Strain identifier

BacDive ID: 6098

Type strain: Yes

Species: Helicobacter cinaedi

Strain Designation: Fennel 165

Strain history: CIP <- 1994, CCUG <- 1986, C.L. Fennell, Seattle, USA: strain 165, Campylobacter cinaedi

NCBI tax ID(s): 537971 (strain), 213 (species)

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General

@ref: 2001

BacDive-ID: 6098

DSM-Number: 5359

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, motile, human pathogen

description: Helicobacter cinaedi Fennel 165 is a microaerophile, mesophilic, motile human pathogen that was isolated from human male; rectal swab.

NCBI tax id

NCBI tax idMatching level
537971strain
213species

strain history

@refhistory
2001<- BCCM; LMG 7543 <- CCUG; CCUG 18818 <- C.L. Flennel; Fennel 165
118282CIP <- 1994, CCUG <- 1986, C.L. Fennell, Seattle, USA: strain 165, Campylobacter cinaedi

doi: 10.13145/bacdive6098.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Epsilonproteobacteria
  • order: Campylobacterales
  • family: Helicobacteraceae
  • genus: Helicobacter
  • species: Helicobacter cinaedi
  • full scientific name: Helicobacter cinaedi (Totten et al. 1988) Vandamme et al. 1991

  • synonyms

    • @ref: 20215
    • synonym: Campylobacter cinaedi

@ref: 2001

domain: Bacteria

phylum: Proteobacteria

class: Epsilonproteobacteria

order: Campylobacterales

family: Helicobacteraceae

genus: Helicobacter

species: Helicobacter cinaedi

full scientific name: Helicobacter cinaedi (Totten et al. 1988) Vandamme et al. 1991

strain designation: Fennel 165

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes94.54
6948099.996negative
118282yesnegativerod-shaped

colony morphology

  • @ref: 46903
  • incubation period: 5 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2001COLUMBIA 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
38146MEDIUM 45 - for Columbia agar with sheep bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Sheepblood (100.000 ml)
118282CIP Medium 45yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=45

culture temp

@refgrowthtypetemperaturerange
2001positivegrowth37mesophilic
38146positivegrowth37mesophilic
46903positivegrowth37mesophilic
118282positivegrowth37mesophilic
118282nogrowth10psychrophilic
118282nogrowth30mesophilic
118282nogrowth41thermophilic
118282nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
2001microaerophile
46903microaerophile

spore formation

@refspore formationconfidence
69481no99
69480no99.997

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
118282606565hippurate+hydrolysis
11828217632nitrate+reduction
11828216301nitrite-reduction
118282132112sodium thiosulfate-builds gas from
6837316199urea-hydrolysis
6837330031succinate-assimilation

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.
6837348923erythromycinyesyes14 µg
68373474053cefazolinyesyes224 µg
68373100147nalidixic acidyesyes84 µg

metabolite production

@refChebi-IDmetaboliteproduction
6837316136hydrogen sulfideno
11828235581indoleno

enzymes

@refvalueactivityec
2001catalase+1.11.1.6
2001cytochrome-c oxidase-1.9.3.1
68373L-aspartate arylamidase-3.4.11.21
68373gamma-glutamyltransferase-2.3.2.2
68373urease-3.5.1.5
118282oxidase+
118282gelatinase-
118282catalase+1.11.1.6
118282urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    46903C12:06.812
    46903C13:00.513
    46903C14:02914
    46903C15:01.215
    46903C16:030.716
    46903C17:00.317
    46903C18:00.418
    46903C12:0 3OH2.713.455
    46903C13:0 ISO 2OH0.413.814
    46903C14:0 ISO1.113.618
    46903C16:0 3OH3.217.52
    46903C16:0 iso0.315.626
    46903C16:1 ω7c0.715.819
    46903C18:1 ω7c /12t/9t19.917.824
    46903C18:2 ω6,9c/C18:0 ANTE1.617.724
    46903Unidentified0.415.941
    46903Unidentified0.417.473
    46903unknown 12.4860.612.486
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API CAM

