zaisan, 17024 Ulaanbaatar, Mongolia
| | - Keisuke Aoshima
- Laboratory of Comparative Pathology, Department of Clinical Sciences, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Atsushi Kobayashi
- Department of Biomedical Models, Graduate School of Biomedical Sciences, Nagasaki University, Sakamoto, Nagasaki, Japan
| | - Vanaabaatar Batbaatar
- Laboratory of Infectious Disease and Immunology, Institute of Veterinary Medicine, Mongolian University of Life Sciences, Khan-Uul district, Zaisan, 17024 Ulaanbaatar, Mongolia
| | - Takashi Kimura
- Laboratory of Comparative Pathology, Department of Clinical Sciences, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan.
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Hu X, Yang F, Yang S, Guo W, Ren J, Liu S, Xiao X, Zhu L, Wei W. Roseinatronobacter alkalisoli sp. nov., an alkaliphilic bacterium isolated from soda soil, and genome-based reclassification of the genera Rhodobaca and Roseinatronobacter. Int J Syst Evol Microbiol 2024; 74. [PMID: 38832859 DOI: 10.1099/ijsem.0.006402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024] Open
Abstract
The genera Rhodobaca and Roseinatronobacter are phylogenetically related genera within the family Paracoccaceae. Species of these genera were described using 16S rRNA gene-based phylogeny and phenotypic characteristics. However, the 16S rRNA gene identity and phylogeny reveal the controversy of the taxonomic status of these two genera. In this work, we examined the taxonomic positions of members of both genera using 16S rRNA gene phylogeny, phylogenomic analysis and further validated using overall genome-related indexes, including digital DNA-DNA hybridization, average nucleotide identity, average amino acid identity and percentage of conserved proteins. Based on phylogenetic and phylogenomic results, the current four species of the two genera clustered tightly into one clade with high bootstrap values, suggesting that the genus Rhodobaca should be merged with Roseinatronobacter. In addition, a novel species isolated from a soda soil sample collected from Anda City, PR China, and designated as HJB301T was also described. Phenotypic, chemotaxonomic, genomic and phylogenetic properties suggested that strain HJB301T (=CCTCC AB 2021113T=KCTC 82977T) represents a novel species of the genus Roseinatronobacter, for which the name Roseinatronobacter alkalisoli sp. nov. is proposed.
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Affiliation(s)
- Xinyu Hu
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, PR China
| | - Fan Yang
- School of Agricultural Engineering, Jiangsu University, Zhenjiang, PR China
| | - Shujing Yang
- School of Agricultural Engineering, Jiangsu University, Zhenjiang, PR China
| | - Wenjun Guo
- School of Agricultural Engineering, Jiangsu University, Zhenjiang, PR China
| | - Jiangtao Ren
- School of Agricultural Engineering, Jiangsu University, Zhenjiang, PR China
| | - Shenkui Liu
- State Key Laboratory of Subtropical Forest Cultivation, Zhejiang Agriculture and Forestry University, Hangzhou, PR China
| | - Xiang Xiao
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, PR China
| | - Lin Zhu
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, PR China
| | - Wei Wei
- School of Agricultural Engineering, Jiangsu University, Zhenjiang, PR China
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8
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Krul D, Rodrigues LS, Siqueira AC, Mesa D, Dos Santos ÉM, Vasconcelos TM, Spalanzani RN, Cardoso R, Ricieri MC, de Araújo Motta F, Conte D, Dalla-Costa LM. High-risk clones of carbapenem resistant Klebsiella pneumoniae recovered from pediatric patients in Southern Brazil. Braz J Microbiol 2024; 55:1437-1443. [PMID: 38499916 PMCID: PMC11153399 DOI: 10.1007/s42770-024-01299-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 03/03/2024] [Indexed: 03/20/2024] Open
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CRKP) exhibit high mortality rates in pediatric patients and usually belong to international high-risk clones. This study aimed to investigate the molecular epidemiology and carbapenem resistance mechanisms of K. pneumoniae isolates recovered from pediatric patients, and correlate them with phenotypical data. Twenty-five CRKP isolates were identified, and antimicrobial susceptibility was assessed using broth microdilution. Carbapenemase production and β-lactamase genes were detected by phenotypic and genotypic tests. Multilocus sequence typing was performed to differentiate the strains and whole-genome sequencing was assessed to characterize a new sequence type. Admission to the intensive care unit and the use of catheters were significantly positive correlates of CRKP infection, and the mortality rate was 36%. Almost all isolates showed multidrug-resistant phenotype, and most frequent resistant gene was blaKPC. We observed the dissemination of ST307 and clones belonging to CG258, which are considered high risk. In pediatric patients, these clones present with high genomic plasticity, favoring adaptation of the KPC and NDM enzymes to healthcare environments.
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Affiliation(s)
- Damaris Krul
- Faculdades Pequeno Príncipe (FPP), Curitiba, Paraná, Brazil
- Instituto de Pesquisa Pelé Pequeno Príncipe (IPPPP), Av. Silva Jardim, 1632 -Rebouças, Curitiba, Paraná, CEP 80250-060, Brazil
| | - Luiza Souza Rodrigues
- Instituto de Pesquisa Pelé Pequeno Príncipe (IPPPP), Av. Silva Jardim, 1632 -Rebouças, Curitiba, Paraná, CEP 80250-060, Brazil
| | - Adriele Celine Siqueira
- Faculdades Pequeno Príncipe (FPP), Curitiba, Paraná, Brazil
- Instituto de Pesquisa Pelé Pequeno Príncipe (IPPPP), Av. Silva Jardim, 1632 -Rebouças, Curitiba, Paraná, CEP 80250-060, Brazil
| | - Dany Mesa
- Faculdades Pequeno Príncipe (FPP), Curitiba, Paraná, Brazil
- Instituto de Pesquisa Pelé Pequeno Príncipe (IPPPP), Av. Silva Jardim, 1632 -Rebouças, Curitiba, Paraná, CEP 80250-060, Brazil
| | - Érika Medeiros Dos Santos
- Faculdades Pequeno Príncipe (FPP), Curitiba, Paraná, Brazil
- Instituto de Pesquisa Pelé Pequeno Príncipe (IPPPP), Av. Silva Jardim, 1632 -Rebouças, Curitiba, Paraná, CEP 80250-060, Brazil
- Hospital Pequeno Príncipe (HPP), Curitiba, Paraná, Brazil
| | - Thaís Muniz Vasconcelos
- Faculdades Pequeno Príncipe (FPP), Curitiba, Paraná, Brazil
- Instituto de Pesquisa Pelé Pequeno Príncipe (IPPPP), Av. Silva Jardim, 1632 -Rebouças, Curitiba, Paraná, CEP 80250-060, Brazil
| | - Regiane Nogueira Spalanzani
- Faculdades Pequeno Príncipe (FPP), Curitiba, Paraná, Brazil
- Instituto de Pesquisa Pelé Pequeno Príncipe (IPPPP), Av. Silva Jardim, 1632 -Rebouças, Curitiba, Paraná, CEP 80250-060, Brazil
| | | | | | | | - Danieli Conte
- Faculdades Pequeno Príncipe (FPP), Curitiba, Paraná, Brazil
- Instituto de Pesquisa Pelé Pequeno Príncipe (IPPPP), Av. Silva Jardim, 1632 -Rebouças, Curitiba, Paraná, CEP 80250-060, Brazil
| | - Libera Maria Dalla-Costa
- Faculdades Pequeno Príncipe (FPP), Curitiba, Paraná, Brazil.
- Instituto de Pesquisa Pelé Pequeno Príncipe (IPPPP), Av. Silva Jardim, 1632 -Rebouças, Curitiba, Paraná, CEP 80250-060, Brazil.
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9
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Katayama Y, Morita M, Chang B, Katagiri D, Ishikane M, Yamada G, Mezaki K, Kurokawa M, Takano H, Akeda Y. Identification and characterization of a novel α-haemolytic streptococci, Streptococcus parapneumoniae sp. nov., which caused bacteremia with pyelonephritis. Int J Med Microbiol 2024; 315:151625. [PMID: 38824713 DOI: 10.1016/j.ijmm.2024.151625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 05/23/2024] [Accepted: 05/23/2024] [Indexed: 06/04/2024] Open
Abstract
OBJECTIVES We report a case of bacteremia with pyelonephritis in an adult male with an underlying disease caused by α-hemolytic streptococci. α-Hemolytic streptococci were isolated from blood, but it was challenging to identify its species. This study aimed to characterize the causative bacterium SP4011 and to elucidate its species. METHODS The whole-genome sequence and biochemical characteristics of SP4011 were determined. Based on the genome sequence, phylogenetic analysis was performed with standard strains of each species of α-hemolytic streptococci. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values were calculated. RESULTS SP4011 showed optochin susceptibility and bile solubility, but did not react with pneumococcal omni antiserum. Phylogenetic analysis of the whole-genome sequence showed that SP4011 clustered with S. pneumoniae and S. pseodopneumoniae and was most closely related to S. pseodopneumoniae. Genomic analysis revealed that ANI and dDDH values between SP4011 and S. pseodopneumoniae were 94.0 % and 56.0 %, respectively, and between SP4011 and S. pneumoniae were 93.3 % and 52.2 %, respectively. Biochemical characteristics also showed differences between SP4011 and S. pseodopneumoniae and between SP4011 and S. pneumoniae. These results indicate that SP4011 is a novel species. CONCLUSION Our findings indicate that SP4011 is a novel species of the genus Streptococcus. SP4011 has biochemical characteristics similar to S. pneumoniae, making it challenging to differentiate and requiring careful clinical diagnosis. This isolate was proposed to be a novel species, Streptococcus parapneumoniae sp. nov. The strain type is SP4011T (= JCM 36068T = KCTC 21228T).
