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Kang T, Choi YJ, Kim J, Park HJ, Jang WJ. Whole genome sequence and comparative genomic analysis of novel Rickettsia koreansis strain CNH17-7 isolated from human. Eur J Clin Microbiol Infect Dis 2024; 43:1909-1918. [PMID: 39031268 DOI: 10.1007/s10096-024-04876-x] [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: 04/19/2024] [Accepted: 06/15/2024] [Indexed: 07/22/2024]
Abstract
PURPOSE To determine the genomic feature of novel spotted fever-causing Rickettsia koreansis strain CNH17-7, which is different from R. japonica that is a causative agent for Japanese spotted fever (JSF), and to perform its comparative genomic analysis. METHODS Whole genome sequencing (WGS) was performed on R. koreansis strain CNH17-7 by using the Illumina Miseq system. After WGS, assembly and annotation were done by SPAdes. Then, its genomic features were compared with 19 different Rickettsia species. Based on the average nucleotide identity (ANI) value, an unweighted pair group method with an arithmetic mean (UPGMA) dendrogram was generated. Following the dendrogram analysis, pan-and core-genome analysis was performed. Then additional comparative analyses with two genetically closest Rickettsia species were conducted based on gene repertoire. RESULTS R. koreansis strain CNH17-7 has a chromosome consisting of 1,392,633 bp with GC content of 32.4%. The ANI-derived UPGMA showed that R. koreansis strain CNH17-7 is genetically close to R. japonica YH and R. heilongjiangensis 054 but is distinctively differentiated. The ANI value of R. koreansis strain CNH17-7 to R. japonica YH and R. heilongjiangensis 054 are 98.14% and 98.04% respectively, indicating R. koreansis strain CNH17-7 is sufficient to be classified as a new species. Other than ANI, R. koreansis strain CNH17-7 also contains novel CDS and its COG functional category proportion which is distinct compared to R. japonica YH and R. heilongjiangensis 054. CONCLUSION We have revealed genomic features of the novel R. koreansis strain CNH17-7. Hence, we propose R. koreansis strain CNH17-7 as new Rickettsia species.
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Affiliation(s)
- Taeuk Kang
- Department of Microbiology, Konkuk University School of Medicine, College of Medicine, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
- Research Institute of Medical Science, Konkuk University School of Medicine, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
| | - Yeon-Joo Choi
- Department of Microbiology, Konkuk University School of Medicine, College of Medicine, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
- Research Institute of Medical Science, Konkuk University School of Medicine, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
| | - Jeoungyeon Kim
- Department of Microbiology, Konkuk University School of Medicine, College of Medicine, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
- Research Institute of Medical Science, Konkuk University School of Medicine, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
| | - Hye-Jin Park
- Department of Microbiology, Konkuk University School of Medicine, College of Medicine, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
- Research Institute of Medical Science, Konkuk University School of Medicine, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
| | - Won-Jong Jang
- Department of Microbiology, Konkuk University School of Medicine, College of Medicine, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea.
- Research Institute of Medical Science, Konkuk University School of Medicine, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea.
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Rouard C, Greig DR, Tauhid T, Dupke S, Njamkepo E, Amato E, van der Putten B, Naseer U, Blaschitz M, Mandilara GD, Cohen Stuart J, Indra A, Noël H, Sideroglou T, Heger F, van den Beld M, Wester AL, Quilici ML, Scholz HC, Fröding I, Jenkins C, Weill FX. Genomic analysis of Vibrio cholerae O1 isolates from cholera cases, Europe, 2022. Euro Surveill 2024; 29. [PMID: 39239731 PMCID: PMC11378513 DOI: 10.2807/1560-7917.es.2024.29.36.2400069] [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: 09/07/2024] Open
Abstract
BackgroundThe number of cholera cases reported to the World Health Organization (WHO) in 2022 was more than double that of 2021. Nine countries of the WHO European Region reported 51 cases of cholera in 2022 vs five reported cases in 2021.AimWe aimed to confirm that the Vibrio cholerae O1 isolates reported by WHO European Region countries in 2022 belonged to the seventh pandemic El Tor lineage (7PET). We also studied their virulence, antimicrobial resistance (AMR) determinants and phylogenetic relationships.MethodsWe used microbial genomics to study the 49 V. cholerae O1 isolates recovered from the 51 European cases. We also used > 1,450 publicly available 7PET genomes to provide a global phylogenetic context for these 49 isolates.ResultsAll 46 good-quality genomes obtained belonged to the 7PET lineage. All but two isolates belonged to genomic Wave 3 and were grouped within three sub-lineages, one of which, Pre-AFR15, predominated (34/44). This sub-lineage, corresponding to isolates from several countries in Southern Asia, the Middle East and Eastern or Southern Africa, was probably a major contributor to the global upsurge of cholera cases in 2022. No unusual AMR profiles were inferred from analysis of the AMR gene content of the 46 genomes.ConclusionReference laboratories in high-income countries should use whole genome sequencing to assign V. cholerae O1 isolates formally to the 7PET or non-epidemic lineages. Periodic collaborative genomic studies based on isolates from travellers can provide useful information on the circulating strains and their evolution, particularly as concerns AMR.
