1
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Verma N, Choksket S, Singla R, Pinnaka AK, Korpole S. Chromobacterium indicum sp. nov., a Pigment-Producing Bacterium Isolated from Soil. Curr Microbiol 2024; 81:385. [PMID: 39356301 DOI: 10.1007/s00284-024-03910-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 09/17/2024] [Indexed: 10/03/2024]
Abstract
A purple colony, designated as TRC1.1.SA was isolated from a tea garden soil sample. It was a Gram-negative, rod-shaped, non-spore-forming and motile bacterium. The strain TRC1.1.SAT grew aerobically at temperatures 15-37 ℃ and pH levels 5.0-9.0. It showed both oxidase and catalase activity. The 16S rRNA gene sequence blast analysis revealed identity with the members of the genus Chromobacterium. The maximum identity was with the type strains of species Chromobacterium piscinae CCM 3329T (99.8%), C. vaccinii MWU205T (99.7%), and C. violaceum ATCC 12472T (98.7%). However, the average nucleotide identity (ANI) of the genome sequence showed less than 96% similarity with all species of the genus Chromobacterium. Further, digital DNA-DNA hybridization (dDDH) revealed the highest identity of 63.4% with its phylogenetic relative C. piscinae CCM 3329T. The G + C content of the strain was 63.9%. The major polar lipids identified were phosphatidylethanolamine (PE), diphosphatidylglycerol (DPG), and phosphoglyceraldehyde (PG). Fatty acid analysis showed C16:0, C16:1ω7c, C17:0 cyclo, and C18:1ω7c as the major fatty acids. RAST and antiSMASH analyses of the genome revealed the presence of a biosynthetic gene cluster (BGC) involved in the production of violacein pigment, as observed for type species C. violaceum ATCC 12472T. Considering the phenotypic differences and genomic identity, strain TRC1.1.SAT is assigned as a novel species of the genus Chromobacterium, for which the name Chromobacterium indicum is proposed. The type strain of prospective species is designated as TRC1.1.SAT (= MTCC 13391T; JCM 36723T; = KCTC 8324T).
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Affiliation(s)
- Nandini Verma
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India
| | - Stanzin Choksket
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India
| | - Riya Singla
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India
| | - Anil Kumar Pinnaka
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India
| | - Suresh Korpole
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India.
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2
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Kang Z, Martinson VG, Wang Y, Coon KL, Valzania L, Strand MR. Increased environmental microbial diversity reduces the disease risk of a mosquitocidal pathogen. mBio 2024; 15:e0272623. [PMID: 38055338 PMCID: PMC10790785 DOI: 10.1128/mbio.02726-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 10/25/2023] [Indexed: 12/08/2023] Open
Abstract
IMPORTANCE The host-specific microbiotas of animals can both reduce and increase disease risks from pathogens. In contrast, how environmental microbial communities affect pathogens is largely unexplored. Aquatic habitats are of interest because water enables environmental microbes to readily interact with animal pathogens. Here, we focused on mosquitoes, which are important disease vectors as terrestrial adults but are strictly aquatic as larvae. We identified a pathogen of mosquito larvae from the field as a strain of Chromobacterium haemolyticum. Comparative genomic analyses and functional assays indicate this strain and other Chromobacterium are mosquitocidal but are also opportunistic pathogens of other animals. We also identify a critical role for diversity of the environmental microbiota in disease risk. Our study characterizes both the virulence mechanisms of a pathogen and the role of the environmental microbiota in disease risk to an aquatic animal of significant importance to human health.
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Affiliation(s)
- Zhiwei Kang
- Hebei University, College of Life Sciences, Baoding, Hebei, China
| | - Vincent G. Martinson
- Department of Entomology, University of Georgia, Athens, Georgia, USA
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, USA
| | - Yin Wang
- Department of Entomology, University of Georgia, Athens, Georgia, USA
| | - Kerri L. Coon
- Department of Entomology, University of Georgia, Athens, Georgia, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Luca Valzania
- Department of Entomology, University of Georgia, Athens, Georgia, USA
- Institut Curie, Paris, France
| | - Michael R. Strand
- Department of Entomology, University of Georgia, Athens, Georgia, USA
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3
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Brunetti F, Ghiglione B, Gudeta DD, Gutkind G, Guardabassi L, Klinke S, Power P. Biochemical and Structural Characterization of CRH-1, a Carbapenemase from Chromobacterium haemolyticum Related to KPC β-Lactamases. Antimicrob Agents Chemother 2023; 67:e0006123. [PMID: 37272821 PMCID: PMC10353377 DOI: 10.1128/aac.00061-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 05/10/2023] [Indexed: 06/06/2023] Open
Abstract
KPC-2 is one of the most relevant serine-carbapenemases among the carbapenem-resistant Enterobacterales. We previously isolated from the environmental species Chromobacterium haemolyticum a class A CRH-1 β-lactamase displaying 69% amino acid sequence identity with KPC-2. The objective of this study was to analyze the kinetic behavior and crystallographic structure of this β-lactamase. Our results showed that CRH-1 can hydrolyze penicillins, cephalosporins (except ceftazidime), and carbapenems with similar efficacy compared to KPC-2. Inhibition kinetics showed that CRH-1 is not well inhibited by clavulanic acid, in contrast to efficient inhibition by avibactam (AVI). The high-resolution crystal of the apoenzyme showed that CRH-1 has a similar folding compared to other class A β-lactamases. The CRH-1/AVI complex showed that AVI adopts a chair conformation, stabilized by hydrogen bonds to Ser70, Ser237, Asn132, and Thr235. Our findings highlight the biochemical and structural similarities of CRH-1 and KPC-2 and the potential clinical impact of this carbapenemase in the event of recruitment by pathogenic bacterial species.
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Affiliation(s)
- Florencia Brunetti
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Barbara Ghiglione
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Dereje D. Gudeta
- Division of Microbiology, U.S. Food and Drug Administration, National Center for Toxicological Research, Jefferson, Arkansas, USA
| | - Gabriel Gutkind
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Luca Guardabassi
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Sebastián Klinke
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Fundación Instituto Leloir, Buenos Aires, Argentina
- Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Buenos Aires, Argentina
| | - Pablo Power
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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4
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Zwe YH, Li D. Pathogenic and transmissional potentials of a Chromobacterium haemolyticum isolate from a hydroponic farm. J Appl Microbiol 2023; 134:lxad149. [PMID: 37442627 DOI: 10.1093/jambio/lxad149] [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: 05/25/2023] [Revised: 06/26/2023] [Accepted: 07/12/2023] [Indexed: 07/15/2023]
Abstract
AIMS This study aims to investigate the in vitro pathogenicity of Chromobacterium haemolyticum strain WI5 toward the intestinal tract, its resistance to water treatments, and its potential for foodborne transmission through leafy greens produced in hydroponic systems. METHODS AND RESULTS C. haemolyticum WI5 caused cytopathic effects in human colon cells HCT116 and exhibited an 8.2-fold higher cell attachment compared to Salmonella serotype Typhimurium. It showed comparable resistance to sodium hypochlorite (NaOCl) and ultraviolet (UV) treatments as Escherichia coli O157: H7 and Pseudomonas aeruginosa but was more susceptible to desiccation. On lettuce, C. haemolyticum WI5 failed to persist, with counts decreasing below the detection limit (≥4 log reductions) after 3 and 2 days at 4 and 25°C, respectively. CONCLUSIONS C. haemolyticum WI5 demonstrated considerable virulence features and high in vitro pathogenicity toward the intestinal tract. NaOCl and UV treatments were effective in disinfecting C. haemolyticum in water. Due to its high susceptibility to desiccation and poor survivability on lettuce, the foodborne transmission potential of C. haemolyticum is considered limited.
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Affiliation(s)
- Ye Htut Zwe
- Department of Food Science and Technology, National University of Singapore, Singapore 117543
| | - Dan Li
- Department of Food Science and Technology, National University of Singapore, Singapore 117543
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5
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Patterson K, Suleta K, Shearen S, Chapman K. Chromobacterium haemolyticum infection from hot springs near Yellowstone National Park: a case report. J Med Case Rep 2023; 17:259. [PMID: 37349786 DOI: 10.1186/s13256-023-04005-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 05/22/2023] [Indexed: 06/24/2023] Open
Abstract
BACKGROUND Chromobacterium haemolyticum is a gram-negative anaerobic sporulated rod and was only first identified in 2008. It is very rare in people with only a handful of cases having been diagnosed around the world. CASE PRESENTATION After suffering a fall near Yellowstone National Park, a white male patient in his 50 s presented to a hospital in Eastern Idaho. With many unexplained symptoms, several changes in patient stability and recovery, over a course of 18 days in the hospital, the infecting organism could not be easily identified. Labs in the hospital, state, and eventually outside of the state were consulted for pathogen identification, which was only accomplished after the patient was discharged. CONCLUSIONS To our knowledge, this is only the seven reported human infection with Chromobacterium haemolyticum. This bacterium is difficult to identify and may be occur in rural areas without the proper testing facilities to quickly identify the pathogen, which is essential to timely treatment.
