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Comprehensive genomic analysis reveals virulence factors and antibiotic resistance genes in Pantoea agglomerans KM1, a potential opportunistic pathogen

(2021) PLOS ONE. 16(1).
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Abstract
Pantoea agglomerans is a Gram-negative facultative anaerobic bacillus causing a wide range of opportunistic infections in humans including septicemia, pneumonia, septic arthritis, wound infections and meningitis. To date, the determinants of virulence, antibiotic resistance, metabolic features conferring survival and host-associated pathogenic potential of this bacterium remain largely underexplored. In this study, we sequenced and assembled the whole-genome of P. agglomerans KM1 isolated from kimchi in South Korea. The genome contained one circular chromosome of 4,039,945 bp, 3 mega plasmids, and 2 prophages. The phage-derived genes encoded integrase, lysozyme and terminase. Six CRISPR loci were identified within the bacterial chromosome. Further in-depth analysis showed that the genome contained 13 antibiotic resistance genes conferring resistance to clinically important antibiotics such as penicillin G, bacitracin, rifampicin, vancomycin, and fosfomycin. Genes involved in adaptations to environmental stress were also identified which included factors providing resistance to osmotic lysis, oxidative stress, as well as heat and cold shock. The genomic analysis of virulence factors led to identification of a type VI secretion system, hemolysin, filamentous hemagglutinin, and genes involved in iron uptake and sequestration. Finally, the data provided here show that, the KM1 isolate exerted strong immunostimulatory properties on RAW 264.7 macrophages in vitro. Stimulated cells produced Nitric Oxide (NO) and pro-inflammatory cytokines TNF-alpha, IL-6 and the anti-inflammatory cytokine IL-10. The upstream signaling for production of TNF-alpha, IL-6, IL-10, and NO depended on TLR4 and TLR1/2. While production of TNF-alpha, IL-6 and NO involved solely activation of the NF-kappa B, IL-10 secretion was largely dependent on NF-kappa B and to a lesser extent on MAPK Kinases. Taken together, the analysis of the whole-genome and immunostimulatory properties provided in-depth characterization of the P. agglomerans KM1 isolate shedding a new light on determinants of virulence that drive its interactions with the environment, other microorganisms and eukaryotic hosts
Keywords
General Biochemistry, Genetics and Molecular Biology, General Agricultural and Biological Sciences, General Medicine, DUST-BORNE ENDOTOXINS, MYSTERIOUS BACTERIUM, FILAMENTOUS HEMAGGLUTININ, PSEUDOMONAS-AERUGINOSA, ESCHERICHIA-COLI, IL-10 PRODUCTION, WATER ACTIVITY, ANNOTATION, SEQUENCE, KIMCHI