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Affiliation(s)
- Caroline Rouard
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Centre National de Référence des Vibrions et du choléra, Paris, France
| | - David R Greig
- Gastrointestinal Bacteria Reference Unit (GBRU), UK Health Security Agency, London, United Kingdom
| | - Thamida Tauhid
- Public Health Agency of Sweden, Unit for Laboratory Surveillance of Bacterial Pathogens, Solna, Sweden
| | - Susann Dupke
- Centre for Biological Threats and Special Pathogens (ZBS 2), National Consultant Laboratory for Human Pathogenic Vibrio species, Robert Koch Institute, Berlin, Germany
| | - Elisabeth Njamkepo
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Centre National de Référence des Vibrions et du choléra, Paris, France
| | - Ettore Amato
- Norwegian Institute of Public Health, Department of Infection Control and Preparedness, Oslo, Norway
| | - Boas van der Putten
- Centre for Infectious Disease Control, Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Umaer Naseer
- Norwegian Institute of Public Health, Department of Infection Control and Preparedness, Oslo, Norway
| | | | - Georgia D Mandilara
- National Reference Centre for Salmonella, School of Public Health, University of West Attica, Athens, Greece
| | - James Cohen Stuart
- Department of Medical Microbiology, Noordwest Ziekenhuisgroep, Alkmaar, The Netherlands
| | - Alexander Indra
- Paracelsus Medical University of Salzburg, Salzburg, Austria
| | - Harold Noël
- Santé publique France, Saint Maurice, France
| | - Theologia Sideroglou
- Directorate of Epidemiological Surveillance and Intervention for Infectious Diseases, National Public Health Organization (NPHO), Athens, Greece
| | - Florian Heger
- Austrian Agency for Health and Food Safety, Vienna, Austria
| | - Maaike van den Beld
- Centre for Infectious Disease Control, Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Astrid Louise Wester
- Norwegian Institute of Public Health, Department of Bacteriology, Norwegian Reference Laboratory for Cholera, Oslo, Norway
| | - Marie-Laure Quilici
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Centre National de Référence des Vibrions et du choléra, Paris, France
| | - Holger C Scholz
- Centre for Biological Threats and Special Pathogens (ZBS 2), National Consultant Laboratory for Human Pathogenic Vibrio species, Robert Koch Institute, Berlin, Germany
| | - Inga Fröding
- Public Health Agency of Sweden, Unit for Laboratory Surveillance of Bacterial Pathogens, Solna, Sweden
| | - Claire Jenkins
- Gastrointestinal Bacteria Reference Unit (GBRU), UK Health Security Agency, London, United Kingdom
| | - François-Xavier Weill
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Centre National de Référence des Vibrions et du choléra, Paris, France
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Effects of NaCl Concentration on the Behavior of Vibrio brasiliensis and Transcriptome Analysis. Foods 2022; 11:foods11060840. [PMID: 35327263 PMCID: PMC8955013 DOI: 10.3390/foods11060840] [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] [Received: 02/19/2022] [Revised: 03/08/2022] [Accepted: 03/10/2022] [Indexed: 11/26/2022] Open
Abstract
The growth of Vibrio bacteria is affected by environmental conditions, and unfavorable conditions will produce different degrees of stress on Vibrio. The cells respond to the stress on the bacteria through changes in biological characteristics and transcriptomes. To study the effect of NaCl concentration on Vibrio brasiliensis, we have determined the biological characteristics of the 0%, 1%, 2%, 3%, 5%, and 7% NaCl concentrations cultured V. brasiliensis to research the salt stress to bacteria. We found that the biological properties of V. brasiliensis cultured with different NaCl concentrations were different, and the expression of outer membrane proteins of V. brasiliensis changed when it was grown under different NaCl concentrations. When bacteria cultured in higher NaCl concentrations (3%, 5% and 7% NaCl), the sodium-type flagellar protein MotY was found. Finally, the transcriptome analysis of V. brasiliensis cultured with 0% NaCl and 7% NaCl was carried out to find out the differentially expressed genes. We found that the same gene have opposite up-regulated and down-regulated expression in two treatments, indicating that these types of genes are regulated different in low and high osmotic stress.