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Affiliation(s)
- Kyle Patterson
- Eastern Idaho Regional Medical Center, 3100 Channing Way, Idaho Falls, ID, 83404, USA
| | - Katie Suleta
- HCA Healthcare, 4900 S. Monaco St., Denver, CO, 80237, USA.
| | - Sean Shearen
- Eastern Idaho Regional Medical Center, 3100 Channing Way, Idaho Falls, ID, 83404, USA
| | - Kenneth Chapman
- Eastern Idaho Regional Medical Center, 3100 Channing Way, Idaho Falls, ID, 83404, USA
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6
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Iwamoto K, Yamamoto M, Yamamoto A, Sai T, Mukai T, Miura N, Kozono H, Onishi S, Ohno S, Iwamoto N, Matsumura Y, Nagao M, Urata Y. Meningitis caused by Chromobacterium haemolyticum suspected to be derived from a canal in Japan: a case report. J Med Case Rep 2023; 17:171. [PMID: 37120580 PMCID: PMC10149000 DOI: 10.1186/s13256-023-03913-1] [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: 12/08/2022] [Accepted: 03/28/2023] [Indexed: 05/01/2023] Open
Abstract
BACKGROUND The genus Chromobacterium, of which 12 species have been recognized, comprises bacteria that reside in tropical and subtropical environments. Of these species, Chromobacterium violaceum and Chromobacterium haemolyticum are known to cause infections in humans. There have been few reports of infections caused by Chromobacterium haemolyticum. CASE PRESENTATION Chromobacterium haemolyticum was detected in spinal fluid and blood samples isolated from a 73-year-old Japanese male patient who fell into a canal in Kyoto City, Japan and developed bacteremia and meningitis. Although meropenem and vancomycin were administered, this patient died 9 days after admission. Although the infection was misidentified as being caused by Chromobacterium violaceum by conventional identification methods, average nucleotide identity analysis revealed that the causative pathogen was Chromobacterium haemolyticum. The same bacteria were also detected in the canal in which the accident occurred. Phylogenetic analysis of the strain isolated from the patient and the strain isolated from the canal suggested that the two strains were very closely related. CONCLUSIONS Chromobacterium haemolyticum can be misidentified as Chromobacterium violaceum by conventional identification methods and tends to be more resistant to β-lactams than Chromobacterium violaceum. Pigment production and β-hemolysis on blood sheep agar can provide clues for the early identification of Chromobacterium haemolyticum.
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Affiliation(s)
- Kumi Iwamoto
- Department of Medical Laboratory, Japanese Red Cross Kyoto Daiichi Hospital, Kyoto, Japan
| | - Masaki Yamamoto
- Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, 54 Shogoin-Kawaharacho, Sakyo-Ku, Kyoto, 6068507, Japan.
| | - Atsushi Yamamoto
- Department of Cerebral Neurology and Stroke, Japanese Red Cross Kyoto Daiichi Hospital, Kyoto, Japan
| | - Toshi Sai
- Department of Cerebral Neurology and Stroke, Japanese Red Cross Kyoto Daiichi Hospital, Kyoto, Japan
| | - Toshiko Mukai
- Department of Medical Laboratory, Japanese Red Cross Kyoto Daiichi Hospital, Kyoto, Japan
| | - Noriko Miura
- Department of Medical Laboratory, Japanese Red Cross Kyoto Daiichi Hospital, Kyoto, Japan
| | - Haruhisa Kozono
- Department of Medical Laboratory, Japanese Red Cross Kyoto Daiichi Hospital, Kyoto, Japan
| | - Shigeki Onishi
- Department of Medical Laboratory, Japanese Red Cross Kyoto Daiichi Hospital, Kyoto, Japan
| | - Seiko Ohno
- Department of Infection Control, Japanese Red Cross Kyoto Daiichi Hospital, Kyoto, Japan
| | - Nobuki Iwamoto
- Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, 54 Shogoin-Kawaharacho, Sakyo-Ku, Kyoto, 6068507, Japan
| | - Yasufumi Matsumura
- Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, 54 Shogoin-Kawaharacho, Sakyo-Ku, Kyoto, 6068507, Japan
| | - Miki Nagao
- Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, 54 Shogoin-Kawaharacho, Sakyo-Ku, Kyoto, 6068507, Japan
| | - Yoji Urata
- Department of Medical Laboratory, Japanese Red Cross Kyoto Daiichi Hospital, Kyoto, Japan
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7
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Outbreak of Fatal Piglet Diarrhea Caused by Chromobacterium haemolyticum in China. Transbound Emerg Dis 2023. [DOI: 10.1155/2023/6694913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Chromobacterium haemolyticum is a fatal Gram-negative bacterium which could infect human beings. Our investigation found severe piglet diarrhea in one farm; the morbidity rate of piglets was 30.65%. Then, we isolated a nonpigmented, β-hemolytic Gram-negative bacillus from the clinical samples of this farm, which was designated GDHYZ30 strain. The 16S rRNA gene sequence indicated it was most closely related to Chromobacterium haemolyticum. Similar clinical symptoms were successfully reproduced in experimental piglets with this isolate, and the isolate was also subjected to whole genome-sequencing. It is worth noting that this Chromobacterium haemolyticum has been isolated from several other pig farms with diarrhea of unknown causes. To our knowledge, this is the first report that discusses Chromobacterium haemolyticum as a new pathogen causing diarrhea and death in piglets and transmitting through water sources, and it provides a reference for the prevention and control of human/animal infections as well as food safety.
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8
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Rogers TJ, Buongiorno J, Jessen GL, Schrenk MO, Fordyce JA, de Moor JM, Ramírez CJ, Barry PH, Yücel M, Selci M, Cordone A, Giovannelli D, Lloyd KG. Chemolithoautotroph distributions across the subsurface of a convergent margin. THE ISME JOURNAL 2023; 17:140-150. [PMID: 36257972 PMCID: PMC9751116 DOI: 10.1038/s41396-022-01331-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 10/03/2022] [Accepted: 10/06/2022] [Indexed: 12/15/2022]
Abstract
Subducting oceanic crusts release fluids rich in biologically relevant compounds into the overriding plate, fueling subsurface chemolithoautotrophic ecosystems. To understand the impact of subsurface geochemistry on microbial communities, we collected fluid and sediments from 14 natural springs across a ~200 km transect across the Costa Rican convergent margin and performed shotgun metagenomics. The resulting 404 metagenome-assembled genomes (MAGs) cluster into geologically distinct regions based on MAG abundance patterns: outer forearc-only (25% of total relative abundance), forearc/arc-only (38% of total relative abundance), and delocalized (37% of total relative abundance) clusters. In the outer forearc, Thermodesulfovibrionia, Candidatus Bipolaricaulia, and Firmicutes have hydrogenotrophic sulfate reduction and Wood-Ljungdahl (WL) carbon fixation pathways. In the forearc/arc, Anaerolineae, Ca. Bipolaricaulia, and Thermodesulfovibrionia have sulfur oxidation, nitrogen cycling, microaerophilic respiration, and WL, while Aquificae have aerobic sulfur oxidation and reverse tricarboxylic acid carbon fixation pathway. Transformation-based canonical correspondence analysis shows that MAG distribution corresponds to concentrations of aluminum, iron, nickel, dissolved inorganic carbon, and phosphate. While delocalized MAGs appear surface-derived, the subsurface chemolithoautotrophic, metabolic, and taxonomic landscape varies by the availability of minerals/metals and volcanically derived inorganic carbon. However, the WL pathway persists across all samples, suggesting that this versatile, energy-efficient carbon fixation pathway helps shape convergent margin subsurface ecosystems.
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Affiliation(s)
| | - Joy Buongiorno
- Division of Natural Sciences, Maryville College, Maryville, TN, USA
| | - Gerdhard L Jessen
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile
- Center for Oceanographic Research COPAS COASTAL, Universidad de Concepción, Valdivia, Chile
| | | | | | - J Maarten de Moor
- National University of Costa Rica, Heredia, Costa Rica
- University of New Mexico, Albuquerque, NM, USA
| | | | - Peter H Barry
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Mustafa Yücel
- Institute of Marine Sciences, Middle East Technical University, Erdemli, Turkey
| | - Matteo Selci
- Department of Biology, University of Naples -Federico II, Naples, Italy
| | - Angela Cordone
- Department of Biology, University of Naples -Federico II, Naples, Italy
| | - Donato Giovannelli
- Department of Biology, University of Naples -Federico II, Naples, Italy
- Department of Marine and Coastal Science, Rutgers University, Rutgers, NJ, USA
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- National Research Council - Institute of Marine Biological Resources and Biotechnologies - CNR-IRBIM, Ancona, Italy
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O'Hara-Hanley K, Harrison A, Soby SD. Chromobacterium alticapitis sp. nov. and Chromobacterium sinusclupearum sp. nov. isolated from wild cranberry bogs in the Cape Cod National Seashore, USA. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005410] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Two non-pigmented strains in the genus
Chromobacterium
, MWU14-2602T and MWU13-2610T, were isolated from wild cranberry bogs in the Cape Cod National Seashore, USA. The isolates were characterized by genomic and phenotypic analyses, the results of which indicated that they represent two novel species. Based on total genome sequences, the closest relatives were in the
Chromobacterium amazonense
group, which includes the recently described
Chromobacterium paludis
. Whole genome sequences were compared by genome blast distance phylogeny, digital DNA–DNA hybridization and average nucleotide identity analyses with each other and with the type strains of their nearest species. MWU14-2602T and MWU13-2610T fell well below the accepted cutoff values for species relatedness, clearly indicating that they represent novel species. Although little is known about these organisms in situ, under laboratory conditions, MWU13-2610T produced a modest amount of HCN and was strongly positive for exoprotease activity, whereas MWU14-2602T did not produce HCN or exoproteases. The predominant fatty acids for both isolates were summed C16 : 1ω7cis/C16 : 1ω6cis. Both isolates produced siderophores and pyomelanin pigment on rich media, and neither was haemolytic on sheep blood agar. We propose the names Chromobacterium alticapitis sp. nov. (type strain MWU14-2602T=ATCC TSD 260T=CCOS 1979T) and Chromobacterium sinusclupearum sp. nov. (type strain MWU13-2610T=ATCC TSD-259T=CCOS 1981T) for these taxa.
