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

Bhatti, Micah D.; Kalia, Awdhesh; Sahasrabhojane, Pranoti; Kim, Jiwoong; Greenberg, David E.; Shelburne, Samuel A.

doi:10.3389/fmicb.2017.00062

Cited by 18 publications

(14 citation statements)

References 15 publications

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“…Our baseline (T0) evaluations ( Figure 4 ) confirm recent publications arguing a decreased gut microbial alpha diversity in PCOS women compared to healthy controls [ 2 , 108 ]. These data also align with the common concept of a fast adapting diet-induced change of the microbiome [ 109 , 110 , 111 , 112 ].…”

Section: Discussionsupporting

confidence: 87%

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Impact of Short-Term Isoflavone Intervention in Polycystic Ovary Syndrome (PCOS) Patients on Microbiota Composition and Metagenomics

et al. 2020

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Background: Polycystic ovary syndrome (PCOS) affects 5–20% of women of reproductive age worldwide and is associated with disorders of glucose metabolism. Hormone and metabolic signaling may be influenced by phytoestrogens, such as isoflavones. Their endocrine effects may modify symptom penetrance in PCOS. Equol is one of the most active isoflavone metabolites, produced by intestinal bacteria, and acts as a selective estrogen receptor modulator. Method: In this interventional study of clinical and biochemical characterization, urine isoflavone levels were measured in PCOS and control women before and three days after a defined isoflavone intervention via soy milk. In this interventional study, bacterial equol production was evaluated using the log(equol: daidzein ratio) and microbiome, metabolic, and predicted metagenome analyses were performed. Results: After isoflavone intervention, predicted stool metagenomic pathways, microbial alpha diversity, and glucose homeostasis in PCOS improved resembling the profile of the control group at baseline. In the whole cohort, larger equol production was associated with lower androgen as well as fertility markers. Conclusion: The dynamics in our metabolic, microbiome, and predicted metagenomic profiles underline the importance of external phytohormones on PCOS characteristics and a potential therapeutic approach or prebiotic in the future.

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Section: Discussionsupporting

confidence: 87%

“…Polycystic ovary syndrome (PCOS) is one of the most prevalent endocrine and metabolic disorders in women, affecting 5–20% already from reproductive age worldwide, with phenotypes of various degrees of hyperandrogenism, anovulation and polycystic ovarian morphology [ 1 , 2 ].…”

Section: Introductionmentioning

confidence: 99%

Impact of Short-Term Isoflavone Intervention in Polycystic Ovary Syndrome (PCOS) Patients on Microbiota Composition and Metagenomics

et al. 2020

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“…This study further demonstrates the utility of whole genome sequencing for pathogen identification in a clinical setting. Similarity, another report found that Vitek2 identified a blood culture derived isolate as E. cloacae but Illumina whole genome sequencing unequivocally determined it to be Kosakonia radicincitans (Bhatti et al, 2017 ). Further comprehensive work is therefore warranted to investigate clinical outcomes that result from these species misidentification.…”

Section: Discussionmentioning

confidence: 69%

Superficieibacter electus gen. nov., sp. nov., an Extended-Spectrum β-Lactamase Possessing Member of the Enterobacteriaceae Family, Isolated From Intensive Care Unit Surfaces

et al. 2018

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Two Gram-negative bacilli strains, designated BP-1(T) and BP-2, were recovered from two different Intensive Care Unit surfaces during a longitudinal survey in Pakistan. Both strains were unidentified using the bioMerieux VITEK MS IVD v2.3.3 and Bruker BioTyper MALDI-TOF mass spectrometry platforms. To more precisely determine the taxonomic identity of BP-1(T) and BP-2, we employed a biochemical and phylogenomic approach. The 16S rRNA gene sequence of strain BP-1(T) had the highest identity to Citrobacter farmeri CDC 2991-81(T) (98.63%) Citrobacter amalonaticus CECT 863(T) (98.56%), Citrobacter sedlakii NBRC 105722(T) (97.74%) and Citrobacter rodentium NBRC 105723(T) (97.74%). The biochemical utilization scheme of BP-1(T) using the Analytic Profile Index for Enterobacteriaceae (API20E) indicated its enzymatic functions are unique within the Enterobacteriaceae but most closely resemble Kluyvera spp., Enterobacter cloacae and Citrobacter koseri/farmeri. Phylogenomic analysis of the shared genes between BP-1(T), BP-2 and type strains from Kluyvera, Citrobacter, Escherichia, Salmonella, Kosakonia, Siccibacter and Shigella indicate that BP-1(T) and BP-2 isolates form a distinct branch from these genera. Average Nucleotide Identity analysis indicates that BP-1(T) and BP-2 are the same species. The biochemical and phylogenomic analysis indicate strains BP-1(T) and BP-2 represent a novel species from a new genus within the Enterobacteriaceae family, for which the name Superficieibacter electus gen. nov., sp. nov., is proposed. The type strain is BP-1(T) (= ATCC BAA-2937, = NBRC 113412).

