Genome sequence of<i>Kosakonia radicincitans</i>UMEnt01/12, a bacterium associated with bacterial wilt diseased banana plant

Suhaimi, Nurul Shamsinah Mohd; Yap, Kien-Pong; Ajam, Noni; Thong, Kwai Lin

doi:10.1111/1574-6968.12537

Cited by 11 publications

(8 citation statements)

References 17 publications

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“…Previously known as Enterobacter radicincitans , all prior reports of this organism have described it as a plant associated bacteria and have mainly focused on its growth promoting properties (Kampfer et al, 2005; Schreiner et al, 2009; Witzel et al, 2012; Brock et al, 2013; Suhaimi et al, 2014; Bergottini et al, 2015). However, there is a report of K. radicincitans causing bacterial wilt disease in bananas, suggesting its pathogenic potential (Suhaimi et al, 2014). Given the difficulties in accurately identifying organisms previously labeled as part of the Enterobacter genus, we cannot determine whether this is actually the first case of human infection due to K. radicincitans or whether the organism has been previously misidentified, as originally occurred with our isolate.…”

Section: Discussionmentioning

confidence: 99%

Identification and Whole Genome Sequencing of the First Case of Kosakonia radicincitans Causing a Human Bloodstream Infection

et al. 2017

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The taxonomy of Enterobacter species is rapidly changing. Herein we report a bloodstream infection isolate originally identified as Enterobacter cloacae by Vitek2 methodology that we found to be Kosakonia radicincitans using genetic means. Comparative whole genome sequencing of our isolate and other published Kosakonia genomes revealed these organisms lack the AmpC β-lactamase present on the chromosome of Enterobacter sp. A fimbriae operon primarily found in Escherichia coli O157:H7 isolates was present in our organism and other available K. radicincitans genomes. This is the first report of a Kosakonia species, which are typically associated with plants, causing a human infection.

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Section: Discussionmentioning

confidence: 99%

Identification and Whole Genome Sequencing of the First Case of Kosakonia radicincitans Causing a Human Bloodstream Infection

et al. 2017

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“…The assembled genomes were annotated and mapped to the reference genomes (CT18) as previously described ( Ho et al, 2012 ; Yap et al, 2012a ). The tRNA and tmRNA were predicted using Aragorn ( Laslett and Canback, 2004 ) whereas the rRNA was predicted with rRNAMMer ( Lagesen et al, 2007 ), and manually validated as described earlier ( Osama et al, 2012 ; Suhaimi et al, 2014 ). To compare, we have included three reference genomes and six of our own published sequenced genomes (described earlier), representing ST1 (Ty2, P-stx-12, Ty21a, BL196, CR0044) and ST2 populations (CT18, CR0063, UJ308A, UJ816A, ST0208).…”

Section: Methodsmentioning

confidence: 99%

Global MLST of Salmonella Typhi Revisited in Post-genomic Era: Genetic Conservation, Population Structure, and Comparative Genomics of Rare Sequence Types

Yap

Gan

et al. 2016

Front. Microbiol.

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Typhoid fever, caused by Salmonella enterica serovar Typhi, remains an important public health burden in Southeast Asia and other endemic countries. Various genotyping methods have been applied to study the genetic variations of this human-restricted pathogen. Multilocus sequence typing (MLST) is one of the widely accepted methods, and recently, there is a growing interest in the re-application of MLST in the post-genomic era. In this study, we provide the global MLST distribution of S. Typhi utilizing both publicly available 1,826 S. Typhi genome sequences in addition to performing conventional MLST on S. Typhi strains isolated from various endemic regions spanning over a century. Our global MLST analysis confirms the predominance of two sequence types (ST1 and ST2) co-existing in the endemic regions. Interestingly, S. Typhi strains with ST8 are currently confined within the African continent. Comparative genomic analyses of ST8 and other rare STs with genomes of ST1/ST2 revealed unique mutations in important virulence genes such as flhB, sipC, and tviD that may explain the variations that differentiate between seemingly successful (widespread) and unsuccessful (poor dissemination) S. Typhi populations. Large scale whole-genome phylogeny demonstrated evidence of phylogeographical structuring and showed that ST8 may have diverged from the earlier ancestral population of ST1 and ST2, which later lost some of its fitness advantages, leading to poor worldwide dissemination. In response to the unprecedented increase in genomic data, this study demonstrates and highlights the utility of large-scale genome-based MLST as a quick and effective approach to narrow the scope of in-depth comparative genomic analysis and consequently provide new insights into the fine scale of pathogen evolution and population structure.