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Affiliation(s)
- Yuri Katayama
- Department of Nephrology, National Center for Global Health and Medicine, Tokyo, Japan
| | - Masatomo Morita
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Bin Chang
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Daisuke Katagiri
- Department of Nephrology, National Center for Global Health and Medicine, Tokyo, Japan.
| | - Masahiro Ishikane
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Tokyo, Japan.
| | - Gen Yamada
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Kazuhisa Mezaki
- Department of Clinical Laboratory, National Center for Global Health and Medicine, Tokyo, Japan
| | - Masami Kurokawa
- Department of Clinical Laboratory, National Center for Global Health and Medicine, Tokyo, Japan
| | - Hideki Takano
- Department of Nephrology, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yukihiro Akeda
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
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10
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Narihara S, Chida S, Matsunaga N, Akimoto R, Akimoto M, Hagio A, Mori T, Nittami T, Sato M, Mun S, Kang H, Back JH, Takeda M. Taxonomic characterization of Sphaerotilus microaerophilus sp. nov., a sheath-forming microaerophilic bacterium of activated sludge origin. Arch Microbiol 2024; 206:252. [PMID: 38727820 PMCID: PMC11087309 DOI: 10.1007/s00203-024-03991-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 04/30/2024] [Accepted: 05/01/2024] [Indexed: 05/13/2024]
Abstract
A microaerophilic Gram-stain-negative bacilliform bacterial strain, FB-5 T, was isolated from activated sludge in Yokohama, Japan, that exhibited filamentous growth and formed a microtube (sheath). Cells were motile using a single polar flagellum. The optimum growth temperature and pH were 30 °C and 7.5, respectively. Strain FB-5 T was catalase-negative. Peptides and amino acids were utilized as energy and carbon sources. Sugars and organic acids were not utilized. Vitamin B12 enhanced the growth of strain FB-5 T. Sulfur-dependent lithotrophic growth was possible. Major respiratory quinone was UQ-8. Major fatty acids were C16:1ω7 and C16:0. The genomic DNA G + C content was 69.16%. Phylogenetic analysis of the 16S rRNA gene suggested that strain FB-5 T belongs to the genus Sphaerotilus. The close relatives were S. natans subsup. sulfidivorans and S. natans subsup. natans with 98.0% and 97.8% similarity based on the 16S rRNA gene analysis, respectively. The genome size (6.06 Mbp) was larger than that (4.39-5.07 Mbp) of the Sphaerotilus strains. The AAI values against the related strains ranged from 71.0 to 72.5%. The range of ANI values was 81.7 - 82.5%. In addition to these distinguishable features of the genome, the core genome and dDDH analyses suggested that this strain is a novel member of the genus Sphaerotilus. Based on its physiological properties and genomic features, strain FB-5 T is considered as a novel species of the genus Sphaerotilus, for which the name S. microaerophilus sp. nov. is proposed. The type strain is FB-5 T (= JCM 35424 T = KACC 23146 T).
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Affiliation(s)
- Shiori Narihara
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5, Hodogaya, Yokohama, 240-8501, Japan
| | - Shun Chida
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5, Hodogaya, Yokohama, 240-8501, Japan
| | - Naoki Matsunaga
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5, Hodogaya, Yokohama, 240-8501, Japan
| | - Ryosuke Akimoto
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5, Hodogaya, Yokohama, 240-8501, Japan
| | - Mizuki Akimoto
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5, Hodogaya, Yokohama, 240-8501, Japan
| | - Aoi Hagio
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5, Hodogaya, Yokohama, 240-8501, Japan
| | - Tomomi Mori
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5, Hodogaya, Yokohama, 240-8501, Japan
| | - Tadashi Nittami
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5, Hodogaya, Yokohama, 240-8501, Japan
| | - Michio Sato
- School of Agriculture, Meiji University, 1-1-1 Higashimita, Tama, Kawasaki, 214-8571, Japan
| | - Sehui Mun
- Department of Food Science and Nutrition, Gwangju University, 277, Hyodeok-Ro, Nam-Gu, Gwangju, 61743, Korea
| | - Hyeonjin Kang
- Department of Food Science and Nutrition, Gwangju University, 277, Hyodeok-Ro, Nam-Gu, Gwangju, 61743, Korea
| | - Ji Hwan Back
- Department of Food Science and Nutrition, Gwangju University, 277, Hyodeok-Ro, Nam-Gu, Gwangju, 61743, Korea
| | - Minoru Takeda
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5, Hodogaya, Yokohama, 240-8501, Japan.
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11
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Takei K, Ogawa M, Sakata R, Kanamori H. Molecular Epidemiology of Carbapenem-Resistant Klebsiella aerogenes in Japan. Int J Mol Sci 2024; 25:4494. [PMID: 38674079 PMCID: PMC11049973 DOI: 10.3390/ijms25084494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/07/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
Information regarding Klebsiella aerogenes haboring carbapenemase in Japan is limited. A comprehensive nationwide survey was conducted from September 2014 to December 2022, and 67 non-duplicate strains of carbapenem-resistant K. aerogenes were isolated from 57 healthcare facilities in Japan. Through genetic testing and whole-genome sequencing, six strains were found to possess carbapenemases, including imipenemase (IMP)-1, IMP-6, New Delhi metallo-β-lactamase (NDM)-1, and NDM-5. The strain harboring blaNDM-5 was the novel strain ST709, which belongs to the clonal complex of the predominant ST4 in China. The novel integron containing blaIMP-1 featured the oxacillinase-101 gene, which is a previously unreported structure, with an IncN4 plasmid type. However, integrons found in the strains possessing blaIMP-6, which were the most commonly identified, matched those reported domestically in Klebsiella pneumoniae, suggesting the prevalence of identical integrons. Transposons containing blaNDM are similar or identical to the transposon structure of K. aerogenes harboring blaNDM-5 previously reported in Japan, suggesting that the same type of transposon could have been transmitted to K. aerogenes in Japan. This investigation analyzed mobile genetic elements, such as integrons and transposons, to understand the spread of carbapenemases, highlighting the growing challenge of carbapenem-resistant Enterobacterales in Japan and underscoring the critical need for ongoing surveillance to control these pathogens.
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Affiliation(s)
- Kentarou Takei
- Department of Infectious Diseases, Internal Medicine, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan;
| | - Miho Ogawa
- Department of Bacteriology, BML Inc., Kawagoe 350-1101, Japan
| | - Ryuji Sakata
- Department of Bacteriology, BML Inc., Kawagoe 350-1101, Japan
| | - Hajime Kanamori
- Department of Infectious Diseases, Internal Medicine, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan;
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12
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Handayani DP, Isnansetyo A, Istiqomah I. New investigation of encoding secondary metabolites gene by genome mining of a marine bacterium, Pseudoalteromonas viridis BBR56. BMC Genomics 2024; 25:364. [PMID: 38615000 PMCID: PMC11015633 DOI: 10.1186/s12864-024-10266-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 03/27/2024] [Indexed: 04/15/2024] Open
Abstract
Pseudoalteromonas viridis strain BBR56 was isolated from seawater at Dutungan Island, South Sulawesi, Indonesia. Bacterial DNA was isolated using Promega Genomic DNA TM050. DNA purity and quantity were assessed using NanoDrop spectrophotometers and Qubit fluorometers. The DNA library and sequencing were prepared using Oxford Nanopore Technology GridION MinKNOW 20.06.9 with long read, direct, and comprehensive analysis. High accuracy base calling was assessed with Guppy version 4.0.11. Filtlong and NanoPlot were used for filtering and visualizing the FASTQ data. Flye (2.8.1) was used for de novo assembly analysis. Variant calls and consensus sequences were created using Medaka. The annotation of the genome was elaborated by DFAST. The assembled genome and annotation were tested using Busco and CheckM. Herein, we found that the highest similarity of the BBR56 isolate was 98.37% with the 16 S rRNA gene sequence of P. viridis G-1387. The genome size was 5.5 Mb and included chromosome 1 (4.2 Mbp) and chromosome 2 (1.3 Mbp), which encoded 61 pseudogenes, 4 noncoding RNAs, 113 tRNAs, 31 rRNAs, 4,505 coding DNA sequences, 4 clustered regularly interspaced short palindromic repeats, 4,444 coding genes, and a GC content of 49.5%. The sequence of the whole genome of P. viridis BBR56 was uploaded to GenBank under the accession numbers CP072425-CP072426, biosample number SAMN18435505, and bioproject number PRJNA716373. The sequence read archive (SRR14179986) was successfully obtained from NCBI for BBR56 raw sequencing reads. Digital DNA-DNA hybridization results showed that the genome of BBR56 had the potential to be a new species because no other bacterial genomes were similar to the sample. Biosynthetic gene clusters (BGCs) were assessed using BAGEL4 and the antiSMASH bacterial version. The genome harbored diverse BGCs, including genes that encoded polyketide synthase, nonribosomal peptide synthase, RiPP-like, NRP-metallophore, hydrogen cyanide, betalactone, thioamide-NRP, Lant class I, sactipeptide, and prodigiosin. Thus, BBR56 has considerable potential for further exploration regarding the use of its secondary metabolite products in the human and fisheries sectors.
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Affiliation(s)
- Desy Putri Handayani
- Department of Fisheries, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Alim Isnansetyo
- Department of Fisheries, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta, Indonesia.
| | - Indah Istiqomah
- Department of Fisheries, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta, Indonesia
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13
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Shu HY, Chen CC, Ku HT, Wang CL, Wu KM, Weng HY, Liu ST, Chen CL, Chiu CH. Complete genome sequence of Bacillus halotolerans F29-3, a fengycin-producing strain. Microbiol Resour Announc 2024; 13:e0124623. [PMID: 38451104 PMCID: PMC11008187 DOI: 10.1128/mra.01246-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 02/11/2024] [Indexed: 03/08/2024] Open
Abstract
Bacillus halotolerans F29-3, a Gram-positive bacterium, is recognized for its synthesis of the antifungal substance fengycin. This announcement introduces the complete genome sequence and provides insights into the genetic products related to antibiotic secondary metabolites, including non-ribosomal peptide synthetase (NRPS), polyketide synthase (PKS), and NRPS/PKS combination.
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Affiliation(s)
- Hung-Yu Shu
- Department of Bioscience Technology, Chang Jung Christian University, Tainan, Taiwan
| | - Chien-Chi Chen
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan
| | - Hsin-Tzu Ku
- Department of Bioscience Technology, Chang Jung Christian University, Tainan, Taiwan
| | - Chun-Lin Wang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan
| | - Keh-Ming Wu
- Bioinformatics Department, Welgene Biotech Co., Ltd., Taipei, Taiwan
| | - Hui-Ying Weng
- Biomedical Industry Ph.D. Program, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Shih-Tung Liu
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chyi-Liang Chen
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Cheng-Hsun Chiu
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan
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14
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Kagawa N, Aoki K, Komori K, Ishii Y, Shimuta K, Ohnishi M, Tateda K. Molecular epidemiological and antimicrobial-resistant mechanisms analysis of prolonged Neisseria gonorrhoeae collection between 1971 and 2005 in Japan. JAC Antimicrob Resist 2024; 6:dlae040. [PMID: 38476773 PMCID: PMC10928670 DOI: 10.1093/jacamr/dlae040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
Objectives As antimicrobial-resistant (AMR) Neisseria gonorrhoeae strains have emerged, humans have adjusted the antimicrobials used to treat infections. We identified shifts in the N. gonorrhoeae population and the determinants of AMR strains isolated during the recurring emergence of resistant strains and changes in antimicrobial therapies. Methods We examined 243 N. gonorrhoeae strains corrected at the Kanagawa Prefectural Institute of Public Health, Kanagawa, Japan, these isolated in 1971-2005. We performed multilocus sequence typing and AMR determinants (penA, mtrR, porB, ponA, 23S rRNA, gyrA and parC) mainly using high-throughput genotyping methods together with draft whole-genome sequencing on the MiSeq (Illumina) platform. Results All 243 strains were divided into 83 STs. ST1901 (n = 17) was predominant and first identified after 2001. Forty-two STs were isolated in the 1970s, 34 in the 1980s, 22 in the 1990s and 13 in the 2000s, indicating a decline in ST diversity over these decades. Among the 29 strains isolated after 2001, 28 were highly resistant to ciprofloxacin (MIC ≥ 8 mg/L) with two or more amino-acid substitutions in quinolone-resistance-determining regions. Seven strains belonging to ST7363 (n = 3), ST1596 (n = 3) and ST1901 (n = 1) were not susceptible to cefixime, and six strains carried penA alleles with mosaic-like penicillin-binding protein 2 (PBP2; penA 10.001 and 10.016) or PBP2 substitutions A501V and A517G. Conclusions We observed a significant reduction in the diversity of N. gonorrhoeae over 35 years in Japan. Since 2001, ST1901, which is resistant to ciprofloxacin, has superseded previous strains, becoming the predominant ST population.
