Citrobacter portucalensis (DSM 104542, CECT 9236, A60)

Name: Citrobacter portucalensis (DSM 104542, CECT 9236, A60)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 140426

Type strain

Strain Designation A60

Culture col. no. DSM 104542 CECT 9236 A60 CIP 111602

NCBI tax ID(s) 1639133

Special Collections DSMZ Literature strains CIP

History DSMZ <- L. Vieira Peixe; Faculty of Pharmacy, University of Porto, Porto, Portugal; A60 <- E. Machado CIP <- 2017, L. Peixe, Porto Univ., Porto, Portugal: strain A60

Links

Citrobacter portucalensis A60 is a facultative anaerobe, Gram-negative, motile bacterium that was isolated from water well.

Gram-negative motile rod-shaped facultative anaerobe genome sequence Bacteria

Name and taxonomic classification

SI-ID 408082

CECT 9236,DSM 104542

@ref 20215

Last LPSN update 2026-05-29 08:39:43

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Enterobacterales

Family Enterobacteriaceae

Genus Citrobacter

Species Citrobacter portucalensis

Full scientific name Citrobacter portucalensis Ribeiro et al. 2017

BacDive ID	Other strains from **Citrobacter portucalensis** (4)	Type strain
134584	C. portucalensis DM2.TOL, CIP 106652
137394	C. portucalensis DM2.SSS, CIP 106650
137724	C. portucalensis DM2.CC, CIP 106653
139128	C. portucalensis DM2.TOO, CIP 106651

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
43514	negative	4-5 µm	1-2 µm	rod-shaped
121947	negative			rod-shaped
125439	negative				96.131

Colony morphology

@ref	Colony color	Medium used
43514	bright, translucent	TSB

Multimedia

@ref:	43033
multimedia content:	DSM_104542.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_104542.jpg
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
43514	TSB
43033	COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)	Medium recipe at MediaDive	Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
43033	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)	Medium recipe at MediaDive	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
121947	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
43033	positive	growth	37
43514	positive	growth	20-37
43514	positive	growth	50

Culture pH

@ref	Ability	Type	PH	PH range
43514	positive	growth	5-10	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
43514	facultative anaerobe
125439	obligate aerobe	95.883

Spore formation

@ref	Spore formation	Confidence
43514
125439		99.489

Halophily

@ref	Salt	Growth	Tested relation	Concentration
43514	NaCl	positive	growth	0-15 %(w/v)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43514	16808 ChEBI	2-dehydro-D-gluconate	+	builds acid from
43514	58143 ChEBI	5-dehydro-D-gluconate	+	builds acid from
43514	27613 ChEBI	amygdalin	-	builds acid from
68368	27613 ChEBI	amygdalin	+	fermentation	from API 20E
43514	18305 ChEBI	arbutin	+	builds acid from
68368	29016 ChEBI	arginine	-	hydrolysis	from API 20E
43514	17057 ChEBI	cellobiose	+	builds acid from
43514	16947 ChEBI	citrate	+	carbon source
68368	16947 ChEBI	citrate	+	assimilation	from API 20E
43514	17108 ChEBI	D-arabinose	-	builds acid from
43514	18333 ChEBI	D-arabitol	-	builds acid from
43514	15824 ChEBI	D-fructose	+	builds acid from
43514	28847 ChEBI	D-fucose	-	builds acid from
43514	12936 ChEBI	D-galactose	+	builds acid from
43514	17634 ChEBI	D-glucose	+	builds acid from
68368	17634 ChEBI	D-glucose	+	fermentation	from API 20E
43514	62318 ChEBI	D-lyxose	-	builds acid from
43514	16899 ChEBI	D-mannitol	+	builds acid from
68368	16899 ChEBI	D-mannitol	+	fermentation	from API 20E
43514	16024 ChEBI	D-mannose	+	builds acid from
43514	16988 ChEBI	D-ribose	+	builds acid from
43514	17924 ChEBI	D-sorbitol	+	builds acid from
43514	16443 ChEBI	D-tagatose	-	builds acid from
43514	65327 ChEBI	D-xylose	+	builds acid from
43514	17113 ChEBI	erythritol	-	builds acid from
43514		esculin ferric citrate	-	builds acid from
43514	16813 ChEBI	galactitol	-	builds acid from
43514	5291 ChEBI	gelatin	-	degradation
68368	5291 ChEBI	gelatin	-	hydrolysis	from API 20E
43514	28066 ChEBI	gentiobiose	+	builds acid from
43514	17234 ChEBI	glucose	+	fermentation
43514	17754 ChEBI	glycerol	+	builds acid from
43514	28087 ChEBI	glycogen	-	builds acid from
43514	15443 ChEBI	inulin	-	builds acid from
43514	30849 ChEBI	L-arabinose	+	builds acid from
68368	30849 ChEBI	L-arabinose	+	fermentation	from API 20E
43514	18403 ChEBI	L-arabitol	-	builds acid from
43514	16467 ChEBI	L-arginine	-	assimilation
43514	18287 ChEBI	L-fucose	+	builds acid from
43514	18019 ChEBI	L-lysine	-	assimilation
43514	15729 ChEBI	L-ornithine	-	assimilation
43514	62345 ChEBI	L-rhamnose	+	builds acid from
68368	62345 ChEBI	L-rhamnose	+	fermentation	from API 20E
43514	17266 ChEBI	L-sorbose	+	builds acid from
43514	16828 ChEBI	L-tryptophan	-	assimilation
43514	65328 ChEBI	L-xylose	-	builds acid from
43514	17716 ChEBI	lactose	+	builds acid from
68368	25094 ChEBI	lysine	-	degradation	from API 20E
43514	17306 ChEBI	maltose	+	builds acid from
43514	6731 ChEBI	melezitose	-	builds acid from
43514	28053 ChEBI	melibiose	+	builds acid from
68368	28053 ChEBI	melibiose	+	fermentation	from API 20E
43514	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from
43514	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from
43514	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from
43514	17268 ChEBI	myo-inositol	+	builds acid from
43514	506227 ChEBI	N-acetylglucosamine	+	builds acid from
43514	17632 ChEBI	nitrate	+	reduction
68368	18257 ChEBI	ornithine	-	degradation	from API 20E
43514	32032 ChEBI	potassium gluconate	+	builds acid from
43514	16634 ChEBI	raffinose	+	builds acid from
43514	15963 ChEBI	ribitol	-	builds acid from
43514	17814 ChEBI	salicin	+	builds acid from
68368	30911 ChEBI	sorbitol	+	fermentation	from API 20E
43514	28017 ChEBI	starch	-	builds acid from
43514	17992 ChEBI	sucrose	+	builds acid from
68368	17992 ChEBI	sucrose	+	fermentation	from API 20E
43514	27082 ChEBI	trehalose	+	builds acid from
43514	27897 ChEBI	tryptophan	-	energy source
68368	27897 ChEBI	tryptophan	-	energy source	from API 20E
43514	32528 ChEBI	turanose	-	builds acid from
68368	16199 ChEBI	urea	-	hydrolysis	from API 20E
43514	17151 ChEBI	xylitol	-	builds acid from