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“…It is not yet known which of K. radicincitans genes contribute to the growth improvements observed in inoculated plants; however biochemical tests confirmed that K. radicincitans is diazotrophic (Ruppel and Merbach 1997;Scholz-Seidel and Ruppel 1992). This is also strengthened by genome publications revealing a nitrogenase-encoding nifHDK operon in K. radicincitans strains (Bergottini et al 2015;Mohd Suhaimi et al 2014;Witzel et al 2012) (https://www.ncbi.nlm.nih.gov/nuccore/CP015113.1). Through sequence analysis of the published genomes, we discovered that K. radicincitans DSM16656 T , YD4, UMEnt01/12 and D r a f t GXGL-4A also have an anfHDGK operon encoding an additional nitrogenase.…”

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Site-directed mutagenesis to deactivate two nitrogenase isozymes of Kosakonia radicincitans DSM16656^T

et al. 2018

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Biological nitrogen fixation (BNF) is considered one of the key plant-growth-promoting (PGP) factors for diazotrophic organisms. Whether the iron and iron-molybdenum nitrogenases of Kosakonia radicincitans contribute to its PGP effect is yet to be proven. Hence, for the first time, we conducted site-directed mutagenesis in K. radicincitans to knock out anfH and (or) nifH as a mean to deactivate BNF in this strain. We used N-labeled air to trace BNF activities in ΔanfH, ΔnifH, and ΔanfHΔnifH mutants. Assessing bacterial growth, nitrogen content, and N incorporation revealed that BNF is impaired in K. radicincitans DSM16656 ΔnifH and ΔanfHΔnifH. However, we detected no significant contribution of the Fe nitrogenase to biological dinitrogen assimilation under our pure bacterial culture experimental conditions. Such nondiazotrophic K. radicincitans DSM16656 mutants represent excellent tools for investigating nitrogen nutrition in K. radicincitans-inoculated plants.

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Genome sequence ofKosakonia radicincitansUMEnt01/12, a bacterium associated with bacterial wilt diseased banana plant

Cited by 11 publications

References 17 publications

Identification and Whole Genome Sequencing of the First Case of Kosakonia radicincitans Causing a Human Bloodstream Infection

Identification and Whole Genome Sequencing of the First Case of Kosakonia radicincitans Causing a Human Bloodstream Infection

Global MLST of Salmonella Typhi Revisited in Post-genomic Era: Genetic Conservation, Population Structure, and Comparative Genomics of Rare Sequence Types

Site-directed mutagenesis to deactivate two nitrogenase isozymes of Kosakonia radicincitans DSM16656^T

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Genome sequence ofKosakonia radicincitansUMEnt01/12, a bacterium associated with bacterial wilt diseased banana plant

Cited by 11 publications

References 17 publications

Identification and Whole Genome Sequencing of the First Case of Kosakonia radicincitans Causing a Human Bloodstream Infection

Identification and Whole Genome Sequencing of the First Case of Kosakonia radicincitans Causing a Human Bloodstream Infection

Global MLST of Salmonella Typhi Revisited in Post-genomic Era: Genetic Conservation, Population Structure, and Comparative Genomics of Rare Sequence Types

Site-directed mutagenesis to deactivate two nitrogenase isozymes of Kosakonia radicincitans DSM16656T

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Site-directed mutagenesis to deactivate two nitrogenase isozymes of Kosakonia radicincitans DSM16656^T