@refURENITESTHIPGGTTTCPYRAArgAAspAPALH2SGLUSUTNALCFZACEPROPMLTCITEROCAT
2001---------+/--+/---------+
46903---------------+-----
46903-++--+++-+------+---+
46903-++--+---+-----------
2001-+-+/--+-+-+------++/-+-+
2001-++--++----+---+/-+/----+
2001-----+--------------+
2001-+-----+/--+----------+
2001-+------------------+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
2001human male; rectal swabSeattleUSAUSANorth America47.61-122.34
46903Human rectal swabSeattleUSAUSANorth America
118282Human, Homosexual man, rectal swabSeattle, WashingtonUnited States of AmericaUSANorth America

isolation source categories

Cat1Cat2Cat3
#Infection#Patient
#Infection#Patient#Swab
#Host Body-Site#Gastrointestinal tract#Rectum
#Host#Human#Male

Safety information

risk assessment

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
2001yesyes2Risk group (German classification)
1182822Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Helicobacter fennelliae strain ATCC 35683 16S ribosomal RNA gene, partial sequenceAF3487451676ena215
20218Helicobacter cinaedi gene for 16S rRNA, partial sequence, strain: PAGU0597 (= CCUG18818)AB2753171430ena213
20218Helicobacter cinaedi strain CCUG 18818 16S ribosomal RNA gene, partial sequenceAF3487481327ena537971
2001Helicobacter cinaedi strain CCUG 18818 16S ribosomal RNA gene, partial sequenceM881501473ena537971

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Helicobacter cinaedi CCUG 18818 = ATCC BAA-847GCA_000349975completencbi537971
66792Helicobacter cinaedi DSM 5359GCA_017979495contigncbi213
66792Helicobacter cinaedi CCUG 18818 = ATCC BAA-847GCA_000155475scaffoldncbi537971
66792Helicobacter cinaedi CCUG 18818 = ATCC BAA-847GCA_003215615contigncbi537971
66792Helicobacter cinaedi CCUG 18818537971.5wgspatric537971
66792Helicobacter cinaedi CCUG 18818 = ATCC BAA-847537971.15wgspatric537971
66792Helicobacter cinaedi strain DSM 5359213.64wgspatric213
66792Helicobacter cinaedi CCUG 18818643886141draftimg537971

GC content

  • @ref: 2001
  • GC-content: 36.1
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileyes92.521no
flagellatedyes54.428no
gram-positiveno99.225no
anaerobicno61.564no
aerobicno97.434yes
halophileno88.731no
spore-formingno95.235no
glucose-utilno89.585no
thermophileno62.204yes
glucose-fermentno88.746no

External links

@ref: 2001

culture collection no.: DSM 5359, ATCC 35683, CCUG 18818, LMG 7543, NCTC 12423, CIP 103752