Metabolite production

@ref	Chebi-ID	Metabolite
43514	15688 ChEBI	acetoin
68368	15688 ChEBI	acetoin	from API 20E
43514	17997 ChEBI	dinitrogen
43514	16136 ChEBI	hydrogen sulfide
68368	16136 ChEBI	hydrogen sulfide	from API 20E
43514	35581 ChEBI	indole
68368	35581 ChEBI	indole	from API 20E

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test	Indole test
43514	15688 ChEBI	acetoin	-
68368	15688 ChEBI	acetoin	-			from API 20E
43514	17234 ChEBI	glucose		+
43514	35581 ChEBI	indole			-
68368	35581 ChEBI	indole			-	from API 20E

Enzymes

@ref	Value	Activity	Ec
68368	arginine dihydrolase	-	3.5.3.6	from API 20E
68368	beta-galactosidase	+	3.2.1.23	from API 20E
43514	catalase	-	1.11.1.6
43514	cytochrome oxidase	-	1.9.3.1
68368	cytochrome oxidase	-	1.9.3.1	from API 20E
68368	gelatinase	-		from API 20E
68368	lysine decarboxylase	-	4.1.1.18	from API 20E
68368	ornithine decarboxylase	-	4.1.1.17	from API 20E
43514	tryptophan deaminase	-	4.1.99.1
68368	tryptophan deaminase	-	4.1.99.1	from API 20E
43514	urease	+	3.5.1.5
68368	urease	-	3.5.1.5	from API 20E

API 20E

@ref	ONPG	ADH (Arg)	LDC (Lys)	ODC	CIT	H2S productionH2S	URE	TDA (Trp)	IND	Acetoin production (Voges Proskauer test)VP	GEL	GLU	MAN	INO	Sor	RHA	SAC	MEL	AMY	ARA	OX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	OF-O	OF-F
43033	+	-	-	-	+	+	-	-	-	-	-	+	+	-	+	+	+	+	+	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.
43033	+	-	-	-	+	+	-	-	-	-	-	+	+	+	+	+	+	+	+	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Environmental	#Aquatic

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
43033	water well	Taboeira, Cadima, Cantanhede	Portugal	PRT	Europe
43514	water well sample collected in Cantanhede City	Cantanhede City	Portugal	PRT	Europe	2008
121947	Environment, Water well		Portugal	PRT	Europe	2006

Interaction and safety

Risk assessment

@ref	Pathogenicity human	Biosafety level	Biosafety level comment
43033	yes, in single cases	1	Risk group (German classification)
121947		1	Risk group (French classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM204288v1 assembly for Citrobacter portucalensis A60	contig	GCA_002042885	1639133.3	2874289006	1639133	71.84

GC content

@ref	GC-content (mol%)
43514	52
43033	52.0

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM204288v1 assembly for Citrobacter portucalensis A60
NCBI: GCA_002042885