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“…In 2013, Enterobacter was divided into 5 new genera: Lelliottia, Pluralibacter, Kosakonia, epidemiological data on the occurrence of Kosakonia species in human samples. The first case of a human bloodstream infection with K. radicincitans was reported in a 61-year-old man with cholangiocarcinoma in Houston, TX, USA, in Dec. 2016 4 . Unfortunately, the authors of this report considered some common features of enteric bacteria to be virulence factors, and confused type IV secretion systems with type IV pili that are involved in several phenomena, not only pathogenicity 12 .…”

Section: Discussionmentioning

confidence: 99%

First Report of Kosakonia radicincitans Bacteraemia from Europe (Austria) - Identification and Whole-Genome Sequencing of Strain DSM 107547

Mertschnigg

Patz

Becker

et al. 2020

Sci Rep

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Kosakonia radicincitans is a species within the new genus Kosakonia. Many strains of this genus have been isolated from plants, but some strains are assumed to act as facultative human pathogens. in this study, an in-depth analysis of a Kosakonia isolate from human blood was performed. the strain was originally isolated from blood and identified as a member of the Enterobacter cloacae complex, exhibiting an atypical result in susceptibility testing. therefore, the genetic background was examined, including phylogenetic classification and screening for virulence factors. Using whole-genome sequencing, the isolate was identified as a K. radicincitans strain, revealing a virulence gene cluster for yersiniabactin biosynthesis in contrast to all other strains of the species. Whole-genome sequencing was the perfect method for identifying putative virulence factors of a particular Kosakonia strain and will help distinguish beneficial strains from pathogenic strains in the future. To our knowledge, this is the first report of Kosakonia-related bacteraemia from europe. Kosakonia radicincitans is a species within the new genus Kosakonia, until recently part of the genus Enterobacter. Many Kosakonia species have been isolated from plants and are known to improve plant performance 1,2 , but there are also rare reports that assume that some Kosakonia spp., such as Kosakonia cowanii, can act as facultative human pathogens 3. There are also rare reports of Kosakonia radicincitans involved in human infections; however, all these reports are from outside Europe (mainly Asia and America). The first case of a human bloodstream infection with K. radicincitans was reported in a 61-year-old man with cholangiocarcinoma in Houston, Texas, USA, in December 2016 4. However, the actual number of infections could have been underestimated, as this genus is relatively new and is therefore probably not yet included in all automated databases of bacterial diagnostic tools. It seems that Kosakonia has no higher pathogenic or resistance properties than Enterobacter, making a more precise diagnosis unnecessary in many cases 4. Therefore, this study used the rare opportunity to diagnose such an infection by careful evaluation. The aim of the study was to analyse the genetic background of a Kosakonia isolate from a patient with bacteraemia, including phylogenetic classification and screening for virulence factors. Description of the case: An 85-year-old woman presented at the Department of Internal Medicine, in Graz, Austria, with icterus, occasionally diffuse abdominal pain and loss of appetite. Upon admission, she was afebrile, showed atrial flutter (3:1), and a heart rate of 100/min; she was in slightly poor general condition and had pressure pain in the middle and lower abdomen. Her liver values were significantly increased. She was diagnosed with bile duct stenosis and received a stent by endoscopic retrograde cholangiopancreatography (ERCP) on the third day

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

Cited by 18 publications

References 15 publications

Impact of Short-Term Isoflavone Intervention in Polycystic Ovary Syndrome (PCOS) Patients on Microbiota Composition and Metagenomics

Impact of Short-Term Isoflavone Intervention in Polycystic Ovary Syndrome (PCOS) Patients on Microbiota Composition and Metagenomics

Superficieibacter electus gen. nov., sp. nov., an Extended-Spectrum β-Lactamase Possessing Member of the Enterobacteriaceae Family, Isolated From Intensive Care Unit Surfaces

First Report of Kosakonia radicincitans Bacteraemia from Europe (Austria) - Identification and Whole-Genome Sequencing of Strain DSM 107547

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