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Affiliation(s)
- Kory O'Hara-Hanley
- Arizona College of Osteopathic Medicine, Midwestern University, Glendale, AZ, USA
| | - Alisha Harrison
- Biomedical Sciences Program, College of Graduate Studies, Midwestern University, Glendale, AZ, USA
| | - Scott D. Soby
- Biomedical Sciences Program, College of Graduate Studies, Midwestern University, Glendale, AZ, USA
- College of Veterinary Medicine, Midwestern University, Glendale, AZ, USA
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10
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Zwe YH, Yadav M, Zhen Ten MM, Srinivasan M, Jobichen C, Sivaraman J, Li D. Bacterial Antagonism of Chromobacterium haemolyticum and Characterization of its Putative Type VI Secretion System. Res Microbiol 2021; 173:103918. [PMID: 34906677 DOI: 10.1016/j.resmic.2021.103918] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 12/08/2021] [Accepted: 12/08/2021] [Indexed: 10/19/2022]
Abstract
This study reports the isolation of a new Chromobacterium haemolyticum strain named WI5 from a hydroponic farming facility. WI5 exhibited remarkable bacterial antagonistic properties, eliminating Salmonella, Escherichia coli, Listeria monocytogenes and Staphylococcus aureus (initial inoculum load ∼105 CFU/ml) in dual-species co-culture biofilms. Antagonism was strictly contact-dependent and highly influenced by nutrient availability. Next, we identified a complete suite of putative Type VI secretion system (T6SS) genes in the WI5 genome, annotated the gene locus architecture, and determined the crystal structure of hallmark T6SS tube protein Hcp1, which revealed a hexameric ring structure with an outer and inner diameter of 77 and 45Å, respectively. Structural comparison with homologs showed differences in the key loops connecting the β-strands in which the conserved residues are located, suggesting a role of these residues in the protein function. The T6SS is well-known to facilitate interbacterial competition, and the putative T6SS characterized herein might be responsible for the remarkable antagonism by C. haemolyticum WI5. Collectively, these findings shed light on the nature of bacterial antagonism and a putative key virulence determinant of C. haemolyticum, which might aid in further understanding its potential ecological role in natural habitats.
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Affiliation(s)
- Ye Htut Zwe
- Department of Food Science & Technology, 2 Science Drive 2, Faculty of Science, National University of Singapore, Singapore 117543
| | - Manisha Yadav
- Department of Biological Sciences, 14 Science Drive 4, Faculty of Science, National University of Singapore, Singapore 117543
| | - Michelle Mei Zhen Ten
- Department of Food Science & Technology, 2 Science Drive 2, Faculty of Science, National University of Singapore, Singapore 117543
| | - Mahalashmi Srinivasan
- Department of Biological Sciences, 14 Science Drive 4, Faculty of Science, National University of Singapore, Singapore 117543
| | - Chacko Jobichen
- Department of Biological Sciences, 14 Science Drive 4, Faculty of Science, National University of Singapore, Singapore 117543
| | - J Sivaraman
- Department of Biological Sciences, 14 Science Drive 4, Faculty of Science, National University of Singapore, Singapore 117543
| | - Dan Li
- Department of Food Science & Technology, 2 Science Drive 2, Faculty of Science, National University of Singapore, Singapore 117543.
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11
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Lyakhovchenko NS, Abashina TN, Polivtseva VN, Senchenkov VY, Pribylov DA, Chepurina AA, Nikishin IA, Avakova AA, Goyanov MA, Gubina ED, Churikova DA, Sirotin AA, Suzina NE, Solyanikova IP. A Blue-Purple Pigment-Producing Bacterium Isolated from the Vezelka River in the City of Belgorod. Microorganisms 2021; 9:E102. [PMID: 33466248 PMCID: PMC7824796 DOI: 10.3390/microorganisms9010102] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/23/2020] [Accepted: 12/30/2020] [Indexed: 02/07/2023] Open
Abstract
Violacein is a biotechnologically significant secondary metabolite due to its antibacterial, antifungal, and other properties. Isolation, research, and identification of violacein producing strains are of interest for the development of biotechnological processes, in order to enhance the biosynthesis of this compound. The purpose of the present work was to study the properties of a newly isolated bacterium capable of synthesizing blue-purple pigment. An aboriginal bacterium was isolated from the coastal zone of the Vezelka River in the city of Belgorod. Based on chemical and spectrophotometric studies of the crude ethanol extract, the pigment was identified as violacein, and the isolate was assigned to the group of violacein-forming bacteria, which includes bacteria of the genera Chromobacterium, Iodobacter, Janthinobacterium, Duganella, Collimonas, and Massilia. Based on cultural, morphological, tinctorial, physiological, and biochemical properties, as well as analysis of the 16S rRNA gene sequence, the new isolated strain was assigned to the genus Janthinobacterium. The isolated strain is capable of suppressing the growth of a number of fungal and bacterial phytopathogens. For representatives of the genus Janthinobacterium, their inhibitory influence on cyanobacteria was shown for the first time.
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Affiliation(s)
- Nikita S. Lyakhovchenko
- Federal State Autonomous Educational Institution of Higher Education, Belgorod National Research University, 308015 Belgorod, Russia; (N.S.L.); (V.Y.S.); (D.A.P.); (A.A.C.); (I.A.N.); (A.A.A.); (M.A.G.); (E.D.G.); (D.A.C.); (A.A.S.)
| | - Tatiana N. Abashina
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Center for Biological Research of the Russian Academy of Sciences, Pushchino, 142290 Moscow, Russia; (T.N.A.); (V.N.P.); (N.E.S.)
| | - Valentina N. Polivtseva
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Center for Biological Research of the Russian Academy of Sciences, Pushchino, 142290 Moscow, Russia; (T.N.A.); (V.N.P.); (N.E.S.)
| | - Vladislav Yu. Senchenkov
- Federal State Autonomous Educational Institution of Higher Education, Belgorod National Research University, 308015 Belgorod, Russia; (N.S.L.); (V.Y.S.); (D.A.P.); (A.A.C.); (I.A.N.); (A.A.A.); (M.A.G.); (E.D.G.); (D.A.C.); (A.A.S.)
| | - Daniil A. Pribylov
- Federal State Autonomous Educational Institution of Higher Education, Belgorod National Research University, 308015 Belgorod, Russia; (N.S.L.); (V.Y.S.); (D.A.P.); (A.A.C.); (I.A.N.); (A.A.A.); (M.A.G.); (E.D.G.); (D.A.C.); (A.A.S.)
| | - Anna A. Chepurina
- Federal State Autonomous Educational Institution of Higher Education, Belgorod National Research University, 308015 Belgorod, Russia; (N.S.L.); (V.Y.S.); (D.A.P.); (A.A.C.); (I.A.N.); (A.A.A.); (M.A.G.); (E.D.G.); (D.A.C.); (A.A.S.)
| | - Ilja A. Nikishin
- Federal State Autonomous Educational Institution of Higher Education, Belgorod National Research University, 308015 Belgorod, Russia; (N.S.L.); (V.Y.S.); (D.A.P.); (A.A.C.); (I.A.N.); (A.A.A.); (M.A.G.); (E.D.G.); (D.A.C.); (A.A.S.)
| | - Alina A. Avakova
- Federal State Autonomous Educational Institution of Higher Education, Belgorod National Research University, 308015 Belgorod, Russia; (N.S.L.); (V.Y.S.); (D.A.P.); (A.A.C.); (I.A.N.); (A.A.A.); (M.A.G.); (E.D.G.); (D.A.C.); (A.A.S.)
| | - Michael A. Goyanov
- Federal State Autonomous Educational Institution of Higher Education, Belgorod National Research University, 308015 Belgorod, Russia; (N.S.L.); (V.Y.S.); (D.A.P.); (A.A.C.); (I.A.N.); (A.A.A.); (M.A.G.); (E.D.G.); (D.A.C.); (A.A.S.)
| | - Elizaveta D. Gubina
- Federal State Autonomous Educational Institution of Higher Education, Belgorod National Research University, 308015 Belgorod, Russia; (N.S.L.); (V.Y.S.); (D.A.P.); (A.A.C.); (I.A.N.); (A.A.A.); (M.A.G.); (E.D.G.); (D.A.C.); (A.A.S.)
| | - Daria A. Churikova
- Federal State Autonomous Educational Institution of Higher Education, Belgorod National Research University, 308015 Belgorod, Russia; (N.S.L.); (V.Y.S.); (D.A.P.); (A.A.C.); (I.A.N.); (A.A.A.); (M.A.G.); (E.D.G.); (D.A.C.); (A.A.S.)
| | - Alexander A. Sirotin
- Federal State Autonomous Educational Institution of Higher Education, Belgorod National Research University, 308015 Belgorod, Russia; (N.S.L.); (V.Y.S.); (D.A.P.); (A.A.C.); (I.A.N.); (A.A.A.); (M.A.G.); (E.D.G.); (D.A.C.); (A.A.S.)
| | - Nataliya E. Suzina
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Center for Biological Research of the Russian Academy of Sciences, Pushchino, 142290 Moscow, Russia; (T.N.A.); (V.N.P.); (N.E.S.)
| | - Inna P. Solyanikova
- Federal State Autonomous Educational Institution of Higher Education, Belgorod National Research University, 308015 Belgorod, Russia; (N.S.L.); (V.Y.S.); (D.A.P.); (A.A.C.); (I.A.N.); (A.A.A.); (M.A.G.); (E.D.G.); (D.A.C.); (A.A.S.)
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Center for Biological Research of the Russian Academy of Sciences, Pushchino, 142290 Moscow, Russia; (T.N.A.); (V.N.P.); (N.E.S.)
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12
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Egorova DA, Voronina OL, Solovyev AI, Kunda MS, Aksenova EI, Ryzhova NN, Danilova KV, Rykova VS, Scherbakova AA, Semenov AN, Polyakov NB, Grumov DA, Shevlyagina NV, Dolzhikova IV, Romanova YM, Gintsburg AL. Integrated into Environmental Biofilm Chromobacterium vaccinii Survives Winter with Support of Bacterial Community. Microorganisms 2020; 8:E1696. [PMID: 33143246 PMCID: PMC7716238 DOI: 10.3390/microorganisms8111696] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 09/30/2020] [Accepted: 10/29/2020] [Indexed: 12/27/2022] Open
Abstract
Chromobacterium species are common in tropical and subtropical zones in environmental samples according to numerous studies. Here, we describe an environmental case of resident Chromobacterium vaccinii in biofilms associated with Carex spp. roots in Moscow region, Russia (warm-summer humid continental climate zone). We performed broad characterization of individual properties as well as surrounding context for better understanding of the premise of C. vaccinii survival during the winter season. Genome properties of isolated strains propose some insights into adaptation to habit and biofilm mode of life, including social cheaters carrying ΔluxR mutation. Isolated C. vaccinii differs from previously described strains in some biochemical properties and some basic characteristics like fatty acid composition as well as unique genome features. Despite potential to modulate membrane fluidity and presence of several genes responsible for cold shock response, isolated C. vaccinii did not survive during exposure to 4 °C, while in the complex biofilm sample, it was safely preserved for at least half a year in vitro at 4 °C. The surrounding bacterial community within the same biofilm with C. vaccinii represented a series of psychrophilic bacterial species, which may share resistance to low temperatures with other species within biofilm and provide C. vaccinii an opportunity to survive during the cold winter season.