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	95.88	no
125439	gram_stain	BacteriaNetⓘ	negative	96.13	no
125439	spore_formation	BacteriaNetⓘ	no	99.49	no
125439	motility	BacteriaNetⓘ	yes	66.36	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Mutagenesis and Characterization of Hyaluronidase Production by a New Isolate of Citrobacter portucalensis.	Yao Y, Feng W, Li F, Qu Y, Zhu Y, Li X, Feng S, Yue H.	J Agric Food Chem	10.1021/acs.jafc.5c00145	2025
	Foodborne diarrhea outbreaks linked to Citrobacter species in East China 2022-2023.	Jiang G, Guo C, Kuai X, Ji L, Zhao J, Zhou Y, Wang X, Zhang M, Zhou Z, Li H.	Food Microbiol	10.1016/j.fm.2025.104839	2025
	Broadly reactive monoclonal antibodies against beta-lactamases for immunodetection of bacterial resistance to antibiotics.	Bielske K, Petraityte-Burneikiene R, Aviziniene A, Dapkunas J, Plikusiene I, Juciute S, Stanciauskaite M, Zvirbliene A, Kucinskaite-Kodze I.	Sci Rep	10.1038/s41598-025-04603-2	2025
	Genomic characterization of a multidrug-resistant Citrobacter portucalensis isolate co-harboring bla _KPC-2 and bla _NDM-1 on distinct plasmids.	Huang J, Shen K, Chen K, Wu J, Zhu Y, Shi J.	Front Microbiol	10.3389/fmicb.2025.1633493	2025
	Emergence of an Extensive Drug Resistant Citrobacter portucalensis Clinical Strain Harboring bla _SFO-1, bla _KPC-2, and bla _NDM-1.	Guo K, Zhao Z, Yang Y, Jiang X, Xu H, Tao F, Xu Y, Liu W.	Infect Drug Resist	10.2147/idr.s461118	2024
Genetics	The Gut Microbiome of the Asiatic Toad (Bufo gargarizans) Reflects Environmental Changes and Human Activities.	Kang X, Shao M, Jiang J, He L, Lu Y, Song J, Xu J, Fan Z.	Ecol Evol	10.1002/ece3.71394	2025
	Identification of enterobacteriaceae causing septicemia in the axolotl Ambystoma mexicanum.	Diaz OL, Buendia A, Sanchez J, Villalobos G, Rojas-Serrania N, Cervantes JAO, Uranga-Munoz F, Martinez-Hernandez F, Rendon-Franco E, Munoz-Garcia CI.	Antonie Van Leeuwenhoek	10.1007/s10482-025-02067-y	2025
	A comprehensive analysis of antibiotic resistance genes in the giant panda gut.	Deng F, Han Y, Huang Y, Li D, Chai J, Deng L, Wei M, Wu K, Zhao H, Yang G, Zhao J, Li Y, Wang C.	Imeta	10.1002/imt2.171	2024
Genetics	Antibiotic Resistance Hotspot: Comparative Genomics Reveals Multiple Strains of Multidrug-Resistant Citrobacter portucalensis in Edible Snails.	Okafor AC, Rosel AC, Ogbo FC, Adetunji CO, Imarhiagbe O, Gamp L, Stoger A, Allerberger F, Ruppitsch W.	Int J Mol Sci	10.3390/ijms25189889	2024
Genetics	Integrating metagenomic and isolation strategies revealed high contamination of pathogenies and resistome in market shrimps.	Ye L, Zheng Z, Wang Y, Hu Q, Zhong L, Heng H, Guo Z, Li R, Chan EWC, Chen S.	Sci Total Environ	10.1016/j.scitotenv.2024.171924	2024
	Comprehensive analysis of the microbial consortium in the culture of flagellate Monocercomonoides exilis.	Jimenez-Gonzalez A, Treitli SC, Pena-Diaz P, Janovska A, Benes V, Zacek P, Hampl V.	Environ Microbiome	10.1186/s40793-025-00758-7	2025
Genetics	Is a floodplain forest a valuable source for lignin-degrading anaerobic microbial communities: A metagenomic approach.	Ozsefil IC, Miraloglu IH, Ozbayram EG, Uzun O, Ince B, Ince O.	Chemosphere	10.1016/j.chemosphere.2023.139675	2023
	Genomic characterization of New Delhi metallo-beta-lactamase-producing species of Morganellaceae, Yersiniaceae, and Enterobacteriaceae (other than Klebsiella) from Brazil over 2013-2022.	Camargo CH, Yamada AY, de Souza AR, Sacchi CT, Reis AD, Santos MBN, de Assis DB, de Carvalho E, Takagi EH, Cunha MPV, Tiba-Casas MR.	Microbiol Immunol	10.1111/1348-0421.13100	2024
	Citrobacter portucalensis Sb-2 contains a metalloid resistance determinant transmitted by Citrobacter phage Chris1.	Yu Y, Xie Z, Yang J, Yang R, Li Y, Zhu Y, Zhao Y, Yang Q, Chen J, Alwathnani HA, Feng R, Rensing C, Herzberg M.	J Hazard Mater	10.1016/j.jhazmat.2022.130184	2023
	Bullfrogs (Lithobates catesbeianus) as a Potential Source of Foodborne Disease.	Zepeda-Velazquez AP, Gomez-De-Anda FR, Aguilar-Mendoza LF, Castrejon-Jimenez NS, Hernandez-Gonzalez JC, Varela-Guerrero JA, de-la-Rosa-Arana JL, Vega-Sanchez V, Reyes-Rodriguez NE.	J Food Prot	10.1016/j.jfp.2023.100067	2023