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Affiliation(s)
- Narito Kagawa
- Department of Microbiology and Infection Control and Prevention, Toho University Graduate School of Medicine, 5-21-16 Omori-nishi, Ota-ku, Tokyo 143-8540, Japan
- Department of Microbiology, School of Life and Environmental Science, Azabu University, Kanagawa, Japan
| | - Kotaro Aoki
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
| | - Kohji Komori
- Department of Microbiology and Infection Control and Prevention, Toho University Graduate School of Medicine, 5-21-16 Omori-nishi, Ota-ku, Tokyo 143-8540, Japan
| | - Yoshikazu Ishii
- Department of Microbiology and Infection Control and Prevention, Toho University Graduate School of Medicine, 5-21-16 Omori-nishi, Ota-ku, Tokyo 143-8540, Japan
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
| | - Ken Shimuta
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kazuhiro Tateda
- Department of Microbiology and Infection Control and Prevention, Toho University Graduate School of Medicine, 5-21-16 Omori-nishi, Ota-ku, Tokyo 143-8540, Japan
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
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15
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Matsuda K, Maruyama H, Imachi K, Ikeda H, Wakimoto T. Actinobacterial chalkophores: the biosynthesis of hazimycins. J Antibiot (Tokyo) 2024; 77:228-237. [PMID: 38378905 DOI: 10.1038/s41429-024-00706-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 02/22/2024]
Abstract
Copper is a transition metal element with significant effects on the morphological development and secondary metabolism of actinobacteria. In some microorganisms, copper-binding natural products are employed to modulate copper homeostasis, although their significance in actinobacteria remains largely unknown. Here, we identified the biosynthetic genes of the diisocyanide natural product hazimycin in Kitasatospora purpeofusca HV058, through gene knock-out and heterologous expression. Biochemical analyses revealed that hazimycin A specifically binds to copper, which diminishes its antimicrobial activity. The presence of a set of putative importer/exporter genes surrounding the biosynthetic genes suggested that hazimycin is a chalkophore that modulates the intracellular copper level. A bioinformatic survey of homologous gene cassettes, as well as the identification of two previously unknown hazimycin-producing Streptomyces strains, indicated that the isocyanide-based mechanism of copper homeostasis is prevalent in actinobacteria.
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Affiliation(s)
- Kenichi Matsuda
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan.
| | - Hiroto Maruyama
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan
| | - Kumiko Imachi
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan
| | - Haruo Ikeda
- Technology Research Association for Next generation natural products chemistry, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Toshiyuki Wakimoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan.
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16
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Roncero-Ramos B, Savaglia V, Durieu B, Van de Vreken I, Richel A, Wilmotte A. Ecophysiological and genomic approaches to cyanobacterial hardening for restoration. JOURNAL OF PHYCOLOGY 2024; 60:465-482. [PMID: 38373045 DOI: 10.1111/jpy.13436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/15/2023] [Accepted: 12/15/2023] [Indexed: 02/20/2024]
Abstract
Cyanobacteria inhabit extreme environments, including drylands, providing multiple benefits to the ecosystem. Soil degradation in warm drylands is increasing due to land use intensification. Restoration methods adapted to the extreme stress in drylands are being developed, such as cyanobacteria inoculation to recover biocrusts. For this type of restoration method to be a success, it is crucial to optimize the survival of inoculated cyanobacteria in the field. One strategy is to harden them to be acclimated to stressful conditions after laboratory culturing. Here, we analyzed the genome and ecophysiological response to osmotic desiccation and UVR stresses of an Antarctic cyanobacterium, Stenomitos frigidus ULC029, which is closely related to other cyanobacteria from warm and cold dryland soils. Chlorophyll a concentrations showed that preculturing ULC029 under moderate osmotic stress improved its survival during an assay of desiccation plus rehydration under UVR. Additionally, its sequential exposure to these stress factors increased the production of exopolysaccharides, carotenoids, and scytonemin. Desiccation, but not osmotic stress, increased the concentrations of the osmoprotectants trehalose and sucrose. However, osmotic stress might induce the production of other osmoprotectants, for which the complete pathways were observed in the ULC029 genome. In total, 140 genes known to be involved in stress resistance were annotated. Here, we confirm that the sequential application of moderate osmotic stress and dehydration could improve cyanobacterial hardening for soil restoration by inducing several resistance mechanisms. We provide a high-quality genome of ULC029 and a description of the main resistance mechanisms (i.e., production of exopolysaccharides, osmoprotectants, chlorophyll, and carotenoids; DNA repair; and oxidative stress protection).
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Affiliation(s)
- Beatriz Roncero-Ramos
- InBios-Molecular Diversity and Ecology of Cyanobacteria, University of Liège, Liege, Belgium
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Sevilla, Spain
| | - Valentina Savaglia
- InBios-Molecular Diversity and Ecology of Cyanobacteria, University of Liège, Liege, Belgium
- Laboratory of Protistology & Aquatic Ecology, Ghent University, Ghent, Belgium
| | - Benoit Durieu
- InBios-Molecular Diversity and Ecology of Cyanobacteria, University of Liège, Liege, Belgium
| | | | - Aurore Richel
- TERRA-Biomass and Green Technologies, University of Liège, Gembloux, Belgium
| | - Annick Wilmotte
- InBios-Molecular Diversity and Ecology of Cyanobacteria, University of Liège, Liege, Belgium
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17
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Oba K, Yasuda S, Terada A. Complete genome sequence of Afipia carboxidovorans strain SH125, a non-denitrifying nitrous oxide-reducing bacterium isolated from anammox biomass. Microbiol Resour Announc 2024; 13:e0127923. [PMID: 38385666 DOI: 10.1128/mra.01279-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 02/13/2024] [Indexed: 02/23/2024] Open
Abstract
Here, we report a genome sequence of Afipia carboxidovorans strain SH125 isolated from an anammox reactor. This facultative anaerobic strain possesses the clade I-type nitrous oxide (N2O) reductase gene, devoid of nitrite- and nitric oxide reductase genes. Deciphering the genome will help explore N2O reducers instrumental in N2O mitigation.
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Affiliation(s)
- Kohei Oba
- Department of Applied Physics and Chemical Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan
| | - Shohei Yasuda
- Civil Engineering, School of Engineering, College of Science and Engineering, University of Galway, Galway, Ireland
| | - Akihiko Terada
- Department of Applied Physics and Chemical Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan
- Global Innovation Research Institute, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
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18
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Bedoya-Urrego K, Alzate JF. Phylogenomic discernments into Anaerolineaceae thermal adaptations and the proposal of a candidate genus Mesolinea. Front Microbiol 2024; 15:1349453. [PMID: 38486696 PMCID: PMC10937449 DOI: 10.3389/fmicb.2024.1349453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/14/2024] [Indexed: 03/17/2024] Open
Abstract
This study delves into the evolutionary history of Anaerolineaceae, a diverse bacterial family within the Chloroflexota phylum. Employing a multi-faceted approach, including phylogenetic analyses, genomic comparisons, and exploration of adaptive features, the research unveils novel insights into the family's taxonomy and evolutionary dynamics. The investigation employs metagenome-assembled genomes (MAGs), emphasizing their prevalence in anaerobic environments. Notably, a novel mesophilic lineage, tentatively named Mesolinea, emerges within Anaerolineaceae, showcasing a distinctive genomic profile and apparent adaptation to a mesophilic lifestyle. The comprehensive genomic analyses shed light on the family's complex evolutionary patterns, including the conservation of key operons in thermophiles, providing a foundation for understanding the diverse ecological roles and adaptive strategies of Anaerolineaceae members.
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Affiliation(s)
- Katherine Bedoya-Urrego
- Centro Nacional de Secuenciación Genómica, Sede de Investigación Universitaria, Universidad de Antioquia, Medellín, Colombia
| | - Juan F. Alzate
- Centro Nacional de Secuenciación Genómica, Sede de Investigación Universitaria, Universidad de Antioquia, Medellín, Colombia
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
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19
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Erban T, Sopko B, Klimov PB, Hubert J. Mixta mediterraneensis as a novel and abundant gut symbiont of the allergen-producing domestic mite Blomia tropicalis. EXPERIMENTAL & APPLIED ACAROLOGY 2024; 92:161-181. [PMID: 38227156 DOI: 10.1007/s10493-023-00875-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/12/2023] [Indexed: 01/17/2024]
Abstract
Blomia tropicalis is an allergen-producing mite in the human environment in tropical regions. The microbiome of B. tropicalis was described using the barcode sequencing region of V4 16S rDNA and genome assemblage. Mixta mediterraneensis, previously isolated from human skin swabs, was identified as a B. tropicalis gut symbiont based on genome assembly. The microbiome contains two bacteria, Staphylococcus and M. mediterraneensis. The number of M. mediterraneensis 16S DNA copies was 106 per mite and 109 per feces in the rearing chamber based on qPCR quantification. The profile of this bacterium reached 50% of reads in the mite gut and feces. Genomic analyses revealed that the bacterium has several metabolic pathways that suggest metabolic cooperation with the mite host in vitamin and amino acid synthesis, nitrogen recycling, and antimicrobial defense. Lysozyme is present in the symbiotic bacterium but absent in the mite. The B. tropicalis microbiome contained Staphylococcus, which accelerates mite population growth. Mites can digest Staphylococcus by using specific enzymes with hydrolytic functions against bacterial cell walls (chitinases and cathepsin D), leading to endocytosis of bacteria and their degradation in lysosomes and phagosomes. Gene expression analysis of B. tropicalis indicated that phagocytosis was mediated by the PI3-kinase/Akt pathway interacting with the invasins produced by M. mediterraneensis. Moreover, the symbiont had metabolic pathways that allowed it to recycle the mite metabolic waste product guanine, known as a mite attractant. The mite host symbiont enhances mite aggregation in the feces, and the fecal-oral transmission route is excepted.
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Affiliation(s)
- Tomas Erban
- Crop Research Institute, Drnovska 507/73, 161 06, Prague 6 - Ruzyne, Czechia
| | - Bruno Sopko
- Crop Research Institute, Drnovska 507/73, 161 06, Prague 6 - Ruzyne, Czechia
| | - Pavel B Klimov
- Purdue University, Lilly Hall of Life Sciences, G-225, 915 W State St, West Lafayette, IN, 47907, USA
| | - Jan Hubert
- Crop Research Institute, Drnovska 507/73, 161 06, Prague 6 - Ruzyne, Czechia.
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00, Prague 6 - Suchdol, Czechia.