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MLA
Guevarra, Robin, et al. “Comprehensive Genomic Analysis Reveals Virulence Factors and Antibiotic Resistance Genes in Pantoea Agglomerans KM1, a Potential Opportunistic Pathogen.” PLOS ONE, edited by Feng Gao, vol. 16, no. 1, 2021, doi:10.1371/journal.pone.0239792.
APA
Guevarra, R., Magez, S., Peeters, E., Chung, M. S., Kim, K. H., & Radwanska, M. (2021). Comprehensive genomic analysis reveals virulence factors and antibiotic resistance genes in Pantoea agglomerans KM1, a potential opportunistic pathogen. PLOS ONE, 16(1). https://doi.org/10.1371/journal.pone.0239792
Chicago author-date
Guevarra, Robin, Stefan Magez, Eveline Peeters, Mi Sook Chung, Kyung Hyun Kim, and Magdalena Radwanska. 2021. “Comprehensive Genomic Analysis Reveals Virulence Factors and Antibiotic Resistance Genes in Pantoea Agglomerans KM1, a Potential Opportunistic Pathogen.” Edited by Feng Gao. PLOS ONE 16 (1). https://doi.org/10.1371/journal.pone.0239792.
Chicago author-date (all authors)
Guevarra, Robin, Stefan Magez, Eveline Peeters, Mi Sook Chung, Kyung Hyun Kim, and Magdalena Radwanska. 2021. “Comprehensive Genomic Analysis Reveals Virulence Factors and Antibiotic Resistance Genes in Pantoea Agglomerans KM1, a Potential Opportunistic Pathogen.” Ed by. Feng Gao. PLOS ONE 16 (1). doi:10.1371/journal.pone.0239792.
Vancouver
1.
Guevarra R, Magez S, Peeters E, Chung MS, Kim KH, Radwanska M. Comprehensive genomic analysis reveals virulence factors and antibiotic resistance genes in Pantoea agglomerans KM1, a potential opportunistic pathogen. Gao F, editor. PLOS ONE. 2021;16(1).
IEEE
[1]
R. Guevarra, S. Magez, E. Peeters, M. S. Chung, K. H. Kim, and M. Radwanska, “Comprehensive genomic analysis reveals virulence factors and antibiotic resistance genes in Pantoea agglomerans KM1, a potential opportunistic pathogen,” PLOS ONE, vol. 16, no. 1, 2021.
@article{8689157,
  abstract     = {{Pantoea agglomerans is a Gram-negative facultative anaerobic bacillus causing a wide range of opportunistic infections in humans including septicemia, pneumonia, septic arthritis, wound infections and meningitis. To date, the determinants of virulence, antibiotic resistance, metabolic features conferring survival and host-associated pathogenic potential of this bacterium remain largely underexplored. In this study, we sequenced and assembled the whole-genome of P. agglomerans KM1 isolated from kimchi in South Korea. The genome contained one circular chromosome of 4,039,945 bp, 3 mega plasmids, and 2 prophages. The phage-derived genes encoded integrase, lysozyme and terminase. Six CRISPR loci were identified within the bacterial chromosome. Further in-depth analysis showed that the genome contained 13 antibiotic resistance genes conferring resistance to clinically important antibiotics such as penicillin G, bacitracin, rifampicin, vancomycin, and fosfomycin. Genes involved in adaptations to environmental stress were also identified which included factors providing resistance to osmotic lysis, oxidative stress, as well as heat and cold shock. The genomic analysis of virulence factors led to identification of a type VI secretion system, hemolysin, filamentous hemagglutinin, and genes involved in iron uptake and sequestration. Finally, the data provided here show that, the KM1 isolate exerted strong immunostimulatory properties on RAW 264.7 macrophages in vitro. Stimulated cells produced Nitric Oxide (NO) and pro-inflammatory cytokines TNF-alpha, IL-6 and the anti-inflammatory cytokine IL-10. The upstream signaling for production of TNF-alpha, IL-6, IL-10, and NO depended on TLR4 and TLR1/2. While production of TNF-alpha, IL-6 and NO involved solely activation of the NF-kappa B, IL-10 secretion was largely dependent on NF-kappa B and to a lesser extent on MAPK Kinases. Taken together, the analysis of the whole-genome and immunostimulatory properties provided in-depth characterization of the P. agglomerans KM1 isolate shedding a new light on determinants of virulence that drive its interactions with the environment, other microorganisms and eukaryotic hosts}},
  articleno    = {{e0239792}},
  author       = {{Guevarra, Robin and Magez, Stefan and Peeters, Eveline and Chung, Mi Sook and Kim, Kyung Hyun and Radwanska, Magdalena}},
  editor       = {{Gao, Feng}},
  issn         = {{1932-6203}},
  journal      = {{PLOS ONE}},
  keywords     = {{General Biochemistry,Genetics and Molecular Biology,General Agricultural and Biological Sciences,General Medicine,DUST-BORNE ENDOTOXINS,MYSTERIOUS BACTERIUM,FILAMENTOUS HEMAGGLUTININ,PSEUDOMONAS-AERUGINOSA,ESCHERICHIA-COLI,IL-10 PRODUCTION,WATER ACTIVITY,ANNOTATION,SEQUENCE,KIMCHI}},
  language     = {{eng}},
  number       = {{1}},
  pages        = {{27}},
  title        = {{Comprehensive genomic analysis reveals virulence factors and antibiotic resistance genes in Pantoea agglomerans KM1, a potential opportunistic pathogen}},
  url          = {{http://dx.doi.org/10.1371/journal.pone.0239792}},
  volume       = {{16}},
  year         = {{2021}},
}

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