Metabolism	Phylogenomic analysis of Citrobacter sp. strain AAK_AS5 and its metabolic capabilities to support nitrogen removal behavior.	Gupta RK, Singh AK, Bajaj A, Khardenavis AA, Purohit HJ.	J Basic Microbiol	10.1002/jobm.202200323	2023
	New Delhi metallo-beta-lactamase-1-producing Citrobacter portucalensis belonging to the novel ST264 causing fatal sepsis in a vulnerable migratory sea turtle.	Sellera FP, Fuentes-Castillo D, Fuga B, Goldberg DW, Kolesnikovas CKM, Lincopan N.	One Health	10.1016/j.onehlt.2023.100590	2023
Genetics	Analyzing Antibiotic Resistance in Bacteria from Wastewater in Pakistan Using Whole-Genome Sequencing.	Sattar F, Hu X, Saxena A, Mou K, Shen H, Ali H, Ghauri MA, Sarwar Y, Ali A, Li G.	Antibiotics (Basel)	10.3390/antibiotics13100937	2024
	Diverse new plasmid structures and antimicrobial resistance in strains isolated from perianal abscess patients.	Xu Z, Shi L, Meng T, Luo M, Zhu J, Wang M, Shen W.	Front Microbiol	10.3389/fmicb.2024.1452795	2024
	Observed Prevalence and Characterization of Fluoroquinolone-Resistant and Multidrug-Resistant Bacteria in Loggerhead Sea Turtles (Caretta caretta) from the Adriatic Sea.	Lai O, Tinelli A, Soloperto S, Crescenzo G, Galante D, Calarco A, Tribuzio M, Manzulli V, Caioni G, Zizzadoro C, Damiano A, Camarda A, Pugliese N.	Antibiotics (Basel)	10.3390/antibiotics14030252	2025
	Removal of Ibuprofen from Contaminated Water by Bioaugmentation with Novel Bacterial Strains Isolated from Sewage Sludge	Aguilar-Romero I, Lara-Moreno A, Madrid F, Villaverde J, Alonso E, Santos J, Morillo E.	Microorganisms		2025
	Detection of a clinical carbapenem-resistant Citrobacter portucalensis strain and the dissemination of C. portucalensis in clinical settings.	Cao X, Xie H, Huang D, Zhou W, Liu Y, Shen H, Zhou K.	J Glob Antimicrob Resist	10.1016/j.jgar.2021.04.027	2021
Pathogenicity	Comprehensive discovery and functional characterization of diverse prophages in the pig gut microbiome.	Wei C, Wang Y, Chen Z.	Front Microbiol	10.3389/fmicb.2025.1662087	2025
	First Report of OXA-181-Producing Enterobacterales Isolates in Latin America.	Cuicapuza D, Alvarado L, Tocasca N, Aguilar D, Gomez-de-la-Torre JC, Salvatierra G, Tsukayama P, Tamariz J.	Microbiol Spectr	10.1128/spectrum.04584-22	2023
Genetics	Mechanisms of Cefiderocol Resistance in Carbapenemase-Producing Enterobacterales: Insights from Comparative Genomics.	Tristancho-Baro A, Lopez-Calleja AI, Milagro A, Ariza M, Vineta V, Fortuno B, Lopez C, Latorre-Millan M, Clusa L, Badenas-Alzugaray D, Martinez R, Torres C, Rezusta A.	Antibiotics (Basel)	10.3390/antibiotics14070703	2025
	Mobile Colistin-Resistant Genes mcr-1, mcr-2, and mcr-3 Identified in Diarrheal Pathogens among Infants, Children, and Adults in Bangladesh: Implications for the Future	Sarker S, Neeloy R, Habib M, Urmi U, Al Asad M, Mosaddek A, Khan M, Nahar S, Godman B, Islam S.	Antibiotics (Basel)		2024
	Detection and Antimicrobial Resistance of Enterobacteriaceae other than Escherichia Coli in Raccoons from the Madrid Region of Spain.	Orden JA, Martinez-Rodrigo A, Vela AI, Fernandez-Garayzabal JF, Hurtado-Morillas C, Mas A, Dominguez-Bernal G.	J Vet Res	10.2478/jvetres-2022-0058	2022
	Carbapenemase-Producing Enterobacterales from Patients Arriving from Ukraine in Poland, March 2022-February 2023.	Biedrzycka M, Izdebski R, Hryniewicz W, Gniadkowski M, Zabicka D.	Infect Dis Ther	10.1007/s40121-024-01097-9	2025
	Emergence of carbapenem-resistant Serratia marcescens co-harboring bla_NDM-1, bla_KPC-2, and bla_SRT-2 in bloodstream infection.	Wang X, Fan F, Dong S, Zhang Y.	Microbiol Spectr	10.1128/spectrum.00545-25	2025
Genetics	Genetic Characterization of bla _NDM-1-Carrying Citrobacter portucalensis Sequence Type 328 and Citrobacter freundii Sequence Type 98.	Wang L, Li Z, Xiao N, Tang J, He Y, Guo J, Zhao X.	Infect Drug Resist	10.2147/idr.s361761	2022
	Novel monoclonal antibodies for immunodetection of AmpC beta-lactamases.	Bielske K, Simanavicius M, Nuttens J, Armalyte J, Dapkunas J, Valancauskas L, Zvirbliene A.	PeerJ	10.7717/peerj.20036	2025