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Affiliation(s)
- Daria A. Egorova
- N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health, 123098 Moscow, Russia; (A.I.S.); (M.S.K.); (E.I.A.); (N.N.R.); (K.V.D.); (V.S.R.); (A.A.S.); (A.N.S.); (N.B.P.); (D.A.G.); (N.V.S.); (I.V.D.); (Y.M.R.); (A.L.G.)
| | - Olga L. Voronina
- N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health, 123098 Moscow, Russia; (A.I.S.); (M.S.K.); (E.I.A.); (N.N.R.); (K.V.D.); (V.S.R.); (A.A.S.); (A.N.S.); (N.B.P.); (D.A.G.); (N.V.S.); (I.V.D.); (Y.M.R.); (A.L.G.)
| | - Andrey I. Solovyev
- N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health, 123098 Moscow, Russia; (A.I.S.); (M.S.K.); (E.I.A.); (N.N.R.); (K.V.D.); (V.S.R.); (A.A.S.); (A.N.S.); (N.B.P.); (D.A.G.); (N.V.S.); (I.V.D.); (Y.M.R.); (A.L.G.)
| | - Marina S. Kunda
- N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health, 123098 Moscow, Russia; (A.I.S.); (M.S.K.); (E.I.A.); (N.N.R.); (K.V.D.); (V.S.R.); (A.A.S.); (A.N.S.); (N.B.P.); (D.A.G.); (N.V.S.); (I.V.D.); (Y.M.R.); (A.L.G.)
| | - Ekaterina I. Aksenova
- N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health, 123098 Moscow, Russia; (A.I.S.); (M.S.K.); (E.I.A.); (N.N.R.); (K.V.D.); (V.S.R.); (A.A.S.); (A.N.S.); (N.B.P.); (D.A.G.); (N.V.S.); (I.V.D.); (Y.M.R.); (A.L.G.)
| | - Natalia N. Ryzhova
- N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health, 123098 Moscow, Russia; (A.I.S.); (M.S.K.); (E.I.A.); (N.N.R.); (K.V.D.); (V.S.R.); (A.A.S.); (A.N.S.); (N.B.P.); (D.A.G.); (N.V.S.); (I.V.D.); (Y.M.R.); (A.L.G.)
| | - Ksenya V. Danilova
- N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health, 123098 Moscow, Russia; (A.I.S.); (M.S.K.); (E.I.A.); (N.N.R.); (K.V.D.); (V.S.R.); (A.A.S.); (A.N.S.); (N.B.P.); (D.A.G.); (N.V.S.); (I.V.D.); (Y.M.R.); (A.L.G.)
| | - Valentina S. Rykova
- N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health, 123098 Moscow, Russia; (A.I.S.); (M.S.K.); (E.I.A.); (N.N.R.); (K.V.D.); (V.S.R.); (A.A.S.); (A.N.S.); (N.B.P.); (D.A.G.); (N.V.S.); (I.V.D.); (Y.M.R.); (A.L.G.)
| | - Anastasya A. Scherbakova
- N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health, 123098 Moscow, Russia; (A.I.S.); (M.S.K.); (E.I.A.); (N.N.R.); (K.V.D.); (V.S.R.); (A.A.S.); (A.N.S.); (N.B.P.); (D.A.G.); (N.V.S.); (I.V.D.); (Y.M.R.); (A.L.G.)
| | - Andrey N. Semenov
- N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health, 123098 Moscow, Russia; (A.I.S.); (M.S.K.); (E.I.A.); (N.N.R.); (K.V.D.); (V.S.R.); (A.A.S.); (A.N.S.); (N.B.P.); (D.A.G.); (N.V.S.); (I.V.D.); (Y.M.R.); (A.L.G.)
| | - Nikita B. Polyakov
- N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health, 123098 Moscow, Russia; (A.I.S.); (M.S.K.); (E.I.A.); (N.N.R.); (K.V.D.); (V.S.R.); (A.A.S.); (A.N.S.); (N.B.P.); (D.A.G.); (N.V.S.); (I.V.D.); (Y.M.R.); (A.L.G.)
- Vernadsky Institute of Geochemistry and Analytical Chemistry of Russian Academy of Sciences, 119991 Moscow, Russia
| | - Daniil A. Grumov
- N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health, 123098 Moscow, Russia; (A.I.S.); (M.S.K.); (E.I.A.); (N.N.R.); (K.V.D.); (V.S.R.); (A.A.S.); (A.N.S.); (N.B.P.); (D.A.G.); (N.V.S.); (I.V.D.); (Y.M.R.); (A.L.G.)
| | - Natalia V. Shevlyagina
- N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health, 123098 Moscow, Russia; (A.I.S.); (M.S.K.); (E.I.A.); (N.N.R.); (K.V.D.); (V.S.R.); (A.A.S.); (A.N.S.); (N.B.P.); (D.A.G.); (N.V.S.); (I.V.D.); (Y.M.R.); (A.L.G.)
| | - Inna V. Dolzhikova
- N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health, 123098 Moscow, Russia; (A.I.S.); (M.S.K.); (E.I.A.); (N.N.R.); (K.V.D.); (V.S.R.); (A.A.S.); (A.N.S.); (N.B.P.); (D.A.G.); (N.V.S.); (I.V.D.); (Y.M.R.); (A.L.G.)
| | - Yulia M. Romanova
- N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health, 123098 Moscow, Russia; (A.I.S.); (M.S.K.); (E.I.A.); (N.N.R.); (K.V.D.); (V.S.R.); (A.A.S.); (A.N.S.); (N.B.P.); (D.A.G.); (N.V.S.); (I.V.D.); (Y.M.R.); (A.L.G.)
- Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation, 119991 Moscow, Russia
| | - Alexander L. Gintsburg
- N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health, 123098 Moscow, Russia; (A.I.S.); (M.S.K.); (E.I.A.); (N.N.R.); (K.V.D.); (V.S.R.); (A.A.S.); (A.N.S.); (N.B.P.); (D.A.G.); (N.V.S.); (I.V.D.); (Y.M.R.); (A.L.G.)
- Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation, 119991 Moscow, Russia
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13
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Blackburn MB, Farrar RR, Sparks ME, Kuhar D, Mowery JD, Mitchell A, Gundersen-Rindal DE. Chromobacterium paludis sp. nov., a novel bacterium isolated from a Chesapeake Bay marsh. Int J Syst Evol Microbiol 2020; 70:6142-6146. [PMID: 33054903 DOI: 10.1099/ijsem.0.004509] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two isolates of Gram-reaction-negative, motile, violet-pigmented bacteria were isolated from a small pool in marshland near the mouth of the Nanticoke River in Maryland, USA. The isolates IIBBL 257-1T and IIBBL 257-2 had identical 16S rRNA gene sequences as determined by PCR, and highly similar fatty acid and biochemical profiles. The 16S rRNA gene sequences indicated the isolates belonged to the genus Chromobacterium. Genomic sequencing of IIBBL 257-1T revealed a genome of 4.27 Mb, with a G+C content of 63.6 %. Whole genome comparisons with other members of the Chromobacterium using JSpecies and the genome blast distance phylogeny approach indicated that among described species, IIBBL 257-1T was most closely related to C. amazonense and C. phragmitis. Comparison of the IIBBL 257-1T genome with those of type strains of these species resulted in ANIb and dDDH values of ca. 85 and 30 %, respectively, for both. These results demonstrate that IIBBL 257-1T and IIBBL 257-2 represent a new taxon within the genus Chromobacterium. We propose the name Chromobacterium paludis sp. nov. for this taxon; the type strain is IIBBL 257-1T (=NRRL B-65555T=JCM 33770T).
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Affiliation(s)
- Michael B Blackburn
- Invasive Insect Biocontrol and Behavior Laboratory, USDA-ARS, Beltsville, MD 20705, USA
| | - Robert R Farrar
- Invasive Insect Biocontrol and Behavior Laboratory, USDA-ARS, Beltsville, MD 20705, USA
| | - Michael E Sparks
- Invasive Insect Biocontrol and Behavior Laboratory, USDA-ARS, Beltsville, MD 20705, USA
| | - Daniel Kuhar
- Invasive Insect Biocontrol and Behavior Laboratory, USDA-ARS, Beltsville, MD 20705, USA
| | - Joseph D Mowery
- Electron and Confocal Microscopy Unit, USDA-ARS, Beltsville, MD 20705, USA
| | - Ashaki Mitchell
- Invasive Insect Biocontrol and Behavior Laboratory, USDA-ARS, Beltsville, MD 20705, USA
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14
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Kanamori H, Aoyagi T, Kuroda M, Sekizuka T, Katsumi M, Ishikawa K, Hosaka T, Baba H, Oshima K, Tokuda K, Hasegawa M, Kawazoe Y, Kushimoto S, Kaku M. Chromobacterium haemolyticum Pneumonia Associated with Near-Drowning and River Water, Japan. Emerg Infect Dis 2020; 26:2186-2189. [PMID: 32818399 PMCID: PMC7454080 DOI: 10.3201/eid2609.190670] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
We report a severe case of Chromobacterium haemolyticum pneumonia associated with near-drowning and detail the investigation of the pathogen and river water. Our genomic and environmental investigation demonstrated that river water in a temperate region can be a source of C. haemolyticum causing human infections.