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20
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FUKAO M, OKI A, SEGAWA S. Genome-based assessment of safety characteristics of Lacticaseibacillus paracasei NY1301 and genomic differences in closely related strains marketed as probiotics. BIOSCIENCE OF MICROBIOTA, FOOD AND HEALTH 2024; 43:145-149. [PMID: 38562548 PMCID: PMC10981942 DOI: 10.12938/bmfh.2023-072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 12/29/2023] [Indexed: 04/04/2024]
Abstract
The probiotic attributes of Lacticaseibacillus paracasei NY1301 were comprehensively characterized, and a comparison between the closely related LcA (Actimel) and LcY (Yakult) probiotic strains was conducted using genomic tools. All strains exhibited high genetic similarity and likely shared a common ancestor; differences were primarily expressed as minor chromosomal re-arrangements, substitutions, insertions, and deletions. Compared with LcY, NY1301 exhibited 125 single-nucleotide polymorphisms. NY1301 lacked virulence factors, antibiotic resistance genes, and mutations associated with antibiotic resistance and had a 46-kbp prophage. This prophage is spontaneously induced at low levels and remains in a non-lytic state under standard culture conditions. The observed causal adaptive mutations were likely related to niche adaptation within the respective laboratory or manufacturing processes that occurred during the maintenance of the strains. However, the phenotypic effects of these genomic differences remain unclear. To validate the safety of NY1301, we conducted an open-label trial with healthy participants who consumed excessive amounts of NY1301 (3.0 × 1011 cfu) daily for 28 days. The results of this trial and those of other in vivo studies, coupled with the long history of human consumption without established risks to humans, provide strong evidence confirming the safety of NY1301.
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Affiliation(s)
- Masanori FUKAO
- Nissin York Co., Ltd., 3-6-11 Higashi-Nihonbashi, Chuo-ku,
Tokyo 103-0004, Japan
| | - Atsushi OKI
- Nissin Foods Holdings Co., Ltd., 2100 Tobuki, Hachioji-shi,
Tokyo 192-0001, Japan
| | - Shuichi SEGAWA
- Nissin York Co., Ltd., 3-6-11 Higashi-Nihonbashi, Chuo-ku,
Tokyo 103-0004, Japan
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21
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Wokorach G, Erima B, Najjuka F, Kiyengo J, Kibuuka H, Musinguzi AK, Wabwire-Mangen F, Byarugaba DK. Draft genome sequence of Staphylococcus urealyticus strain MUWRP0921, isolated from the urine of an adult female Ugandan. Microbiol Resour Announc 2024; 13:e0081723. [PMID: 38078696 DOI: 10.1128/mra.00817-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/19/2023] [Indexed: 01/18/2024] Open
Abstract
Staphylococcus urealyticus bacteria are pathogenic among immune-compromised individuals. A strain (MUWRP0921) of Staphylococcus urealyticus with a genome of 2,708,354 bp was isolated from Uganda and carries genes that are associated with antibiotic resistance, including resistance to macrolides (erm(C) and mph(C')), aminoglycosides (aac(6")-aph(2")), tetracyclines (tet(K)), and trimethoprim (dfrG).
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Affiliation(s)
- Godfrey Wokorach
- Makerere University Walter Reed Project , Kampala, Uganda
- Multifunctional Research Laboratories, Gulu University , Gulu, Uganda
| | - Bernard Erima
- Makerere University Walter Reed Project , Kampala, Uganda
| | | | | | - Hannah Kibuuka
- Makerere University Walter Reed Project , Kampala, Uganda
| | | | - Fred Wabwire-Mangen
- Makerere University Walter Reed Project , Kampala, Uganda
- Makerere University , Kampala, Uganda
| | - Denis K Byarugaba
- Makerere University Walter Reed Project , Kampala, Uganda
- Makerere University , Kampala, Uganda
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22
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Kato H, Ohtsubo Y, Hirano S, Masuda S, Shibata A, Shirasu K, Nagata Y. Draft genome sequence of Cupriavidus sp. strain TKC, isolated from a γ-hexachlorocyclohexane-degrading community. Microbiol Resour Announc 2023; 12:e0056723. [PMID: 37937996 PMCID: PMC10720496 DOI: 10.1128/mra.00567-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 09/26/2023] [Indexed: 11/09/2023] Open
Abstract
Cupriavidus sp. strain TKC was isolated from a microbial community enriched with γ-hexachlorocyclohexane (γ-HCH). This strain did not show γ-HCH-degrading activity but was one of the major members of the community. Here, we present the draft genome sequence of the strain TKC with a size of 7 Mb.
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Affiliation(s)
- Hiromi Kato
- Institute for Agro-Environmental Science, National Agriculture and Food Research Organization, Kan-nondai, Tsukuba, Ibaraki, Japan
- Graduate School of Life Sciences, Tohoku University, Katahira, Sendai, Japan
| | - Yoshiyuki Ohtsubo
- Graduate School of Life Sciences, Tohoku University, Katahira, Sendai, Japan
| | - Shoko Hirano
- Graduate School of Life Sciences, Tohoku University, Katahira, Sendai, Japan
| | - Sachiko Masuda
- Plant Immunity Research Group, RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Arisa Shibata
- Plant Immunity Research Group, RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Ken Shirasu
- Plant Immunity Research Group, RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Yuji Nagata
- Graduate School of Life Sciences, Tohoku University, Katahira, Sendai, Japan
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Chowdhury G, Kitahara K, Taniguchi M, Uesaka K, Muzembo BA, Mitra D, Ohno A, Ramamurthy T, Dutta S, Miyoshi SI, Mukhopadhyay AK. Complete genomic sequence of Vibrio fluvialis strain IDH5335 isolated from a patient with diarrhea in Kolkata, India. Microbiol Resour Announc 2023; 12:e0070723. [PMID: 37943041 PMCID: PMC10871063 DOI: 10.1128/mra.00707-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 10/03/2023] [Indexed: 11/10/2023] Open
Abstract
We isolated a Vibrio fluvialis strain (IDH5335) from a stool sample collected from a patient with diarrhea. In this announcement, we report the complete genomic sequence of this organism, which was obtained by combining Illumina and Oxford Nanopore sequencing data.
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Affiliation(s)
- Goutam Chowdhury
- ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
- Collaborative Research Center of Okayama University for Infectious Diseases in India at ICMR-NICED, Kolkata, West Bengal, India
| | - Kei Kitahara
- Collaborative Research Center of Okayama University for Infectious Diseases in India at ICMR-NICED, Kolkata, West Bengal, India
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Makoto Taniguchi
- Oral Microbiome Center, Taniguchi Dental Clinic, Takamatsu, Kagawa, Japan
| | - Kazuma Uesaka
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, Japan
| | - Basilua Andre Muzembo
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Debmalya Mitra
- Collaborative Research Center of Okayama University for Infectious Diseases in India at ICMR-NICED, Kolkata, West Bengal, India
| | - Ayumu Ohno
- Collaborative Research Center of Okayama University for Infectious Diseases in India at ICMR-NICED, Kolkata, West Bengal, India
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | | | - Shanta Dutta
- ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
| | - Shin-ichi Miyoshi
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
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Xu B, Kong J, Lin Y, Tang Z, Liu J, Chen Z, Zeng W, Bai Y, Fan H. Anti- Helicobacter pylori activity and gastroprotective effects of human stomach-derived Lactobacillus paragasseri strain LPG-9. Food Funct 2023; 14:10882-10895. [PMID: 37987614 DOI: 10.1039/d3fo03562j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
The eradication of Helicobacter pylori is an urgent global issue. However, the traditional regimens have several limitations. Thus, we propose the idea of treating bacterial gastric disease with the objective of eliminating gastric pathogenic bacteria and enhancing gastroprotective effects using gastric probiotics. In this study, a total of 12 Lactobacillus strains were isolated from the gastric mucosa of healthy donors. After evaluation using a weight scoring system, Lactobacillus paragasseri strain LPG-9 was identified as the most promising probiotic for gastric disease, with the highest acid-resistance and the best adhesion characteristics. Gastric colonisation, H. pylori inhibition, anti-inflammatory, and gastric homeostasis effects of LPG-9 were confirmed in C57BL/6 mice. Finally, a safety evaluation and whole-genome sequencing were performed. Based on the results of this study, LPG-9 originates from the gastric microbiota and is a promising probiotic for gastric disease, particularly H. pylori-induced gastritis, providing a solution to this global issue.
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Affiliation(s)
- Binyan Xu
- Department of Microbiology, Guangdong Provincial Key Laboratory of Tropical Diseases Research, School of Public Health, Southern Medical University, Guangzhou, China.
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Institute of Gastroenterology of Guangdong Province, Nanfang Hospital, Southern Medical University, Guangzhou, China.
| | - Jingjing Kong
- Department of Microbiology, Guangdong Provincial Key Laboratory of Tropical Diseases Research, School of Public Health, Southern Medical University, Guangzhou, China.
| | - Yangfan Lin
- Department of Microbiology, Guangdong Provincial Key Laboratory of Tropical Diseases Research, School of Public Health, Southern Medical University, Guangzhou, China.
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Institute of Gastroenterology of Guangdong Province, Nanfang Hospital, Southern Medical University, Guangzhou, China.
| | - Ziyu Tang
- Department of Microbiology, Guangdong Provincial Key Laboratory of Tropical Diseases Research, School of Public Health, Southern Medical University, Guangzhou, China.
| | - Jiaxin Liu
- Department of Microbiology, Guangdong Provincial Key Laboratory of Tropical Diseases Research, School of Public Health, Southern Medical University, Guangzhou, China.
| | - Zhenhui Chen
- Department of Microbiology, Guangdong Provincial Key Laboratory of Tropical Diseases Research, School of Public Health, Southern Medical University, Guangzhou, China.
| | - Weiseng Zeng
- Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Yang Bai
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Institute of Gastroenterology of Guangdong Province, Nanfang Hospital, Southern Medical University, Guangzhou, China.
| | - Hongying Fan
- Department of Microbiology, Guangdong Provincial Key Laboratory of Tropical Diseases Research, School of Public Health, Southern Medical University, Guangzhou, China.