	Metagenomic Analyses Expand Bacterial and Functional Profiling Biomarkers for Colorectal Cancer in a Hainan Cohort, China.	Chang H, Mishra R, Cen C, Tang Y, Ma C, Wasti S, Wang Y, Ou Q, Chen K, Zhang J.	Curr Microbiol	10.1007/s00284-020-02299-3	2021
Genetics	Analysis of causal pathogens of mulberry bacterial blight in samples collected from eight provinces of China using culturomics and metagenomic sequencing methods.	Huang X, Yuan T, Huang Y, Qazi IH, Liu J.	Front Plant Sci	10.3389/fpls.2025.1517050	2025
Genetics	Nationwide molecular epidemiology of carbapenemase-producing Citrobacter spp. in France in 2019 and 2020.	Biez L, Bonnin RA, Emeraud C, Birer A, Jousset AB, Naas T, Dortet L.	mSphere	10.1128/msphere.00366-23	2023
Genetics	Complete genome arrangement revealed the emergence of a poultry origin superbug Citrobacter portucalensis strain NR-12.	Hasan MS, Sultana M, Hossain MA.	J Glob Antimicrob Resist	10.1016/j.jgar.2019.05.031	2019
	Phylogeographical Landscape of Citrobacter portucalensis Carrying Clinically Relevant Resistomes.	Sellera FP, Fernandes MR, Fuga B, Fontana H, Vasquez-Ponce F, Goldberg DW, Monte DF, Rodrigues L, Cardenas-Arias AR, Lopes R, Cardoso B, Costa DGC, Esposito F, Lincopan N.	Microbiol Spectr	10.1128/spectrum.01506-21	2022
Genetics	Metagenomic Investigation of Intestinal Microbiota of Insectivorous Synanthropic Bats: Densoviruses, Antibiotic Resistance Genes, and Functional Profiling of Gut Microbial Communities.	Popov IV, Manakhov AD, Gorobets VE, Diakova KB, Lukbanova EA, Malinovkin AV, Venema K, Ermakov AM, Popov IV.	Int J Mol Sci	10.3390/ijms26135941	2025
	Relative inhibitory activities of newly developed diazabicyclooctanes, boronic acid derivatives, and penicillin-based sulfone beta-lactamase inhibitors against broad-spectrum AmpC beta-lactamases.	Le Terrier C, Mlynarcik P, Sadek M, Nordmann P, Poirel L.	Antimicrob Agents Chemother	10.1128/aac.00775-24	2024
	Genetic basis of transmission of bla_NDM-1 among foodborne Vibrio parahaemolyticus strains in China.	Chen D, Sun R, Wang J, Chen K, Xie M, Lin Q, Li J, Chen S, Liu X.	Appl Microbiol Biotechnol	10.1007/s00253-025-13567-2	2025
	Molecular analysis of clinical Citrobacter spp. isolates: Acquisition of the Yersinia high-pathogenicity island mediated by ICEkp in C. freundii.	Zhang G, Zhao Q, Ye K, Ye L, Ma Y, Yang J.	Front Microbiol	10.3389/fmicb.2023.1056790	2023
	Exploring Protein Functions of Gut Bacteriome and Mycobiome in Thai Infants Associated with Atopic Dermatitis Through Metaproteomic and Host Interaction Analysis.	Chantanaskul T, Patumcharoenpol P, Roytrakul S, Kingkaw A, Vongsangnak W.	Int J Mol Sci	10.3390/ijms252413533	2024
	Draft Genome Sequence of the Redox-Active Enteric Bacterium Citrobacter portucalensis Strain MBL.	Tsypin LM, Saunders SH, Bar-On Y, Leadbetter JR, Newman DK.	Microbiol Resour Announc	10.1128/mra.00695-20	2020
	The Impact of Chlorine Disinfection of Hospital Wastewater on Clonal Similarity and ESBL-Production in Selected Bacteria of the Family Enterobacteriaceae.	Rolbiecki D, Korzeniewska E, Czatzkowska M, Harnisz M.	Int J Environ Res Public Health	10.3390/ijerph192113868	2022
	Repeated biocide treatments cause changes to the microbiome of a food industry floor drain biofilm model.	Kragh ML, Scheel NH, Leekitcharoenphon P, Truelstrup Hansen L.	Front Microbiol	10.3389/fmicb.2025.1542193	2025
	Molecular epidemiology of multidrug-resistant Klebsiella pneumoniae, Enterobacter cloacae, and Escherichia coli outbreak among neonates in Tembisa hospital, South Africa.	Osei Sekyere J, Mmatli M, Bosch A, Ntsoane RV, Naidoo H, Doyisa S, Maningi NE, Mbelle NM, Said M.	Front Cell Infect Microbiol	10.3389/fcimb.2024.1328123	2024
	Emergence of Extensively Drug-Resistant ST170 Citrobacter portucalensis with Plasmids pK218-KPC, pK218-NDM, and pK218-SHV from a Tertiary Hospital, China.	Luo X, Yu L, Feng J, Zhang J, Zheng C, Hu D, Dai P, Xu M, Li P, Lin R, Mu K.	Microbiol Spectr	10.1128/spectrum.02510-22	2022