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Nouioui I, Ha SM, Baek I, Chun J, Goodfellow M. Genome insights into the pharmaceutical and plant growth promoting features of the novel species Nocardia alni sp. nov. BMC Genomics 2022; 23:70. [PMID: 35062865 PMCID: PMC8783487 DOI: 10.1186/s12864-021-08257-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 12/14/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Recent studies highlighted the biosynthetic potential of nocardiae to produce diverse novel natural products comparable to that of Streptomyces, thereby making them an attractive source of new drug leads. Many of the 119 Nocardia validly named species were isolated from natural habitats but little is known about the diversity and the potential of the endophytic nocardiae of root nodule of actinorhizal plants. RESULTS The taxonomic status of an actinobacterium strain, designated ncl2T, was established in a genome-based polyphasic study. The strain was Gram-stain-positive, produced substrate and aerial hyphae that fragmented into coccoid and rod-like elements and showed chemotaxonomic properties that were also typical of the genus Nocardia. It formed a distinct branch in the Nocardia 16S rRNA gene tree and was most closely related to the type strains of Nocardia nova (98.6%), Nocardia jiangxiensis (98.4%), Nocardia miyuensis (97.8%) and Nocardia vaccinii (97.7%). A comparison of the draft genome sequence generated for the isolate with the whole genome sequences of its closest phylogenetic neighbours showed that it was most closely related to the N. jiangxiensis, N. miyuensis and N. vaccinii strains, a result underpinned by average nucleotide identity and digital DNA-DNA hybridization data. Corresponding taxogenomic data, including those from a pan-genome sequence analysis showed that strain ncl2T was most closely related to N. vaccinii DSM 43285T. A combination of genomic, genotypic and phenotypic data distinguished these strains from one another. Consequently, it is proposed that strain ncl2T (= DSM 110931T = CECT 30122T) represents a new species within the genus Nocardia, namely Nocardia alni sp. nov. The genomes of the N. alni and N. vaccinii strains contained 36 and 29 natural product-biosynthetic gene clusters, respectively, many of which were predicted to encode for a broad range of novel specialised products, notably antibiotics. Genome mining of the N. alni strain and the type strains of its closest phylogenetic neighbours revealed the presence of genes associated with direct and indirect mechanisms that promote plant growth. The core genomes of these strains mainly consisted of genes involved in amino acid transport and metabolism, energy production and conversion and transcription. CONCLUSIONS Our genome-based taxonomic study showed that isolate ncl2T formed a new centre of evolutionary variation within the genus Nocardia. This novel endophytic strain contained natural product biosynthetic gene clusters predicted to synthesize novel specialised products, notably antibiotics and genes associated with the expression of plant growth promoting compounds.
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Affiliation(s)
- Imen Nouioui
- Department of Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124, Braunschweig, Germany.
| | - Sung-Min Ha
- Department of Integrative Biology and Physiology, University of California Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA
| | - Inwoo Baek
- School of Biological Sciences & Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea
| | - Jongsik Chun
- School of Biological Sciences & Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea
- ChunLab, Inc, Seoul, Korea
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, NE1 7RU, Newcastle upon Tyne, UK
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Min H, Baek K, Lee A, Seok YJ, Choi Y. Genomic characterization of four Escherichia coli strains isolated from oral lichen planus biopsies. J Oral Microbiol 2021; 13:1905958. [PMID: 33828821 PMCID: PMC8009128 DOI: 10.1080/20002297.2021.1905958] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Oral lichen planus (OLP) is a chronic T cell-mediated inflammatory disease that affects the mucus membrane of the oral cavity. We previously proposed a potential role of intracellular bacteria detected within OLP lesions in the pathogenesis of OLP and isolated four Escherichia coli strains from OLP tissues that were phylogenetically close to K-12 MG1655 strain. We sequenced the genomes of the four OLP-isolated E. coli strains and generated 6.71 Gbp of Illumina MiSeq data (166–195x coverage per strain). The size of the assembled draft genomes was 4.69 Mbp, with a GC content of 50.7%, in which 4360 to 4367 protein-coding sequences per strain were annotated. We also identified 368 virulence factors and 53 antibiotic resistance genes. Comparative genomics revealed that the OLP-isolated strains shared more pangenome orthologous groups with pathogenic strains than did the K-12 MG1655 strain, a derivative of K-12 strain isolated from human feces. Although the OLP-isolated strains did not have the major virulence factors (VFs) of the pathogenic strains, a number of VFs involved in adherence/invasion, colonization, or systemic infection were identified. The genomic characteristics of E. coli first isolated from the oral cavity would benefit future investigations on the pathogenic potential of these bacteria.
