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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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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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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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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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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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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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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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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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