	Tn4661-mediated transfer of bla _CTX-M-15 from Klebsiella michiganensis to an outbreak clone of Pseudomonas aeruginosa.	Bartlett KV, Luo TL, Ong AC, Maybank RA, Stribling W, Thompson B, Powell A, Kwak YI, Bennett JW, Lebreton F, Mc Gann PT.	Microb Genom	10.1099/mgen.0.001303	2024
Genetics	Temporal dynamics and species-level complexity of Prevotella spp. in the human gut microbiota: implications for enterotypes and health.	Han N, Peng X, Zhang T, Qiang Y, Li X, Zhang W.	Front Microbiol	10.3389/fmicb.2024.1414000	2024
Metabolism	Nitrate Reduction Stimulates and Is Stimulated by Phenazine-1-Carboxylic Acid Oxidation by Citrobacter portucalensis MBL.	Tsypin LM, Newman DK.	mBio	10.1128/mbio.02265-21	2021
	Gut microbiome alterations in patients with COVID-19-related coagulopathy.	Chen Y, Li X, Yu C, Wang E, Luo C, Jin Y, Zhang L, Ma Y, Jin Y, Yang L, Sun B, Qiao J, Zhou X, Rasche L, Einsele H, Song J, Bai T, Hou X.	Ann Hematol	10.1007/s00277-023-05186-6	2023
	Draft Genome Sequence of Multidrug-Resistant Strain Citrobacter portucalensis MBTC-1222, Isolated from Uziza (Piper guineense) Leaves in Nigeria.	Igbinosa EO, Rathje J, Habermann D, Brinks E, Cho GS, Franz CMAP.	Genome Announc	10.1128/genomea.00123-18	2018
	Genome analysis of Bifidobacterium adolescentis and investigation of its effects on inflammation and intestinal barrier function.	Li B, Wang H, Wang M, Liang H, Hu T, Yang J, Li S, You X, Xia B, Yuan Y, Zou Y, Miao Y, Sun Y.	Front Microbiol	10.3389/fmicb.2024.1496280	2024
Phylogeny	Genomic Characterization of 16S rRNA Methyltransferase-Producing Enterobacterales Reveals the Emergence of Klebsiella pneumoniae ST6260 Harboring rmtF, rmtB, bla_NDM-5, bla_OXA-232 and bla_SFO-1 Genes in a Cancer Hospital in Bulgaria.	Sabtcheva S, Stoikov I, Georgieva S, Donchev D, Hodzhev Y, Dobreva E, Christova I, Ivanov IN.	Antibiotics (Basel)	10.3390/antibiotics13100950	2024
Genetics	Current Research on Molecular Biomarkers for Colorectal Cancer in Stool Samples.	Ordenes P, Carril Pardo C, Elizondo-Vega R, Oyarce K.	Biology (Basel)	10.3390/biology13010015	2023
	Genomic characterization of a WHO critical priority isolate Enterobacter kobei ST2070 harboring OXA-10, KPC-2, and CTX-M-12 recovered from a water irrigation channel in Ecuador	Corrales-Martinez J, Jaramillo K, Tadesse D, Satan C, Villavicencio F, Sanchez-Gavilanes L, Rivadeneira-Cueva B, Balcazar J, Calero-Caceres W.	Heliyon		2024
Genetics	Analytical Performance of a Novel Nanopore Sequencing for SARS-CoV-2 Genomic Surveillance.	Maimaiti M, Kong L, Yu Q, Wang Z, Liu Y, Yang C, Guo W, Jin L, Yi J.	J Med Virol	10.1002/jmv.70108	2024
Biotechnology	Comparative genomics of the highly halophilic Haloferacaceae.	Griffiths DB, Tiwari RP, Murphy DV, Scott C.	Sci Rep	10.1038/s41598-024-78438-8	2024
	Beneficial effect of consuming milk containing only A2 beta-casein on gut microbiota: A single-center, randomized, double-blind, cross-over study.	Song CH, Kim N, Choi Y, Kim S, Kim KS, Park MH, Lee SH, Lee DH.	PLoS One	10.1371/journal.pone.0323016	2025
Genetics	Metagenomic and metabolite analysis reveals microbial community and metabolite dynamics in fermented Indigo naturalis.	Yuan X, Zhang D, Li D, Ji Q, Gao J, Hou F, Chen Y.	Heliyon	10.1016/j.heliyon.2024.e36733	2024
	Aeromonas hydrophila RIT668 and Citrobacter portucalensis RIT669-Potential Zoonotic Pathogens Isolated from Spotted Turtles.	Thomas SG, Abajorga M, Glover MA, Wengert PC, Parthasarathy A, Savka MA, Wadsworth CB, Shipman PA, Hudson AO.	Microorganisms	10.3390/microorganisms8111805	2020
	Cefiderocol-resistant pathogens in German hospital wastewater: a reservoir for multidrug resistance	Erler T, Carlsen L, Dengler J, Hammerl J, Stroehlein A, Hoffmann M, Knobloch J, Lubbert C, Papan C, Schwanz T, Zweigner J, Bari A, Xavier B, Rossen J, Mutters N, Savin M.	Sci Rep		2025
Cultivation	A Novel Agro-Waste Formulated Medium Enhanced the Growth of Electrogenic Enterobacter Species Isolated Using Microbial Fuel Cell System: Response Surface Methodology Approach.	Bantihun G, Mekonnen A, Kotakadi V, Mohammed S.	Environ Microbiol Rep	10.1111/1758-2229.70232	2025