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Affiliation(s)
- Huitae Min
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, Republic of Korea
| | - Keumjin Baek
- Department of Immunology and Molecular Microbiology, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, Republic of Korea
| | - Ahreum Lee
- Department of Immunology and Molecular Microbiology, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, Republic of Korea
| | - Yeong-Jae Seok
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, Republic of Korea
| | - Youngnim Choi
- Department of Immunology and Molecular Microbiology, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, Republic of Korea
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Bhandari M, Jennison AV, Rathnayake IU, Huygens F. Evolution, distribution and genetics of atypical Vibrio cholerae - A review. INFECTION GENETICS AND EVOLUTION 2021; 89:104726. [PMID: 33482361 DOI: 10.1016/j.meegid.2021.104726] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 01/07/2021] [Accepted: 01/15/2021] [Indexed: 12/21/2022]
Abstract
Vibrio cholerae is the etiological agent of cholera, a severe diarrheal disease, which can occur as either an epidemic or sporadic disease. Cholera pandemic-causing V. cholerae O1 and O139 serogroups originated from the Indian subcontinent and spread globally and millions of lives are lost each year, mainly in developing and underdeveloped countries due to this disease. V. cholerae O1 is further classified as classical and El Tor biotype which can produce biotype specific cholera toxin (CT). Since 1961, the current seventh pandemic El Tor strains replaced the sixth pandemic strains resulting in the classical biotype strain that produces classical CT. The ongoing evolution of Atypical El Tor V. cholerae srains encoding classical CT is of global concern. The severity in the pathophysiology of these Atypical El Tor strains is significantly higher than El Tor or classical strains. Pathogenesis of V. cholerae is a complex process that involves coordinated expression of different sets of virulence-associated genes to cause disease. We are yet to understand the complete virulence profile of V. cholerae, including direct and indirect expression of genes involved in its survival and stress adaptation in the host. In recent years, whole genome sequencing has paved the way for better understanding of the evolution and strain distribution, outbreak identification and pathogen surveillance for the implementation of direct infection control measures in the clinic against many infectious pathogens including V. cholerae. This review provides a synopsis of recent studies that have contributed to the understanding of the evolution, distribution and genetics of the seventh pandemic Atypical El Tor V. cholerae strains.
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Affiliation(s)
- Murari Bhandari
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia; Public Health Microbiology, Forensic and Scientific Services, Queensland Department of Health, Brisbane, QLD, Australia
| | - Amy V Jennison
- Public Health Microbiology, Forensic and Scientific Services, Queensland Department of Health, Brisbane, QLD, Australia
| | - Irani U Rathnayake
- Public Health Microbiology, Forensic and Scientific Services, Queensland Department of Health, Brisbane, QLD, Australia
| | - Flavia Huygens
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia.
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Park S, Steinegger M, Cho HS, Chun J. Metagenomic Association Analysis of Gut Symbiont Limosilactobacillus reuteri Without Host-Specific Genome Isolation. Front Microbiol 2020; 11:585622. [PMID: 33329454 PMCID: PMC7717999 DOI: 10.3389/fmicb.2020.585622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 10/29/2020] [Indexed: 11/13/2022] Open
Abstract
Limosilactobacillus reuteri is a model symbiont that colonizes the guts of vertebrates in studies on host adaptation of the gut symbiont. Previous studies have investigated host-specific phylogenetic and functional properties by isolating the genomic sequence. This dependency on genome isolation is a significant bottleneck. Here, we propose a method to study the association between L. reuteri and its hosts directly from metagenomic reads without strain isolation using pan-genomes. We characterized the host-specificity of L. reuteri in metagenomic samples, not only in previously studied organisms (mice and pigs) but also in dogs. For each sample, two types of profiles were generated: (1) genome-based strain type abundance profiles and (2) gene composition profiles. Our profiles showed host-association of L. reuteri in both phylogenetic and functional aspects without depending on host-specific genome isolation. We observed not only the presence of host-specific lineages, but also the dominant lineages associated with the different hosts. Furthermore, we showed that metagenome-assembled genomes provide detailed insights into the host-specificity of L. reuteri. We inferred evolutionary trajectories of host-associative L. reuteri strains in the metagenomic samples by placing the metagenome-assembled genomes into a phylogenetic tree and identified novel host-specific genes that were unannotated in existing pan-genome databases. Our pan-genomic approach reduces the need for time-consuming and expensive host-specific genome isolation, while producing consistent results with previous host-association findings in mice and pigs. Additionally, we predicted associations that have not yet been studied in dogs.
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Affiliation(s)
- Sein Park
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, South Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
| | - Martin Steinegger
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
- School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Ho-Seong Cho
- Laboratory of Swine Diseases, College of Veterinary Medicine and Bio-Safety Research Institute, Jeonbuk National University, Iksan, South Korea
| | - Jongsik Chun
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, South Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
- School of Biological Sciences, Seoul National University, Seoul, South Korea
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