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25
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Byarugaba DK, Erima B, Wokorach G, Alafi S, Kibuuka H, Mworozi E, Musinguzi AK, Kiyengo J, Najjuka F, Wabwire-Mangen F. Resistome and virulome of high-risk pandemic clones of multidrug-resistant extra-intestinal pathogenic Escherichia coli (ExPEC) isolated from tertiary healthcare settings in Uganda. PLoS One 2023; 18:e0294424. [PMID: 37992119 PMCID: PMC10664879 DOI: 10.1371/journal.pone.0294424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 11/01/2023] [Indexed: 11/24/2023] Open
Abstract
Multi-drug resistant (MDR) globally disseminated extraintestinal pathogenic high-risk Escherichia coli (ExPEC) clones are threatening the gains in bacterial disease management. In this study, we evaluated the genomic structure including the resistome and virulome of the E. coli isolates from extraintestinal infections using whole genome sequencing (WGS). The results highlight that isolates were highly resistant (≥ 90.0%) to commonly used antibiotics (Ampicillin, Trimethoprim-Sulfamethoxazole, Nalidixic acid, and Piperacillin) and were less (<14%) resistant to last resort antibiotics; Imipenem (10.94%) and Meropenem (10.20%). A greater proportion of the E. coli isolates belonged to phylogroup B2 (30.52%) and phylogroup A (27.37%). The sequence types ST131 of phylogroup B2 (21.05%) and ST648 of phylogroup F (9.3%) were the dominant pandemic high-risk clones identified in addition to the ST1193, ST410, ST69, ST38, ST405, and ST10. Many of the isolates were MDR and most (64.58%) carried the blaCTX-M-15 gene for extended-spectrum β-lactamases. There was a high correlation between phylogroups and the occurrence of both antimicrobial resistance and virulence genes. The cephalosporin-resistance gene blaEC-5 was only found in phylogroup B2 while blaEC-8 and blaEC-19, were only found within phylogroup D and phylogroup F respectively. Aminoglycoside gene (aadA1) was only associated with phylogroups D and C. The isolates were armed with a broad range of virulence genes including adhesins, toxins, secreted proteases, iron uptake genes, and others. The yfcv, chuA, and kpsE genes preferentially occurred among isolates of phylogroup B2. The study underlines the predominance of MDR internationally disseminated high-risk ExPEC clones with a broad range of virulence genes known to be highly transmissible in healthcare and community settings.
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Affiliation(s)
- Denis K. Byarugaba
- Makerere University Walter Reed Project, Kampala, Uganda
- College of Veterinary Medicine, Makerere University, Kampala, Uganda
| | - Bernard Erima
- Makerere University Walter Reed Project, Kampala, Uganda
| | - Godfrey Wokorach
- Makerere University Walter Reed Project, Kampala, Uganda
- Gulu University Multifunctional Research Laboratories, Gulu, Uganda
| | - Stephen Alafi
- Makerere University Walter Reed Project, Kampala, Uganda
| | - Hannah Kibuuka
- Makerere University Walter Reed Project, Kampala, Uganda
| | - Edison Mworozi
- Makerere University Walter Reed Project, Kampala, Uganda
- College of Health Sciences, Makerere University, Kampala, Uganda
| | | | - James Kiyengo
- Uganda Peoples’ Defence Forces, Ministry of Defence, Kampala, Uganda
| | - Florence Najjuka
- College of Health Sciences, Makerere University, Kampala, Uganda
| | - Fred Wabwire-Mangen
- Makerere University Walter Reed Project, Kampala, Uganda
- College of Health Sciences, Makerere University, Kampala, Uganda
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26
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Hisatomi A, Tourlousse DM, Hamajima M, Ohkuma M, Sekiguchi Y, Sakamoto M. Complete genome sequences of Ruminococcus torques strains JCM 36208 and JCM 36209, isolated from the feces of a healthy Japanese male. Microbiol Resour Announc 2023; 12:e0063223. [PMID: 37800929 PMCID: PMC10652952 DOI: 10.1128/mra.00632-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 08/25/2023] [Indexed: 10/07/2023] Open
Abstract
Here, we report the complete genome sequences of two Ruminococcus torques strains (JCM 36208 and JCM 36209) that were newly isolated from the feces of a healthy Japanese male. Both genomes consist of a single circular chromosome with a length of ~2.8 Mbp and a G+C content of 41.8%.
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Affiliation(s)
- Atsushi Hisatomi
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Dieter M. Tourlousse
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Mayu Hamajima
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Yuji Sekiguchi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
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27
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Hijikata A, Oshima T, Yura K, Bessho Y. ThermusQ: Toward the cell simulation platform for Thermus thermophilus. J GEN APPL MICROBIOL 2023; 69:59-67. [PMID: 37460312 DOI: 10.2323/jgam.2023.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Abstract
ThermusQ is a website (https://www.thermusq.net/) that aims to gather all the molecular information on Thermus thermophilus and to provide a platform to easily access the whole view of the bacterium. ThermusQ comprises the genome sequences of 22 strains from T. thermophilus and T. oshimai strains, plus the sequences of known Thermus phages. ThermusQ also contains information and map diagrams of pathways unique to Thermus strains. The website provides tools to retrieve sequence data in different ways. By gathering the whole data of T. thermophilus strains, the strainspecific characteristics was found. This bird's-eye view of the whole data will lead the research community to identify missing important data and the integration will provide a platform to conduct future biochemical simulations of the bacterium.
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Affiliation(s)
- Atsushi Hijikata
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences
| | - Tairo Oshima
- Institute of Environmental Microbiology, Kyowa Kako Co., Ltd
| | - Kei Yura
- Graduate School of Humanities and Sciences, Ochanomizu University
- Center for Interdisciplinary AI and Data Science, Ochanomizu University
- Graduate School of Advanced Science and Engineering, Waseda University
| | - Yoshitaka Bessho
- Center for Interdisciplinary AI and Data Science, Ochanomizu University
- RIKEN SPring-8 Center, Harima Institute
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28
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Byarugaba DK, Erima B, Wokorach G, Alafi S, Kibuuka H, Mworozi E, Najjuka F, Kiyengo J, Musinguzi AK, Wabwire-Mangen F. Genome Analysis of Klebsiella pneumoniae Reveals International High-Risk Pandemic MDR Clones Emerging in Tertiary Healthcare Settings in Uganda. Pathogens 2023; 12:1334. [PMID: 38003798 PMCID: PMC10674604 DOI: 10.3390/pathogens12111334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/14/2023] [Accepted: 10/26/2023] [Indexed: 11/26/2023] Open
Abstract
Klebsiella pneumoniae is a threat to public health due to its continued evolution. In this study, we investigated the evolution, convergence, and transmission of hypervirulent and multi-drug resistant (MDR) clones of K. pneumoniae within healthcare facilities in Uganda. There was high resistance to piperacillin (90.91%), cefuroxime (86.96%), ceftazidime (84.62%), cefotaxime (84.00%), amoxicillin/clavulanate (75%), nalidixic acid (73.68%), and nitrofurantoin (71.43%) antibiotics among K. pneumoniae isolates. The isolates were genetically diverse, consisting of 20 different sequence types (STs) and 34 K-serotype groups. Chromosomal fosA (for fosfomycin) and oqxAB efflux pump genes were detected in all isolates. Two carbapenem resistance genes, blaNDM-5 and blaOXA-181 plus extended-spectrum beta-lactamase (blaCTX-M-15) gene (68.12%), quinolone-resistant genes qnrS1 (28.99%), qnrB1 (13.04%), and qnrB6 (13.04%) and others were found. All, except three of the isolates, harbored plasmids. While the isolates carried a repertoire of virulence genes, only two isolates carried hypervirulent genes demonstrating a low prevalence (2.90%) of hypervirulent strains. Our study demonstrated genetically diverse populations of K. pneumoniae, low levels of carbapenem resistance among the isolates, and no convergence of MDR and hypervirulence. Emerging high-risk international pandemic clones (ST11, ST14, ST147, ST 86 and ST307) were detected in these healthcare settings which are difficult to treat.
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Affiliation(s)
- Denis K. Byarugaba
- Makerere University Walter Reed Project, Kampala P.O. Box 16524, Uganda; (B.E.); (G.W.); (S.A.); (H.K.); (E.M.); (F.W.-M.)
- College of Veterinary Medicine, Makerere University, Kampala P.O. Box 7062, Uganda
| | - Bernard Erima
- Makerere University Walter Reed Project, Kampala P.O. Box 16524, Uganda; (B.E.); (G.W.); (S.A.); (H.K.); (E.M.); (F.W.-M.)
| | - Godfrey Wokorach
- Makerere University Walter Reed Project, Kampala P.O. Box 16524, Uganda; (B.E.); (G.W.); (S.A.); (H.K.); (E.M.); (F.W.-M.)
- Multifunctional Research Laboratories, Gulu University, Gulu P.O. Box 166, Uganda
| | - Stephen Alafi
- Makerere University Walter Reed Project, Kampala P.O. Box 16524, Uganda; (B.E.); (G.W.); (S.A.); (H.K.); (E.M.); (F.W.-M.)
| | - Hannah Kibuuka
- Makerere University Walter Reed Project, Kampala P.O. Box 16524, Uganda; (B.E.); (G.W.); (S.A.); (H.K.); (E.M.); (F.W.-M.)
- College of Veterinary Medicine, Makerere University, Kampala P.O. Box 7062, Uganda
| | - Edison Mworozi
- Makerere University Walter Reed Project, Kampala P.O. Box 16524, Uganda; (B.E.); (G.W.); (S.A.); (H.K.); (E.M.); (F.W.-M.)
- College of Health Sciences, Makerere University, Kampala P.O. Box 7062, Uganda;
| | - Florence Najjuka
- College of Health Sciences, Makerere University, Kampala P.O. Box 7062, Uganda;
| | - James Kiyengo
- Uganda Peoples’ Defence Forces, Ministry of Defence, Kampala P.O. Box 3798, Uganda; (J.K.); (A.K.M.)
| | - Ambrose K. Musinguzi
- Uganda Peoples’ Defence Forces, Ministry of Defence, Kampala P.O. Box 3798, Uganda; (J.K.); (A.K.M.)
| | - Fred Wabwire-Mangen
- Makerere University Walter Reed Project, Kampala P.O. Box 16524, Uganda; (B.E.); (G.W.); (S.A.); (H.K.); (E.M.); (F.W.-M.)
- College of Health Sciences, Makerere University, Kampala P.O. Box 7062, Uganda;
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29
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Wasai-Hara S, Itakura M, Fernandes Siqueira A, Takemoto D, Sugawara M, Mitsui H, Sato S, Inagaki N, Yamazaki T, Imaizumi-Anraku H, Shimoda Y, Minamisawa K. Bradyrhizobium ottawaense efficiently reduces nitrous oxide through high nosZ gene expression. Sci Rep 2023; 13:18862. [PMID: 37914789 PMCID: PMC10620151 DOI: 10.1038/s41598-023-46019-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/26/2023] [Indexed: 11/03/2023] Open
Abstract
N2O is an important greenhouse gas influencing global warming, and agricultural land is the predominant (anthropogenic) source of N2O emissions. Here, we report the high N2O-reducing activity of Bradyrhizobium ottawaense, suggesting the potential for efficiently mitigating N2O emission from agricultural lands. Among the 15 B. ottawaense isolates examined, the N2O-reducing activities of most (13) strains were approximately five-fold higher than that of Bradyrhizobium diazoefficiens USDA110T under anaerobic conditions. This robust N2O-reducing activity of B. ottawaense was confirmed by N2O reductase (NosZ) protein levels and by mitigation of N2O emitted by nodule decomposition in laboratory system. While the NosZ of B. ottawaense and B. diazoefficiens showed high homology, nosZ gene expression in B. ottawaense was over 150-fold higher than that in B. diazoefficiens USDA110T, suggesting the high N2O-reducing activity of B. ottawaense is achieved by high nos expression. Furthermore, we examined the nos operon transcription start sites and found that, unlike B. diazoefficiens, B. ottawaense has two transcription start sites under N2O-respiring conditions, which may contribute to the high nosZ expression. Our study indicates the potential of B. ottawaense for effective N2O reduction and unique regulation of nos gene expression towards the high performance of N2O mitigation in the soil.