Genetics	Overrepresentation of Enterobacteriaceae and Escherichia coli is the major gut microbiome signature in Crohn's disease and ulcerative colitis; a comprehensive metagenomic analysis of IBDMDB datasets.	Khorsand B, Asadzadeh Aghdaei H, Nazemalhosseini-Mojarad E, Nadalian B, Nadalian B, Houri H.	Front Cell Infect Microbiol	10.3389/fcimb.2022.1015890	2022
	A cell-cell communication signal from Enterobacter cloacae interfering with the signaling systems and virulence in Shigella sonnei.	Chen X, Wang M, Zhao Z, Ling X, Peng G, Cui B, Wang Q, Gu B, Deng Y.	Appl Environ Microbiol	10.1128/aem.00510-25	2025
Phylogeny	Deciphering the microbial communities in ticks of Inner Mongolia: ecological determinants and pathogen profiles.	Li C, Ma R, Gao A, Jiang N, Sang C, Zhang Y, Tian H, Li J, Hu W, Feng X.	Parasit Vectors	10.1186/s13071-024-06512-1	2024
Metabolism	Insights from metagenomics into gut microbiome associated with acute coronary syndrome therapy.	Guan Y, Zhao S, Li J, Zhang W, Guo Z, Luo Y, Jiang X, Li J, Liu J, Chen X, Zhao Z, Zhang Z.	Front Microbiol	10.3389/fmicb.2024.1369478	2024
Genetics	Monocentric observational cohort study to investigate the transmission of third-generation cephalosporin-resistant Enterobacterales in a neonatal intensive care unit in Heidelberg, Germany.	Nurjadi D, Eichel VM, Poschl J, Gille C, Kranig S, Heeg K, Boutin S.	Microbiol Spectr	10.1128/spectrum.02038-23	2023
	Epidemiology and Molecular Characteristics of mcr-9 in Citrobacter spp. from Healthy Individuals and Patients in China.	Ju X, Wang S, Yang X, Han W, Cai C, Wu Y, Liu C, Qian J, Zhao X, Qian X, Sun Q, Zhang R, Chen G.	Microbiol Spectr	10.1128/spectrum.01346-22	2022
	A novel clinical metaproteomics workflow enables bioinformatic analysis of host-microbe dynamics in disease.	Do K, Mehta S, Wagner R, Bhuming D, Rajczewski AT, Skubitz APN, Johnson JE, Griffin TJ, Jagtap PD.	mSphere	10.1128/msphere.00793-23	2024
	Removal of Ibuprofen in Water by Bioaugmentation with Labrys neptuniae CSW11 Isolated from Sewage Sludge-Assessment of Biodegradation Pathway Based on Metabolite Formation and Genomic Analysis.	Aguilar-Romero I, Madrid F, Villaverde J, Alonso E, Santos JL, Morillo E.	J Xenobiot	10.3390/jox15010005	2024
	Effects of a supplemented diet containing 7 probiotic strains (Honeybeeotic) on honeybee physiology and immune response: analysis of hemolymph cytology, phenoloxidase activity, and gut microbiome.	Robino P, Galosi L, Bellato A, Vincenzetti S, Gonella E, Ferrocino I, Serri E, Biagini L, Roncarati A, Nebbia P, Menzio C, Rossi G.	Biol Res	10.1186/s40659-024-00533-x	2024
Genetics	Genomic Characterization of Carbapenemase-Producing Enterobacteriaceae from Clinical and Epidemiological Human Samples.	Tristancho-Baro A, Franco-Fobe LE, Ariza MP, Milagro A, Lopez-Calleja AI, Fortuno B, Lopez C, Latorre-Millan M, Clusa L, Martinez R, Torres C, Rezusta A.	Antibiotics (Basel)	10.3390/antibiotics14010042	2025
Metabolism	The Scr and Csc pathways for sucrose utilization co-exist in E. coli, but only the Scr pathway is widespread in other Enterobacteriaceae.	Stephens C, Martinez M, Leonardi V, Jaing J, Miller A.	Front Microbiol	10.3389/fmicb.2024.1409295	2024
	Emergence of Tn1999.7, a New Transposon in bla_OXA-48-Harboring Plasmids Associated with Increased Plasmid Stability.	Sattler J, Tsvetkov T, Stelzer Y, Schafer S, Sommer J, Noster J, Gottig S, Hamprecht A.	Antimicrob Agents Chemother	10.1128/aac.00787-22	2022
	Broad-Spectrum Cephalosporin-Resistant and/or Fluoroquinolone-Resistant Enterobacterales Associated with Canine and Feline Urogenital Infections.	Loncaric I, Misic D, Szostak MP, Kunzel F, Schafer-Somi S, Spergser J.	Antibiotics (Basel)	10.3390/antibiotics9070387	2020
Genetics	Microbial and Metabolic Gut Profiling across Seven Malignancies Identifies Fecal Faecalibacillus intestinalis and Formic Acid as Commonly Altered in Cancer Patients.	Kulecka M, Czarnowski P, Balabas A, Turkot M, Kruczkowska-Tarantowicz K, Zeber-Lubecka N, Dabrowska M, Paszkiewicz-Kozik E, Walewski J, Lugowska I, Kosela-Paterczyk H, Rutkowski P, Kluska A, Piatkowska M, Jagiello-Gruszfeld A, Tenderenda M, Gawinski C, Wyrwicz L, Borucka M, Krzakowski M, Zajac L, Kaminski M, Mikula M, Ostrowski J.	Int J Mol Sci	10.3390/ijms25158026	2024