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15
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Teixeira P, Tacão M, Baraúna RA, Silva A, Henriques I. Genomic analysis of Chromobacterium haemolyticum: insights into the species resistome, virulence determinants and genome plasticity. Mol Genet Genomics 2020; 295:1001-1012. [PMID: 32307574 DOI: 10.1007/s00438-020-01676-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 04/02/2020] [Indexed: 12/26/2022]
Abstract
The increasing number of Chromobacterium haemolyticum human infection reports, especially in tropical regions and connected with environmental sources, resulted in an urge to better describe this species. This study aimed to characterize the C. haemolyticum resistome, virulence determinants and genetic platforms related with genome plasticity. A comparative genomic analysis was conducted between clinical C. haemolyticum genomes publicly available and the genome of an environmental isolate obtained in this study. The pangenome of C. haemolyticum was calculated and a total of 3378 core genes were predicted in its core genome, corresponding to 51.7% of the pangenome. Genetic determinants putatively encoding resistance to beta-lactams, fosfomycin, aminoglycosides and trimethoprim were predicted in all genomes, possibly constituting the intrinsic resistome of this species. In terms of resistance to beta-lactams, 4 genes were predicted encoding beta-lactamases of classes A, C and D. Moreover, the analysis of Chromobacterium genomes and C. haemolyticum environmental isolates reinforced the role of this genus as progenitor of the blaKPC gene. Putative virulence factors (VFs) were predicted in all genomes, related to adherence, toxins production, colonization and cell invasion. Secretion systems, including type III, were detected. A significant number of transposases and genomic islands were predicted in C. haemolyticum, in some cases above the average reported for Gram-negative bacterial genomes. We conclude that C. haemolyticum strains, including those of environmental origin, present a noteworthy collection of antibiotic resistance genes and VFs. Furthermore, sequences related to gene mobility and genome plasticity suggest high adaptability potential and a possible role as disseminator of antibiotic resistance.
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Affiliation(s)
- Pedro Teixeira
- CESAM and Department of Biology, University of Aveiro, Aveiro, Portugal
| | - Marta Tacão
- CESAM and Department of Biology, University of Aveiro, Aveiro, Portugal.
| | - Rafael A Baraúna
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Artur Silva
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Isabel Henriques
- CESAM and Department of Life Sciences, Faculty of Science and Technology, University of Coimbra, Coimbra, Portugal
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16
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Blackburn MB, Farrar RR, Sparks ME, Kuhar D, Mowery JD, Mitchell A, Gundersen-Rindal DE. Chromobacterium phragmitis sp. nov., isolated from estuarine marshes. Int J Syst Evol Microbiol 2019; 69:2681-2686. [PMID: 31199223 DOI: 10.1099/ijsem.0.003508] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Thirteen isolates of Gram-stain-negative, motile, violet-pigmented bacteria were isolated from marshes along tidal portions of the Potomac and James rivers in Maryland and Virginia, USA, respectively. 16S rRNA gene sequences and fatty acid analysis revealed a high degree of relatedness among the isolates, and genomic sequencing of two isolates, IIBBL 112-1T and IIBBL 274-1 (from the Potomac and James rivers, respectively), revealed highly similar genomic sequences, with a blast-based average nucleotide identity (ANIb) of ca. 98.7 %. Phylogenetic analysis of 16S rRNA gene sequences suggested that the species most highly related to IIBBL 112-1T were Chromobacterium amazonense, Chromobacterium subtsugae and Chromobacterium sphagni. However, deletion of a 25-nucleotide sequence that may have been horizontally acquired by both IIBBL 112-1T and C. amazonense resulted in a substantially different analysis; in the latter case, the species nearest IIBBL 112-1T were Chromobacterium violaceum, Chromobacterium vaccinii and Chromobacterium piscinae. Whole-genome alignments between either IIBBL 112-1T or IIBBL 274-1 and the type strains of C. vaccinii or C. violaceum resulted in ANIb values in the range of ca. 87 %, while alignment with C. amazonense CBMAI 310T resulted in an ANIb of ca. 83 %. Collectively, these data demonstrate that IIBBL 112-1T and IIBBL 274-1 represent a new taxon within the genus Chromobacterium. We propose the name Chromobacterium phragmitis sp. nov. for this taxon; the type strain is IIBBL 112-1T (=NRRL B-67132T=JCM 31884T).
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Affiliation(s)
- Michael B Blackburn
- Invasive Insect Biocontrol and Behavior Laboratory, USDA-ARS, Beltsville, MD 20705, USA
| | - Robert R Farrar
- Invasive Insect Biocontrol and Behavior Laboratory, USDA-ARS, Beltsville, MD 20705, USA
| | - Michael E Sparks
- Invasive Insect Biocontrol and Behavior Laboratory, USDA-ARS, Beltsville, MD 20705, USA
| | - Daniel Kuhar
- Invasive Insect Biocontrol and Behavior Laboratory, USDA-ARS, Beltsville, MD 20705, USA
| | - Joseph D Mowery
- Electron and Confocal Microscopy Unit, USDA-ARS, Beltsville, MD 20705, USA
| | - Ashaki Mitchell
- Invasive Insect Biocontrol and Behavior Laboratory, USDA-ARS, Beltsville, MD 20705, USA
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17
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Contribution of gyrA and qnrA genes in Ciprofloxacin Resistant Ecsherichia coli Isolates from Patients with Urinary Tract Infections of Imam Khomeini Hospital of Tehran. ARCHIVES OF PEDIATRIC INFECTIOUS DISEASES 2018. [DOI: 10.5812/pedinfect.62129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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18
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Priya K, Sulaiman J, How KY, Yin WF, Chan KG. Production of N-acyl homoserine lactones by Chromobacterium haemolyticum KM2 isolated from the river water in Malaysia. Arch Microbiol 2018; 200:1135-1142. [PMID: 29796703 DOI: 10.1007/s00203-018-1526-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 03/16/2018] [Accepted: 05/14/2018] [Indexed: 10/16/2022]
Abstract
Quorum sensing (QS) is a term used to describe cell-to-cell communication that enables bacteria to orchestrate group behaviours according to density of bacterial cells. In Gram-negative bacteria, this signalling system is widely known to regulate a variety of different phenotypes such as antibiotic production and biofilm formation. In this study, we report the production of N-acyl homoserine lactones produced by Chromobacterium haemolyticum strain KM2, a bacterium isolated from a river water of a reserved tropical national park. Preliminary screening of QS activity using biosensor reporter assays indicated that C. haemolyticum strain KM2 produces both short- and long-chain AHLs. Analysis with high-resolution liquid chromatography-mass spectrometry (LC-MS/MS) analysis revealed the production of three AHLs by strain KM2: N-octanoyl-L-homoserine lactone (C8-HSL), N-dodecanoyl-L-homoserine lactone (C12-HSL), and N-3-oxo-dodecanoyl-L-homoserine lactone (OC12-HSL). This bacterial isolate also exhibited strong β-haemolytic activity. To the best of our knowledge, this is the first documentation of QS activity and multiple AHLs production by C. haemolyticum strain KM2.
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Affiliation(s)
- Kumutha Priya
- International Genome Centre, Jiangsu University, Zhenjiang, China.,Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, 50603, Malaysia
| | - Joanita Sulaiman
- Institute for Public Health, National Institutes of Health Malaysia, Jalan Bangsar, 50590, Kuala Lumpur, Malaysia
| | - Kah Yan How
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, 50603, Malaysia
| | - Wai-Fong Yin
- International Genome Centre, Jiangsu University, Zhenjiang, China.,Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, 50603, Malaysia
| | - Kok-Gan Chan
- International Genome Centre, Jiangsu University, Zhenjiang, China. .,Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, 50603, Malaysia.
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19
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Insights into the Genome Sequence of Chromobacterium amazonense Isolated from a Tropical Freshwater Lake. Int J Genomics 2018; 2018:1062716. [PMID: 29888247 PMCID: PMC5985088 DOI: 10.1155/2018/1062716] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 03/30/2018] [Accepted: 04/19/2018] [Indexed: 12/04/2022] Open
Abstract
Members of the genus Chromobacterium have been isolated from geographically diverse ecosystems and exhibit considerable metabolic flexibility, as well as biotechnological and pathogenic properties in some species. This study reports the draft assembly and detailed sequence analysis of Chromobacterium amazonense strain 56AF. The de novo-assembled genome is 4,556,707 bp in size and contains 4294 protein-coding and 95 RNA genes, including 88 tRNA, six rRNA, and one tmRNA operon. A repertoire of genes implicated in virulence, for example, hemolysin, hemolytic enterotoxins, colicin V, lytic proteins, and Nudix hydrolases, is present. The genome also contains a collection of genes of biotechnological interest, including esterases, lipase, auxins, chitinases, phytoene synthase and phytoene desaturase, polyhydroxyalkanoates, violacein, plastocyanin/azurin, and detoxifying compounds. Importantly, unlike other Chromobacterium species, the 56AF genome contains genes for pore-forming toxin alpha-hemolysin, a type IV secretion system, among others. The analysis of the C. amazonense strain 56AF genome reveals the versatility, adaptability, and biotechnological potential of this bacterium. This study provides molecular information that may pave the way for further comparative genomics and functional studies involving Chromobacterium-related isolates and improves our understanding of the global genomic diversity of Chromobacterium species.