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Affiliation(s)
- Sawa Wasai-Hara
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Manabu Itakura
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
| | | | - Daisaku Takemoto
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Masayuki Sugawara
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Hisayuki Mitsui
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Shusei Sato
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Noritoshi Inagaki
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Toshimasa Yamazaki
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Haruko Imaizumi-Anraku
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Yoshikazu Shimoda
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan.
| | - Kiwamu Minamisawa
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan.
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30
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Fukuoka H, Tourlousse DM, Hamajima M, Koike K, Endo I, Sekiguchi Y. Complete genome sequence of Butyricimonas faecihominis JCM 18676 T. Microbiol Resour Announc 2023; 12:e0051423. [PMID: 37668366 PMCID: PMC10586130 DOI: 10.1128/mra.00514-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 07/12/2023] [Indexed: 09/06/2023] Open
Abstract
We report a complete genome sequence of Butyricimonas faecihominis JCM 18676T, generated by nanopore sequencing. The genome consists of a single circular chromosome of 4,851,806 bp, with a G + C content of 42.9%, and was predicted to contain 15 rRNA and 61 tRNA genes and encode for 3,946 proteins.
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Affiliation(s)
- Hironori Fukuoka
- Department of Gastroenterological Surgery, Yokohama City University, Kanagawa, Japan
| | - Dieter M. Tourlousse
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Mayu Hamajima
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Kazuyoshi Koike
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Itaru Endo
- Department of Gastroenterological Surgery, Yokohama City University, Kanagawa, Japan
| | - Yuji Sekiguchi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
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31
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Fukuoka H, Tourlousse DM, Hamajima M, Koike K, Endo I, Sekiguchi Y. Complete genome sequence of Blautia luti JCM 17040 T. Microbiol Resour Announc 2023; 12:e0051323. [PMID: 37650615 PMCID: PMC10508176 DOI: 10.1128/mra.00513-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 07/17/2023] [Indexed: 09/01/2023] Open
Abstract
We generated a complete genome sequence of the type strain of Blautia luti (JCM 17040T = DSM 14534T) by Nanopore sequencing. The genome consists of a circular chromosome of 3,741,599 bp with a G + C content of 42.9% and was predicted to contain 3,431 protein-coding sequences.
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Affiliation(s)
- Hironori Fukuoka
- Department of Gastroenterological Surgery, Yokohama City University, Kanagawa, Japan
| | - Dieter M. Tourlousse
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Mayu Hamajima
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Kazuyoshi Koike
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Itaru Endo
- Department of Gastroenterological Surgery, Yokohama City University, Kanagawa, Japan
| | - Yuji Sekiguchi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
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32
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Kaneko T, Osaka T, Tsuneda S. Tailoring Effective Phage Cocktails for Long-Term Lysis of Escherichia coli Based on Physiological Properties of Constituent Phages. PHAGE (NEW ROCHELLE, N.Y.) 2023; 4:128-135. [PMID: 37841387 PMCID: PMC10574527 DOI: 10.1089/phage.2023.0016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Background Bacteriophage (phage) therapy has regained attention as an alternative to antimicrobial agents for eliminating bacteria; however, the emergence of phage-resistant bacteria during the therapy is a major concern. One method to control this emergence is to create a cocktail composed of multiple phages. Materials and Methods In this study, we isolated 28 phages infecting Escherichia coli and evaluated their bacteriolysis (lysis) activity, lytic spectrum, adsorption rate constant, burst size, and titer of a 1-day incubation, followed by clustering of the phages based on these physiological characteristics. Results The variation in lysis onset time and duration was more significant for cocktails of phages from different clusters than for phage cocktails from the same cluster. Conclusions This suggests that a combination of phages with different physiological characteristics is necessary to create a cocktail that rapidly and continuously lyses bacteria over a prolonged duration while suppressing the emergence of resistant bacterial strains.
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Affiliation(s)
- Tomoyoshi Kaneko
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
- Phage Therapy Institute, Comprehensive Research Organization, Waseda University, Tokyo, Japan
| | - Toshifumi Osaka
- Department of Microbiology and Immunology, Tokyo Women's Medical University, Tokyo, Japan
| | - Satoshi Tsuneda
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
- Phage Therapy Institute, Comprehensive Research Organization, Waseda University, Tokyo, Japan
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33
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Hisatomi A, Kastawa NWEPG, Song I, Ohkuma M, Fukiya S, Sakamoto M. Claveliimonas bilis gen. nov., sp. nov., deoxycholic acid-producing bacteria isolated from human faeces, and reclassification of Sellimonas monacensis Zenner et al. 2021 as Claveliimonas monacensis comb. nov. Int J Syst Evol Microbiol 2023; 73. [PMID: 37737068 DOI: 10.1099/ijsem.0.006030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023] Open
Abstract
Obligately anaerobic, Gram-stain-positive, bacilli, strains 12BBH14T, 9CFEGH4 and 10CPCBH12, were isolated from faecal samples of healthy Japanese people. Strain 12BBH14T showed the highest 16S rRNA gene sequence similarity to Sellimonas monacensis Cla-CZ-80T (97.5 %) and 'Lachnoclostridium phocaeense' Marseille-P3177T (97.2 %). Strain 12BBH14T was also closely related to Eubacterium sp. c-25 with 99.7 % 16S rRNA gene sequence similarity. The 16S rRNA gene sequence analysis showed that strains 12BBH14T, 9CFEGH4 and 10CPCBH12 formed a monophyletic cluster with Eubacterium sp. c-25. Near this monophyletic cluster, S. monacensis Cla-CZ-80T and 'L. phocaeense' Marseille-P3177T formed a cluster and did not form a cluster with other Sellimonas species. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strains 12BBH14T, 9CFEGH4, 10CPCBH12 and Eubacterium sp. c-25 were higher than the cut-off values of species demarcation (>88 % dDDH and >98 % ANI), indicating that these four strains are the same species. On the other hand, the dDDH and ANI values of these strains were lower than the cut-off values of species demarcation against other strains (<29 % dDDH and <76 % ANI). Moreover, the average amino acid identity values among these strains were higher than the genus boundary. These results indicate that the isolates should be considered to belong to a new genus of the family Lachnospiraceae. Based on the collected data, strains 12BBH14T, 9CFEGH4 and 10CPCBH12 represent a novel species of a novel genus, for which the name Claveliimonas bilis gen. nov., sp. nov. is proposed. The type strain of C. bilis is 12BBH14T (=JCM 35899T=DSM 115701T). Eubacterium sp. c-25 belongs to C. bilis. In addition, S. monacensis is transferred to the genus Claveliimonas as Claveliimonas monacensis comb. nov.
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Affiliation(s)
- Atsushi Hisatomi
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | | | - Isaiah Song
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Satoru Fukiya
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
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Ochi A, Kidaka T, Hakimi H, Asada M, Yamagishi J. Chromosome-level genome assembly of Babesia caballi reveals diversity of multigene families among Babesia species. BMC Genomics 2023; 24:483. [PMID: 37620766 PMCID: PMC10463595 DOI: 10.1186/s12864-023-09540-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 07/27/2023] [Indexed: 08/26/2023] Open
Abstract
BACKGROUND Babesia caballi is an intraerythrocytic parasite from the phylum Apicomplexa, capable of infecting equids and causing equine piroplasmosis. However, since there is limited genome information available on B. caballi, molecular mechanisms involved in host specificity and pathogenicity of this species have not been fully elucidated yet. RESULTS Genomic DNA from a B. caballi subclone was purified and sequenced using both Illumina and Nanopore technologies. The resulting assembled sequence consisted of nine contigs with a size of 12.9 Mbp, rendering a total of 5,910 protein-coding genes. The phylogenetic tree of Apicomplexan species was reconstructed using 263 orthologous genes. We identified 481 ves1-like genes and named "ves1c". In contrast, expansion of the major facilitator superfamily (mfs) observed in closely related B. bigemina and B. ovata species was not found in B. caballi. A set of repetitive units containing an open reading frame with a size of 297 bp was also identified. CONCLUSIONS We present a chromosome-level genome assembly of B. caballi. Our genomic data may contribute to estimating gene expansion events involving multigene families and exploring the evolution of species from this genus.
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Affiliation(s)
- Akihiro Ochi
- Equine Research Institute, Japan Racing Association, Shimotsuke, Tochigi, Japan
| | - Taishi Kidaka
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Hassan Hakimi
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, Japan
- Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Masahito Asada
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, Japan
| | - Junya Yamagishi
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan.
- Global Station for Zoonosis Control, GI-CoRE, Hokkaido University, Sapporo, Hokkaido, Japan.
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Fukuzawa S, Sato T, Aoki K, Yamamoto S, Ogasawara N, Nakajima C, Suzuki Y, Horiuchi M, Takahashi S, Yokota SI. High prevalence of colistin heteroresistance in specific species and lineages of Enterobacter cloacae complex derived from human clinical specimens. Ann Clin Microbiol Antimicrob 2023; 22:60. [PMID: 37454128 DOI: 10.1186/s12941-023-00610-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 07/05/2023] [Indexed: 07/18/2023] Open
Abstract
BACKGROUND Colistin (CST) is a last-line drug for multidrug-resistant Gram-negative bacterial infections. CST-heteroresistant Enterobacter cloacae complex (ECC) has been isolated. However, integrated analysis of epidemiology and resistance mechanisms based on the complete ECC species identification has not been performed. METHODS Clinical isolates identified as "E. cloacae complex" by MALDI-TOF MS Biotyper Compass in a university hospital in Japan were analyzed. Minimum inhibitory concentrations of CST were determined by the broth microdilution method. The population analysis profiling (PAP) was performed for detecting the heteroresistant phenotype. The heat shock protein 60 (hsp60) cluster was determined from its partial nucleotide sequence. From the data of whole-genome sequencing, average nucleotide identity (ANI) for determining ECC species, multilocus sequence type, core genome single-nucleotide-polymorphism-based phylogenetic analysis were performed. phoPQ-, eptA-, and arnT-deleted mutants were established to evaluate the mechanism underlying colistin heteroresistance. The arnT mRNA expression levels were determined by reverse transcription quantitative PCR. RESULTS Thirty-eight CST-resistant isolates, all of which exhibited the heteroresistant phenotype by PAP, were found from 138 ECC clinical isolates (27.5%). The prevalence of CST-resistant isolates did not significantly differ among the origin of specimens (29.0%, 27.8%, and 20.2% for respiratory, urine, and blood specimens, respectively). hsp60 clusters, core genome phylogeny, and ANI revealed that the CST-heteroresistant isolates were found in all or most of Enterobacter roggenkampii (hsp60 cluster IV), Enterobacter kobei (cluster II), Enterobacter chuandaensis (clusters III and IX), and Enterobacter cloacae subspecies (clusters XI and XII). No heteroresistant isolates were found in Enterobacter hormaechei subspecies (clusters VIII, VI, and III) and Enterobacter ludwigii (cluster V). CST-induced mRNA upregulation of arnT, which encodes 4-amino-4-deoxy-L-arabinose transferase, was observed in the CST-heteroresistant isolates, and it is mediated by phoPQ pathway. Isolates possessing mcr-9 and mcr-10 (3.6% and 5.6% of total ECC isolates, respectively) exhibited similar CST susceptibility and PAP compared with mcr-negative isolates. CONCLUSIONS Significant prevalence (approximately 28%) of CST heteroresistance is observed in ECC clinical isolates, and they are accumulated in specific species and lineages. Heteroresistance is occurred by upregulation of arnT mRNA induced by CST. Acquisition of mcr genes contributes less to CST resistance in ECC.