straininfo link

  • @ref: 75586
  • straininfo: 2993

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology2768458Campylobacter cinaedi is normal intestinal flora in hamsters.Gebhart CJ, Fennell CL, Murtaugh MP, Stamm WEJ Clin Microbiol10.1128/jcm.27.7.1692-1694.19891989Animals, Campylobacter/*isolation & purification, Cricetinae/*microbiology, *Disease Reservoirs, Electrophoresis, Polyacrylamide Gel, Feces/microbiology, Intestines/*microbiology, Mesocricetus/*microbiologyPhylogeny
Enzymology22593597Molecular epidemiologic analysis and antimicrobial resistance of Helicobacter cinaedi isolated from seven hospitals in Japan.Rimbara E, Mori S, Matsui M, Suzuki S, Wachino J, Kawamura Y, Shen Z, Fox JG, Shibayama KJ Clin Microbiol10.1128/JCM.06810-112012Adult, Aged, Aged, 80 and over, Animals, Anti-Bacterial Agents/*pharmacology, Ciprofloxacin/pharmacology, Clarithromycin/pharmacology, Cluster Analysis, DNA Gyrase/genetics, *Drug Resistance, Bacterial, Electrophoresis, Gel, Pulsed-Field, Female, Genotype, Helicobacter/*drug effects/*isolation & purification, Helicobacter Infections/*epidemiology/*microbiology, Hospitals, Humans, Japan, Male, Middle Aged, Molecular Epidemiology, Multilocus Sequence Typing/*methods, Mutation, RNA, Ribosomal, 23S/geneticsPathogenicity
Phylogeny23130344A case of Helicobacter cinaedi bacteremia in an asplenic patient.Kim SK, Cho EJ, Sung H, An D, Park SJ, Kim MN, Nam GBAnn Lab Med10.3343/alm.2012.32.6.4332012Aged, Bacteremia/diagnosis/*microbiology, Base Sequence, Helicobacter/classification/genetics/*isolation & purification, Heterotaxy Syndrome/*pathology, Humans, Male, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/chemistry/genetics, Sequence Analysis, RNAPathogenicity
25381744Helicobacter cinaedi induced typhlocolitis in Rag-2-deficient mice.Shen Z, Feng Y, Rickman B, Fox JGHelicobacter10.1111/hel.121792014Animals, Cecum/pathology, Colitis/complications/*microbiology/*pathology, Colon/pathology, Cytokines/biosynthesis, DNA-Binding Proteins/*deficiency, Female, Gene Expression Profiling, Helicobacter/*growth & development/pathogenicity, Male, Mice, Mice, Knockout, Nitric Oxide Synthase Type II/biosynthesis, Typhlitis/complications/*microbiology/*pathology
Phylogeny27381809Proposal of Helicobacter canicola sp. nov., previously identified as Helicobacter cinaedi, isolated from canines.Kawamura Y, Tomida J, Miyoshi-Akiyama T, Okamoto T, Narita M, Hashimoto K, Cnockaert M, Vandamme P, Morita Y, Sawa T, Akaike TSyst Appl Microbiol10.1016/j.syapm.2016.06.0042016Alkaline Phosphatase/genetics, Animals, Chaperonin 60/*genetics, DNA Gyrase/*genetics, DNA, Bacterial/genetics, Dogs/*microbiology, Genome, Bacterial/genetics, *Helicobacter/classification/genetics/isolation & purification, Humans, Molecular Typing/*veterinary, Nitrates/metabolism, Nitrites/metabolism, Phylogeny, RNA, Ribosomal, 16S/*genetics, RNA, Ribosomal, 23S/*genetics, Sequence Analysis, DNAGenetics
Pathogenicity29203490Mutations in Genes Encoding Penicillin-Binding Proteins and Efflux Pumps Play a Role in beta-Lactam Resistance in Helicobacter cinaedi.Rimbara E, Mori S, Kim H, Suzuki M, Shibayama KAntimicrob Agents Chemother10.1128/AAC.02036-172018Amoxicillin/pharmacology, Anti-Bacterial Agents/pharmacology, Carrier Proteins/genetics, Ceftriaxone/pharmacology, Helicobacter Infections/*drug therapy/microbiology, Helicobacter pylori/*drug effects/*genetics, Humans, Microbial Sensitivity Tests/methods, Mutation/*genetics, Penicillin-Binding Proteins/*genetics, beta-Lactam Resistance/*genetics, beta-Lactams/*pharmacology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2001Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5359)https://www.dsmz.de/collection/catalogue/details/culture/DSM-5359
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
38146Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15584
46903Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 18818)https://www.ccug.se/strain?id=18818
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
68373Automatically annotated from API CAM
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
75586Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID2993.1StrainInfo: A central database for resolving microbial strain identifiers
118282Curators of the CIPCollection of Institut Pasteur (CIP 103752)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103752