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Salmonová H, Killer J, Bunešová V, Geigerová M, Vlková E. Cultivable bacteria from Pectinatella magnifica and the surrounding water in South Bohemia indicate potential new Gammaproteobacterial, Betaproteobacterial and Firmicutes taxa. FEMS Microbiol Lett 2018; 365:4995195. [DOI: 10.1093/femsle/fny118] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 05/09/2018] [Indexed: 12/17/2022] Open
Affiliation(s)
- Hana Salmonová
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences Prague, Kamýcká 129, Prague 6, Suchdol 165 00, Czech Republic
| | - Jiří Killer
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences Prague, Kamýcká 129, Prague 6, Suchdol 165 00, Czech Republic
- Institute of Animal Physiology and Genetics v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, Prague 4, Krč, 142 20, Czech Republic
| | - Věra Bunešová
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences Prague, Kamýcká 129, Prague 6, Suchdol 165 00, Czech Republic
| | - Martina Geigerová
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences Prague, Kamýcká 129, Prague 6, Suchdol 165 00, Czech Republic
| | - Eva Vlková
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences Prague, Kamýcká 129, Prague 6, Suchdol 165 00, Czech Republic
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21
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Saraiva RG, Huitt-Roehl CR, Tripathi A, Cheng YQ, Bosch J, Townsend CA, Dimopoulos G. Chromobacterium spp. mediate their anti-Plasmodium activity through secretion of the histone deacetylase inhibitor romidepsin. Sci Rep 2018; 8:6176. [PMID: 29670144 PMCID: PMC5906607 DOI: 10.1038/s41598-018-24296-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 03/19/2018] [Indexed: 12/03/2022] Open
Abstract
The Chromobacterium sp. Panama bacterium has in vivo and in vitro anti-Plasmodium properties. To assess the nature of the Chromobacterium-produced anti-Plasmodium factors, chemical partition was conducted by bioassay-guided fractionation where different fractions were assayed for activity against asexual stages of P. falciparum. The isolated compounds were further partitioned by reversed-phase FPLC followed by size-exclusion chromatography; high resolution UPLC and ESI/MS data were then collected and revealed that the most active fraction contained a cyclic depsipeptide, which was identified as romidepsin. A pure sample of this FDA-approved HDAC inhibitor allowed us to independently verify this finding, and establish that romidepsin also has potent effect against mosquito stages of the parasite's life cycle. Genomic comparisons between C. sp. Panama and multiple species within the Chromobacterium genus further demonstrated a correlation between presence of the gene cluster responsible for romidepsin production and effective antiplasmodial activity. A romidepsin-null Chromobacterium spp. mutant loses its anti-Plasmodium properties by losing the ability to inhibit P. falciparum HDAC activity, and romidepsin is active against resistant parasites to commonly deployed antimalarials. This independent mode of action substantiates exploring a chromobacteria-based approach for malaria transmission-blocking.
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Affiliation(s)
- Raúl G Saraiva
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | | | - Abhai Tripathi
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Yi-Qiang Cheng
- UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Jürgen Bosch
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
- InterRayBio, LLC, Baltimore, Maryland, USA
| | - Craig A Townsend
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - George Dimopoulos
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.
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22
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Draft Genomic Sequences of Chromobacterium sp. nov. Strains MWU13-2610 and MWU14-2602, Isolated from Wild Cranberry Bogs in Massachusetts. GENOME ANNOUNCEMENTS 2018; 6:6/15/e00332-18. [PMID: 29650585 PMCID: PMC5897794 DOI: 10.1128/genomea.00332-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Chromobacterium sp. nov. strains MWU13-2610 and MWU14-2602 were isolated from cranberry bogs in the Cape Cod National Seashore. These nonpigmented bacteria represent two new presumptive species of the rapidly growing genus Chromobacterium. Gene homologs are present for multiple antibiotic resistance, virulence functions, and prophages.
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23
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Novel Weed-Extracted Silver Nanoparticles and Their Antibacterial Appraisal against a Rare Bacterium from River and Sewage Treatment Plan. NANOMATERIALS 2017; 8:nano8010009. [PMID: 29278389 PMCID: PMC5791096 DOI: 10.3390/nano8010009] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 12/12/2017] [Accepted: 12/15/2017] [Indexed: 02/01/2023]
Abstract
This is the first investigation to demonstrate the use of biochemical contents present within Cyperus rotundus, Eleusin indica, Euphorbia hirta, Melastoma malabathricum, Clidemia hirta and Pachyrhizus erosus extracts for the reduction of silver ion to silver nanoparticles (AgNPs) form. In addition, the antibacterial capability of the synthesized AgNPs and plant extracts alone against a rare bacterium, Chromobacterium haemolyticum (C. haemolyticum), was examined. Moreover, ultraviolet-visible spectroscopy (UV-vis), Fourier transform infrared spectroscopy (FTIR), field emission scanning electron microscopy (FESEM), energy-dispersive X-ray spectroscopy (EDX) and inductively coupled plasma atomic emission spectroscopy (ICPOES) of the synthesized AgNPs were characterized. The smallest AgNPs can be produced when Cyperus rotundus extracts were utilized. In addition, this study has found that the synthesis efficiencies using all plant extracts are in the range of 72% to 91% with the highest percentage achieved when Eleusin indica extract was employed. All synthesized AgNPs have antibacterial capability against all examined bacteria depending on their size and bacteria types. Interestingly, Melastoma malabathricum and Clidemia hirta extracts have demonstrated an antibacterial ability against C. haemolyticum.
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24
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Batista JH, da Silva Neto JF. Chromobacterium violaceum Pathogenicity: Updates and Insights from Genome Sequencing of Novel Chromobacterium Species. Front Microbiol 2017; 8:2213. [PMID: 29176969 PMCID: PMC5686120 DOI: 10.3389/fmicb.2017.02213] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 10/27/2017] [Indexed: 11/13/2022] Open
Abstract
Chromobacterium violaceum is an abundant component of the soil and water microbiota in tropical and subtropical regions around the world. For many years, it was mainly known as a producer of violacein and as a reporter for the discovery of quorum sensing molecules. However, C. violaceum has recently emerged as an important model of an environmental opportunistic pathogen. Its high virulence in human infections and a mouse infection model involves the possession of several predicted virulence traits, including two type III secretion systems (T3SSs). In this article, in addition to providing an update on the new clinical cases of human C. violaceum infections, we will focus on recent advances in understanding the molecular mechanisms regarding C. violaceum pathogenesis. It has been demonstrated that the C. violaceum Cpi-1 T3SS plays a pivotal role in interaction with host cells. It is required for the secretion of effector proteins and is the agonist recognized by the Nod-like receptor CARD domain-containing protein 4 (NLRC4) inflammasome from innate immune cells. Pyroptosis and its release of hepatocytes for killing by neutrophils are key events required for the clearance of C. violaceum. Given the prominent role of T3SSs in C. violaceum virulence, we examine their occurrence in the Chromobacterium genus, taking advantage of several draft genome sequences of Chromobacterium species that have recently become available. Our finding that the Cpi-1 T3SS is widespread among Chromobacterium species points toward the pathogenic potential of this genus for humans or to novel roles of the T3SS in the interaction of Chromobacterium species with other organisms.
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Affiliation(s)
- Juliana H Batista
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - José F da Silva Neto
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
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25
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Blackburn MB, Farrar RR, Sparks ME, Kuhar D, Mitchell A, Gundersen-Rindal DE. Chromobacterium sphagni sp. nov., an insecticidal bacterium isolated from Sphagnum bogs. Int J Syst Evol Microbiol 2017; 67:3417-3422. [PMID: 28829025 DOI: 10.1099/ijsem.0.002127] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sixteen isolates of Gram-reaction-negative, motile, violet-pigmented bacteria were isolated from Sphagnum bogs in West Virginia and Maine, USA. 16S rRNA gene sequences and fatty acid analysis revealed a high degree of relatedness among the isolates, and genome sequencing of two isolates, IIBBL 14B-1T and IIBBL 37-2 (from West Virginia and Maine, respectively), revealed highly similar genomic sequences. The average nucleotide identity (gANI) calculated for these two isolates was found to be in excess of 99 %, but did not exceed 88 % when comparing either isolate with genomic sequences of Chromobacterium violaceum ATCC 12472T, C. haemolyticum DSM 19808T, C. piscinae ND17, C. subtsugae PRAA4-1T, C. vaccinii MWU205T or C. amazonense CBMAI 310T. Collectively, gANI and 16S rRNA gene sequence comparisons suggested that isolates IIBBL 14B-1T and IIBBL 37-2 were most closely related to C. subtsugae, but represented a distinct species. We propose the name Chromobacterium sphagni sp. nov. for this taxon; the type strain is IIBBL 14B-1T (=NRRL B-67130T=JCM 31882T).
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Affiliation(s)
- Michael B Blackburn
- Invasive Insect Biocontrol and Behavior Laboratory, USDA, ARS, Bldg 007, Rm 301, BARC-West, Beltsville, MD 20705, USA
| | - Robert R Farrar
- Invasive Insect Biocontrol and Behavior Laboratory, USDA, ARS, Bldg 007, Rm 301, BARC-West, Beltsville, MD 20705, USA
| | - Michael E Sparks
- Invasive Insect Biocontrol and Behavior Laboratory, USDA, ARS, Bldg 007, Rm 301, BARC-West, Beltsville, MD 20705, USA
| | - Daniel Kuhar
- Invasive Insect Biocontrol and Behavior Laboratory, USDA, ARS, Bldg 007, Rm 301, BARC-West, Beltsville, MD 20705, USA
| | - Ashaki Mitchell
- Invasive Insect Biocontrol and Behavior Laboratory, USDA, ARS, Bldg 007, Rm 301, BARC-West, Beltsville, MD 20705, USA
| | - Dawn E Gundersen-Rindal
- Invasive Insect Biocontrol and Behavior Laboratory, USDA, ARS, Bldg 007, Rm 301, BARC-West, Beltsville, MD 20705, USA
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26
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Draft Genome Sequence of Chromobacterium aquaticum CC-SEYA-1, a Nonpigmented Member of the Genus Chromobacterium. GENOME ANNOUNCEMENTS 2017; 5:5/12/e01661-16. [PMID: 28336606 PMCID: PMC5364231 DOI: 10.1128/genomea.01661-16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chromobacterium aquaticum CC-SEYA-1T, isolated from a spring in Taiwan, shares many characteristics with other members of the genus but also contains auxin biosynthesis genes and does not produce the pigment violacein. Chromobacterium sp. 49, isolated from Brazil, is identified here as C. aquaticum, indicating that this is a cosmopolitan species.