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Affiliation(s)
- Shota Fukuzawa
- Department of Microbiology, Sapporo Medical University School of Medicine, Sapporo, Japan
- Clinical Laboratory, National Hospital Organization Hokkaido Cancer Center, Sapporo, Japan
| | - Toyotaka Sato
- Department of Microbiology, Sapporo Medical University School of Medicine, Sapporo, Japan.
- Laboratory of Veterinary Hygiene, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan.
- Graduate School of Infectious Diseases, Hokkaido University, Sapporo, Japan.
- One Health Research Center, Hokkaido University, Sapporo, Japan.
| | - Kotaro Aoki
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
| | - Soh Yamamoto
- Department of Microbiology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Noriko Ogasawara
- Department of Microbiology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- International Collaboration Unit, Hokkaido University, International Institute for Zoonosis Control, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- International Collaboration Unit, Hokkaido University, International Institute for Zoonosis Control, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
| | - Motohiro Horiuchi
- Laboratory of Veterinary Hygiene, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
- Graduate School of Infectious Diseases, Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
| | - Satoshi Takahashi
- Department of Infection Control and Laboratory Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan
- Division of Laboratory Medicine, Sapporo Medical University Hospital, Sapporo, Japan
| | - Shin-Ichi Yokota
- Department of Microbiology, Sapporo Medical University School of Medicine, Sapporo, Japan
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Wakinaka T, Matsutani M, Watanabe J, Mogi Y, Tokuoka M, Ohnishi A. Identification of Capsular Polysaccharide Synthesis Loci Determining Bacteriophage Susceptibility in Tetragenococcus halophilus. Microbiol Spectr 2023; 11:e0038523. [PMID: 37154759 PMCID: PMC10269466 DOI: 10.1128/spectrum.00385-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 04/17/2023] [Indexed: 05/10/2023] Open
Abstract
Bacteriophages infecting Tetragenococcus halophilus, a halophilic lactic acid bacterium, have been a major industrial concern due to their detrimental effects on the quality of food products. Previously characterized tetragenococcal phages displayed narrow host ranges, but there is little information on these mechanisms. Here, we revealed the host's determinant factors for phage susceptibility using two virulent phages, phiYA5_2 and phiYG2_4, that infect T. halophilus YA5 and YG2, respectively. Phage-resistant derivatives were obtained from these host strains, and mutations were found at the capsular polysaccharide (CPS) synthesis (cps) loci. Quantification analysis verified that capsular polysaccharide production by the cps derivatives from YG2 was impaired. Transmission electron microscopy observation confirmed the presence of filamentous structures outside the cell walls of YG2 and their absence in the cps derivatives of YG2. Phage adsorption assays revealed that phiYG2_4 adsorbed to YG2 but not its cps derivatives, which suggests that the capsular polysaccharide of YG2 is the specific receptor for phiYG2_4. Interestingly, phiYA5_2 adsorbed and infected cps derivatives of YG2, although neither adsorption to nor infection of the parental strain YG2 by phiYA5_2 was observed. The plaque-surrounding halos formed by phiYA5_2 implied the presence of the virion-associated depolymerase that degrades the capsular polysaccharide of YA5. These results indicated that the capsular polysaccharide is a physical barrier rather than a binding receptor for phiYA5_2 and that phiYA5_2 specifically overcomes the capsular polysaccharide of YA5. Thus, it is suggested that tetragenococcal phages utilize CPSs as binding receptors and/or degrade CPSs to approach host cells. IMPORTANCE T. halophilus is a halophilic lactic acid bacterium that contributes to the fermentation processes for various salted foods. Bacteriophage infections of T. halophilus have been a major industrial problem causing fermentation failures. Here, we identified the cps loci in T. halophilus as genetic determinants of phage susceptibility. The structural diversity of the capsular polysaccharide is responsible for the narrow host ranges of tetragenococcal phages. The information provided here could facilitate future studies on tetragenococcal phages and the development of efficient methods to prevent bacteriophage infections.
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Affiliation(s)
| | | | - Jun Watanabe
- Manufacturing Division, Yamasa Corporation, Choshi, Japan
- Faculty of Food and Agricultural Sciences, Fukushima University, Fukushima, Japan
- Institute of Fermentation Sciences, Fukushima University, Fukushima, Japan
| | - Yoshinobu Mogi
- Manufacturing Division, Yamasa Corporation, Choshi, Japan
| | - Masafumi Tokuoka
- Department of Fermentation Science, Faculty of Applied Biosciences, Tokyo University of Agriculture, Tokyo, Japan
| | - Akihiro Ohnishi
- Department of Fermentation Science, Faculty of Applied Biosciences, Tokyo University of Agriculture, Tokyo, Japan
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Salvà-Serra F, Pérez-Pantoja D, Donoso RA, Jaén-Luchoro D, Fernández-Juárez V, Engström-Jakobsson H, Moore ERB, Lalucat J, Bennasar-Figueras A. Comparative genomics of Stutzerimonas balearica ( Pseudomonas balearica): diversity, habitats, and biodegradation of aromatic compounds. Front Microbiol 2023; 14:1159176. [PMID: 37275147 PMCID: PMC10234333 DOI: 10.3389/fmicb.2023.1159176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 04/13/2023] [Indexed: 06/07/2023] Open
Abstract
Stutzerimonas balearica (Pseudomonas balearica) has been found principally in oil-polluted environments. The capability of S. balearica to thrive from the degradation of pollutant compounds makes it a species of interest for potential bioremediation applications. However, little has been reported about the diversity of S. balearica. In this study, genome sequences of S. balearica strains from different origins were analyzed, revealing that it is a diverse species with an open pan-genome that will continue revealing new genes and functionalities as the genomes of more strains are sequenced. The nucleotide signatures and intra- and inter-species variation of the 16S rRNA genes of S. balearica were reevaluated. A strategy of screening 16S rRNA gene sequences in public databases enabled the detection of 158 additional strains, of which only 23% were described as S. balearica. The species was detected from a wide range of environments, although mostly from aquatic and polluted environments, predominantly related to petroleum oil. Genomic and phenotypic analyses confirmed that S. balearica possesses varied inherent capabilities for aromatic compounds degradation. This study increases the knowledge of the biology and diversity of S. balearica and will serve as a basis for future work with the species.
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Affiliation(s)
- Francisco Salvà-Serra
- Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Spain
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Danilo Pérez-Pantoja
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación, Universidad Tecnológica Metropolitana, Santiago, Chile
| | - Raúl A. Donoso
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación, Universidad Tecnológica Metropolitana, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
| | - Daniel Jaén-Luchoro
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Víctor Fernández-Juárez
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Hedvig Engström-Jakobsson
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Edward R. B. Moore
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Jorge Lalucat
- Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Spain
| | - Antoni Bennasar-Figueras
- Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Spain
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Kubota H, Serata M, Matsumoto H, Shida K, Okumura T. Detection of Glycolytically Active Lacticaseibacillus paracasei Strain Shirota by Flow Cytometry Targeting the Efflux Activity of Fluorescent Dye: a Potential Tool for Quality Assessment of Probiotic Cells in Milk Products. Appl Environ Microbiol 2023; 89:e0215622. [PMID: 37022200 PMCID: PMC10132099 DOI: 10.1128/aem.02156-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/21/2023] [Indexed: 04/07/2023] Open
Abstract
The rapid and accurate detection of viable probiotic cells in dairy products is important for assessing product quality in manufacturing. Flow cytometry is widely used for the rapid analysis of bacterial cells. However, further investigation is needed into the optimum property to use it for assessing cell viability. Here, we proposed using the efflux activity of a fluorescent dye, carboxyfluorescein (CF), as an indicator of cell viability. CF is generated from 5(6)-carboxyfluorescein diacetate as a result of cleavage by intracellular esterase. It generally accumulates in the cell, but certain bacterial species are known to extrude it. We found here that the probiotic strain Lacticaseibacillus paracasei strain Shirota (LcS) also extruded CF in the presence of energy sources, such as glucose. To investigate the mechanism of its CF-efflux activity, we screened CF-efflux-negative mutants from a random mutagenesis LcS library and examined the whole genome for genes responsible for CF efflux. We identified a base substitution in the pfkA gene in the glycolytic pathway, and we demonstrated that intact pfkA was essential for CF efflux, indicating that CF-efflux-positive cells must have uncompromised glycolytic activity. We also confirmed that there was a good correlation between the rate of CF-efflux-positive cells and that of colony-forming cells of LcS in a fermented milk product, whereas other properties, such as esterase activity and cell membrane integrity, lost their correlation with the colony-forming activity after long storage. We propose that CF-efflux activity could be an appropriate indicator of cell viability in certain probiotic strains. IMPORTANCE To our knowledge, this is the first report to demonstrate that CF efflux requires uncompromised glycolytic activity in certain lactic acid bacteria. Compared with the cell properties currently widely used for cell viability assessment, such as intracellular esterase activity and membrane integrity, CF-efflux activity enables the accurate detection of culturable cells, especially in products stored for long periods at cold temperatures. These results indicate strongly that CF-efflux activity can be an adequate cell-viability indicator and that flow cytometric quantification could be an alternative to conventional CFU counting. Our findings should be especially informative for dairy/probiotic product manufacturing.
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Affiliation(s)
| | | | | | - Kan Shida
- Yakult Central Institute, Tokyo, Japan
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Hisatomi A, Ohkuma M, Sakamoto M. Sellimonas catena sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2023; 73. [PMID: 37185104 DOI: 10.1099/ijsem.0.005853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
Obligately anaerobic, Gram-stain-positive, small-chain coccobacilli, strains 12EGH17T and 18CBH55, were isolated from faecal samples of healthy Japanese humans. Strain 12EGH17T showed the highest 16S rRNA gene sequence similarity to Sellimonas intestinalis BR72T (95.5 %), Coprococcus comes ATCC 27758T (94.4 %) and Clostridium nexile DSM 1787T (93.7 %). The percentage of conserved proteins values between the genome of strain 12EGH17T and that of the members of the genus Sellimonas were >54 %, suggesting that strain 12EGH17T belongs to the genus Sellimonas. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strains 12EGH17T and 18CBH55 were higher than the cut-off values of species demarcation (90 % dDDH and 99 % ANI), indicating these two strains are the same species. However, the dDDH and ANI values of these strains were lower than the cut-off values of species demarcation against other strains (<30 % dDDH and <79 % ANI). These results indicate that the isolates should be considered to represent a new species of the genus Sellimonas. The isolates were differentiated from the type species, S. intestinalis, by the ability of aesculin hydrolysis. Based on the collected data, strains 12EGH17T and 18CBH55 represent a novel species in the genus Sellimonas, for which the name Sellimonas catena sp. nov. is proposed. The type strain of S. catena is 12EGH17T (=JCM 35622T=DSM 114916T).
