{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T01:25:44Z","timestamp":1790904344689,"version":"4.1.0"},"reference-count":92,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2021,1,6]],"date-time":"2021-01-06T00:00:00Z","timestamp":1609891200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:p>\n                    <jats:italic>Pantoea agglomerans<\/jats:italic>\n                    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\n                    <jats:italic>P<\/jats:italic>\n                    .\n                    <jats:italic>agglomerans<\/jats:italic>\n                    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\n                    <jats:italic>in vitr<\/jats:italic>\n                    o. Stimulated cells produced Nitric Oxide (NO) and pro-inflammatory cytokines TNF-\u03b1, IL-6 and the anti-inflammatory cytokine IL-10. The upstream signaling for production of TNF-\u03b1, IL-6, IL-10, and NO depended on TLR4 and TLR1\/2. While production of TNF-\u03b1, IL-6 and NO involved solely activation of the NF-\u03baB, IL-10 secretion was largely dependent on NF-\u03baB 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\n                    <jats:italic>P<\/jats:italic>\n                    .\n                    <jats:italic>agglomerans<\/jats:italic>\n                    KM1 isolate shedding a new light on determinants of virulence that drive its interactions with the environment, other microorganisms and eukaryotic hosts\n                  <\/jats:p>","DOI":"10.1371\/journal.pone.0239792","type":"journal-article","created":{"date-parts":[[2021,1,6]],"date-time":"2021-01-06T14:27:15Z","timestamp":1609943235000},"page":"e0239792","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":47,"title":["Comprehensive genomic analysis reveals virulence factors and antibiotic resistance genes in Pantoea agglomerans KM1, a potential opportunistic pathogen"],"prefix":"10.1371","volume":"16","author":[{"given":"Robin B.","family":"Guevarra","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefan","family":"Magez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eveline","family":"Peeters","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mi Sook","family":"Chung","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kyung Hyun","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0797-6001","authenticated-orcid":true,"given":"Magdalena","family":"Radwanska","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2021,1,6]]},"reference":[{"issue":"1","key":"pone.0239792.ref001","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1089\/jmf.2013.3083","article-title":"Health benefits of kimchi (Korean fermented vegetables) as a probiotic food","volume":"17","author":"KY Park","year":"2014","journal-title":"Journal of medicinal food"},{"key":"pone.0239792.ref002","doi-asserted-by":"crossref","first-page":"1493","DOI":"10.3389\/fmicb.2016.01493","article-title":"Kimchi and other widely consumed traditional fermented foods of Korea: A review","volume":"7","author":"JK Patra","year":"2016","journal-title":"Frontiers in 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disease."},{"issue":"6","key":"pone.0239792.ref006","doi-asserted-by":"crossref","first-page":"942","DOI":"10.4315\/0362-028X.JFP-17-459","article-title":"Pathogenic Escherichia coli and Salmonella can survive in kimchi during fermentation","volume":"81","author":"Y Choi","year":"2018","journal-title":"Journal of food protection"},{"issue":"44","key":"pone.0239792.ref007","doi-asserted-by":"crossref","DOI":"10.1128\/MRA.00828-19","article-title":"Genome sequence of the plant growth-promoting rhizobacterium Pantoea agglomerans C1.","volume":"8","author":"F Luziatelli","year":"2019","journal-title":"Microbiology resource announcements"},{"issue":"1","key":"pone.0239792.ref008","article-title":"Complete genome sequence ofTH81, isolated from a permafrost thaw gradient","volume":"8","author":"J Humphrey","year":"2019","journal-title":"Pantoea agglomeransMicrobiology resource 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