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27
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Bajaj A, Kumar A, Yadav S, Kaur G, Bala M, Singh NK, Mathan Kumar R, Manickam N, Mayilraj S. Isolation and characterization of a novel Gram-negative bacterium Chromobacterium alkanivorans sp. nov., strain IITR-71T degrading halogenated alkanes. Int J Syst Evol Microbiol 2016; 66:5228-5235. [PMID: 27619232 DOI: 10.1099/ijsem.0.001500] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic position of a Gram-stain negative, non-violaceinpigmented bacterium isolated from an insecticide-contaminated site was characterized by a polyphasic approach. The bacterium was able to grow on three different halogenated compounds namely 1-hlorobutane, 1-hloropropane and 1,2-ichloroethane. As a critical step in the degradation of these haloalkanes, stoichiometric amounts of dechlorination were estimated. Based on selective enrichment method for three months, using a highly contaminated mixed chemical soil, a bacterium was obtained and designated as IITR-71T. Its versatility and novelty led us to further characterize it by polyphasic taxonomy. The 16S rRNA gene sequence (1446 bases) comparison showed highest similarity with those of members of the genus Chromobacterium with the most closely related species to strain IITR-71T being Chromobacterium aquaticum (99.3 %) followed by Chromobacterium haemolyticum (98.6 %) and Chromobacterium piscinae (97.1 %). The major ubiquinone was Q-8. Predominant polar lipids are phosphatidylethanolamine (PE), phosphatidylglycerol (PG) and diphosphatidylglycerol (DPG). The DNA G+C content of IITR-71T was estimated to be 61.2 mol%. The genotypic and phenotypic distinctiveness of IITR-71T and its phylogenetic relationships indicate that IITR-71T represents a novel species, for which the name Chromobacterium alkanivorans sp. nov. is proposed. The type strain is IITR-71T (=MTCC 11059T=JCM 30068T=KCTC 52433T).
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Affiliation(s)
- Abhay Bajaj
- Environmental Biotechnology Division, CSIR-Indian Institute of Toxicological Research (IITR), Lucknow, 226 001, India
| | - Anand Kumar
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, 160 036, India
| | - Shivani Yadav
- Environmental Biotechnology Division, CSIR-Indian Institute of Toxicological Research (IITR), Lucknow, 226 001, India
| | - Gurwinder Kaur
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, 160 036, India
| | - Monu Bala
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, 160 036, India
| | - Nitin Kumar Singh
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, 160 036, India
| | - Rajendran Mathan Kumar
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, 160 036, India
| | - Natesan Manickam
- Environmental Biotechnology Division, CSIR-Indian Institute of Toxicological Research (IITR), Lucknow, 226 001, India
| | - Shanmugam Mayilraj
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, 160 036, India
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28
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The genome of the insecticidal Chromobacterium subtsugae PRAA4-1 and its comparison with that of Chromobacterium violaceum ATCC 12472. GENOMICS DATA 2016; 10:1-3. [PMID: 27617206 PMCID: PMC5004236 DOI: 10.1016/j.gdata.2016.08.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 08/22/2016] [Indexed: 01/08/2023]
Abstract
The genome of Chromobacterium subtsugae strain PRAA4-1, a betaproteobacterium producing insecticidal compounds, was sequenced and compared with the genome of C. violaceum ATCC 12472. The genome of C. subtsugae displayed a reduction in genes devoted to capsular and extracellular polysaccharide, possessed no genes encoding nitrate reductases, and exhibited many more phage-related sequences than were observed for C. violaceum. The genomes of both species possess a number of gene clusters predicted to encode biosynthetic complexes for secondary metabolites; these clusters suggest they produce overlapping, but distinct assortments of metabolites.
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29
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Zhou S, Guo X, Wang H, Kong D, Wang Y, Zhu J, Dong W, He M, Hu G, Zhao B, Zhao B, Ruan Z. Chromobacterium rhizoryzae sp. nov., isolated from rice roots. Int J Syst Evol Microbiol 2016; 66:3890-3896. [PMID: 27393690 DOI: 10.1099/ijsem.0.001284] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel facultatively anaerobic, rod-shaped bacterium, designated LAM1188T, was isolated from the roots of rice (Oryzasativa) in Hubei Province. Cells of LAM1188T were Gram-stain-negative and motile. The temperature and pH ranges for growth were 15-40 °C (optimum: 30 °C) and pH 5-10 (optimum: pH 7), respectively. The strain did not require NaCl for growth but tolerated up to 3.5 % NaCl (w/v). Analysis of the 16S rRNA gene sequence indicated that the isolate represented a member of the genus Chromobacterium, and was most closely related to Chromobacterium haemolyticum MDA0585T and Chromobacterium aquaticum CC-SEYA-1T with 98.7 % and 97.3 % sequence similarity, respectively. The values of DNA-DNA hybridization between LAM1188T and C. haemolyticum JCM 14163T and C. aquaticum CCUG 55175T were 54.0±2.1 % and 44.0±1.2 %, respectively. The major cellular fatty acids were C16 : 0 and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c). The main polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, four unidentified aminolipids and four unidentified lipids. The respiratory quinone was ubiquinone Q-8. The DNA G+C content was 64.1 mol% as determined by the Tm method. On the basis of its phenotypic, chemotaxonomic and phylogenetic characteristics, strain LAM1188T is suggested to represent a novel species of the genus Chromobacterium, for which the name Chromobacte riumrhizoryzae sp. nov. is proposed. The type strain is LAM1188T (=ACCC 19900T=JCM 31180T).
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Affiliation(s)
- Shan Zhou
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China.,State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Xiang Guo
- Biomass Energy Technology Research Centre, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Huimin Wang
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Delong Kong
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Yanwei Wang
- Biomass Energy Technology Research Centre, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Jie Zhu
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Weiwei Dong
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Mingxiong He
- Biomass Energy Technology Research Centre, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Guoquan Hu
- Biomass Energy Technology Research Centre, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Bingqiang Zhao
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Bin Zhao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Zhiyong Ruan
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
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30
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Harmon N, Mortensen JE, Robinette E, Powell EA. Pediatric bacteremia caused by Chromobacterium haemolyticum/Chromobacterium aquaticum. Diagn Microbiol Infect Dis 2016; 86:108-11. [PMID: 27344541 DOI: 10.1016/j.diagmicrobio.2016.05.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 05/24/2016] [Accepted: 05/29/2016] [Indexed: 01/08/2023]
Abstract
We present a case of pediatric bacteremia caused by Chromobacterium haemolyticum, a β-hemolytic, non-pigmented, Gram-negative bacilli recovered from a blood culture and initially identified as Chromobacterium violaceum using phenotypic and proteomic methods. 16S rRNA sequencing of the patient isolated demonstrated a high degree of sequence homology with the type strain of C. haemolyticum. The patient recovered following treatment with meropenem, gentamicin, and trimethoprim/sulfamethoxazole. This case highlights the potential misidentification of C. haemolyticum as non-pigmented C. violaceum due to limitations of the currently available identification methodologies.
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Affiliation(s)
- Nicole Harmon
- Diagnostic Infectious Disease Testing Laboratory, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Joel E Mortensen
- Diagnostic Infectious Disease Testing Laboratory, Cincinnati Children's Hospital Medical Center, Cincinnati, OH.
| | - Eric Robinette
- Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Eleanor A Powell
- Diagnostic Infectious Disease Testing Laboratory, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
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31
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Takenaka R, Nureki SI, Ueno T, Shigemitsu O, Miyazaki E, Kadota JI, Miki T, Okada N. Chromobacterium haemolyticum Pneumonia Possibly Due to the Aspiration of Runoff Water. Jpn J Infect Dis 2015; 68:526-9. [PMID: 26073729 DOI: 10.7883/yoken.jjid.2014.285] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Here, we report a case of pneumonia possibly caused by the aspiration of runoff water containing Chromobacterium haemolyticum. A 69-year-old man became intoxicated with alcohol, fell into a ditch, and lost consciousness after suffering a blow to the head. The lower half of his body was completely paralyzed because of damage to his spinal cord, and he aspirated runoff water from the ditch. Chest computed tomography scans revealed consolidation in the right upper lobe and bilateral lower lobes. A sputum culture detected gram-negative bacteria that was identified as C. haemolyticum. Antibacterial chemotherapy was initiated, and the clinical course was favorable. To the best of our knowledge, this is the first report of C. haemolyticum pneumonia in the literature.
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Affiliation(s)
- Ryuichi Takenaka
- Department of Respiratory Medicine and Infectious Diseases, Oita University Faculty of Medicine
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32
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Menezes CBA, Tonin MF, Corrêa DBA, Parma M, de Melo IS, Zucchi TD, Destéfano SAL, Fantinatti-Garboggini F. Chromobacterium amazonense sp. nov. isolated from water samples from the Rio Negro, Amazon, Brazil. Antonie van Leeuwenhoek 2015; 107:1057-63. [PMID: 25663027 DOI: 10.1007/s10482-015-0397-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Accepted: 01/23/2015] [Indexed: 11/25/2022]
Abstract
The taxonomic position of a bacterium isolated from water samples from the Rio Negro, in Amazon, Brazil, was determined by using a polyphasic approach. The organism formed a distinct phyletic line in the Chromobacterium 16S rRNA gene tree and had chemotaxonomic and morphological properties consistent with its classification in this genus. It was found to be closely related to Chromobacterium vaccinii DSM 25150(T) (98.6 % 16S rRNA gene similarity) and shared 98.5 % 16S rRNA gene similarity with Chromobacterium piscinae LGM 3947(T). DNA-DNA relatedness studies showed that isolate CBMAI 310(T) belongs to distinct genomic species. The isolate was readily distinguished from the type strain of these species using a combination of phenotypic and chemotaxonomic properties. Thus, based on genotypic and phenotypic data, it is proposed that isolate CBMAI 310(T) (=DSM 26508(T)) be classified in the genus Chromobacterium as the type strain of a novel species, namely, Chromobacterium amazonense sp. nov.