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Affiliation(s)
- Atsushi Hisatomi
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
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Genomic and phylogenetic characterization of Elizabethkingia anophelis strains: The first two cases of life-threatening infection in Japan. J Infect Chemother 2023; 29:376-383. [PMID: 36682607 DOI: 10.1016/j.jiac.2023.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 01/07/2023] [Accepted: 01/11/2023] [Indexed: 01/22/2023]
Abstract
OBJECTIVE Elizabethkingia anophelis causes meningitis, bloodstream infections, and respiratory infections in immunocompromised individuals. We examined two E. anophelis strains isolated from the first life-threatening cases caused by this species in Japan to determine the phylogenetic origin and genomic features of them. METHODS We performed whole genome-based analysis to clarify the genetic relationship for the two strains (EK0004 and EK0079) and Elizabethkingia sp. strains isolated from worldwide and to characterize the genomic features such as the prevalence of virulence- and antimicrobial resistance (AMR)-related genes. PATIENTS A 29-year-old man with hepatosplenic T-cell lymphoma and a 52-year-old man with systemic lupus erythematosus developed fatal bacteremia and meningitis due to E. anophelis, respectively. RESULTS Two strains, EK0004 and EK0079, were genetically different but most closely related to the strains isolated from the largest outbreak in Wisconsin, USA from 2015 to 2016, and the strain isolated from cerebrospinal fluid of a patient in Florida, USA in 1982, respectively. The two strains contained AMR-related genes such as those encoding for an extended-spectrum β-lactamase and multiple metallo-β-lactamases and several virulence-related genes such as capsular polysaccharide synthesis gene clusters. CONCLUSIONS Although further functional analyses are required to understand the virulence of these clones, these finding suggests that enough caution of E. anophelis infection in immunocompromised patients is required since the number of infections by this species is increasing outside Japan.
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Whole-Genome Sequence of the Sulfate-Reducing Bacterial Strain SYK, Isolated from a Xenic Culture of an Anaerobic Protist. Microbiol Resour Announc 2023; 12:e0125722. [PMID: 36847538 PMCID: PMC10019280 DOI: 10.1128/mra.01257-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
The sulfate-reducing bacterial strain SYK was isolated from a xenic culture of an anaerobic heterolobosean protist which was obtained from a saline lake in Japan. Its draft genome comprises 1 circular chromosome (3,762,062 bp), harboring 3,463 predicted protein- and 65 tRNA-encoding genes and 3 rRNA operons.
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Genome Sequence Analysis of a Wohlfahrtiimonas chitiniclastica Strain Isolated from a Septic Wound of a Hospitalized Patient in Uganda. Microbiol Resour Announc 2023; 12:e0084022. [PMID: 36877041 PMCID: PMC10112062 DOI: 10.1128/mra.00840-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023] Open
Abstract
We report a genome sequence of Wohlfahrtiimonas chitiniclastica strain MUWRP0946, isolated from a hospitalized patient in Uganda. The genome size was 2.08 million bases, and the genome completeness was 94.22%. The strain carries tetracycline, folate pathway antagonist, β-lactam, and aminoglycoside antibiotic resistance genes.
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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] [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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44
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Bacteriobiota of the Cave Church of Sts. Peter and Paul in Serbia-Culturable and Non-Culturable Communities' Assessment in the Bioconservation Potential of a Peculiar Fresco Painting. Int J Mol Sci 2023; 24:ijms24021016. [PMID: 36674536 PMCID: PMC9867463 DOI: 10.3390/ijms24021016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/30/2022] [Accepted: 01/03/2023] [Indexed: 01/07/2023] Open
Abstract
The principal aim of this study was to determine bacterial diversity within the Cave Church of Sts. Peter and Paul, via culturable and non-culturable approaches, and elucidate the antifungal potential of autochthonous antagonistic bacterial isolates against biodeteriogenic fungi. Furthermore, whole-genome sequencing of selected bacterial antagonists and the analysis of genes included in the synthesis of secondary metabolites were performed. With the highest RA values, determined in metabarcoding analysis, phyla Actinobacteriota (12.08-54.00%) and Proteobacteria (25.34-44.97%) dominated most of the samples. A total of 44 different species, out of 96 obtained isolates, were determined as part of the culturable bacteriobiota, with the predominance of species from the genus Bacillus. Bacillus simplex was the only isolated species simultaneously present in all investigated substrata within the church. The best antagonistic activity against 10 biodeteriogenic fungi was documented for Streptomyces anulatus, followed by Bacillus altitudinis, Chryseobacterium viscerum, and Streptomyces sp. with their highest PGI% values ranging of from 55.9% to 80.9%. These promising results indicate that characterized bacteria are excellent candidates for developing biocontrol strategies for suppressing deteriogenic fungi responsible for the deterioration of investigated fresco painting. Finally, isolate 11-11MM, characterized as Streptomyces sp., represents a new species for science prompting the need for further study.
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45
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Genome Sequence of the Sulfate-Reducing Bacterium Pseudodesulfovibrio portus JCM 14722
T. Microbiol Resour Announc 2022; 11:e0094722. [DOI: 10.1128/mra.00947-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Pseudodesulfovibrio portus
JCM 14722
T
is a strictly anaerobic, mesophilic sulfate-reducing bacterium isolated from estuarine sediments in Japan. Its draft genome sequence comprises 1 circular chromosome (3,403,863 bp), harboring 3,182 predicted protein- and 60 tRNA-encoding genes, as well as 2 rRNA operons.
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46
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Complete Genomic Sequences of Two Agarolytic
Vibrio
Species Isolates from the Red Algae
Gracilaria. Microbiol Resour Announc 2022; 11:e0093422. [DOI: 10.1128/mra.00934-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
We report the complete genomic sequences of two agarolytic
Vibrio
species strains, STUT-A11 and STUT-A16, isolated from the red algae
Gracilaria
. Genomic annotations revealed that both strains harbor four β-agarases, α-neoagarooligosaccharide hydrolase, and agarolytic β-galactosidase, which support efficient agarose catabolism.
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47
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Whole-Genome Sequence of an Arsenite-Oxidizing Bacterium,
Pandoraea
sp. Strain NE5, Isolated from the Rhizosphere of the Arsenic Hyperaccumulator Pteris vittata. Microbiol Resour Announc 2022; 11:e0060922. [DOI: 10.1128/mra.00609-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Pandoraea
sp. strain NE5, an arsenite-oxidizing bacterium, was isolated from the rhizosphere of an arsenic hyperaccumulator fern (
Pteris vittate
). Here, the genome sequence of
Pandoraea
sp. strain NE5 is announced.
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Lee AY, Chen CH, Liou JS, Lin YC, Hamada M, Wang YT, Peng LL, Chang SC, Chen CC, Lin CF, Huang L, Huang CH. Micrococcus porci sp. nov., Isolated from Feces of Black Pig ( Sus scrofa). Life (Basel) 2022; 12:life12111749. [PMID: 36362904 PMCID: PMC9697426 DOI: 10.3390/life12111749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 10/25/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022] Open
Abstract
An aerobic bacterium, designated as strain KD337-16T, was isolated from the fecal samples of a black pig. It exhibited spherical, non-motile and non−spore-forming, Gram-positive cells. KD337-16T was identified as a member of the genus Micrococcus through 16S rRNA gene sequencing, and its closest relatives were found to be Micrococcus endophyticus YIM 56238T (99.5% similarity), Micrococcus luteus NCTC 2665T (99.1%), Micrococcus yunnanensis YIM 65004T (99.1%), Micrococcus aloeverae AE-6T (99.1%), Micrococcus antarcticus T2T (98.9%), and Micrococcus flavus LW4T (98.7%). Phylogenomic trees were constructed, and strain KD337-16T was found to form its own cluster as an independent lineage of M. flavus LW4T. Between KD337-16T and its close relatives, the average nucleotide identity, average amino acid identity, and digital DNA−DNA hybridization were below the respective species delineation thresholds at 82.1−86.6%, 78.1−86.1%, and 24.4−34.9%. The major cellular fatty acids and polar lipids were anteiso-C15:0 and iso-C15:0, and DPG and PG, respectively. The predominant menaquinone was MK-8(H2). Taken together, the results indicate that strain KD337-16T is a novel species of the genus Micrococcus, for which the name Micrococcus porci sp. nov. is proposed. The type strain is KD337-16T (=BCRC 81318T = NBRC 115578T).
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Affiliation(s)
- Ai-Yun Lee
- Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute, Hsinchu 30062, Taiwan
| | - Chia-Hsuan Chen
- Livestock Research Institute, Council of Agriculture, Executive Yuan, Tainan 71246, Taiwan
| | - Jong-Shian Liou
- Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute, Hsinchu 30062, Taiwan
| | - Yu-Chun Lin
- Livestock Research Institute, Council of Agriculture, Executive Yuan, Tainan 71246, Taiwan
| | - Moriyuki Hamada
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Yu-Ting Wang
- Division of Research and Analysis, Food and Drug Administration, Ministry of Health and Welfare, Taipei 11561, Taiwan
| | - Lin-Liang Peng
- Kaohsiung Animal Propagation Station, COA-LRI, Pingtung 91247, Taiwan
| | - Shen-Chang Chang
- Kaohsiung Animal Propagation Station, COA-LRI, Pingtung 91247, Taiwan
| | - Chih-Chieh Chen
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
- Rapid Screening Research Center for Toxicology and Biomedicine, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Chuen-Fu Lin
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung 912301, Taiwan
| | - Lina Huang
- Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute, Hsinchu 30062, Taiwan
| | - Chien-Hsun Huang
- Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute, Hsinchu 30062, Taiwan
- Correspondence: ; Tel.: +886-3-522-3191; Fax: +886-3-522-4171
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49
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Complete Genome Sequence of a Macrolide-Resistant Bordetella pertussis Isolated in Japan. Microbiol Resour Announc 2022; 11:e0071822. [PMID: 36129277 PMCID: PMC9584335 DOI: 10.1128/mra.00718-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
We report the complete genome sequence of macrolide-resistant Bordetella pertussis BP616, which was first isolated in 2018 in Japan. The BP616 genome can serve as a valuable specific reference for genomic and epidemiological studies of this resistant bacterium.
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50
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Draft Genome Sequences of Two Listeria monocytogenes Strains Isolated from Raccoon Feces in Japan. Microbiol Resour Announc 2022; 11:e0049522. [PMID: 36005763 PMCID: PMC9476924 DOI: 10.1128/mra.00495-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Listeria monocytogenes serotype 4b strains RF01 and RF06 were isolated from raccoon feces in Japan. Here, we report the draft genome sequences of the two isolated strains; the genome sizes were 2,918,024 and 2,872,491 bp, with 535× and 510× coverage, for the RF01 and RF06 strains, respectively.
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