Strain identifier

BacDive ID: 23999

Type strain: Yes

Species: Pseudocitrobacter faecalis

Strain Designation: 25 CIT

Strain history: CIP <- 2013, P. Kämpfer, J. Liebig Univ., Giessen, Germany: strain 25 CIT

NCBI tax ID(s): 1398493 (species)

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General

@ref: 21331

BacDive-ID: 23999

DSM-Number: 27453

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, motile, antibiotic resistance

description: Pseudocitrobacter faecalis 25 CIT is a mesophilic, motile bacterium that has multiple antibiotic resistances and was isolated from stool from a hospitalized patient.

NCBI tax id

  • NCBI tax id: 1398493
  • Matching level: species

strain history

@refhistory
21331<- P. Kämpfer, Justus-Liebig-Universität, Giessen, Germany; 25 CIT<- S.A. Abbassi, Armed Forces Institute of Pathology, Pakistan
119218CIP <- 2013, P. Kämpfer, J. Liebig Univ., Giessen, Germany: strain 25 CIT

doi: 10.13145/bacdive23999.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Enterobacteriaceae
  • genus: Pseudocitrobacter
  • species: Pseudocitrobacter faecalis
  • full scientific name: Pseudocitrobacter faecalis Kämpfer et al. 2014

  • synonyms

    • @ref: 20215
    • synonym: Pseudocitrobacter anthropi

@ref: 21331

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Enterobacteriaceae

genus: Pseudocitrobacter

species: Pseudocitrobacter faecalis

full scientific name: Pseudocitrobacter faecalis Kämpfer et al. 2014

strain designation: 25 CIT

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes95.741
6948099.962negative
119218yesnegativerod-shaped

multimedia

  • @ref: 21331
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_27453.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
21331TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
21331COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
119218CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

  • @ref: 21331
  • growth: positive
  • type: growth
  • temperature: 28
  • range: mesophilic

Physiology and metabolism

antibiogram

@refmediumincubation temperatureoxygen conditionPenicillin Goxacillinampicillinticarcillinmezlocillincefalotincefazolincefotaximeaztreonamimipenemtetracyclinechloramphenicolgentamycinamikacinvancomycinerythromycinlincomycinofloxacinnorfloxacincolistinpipemidic acidnitrofurantoinbacitracinpolymyxin bkanamycinneomycindoxycyclineceftriaxoneclindamycinfosfomycinmoxifloxacinlinezolidnystatinquinupristin/dalfopristinteicoplaninpiperacillin/tazobactam
21331Mueller-Hinton Agar30aerob000000001020-220020-2222010016-18141618-20200161418-201000616-1800006
21331Mueller-Hinton Agar30aerob000000001020002220010018141418180161618100081600006
21331Mueller-Hinton Agar30aerob000000001020002220010018141418180161618100081600006

spore formation

@refspore formationconfidence
69481no100
69480no99.774

compound production

@refcompound
21331NDM-1 carbapenemase
21331CTX-M15 beta lactamase

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836830849L-arabinose+fermentation
6836827613amygdalin+fermentation
6836828053melibiose-fermentation
6836817992sucrose-fermentation
6836862345L-rhamnose+fermentation
6836830911sorbitol-fermentation
6836817268myo-inositol-fermentation
6836816899D-mannitol+fermentation
6836817634D-glucose+fermentation
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate+assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin-
6836835581indole-

enzymes

@refvalueactivityec
68368cytochrome oxidase-1.9.3.1
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase+3.2.1.23

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
21331+---+------++--+--++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
21331stool from a hospitalized patientRawalpindi, Military HospitalPakistanPAKAsia33.616773.0667
119218HumanRawalpindi, PakistanPakistanPAKAsia

isolation source categories

Cat1Cat2Cat3
#Infection#Patient
#Host Body Product#Gastrointestinal tract#Feces (Stool)

Safety information

risk assessment

  • @ref: 119218
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

  • @ref: 21331
  • description: Pseudocitrobacter faecalis strain 25 CIT 16S ribosomal RNA gene, partial sequence
  • accession: KF057941
  • length: 1459
  • database: ena
  • NCBI tax ID: 1398493

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudocitrobacter faecalis DSM 27453GCA_003315335scaffoldncbi1398493
66792Pseudocitrobacter faecalis strain DSM 274531398493.6wgspatric1398493
66792Pseudocitrobacter faecalis DSM 274532770939623draftimg1398493

GC content

  • @ref: 21331
  • GC-content: 54.2
  • method: fluorimetric

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno63.087no
gram-positiveno97.66no
anaerobicno95.733no
aerobicyes86.756no
halophileno90.042no
spore-formingno93.723no
glucose-utilyes93.056no
thermophileno99.412yes
motileyes86.277no
glucose-fermentyes90.174yes

External links

@ref: 21331

culture collection no.: DSM 27453, CCM 8479, LMG 27751, CIP 110624

straininfo link

  • @ref: 87974
  • straininfo: 406847

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny24182752Pseudocitrobacter gen. nov., a novel genus of the Enterobacteriaceae with two new species Pseudocitrobacter faecalis sp. nov., and Pseudocitrobacter anthropi sp. nov, isolated from fecal samples from hospitalized patients in Pakistan.Kampfer P, Glaeser SP, Raza MW, Abbasi SA, Perry JDSyst Appl Microbiol10.1016/j.syapm.2013.08.0032013Aerobiosis, Anaerobiosis, Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Enterobacteriaceae/*classification/genetics/*isolation & purification/physiology, Feces/*microbiology, Humans, Molecular Sequence Data, Multilocus Sequence Typing, Nucleic Acid Hybridization, Pakistan, Phylogeny, RNA, Ribosomal, 16S/genetics, Random Amplified Polymorphic DNA Technique, beta-Lactamases/metabolismPathogenicity
Phylogeny35997622Pseudocitrobacter corydidari sp. nov., isolated from the Asian emerald cockroach Corydidarum magnifica.Guzman J, Poehlein A, Glaeser SP, Schwengers O, Blom J, Hollensteiner J, Kampfer P, Vilcinskas AInt J Syst Evol Microbiol10.1099/ijsem.0.0054972022Animals, Bacterial Typing Techniques, Base Composition, Birds, *Cockroaches, DNA, Bacterial/genetics, *Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
21331Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-27453Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27453)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
68368Automatically annotated from API 20E
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
87974Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID406847.1
119218Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110624Collection of Institut Pasteur (CIP 110624)