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Affiliation(s)
- Claudia Beatriz Afonso Menezes
- Centro Pluridisciplinar de Pesquisas Químicas Biológicas e Agrícolas, UNICAMP, Avenida Alexandre Cazelatto, 999, Campinas, SP, CEP 13083-218, Brazil
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33
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Draft Genome Sequence of Chromobacterium haemolyticum Causing Human Bacteremia Infection in Japan. GENOME ANNOUNCEMENTS 2014; 2:2/6/e01047-14. [PMID: 25377696 PMCID: PMC4223447 DOI: 10.1128/genomea.01047-14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Chromobacterium haemolyticum is a Gram-negative bacterium displaying remarkable hemolysis against human and sheep erythrocytes. In addition, C. haemolyticum infects humans, in which the infection mechanism remains unknown. We report here the draft genome sequence of C. haemolyticum strain T124, isolated from a young patient with sepsis in Japan.
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34
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Identification of secreted virulence factors of Chromobacterium violaceum. J Microbiol 2014; 52:350-3. [PMID: 24535738 DOI: 10.1007/s12275-014-3202-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 08/01/2013] [Accepted: 08/08/2013] [Indexed: 10/25/2022]
Abstract
Chromobacterium violaceum, a component of tropical soil microbiota, is an opportunistic pathogenic bacterium that can infect humans and other animals. In addition to identifying a large number of genes that demonstrate the vast biotechnological potential of this bacterium, genome sequencing revealed several virulence factors, including different cytolysins, which can be related to its pathogenicity. Here we confirmed these predictions from genomic analyses by identifying, through mass spectrometry, proteins present in the culture supernatant of C. violaceum that may constitute secreted virulence factors. Among them, we identified a secreted collagenase and the product of a gene with sequence similarity to previously characterized bacterial porins.
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35
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Okada M, Inokuchi R, Shinohara K, Matsumoto A, Ono Y, Narita M, Ishida T, Kazuki C, Nakajima S, Yahagi N. Chromobacterium haemolyticum-induced bacteremia in a healthy young man. BMC Infect Dis 2013; 13:406. [PMID: 24004824 PMCID: PMC3766243 DOI: 10.1186/1471-2334-13-406] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 08/28/2013] [Indexed: 11/23/2022] Open
Abstract
Background The genus Chromobacterium consists of 7 recognized species. Among those, only C. violaceum, commonly found in the soil and water of tropical and subtropical regions, has been shown to cause human infection. Although human infection is rare, C. violaceum can cause life-threatening sepsis, with metastatic abscesses, most frequently infecting those who are young and healthy. Case presentation We recently identified a case of severe bacteremia caused by Chromobacterium haemolyticum infection in a healthy young patient following trauma and exposure to river water, in Japan. The patient developed necrotizing fasciitis that was successfully treated with a fasciotomy and intravenous ciprofloxacin and gentamicin. Conclusions C. haemolyticum should be considered in the differential diagnosis of skin lesions that progressively worsen after trauma involving exposure to river or lake water, even in temperate regions. Second, early blood cultures for the isolation and identification of the causative organism were important for initiating proper antimicrobial therapy.
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Affiliation(s)
- Megumi Okada
- Department of Emergency and Critical Care Medicine, Ohta Nishinouchi Hospital, 2-5-20 Nishinouchi, 963-8558 Koriyama, Fukushima, Japan
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Soby SD, Gadagkar SR, Contreras C, Caruso FL. Chromobacterium vaccinii sp. nov., isolated from native and cultivated cranberry (Vaccinium macrocarpon Ait.) bogs and irrigation ponds. Int J Syst Evol Microbiol 2012; 63:1840-1846. [PMID: 22984138 DOI: 10.1099/ijs.0.045161-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A large number of Gram-negative, motile, mesophilic, violacein-producing bacteria were isolated from the soils and roots of Vaccinium macrocarpon Ait. and Kalmia angustifolia L. plants and from irrigation ponds associated with wild and cultivated cranberry bogs in Massachusetts, USA. Phylogenetic analyses of 16S rRNA gene sequences placed these isolates in a clade with Chromobacterium species, but the specialized environment from which they were isolated, their low genomic DNA relatedness with Chromobacterium violaceum ATCC 12472(T) and C. subtsugae PRAA4-1(T), significant differences in fatty acid composition and colony morphology indicate that the cranberry and Kalmia isolates comprise a separate species of Chromobacterium, for which the name Chromobacterium vaccinii sp. nov. is proposed. Strain MWU205(T) ( = ATCC BAA-2314(T) = DSM 25150(T)) is proposed as the type strain for the novel species. Phenotypic analysis of 26 independent isolates of C. vaccinii sp. nov. indicates that, despite close geographical and biological proximity, there is considerable metabolic diversity among individuals within the population.
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Affiliation(s)
- Scott D Soby
- Department of Biomedical Sciences, Midwestern University, 19555 N 59th Avenue, Glendale, AZ 85308, USA
| | - Sudhindra R Gadagkar
- Department of Biomedical Sciences, Midwestern University, 19555 N 59th Avenue, Glendale, AZ 85308, USA
| | - Cristina Contreras
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Frank L Caruso
- Cranberry Station, University of Massachusetts, PO Box 569, East Wareham, MA 02538, USA
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Identification of N-acyl-l-homoserine lactones produced by non-pigmented Chromobacterium aquaticum CC-SEYA-1(T) and pigmented Chromobacterium subtsugae PRAA4-1(T). 3 Biotech 2011; 1:239-245. [PMID: 22558542 PMCID: PMC3339584 DOI: 10.1007/s13205-011-0029-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Accepted: 09/30/2011] [Indexed: 02/08/2023] Open
Abstract
Many members of the genus Chromobacterium produce violacein, a characteristic purple pigment which is induced by small diffusible N-acyl homoserine lactones (AHL) quorum-sensing molecules. In this study, the production of AHL of the non-pigmented C. aquaticum CC-SEYA-1T and the pigmented C. subtsugae PRAA4-1T were determined by using a CV026 biosensor assay. The profile of AHL was identified from the extracts of stationary phase cultures using gas chromatography–mass spectroscopy (GC–MS) and thin layer chromatography (TLC). CV026 biosensor assay revealed that both the non-pigmented C. aquaticum CC-SEYA-1T and the pigmented C. subtsugae PRAA4-1T produced AHL molecules, which were identified, respectively, as N-octanoyl homoserine lactone (OHL) [also known as C-8 homoserine lactone (C8-HSL)] and N-hexanoyl homoserine lactone (HHL) [also known as C-6 homoserine lactone (C6-HSL)]. The pigment produced by C. subtsugae PRAA4-1T was similar to that of Chromobacterium violaceum ATCC12472T but no characteristic visible spectral peaks of the pigment were observed in the extracts of C. aquaticum CC-SEYA-1T. In addition, C. aquaticum CC-SEYA-1T and C. subtsugae PRAA4-1T showed hemolytic activities.
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Lima-Bittencourt CI, Costa PS, Barbosa FAR, Chartone-Souza E, Nascimento AMA. Characterization of a Chromobacterium haemolyticum population from a natural tropical lake. Lett Appl Microbiol 2011; 52:642-50. [PMID: 21466570 DOI: 10.1111/j.1472-765x.2011.03052.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AIM To study genetic diversity of Chromobacterium haemolyticum isolates recovered from a natural tropical lake. METHODS AND RESULTS A set of 31 isolates were recovered from a bacterial freshwater community by conventional plating methods and subjected to genetic and phenotypic characterization. The 16S ribosomal RNA (rRNA) gene phylogeny revealed that the isolates were related most closely with C. haemolyticum. In addition to the molecular data, our isolates exhibited strong β-haemolytic activity, were nonviolacein producers and utilized i-inositol, D-mannitol and D-sorbitol in contrast with the other known chromobacteria. Evaluation of the genetic diversity in the 16S rRNA gene, tRNA intergenic spacers (tDNA) and 16S-23S internal transcribed spacers (ITS) unveiled different levels of genetic heterogeneity in the population, which were also observed with repetitive extragenic palindromic (rep)-PCR genomic fingerprinting using the BOX-AR1 primer. tDNA- and ITS-PCR analyses were partially congruent with the 16S rRNA gene phylogeny. The isolates exhibited high resistance to β-lactamic antibiotics. CONCLUSION The population genetic heterogeneity was revealed by 16S rRNA gene sequence, ITS and BOX-PCR analysis. SIGNIFICANCE AND IMPACT OF THE STUDY This study provides for the first time an insight into the genetic diversity of phylogenetically close isolates to C. haemolyticum species.
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Affiliation(s)
- C I Lima-Bittencourt
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
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Comparative biogeography of Chromobacterium from the neotropics. Antonie van Leeuwenhoek 2010; 99:355-70. [PMID: 20803105 DOI: 10.1007/s10482-010-9501-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Accepted: 08/15/2010] [Indexed: 10/19/2022]
Abstract
The genus Chromobacterium encompasses free-living Gram-negative bacteria. Until 2007, the genus consisted of only one species but six species are now recognized. Chromobacterium violaceum is the type species of the genus and is commonly found in soil and water in tropical and sub-tropical regions. We have investigated a collection of 111 isolates displaying violet pigmentation from undisturbed aquatic and soil environments from Brazilian Cerrado ecosystem. The 16S rRNA gene phylogeny revealed that all isolates were allocated in a monophyletic cluster inside the Chromobacterium genus and formed few clusters related most closely with Chromobacterium piscinae. The two sets of isolates from water and soil were analyzed by the repetitive extragenic palindromic (rep)-PCR genomic fingerprinting technique using a BOX-AR1 primer. The antimicrobial susceptibility and the different carbon sources utilized by these isolates were also investigated. Physiological profiles of the isolates generated by BIOLOG GN2 plates showed great versatility in the substrate utilization, much higher than the C. violaceum ATCC 12472. All isolates exhibited a high minimum inhibitory concentration (MIC) to ampicillin (MIC > 512 μg/ml) and were inhibited by ciprofloxacin, tetracycline and mercury at the lowest concentration tested (MIC < 2 μg/ml). Thirteen BOX-PCR band patterns were identified from 33 individual fingerprints. Eleven patterns provided evidence for endemic distributions. Antimicrobial susceptibility and BOX-PCR fingerprint clustering showed a clear distinction between Chromobacterium isolates from the water and soil. The results suggested that microenvironment barriers such as water and soil can play an important role in the periodic selection and diversification of Chromobacterium population ecotypes.
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