Genetics	Occurrence and Molecular Characterization of Abundant tet(X) Variants Among Diverse Bacterial Species of Chicken Origin in Jiangsu, China.	Li Y, Peng K, Yin Y, Sun X, Zhang W, Li R, Wang Z.	Front Microbiol	10.3389/fmicb.2021.751006	2021
	Gut microbiome alterations in pulmonary hypertension in highlanders and lowlanders.	Dong W, Ma L, Huang Q, Yang X, Mei Z, Kong M, Sun Z, Zhang Z, Li J, Zou J, Chen D, Dai Y, Zhou D, Zheng Y, Kang L.	ERJ Open Res	10.1183/23120541.00617-2022	2023
	Molecular Epidemiology of Global Carbapenemase-Producing Citrobacter spp. (2015-2017).	Nobrega D, Peirano G, Matsumura Y, Pitout JDD.	Microbiol Spectr	10.1128/spectrum.04144-22	2023
	The emergence of the tetrathionate reductase operon in the Escherichia coli/Shigella pan-genome.	Adsit FG, Randall TA, Locklear J, Kurtz DM.	Microbiologyopen	10.1002/mbo3.1333	2022
	Genetic and species rearrangements in microbial consortia impact biodegradation potential.	Saati-Santamaria Z, Navarro-Gomez P, Martinez-Mancebo JA, Juarez-Mugarza M, Flores A, Canosa I.	ISME J	10.1093/ismejo/wraf014	2025
	Environmental and Pathogenic Carbapenem Resistant Bacteria Isolated from a Wastewater Treatment Plant Harbour Distinct Antibiotic Resistance Mechanisms.	Oliveira M, Leonardo IC, Nunes M, Silva AF, Barreto Crespo MT.	Antibiotics (Basel)	10.3390/antibiotics10091118	2021
	Coexistence of bla_IMP-4, bla_NDM-1 and bla_OXA-1 in bla_KPC-2-producing Citrobacter freundii of clinical origin in China.	Qiao J, Chen Y, Ge H, Xu H, Guo X, Liu R, Li C, Chen R, Gou J, Chen M, Zheng B.	Front Microbiol	10.3389/fmicb.2023.1074612	2023
	Antimicrobial resistance situation in animal health of Bangladesh.	Al Amin M, Hoque MN, Siddiki AZ, Saha S, Kamal MM.	Vet World	10.14202/vetworld.2020.2713-2727	2020
	High-Molecular-Weight Plasmids Carrying Carbapenemase Genes bla_NDM-1, bla_KPC-2, and bla_OXA-48 Coexisting in Clinical Klebsiella pneumoniae Strains of ST39.	Kuzina ES, Kislichkina AA, Sizova AA, Skryabin YP, Novikova TS, Ershova ON, Savin IA, Khokhlova OE, Bogun AG, Fursova NK.	Microorganisms	10.3390/microorganisms11020459	2023
	Broadly reactive monoclonal antibodies against beta-lactamases for immunodetection of bacterial resistance to antibiotics	Bielske K, Petraityte-Burneikiene R, Aviziniene A, Dapkunas J, Plikusiene I, Juciute S, Stanciauskaite M, Zvirbliene A, Kucinskaite-Kodze I.	Sci Rep		2025
Genetics	Metagenomic, metabolomic, and lipidomic shifts associated with fecal microbiota transplantation for recurrent Clostridioides difficile infection.	McMillan AS, Zhang G, Dougherty MK, McGill SK, Gulati AS, Baker ES, Theriot CM.	mSphere	10.1128/msphere.00706-24	2024
	Municipal wastewater monitoring revealed the predominance of bla _GES genes with diverse variants among carbapenemase-producing organisms: high occurrence and persistence of Aeromonas caviae harboring the new bla _GES variant bla _GES-48.	Tanabe M, Sugawara Y, Denda T, Sakaguchi K, Takizawa S, Koide S, Hayashi W, Yu L, Kayama S, Sugai M, Nagano Y, Nagano N.	Microbiol Spectr	10.1128/spectrum.02188-23	2023
Genetics	Metagenomic and culture-dependent approaches unveil active microbial community and novel functional genes involved in arsenic mobilization and detoxification in groundwater.	Diba F, Hoque MN, Rahman MS, Haque F, Rahman KMJ, Moniruzzaman M, Khan M, Hossain MA, Sultana M.	BMC Microbiol	10.1186/s12866-023-02980-0	2023
Genetics	The Bacteriophage vB_CbrM_HP1 Protects Crucian Carp Against Citrobacter braakii Infection.	Huang C, Feng C, Liu X, Zhao R, Wang Z, Xi H, Ou H, Han W, Guo Z, Gu J, Zhang L.	Front Vet Sci	10.3389/fvets.2022.888561	2022
	Development of a multi-locus typing scheme for an Enterobacteriaceae linear plasmid that mediates inter-species transfer of flagella.	Robertson J, Lin J, Wren-Hedgus A, Arya G, Carrillo C, Nash JHE.	PLoS One	10.1371/journal.pone.0218638	2019
	Non-enzymatic Transformation of Aflatoxin B₁ by Pseudomonas geniculata m29.	Yao Y, Shu X, Wang D, Kan W, Su P, Hu H, Chen X, Wang D, Huang S, Wu L.	Front Microbiol	10.3389/fmicb.2021.724103	2021
Metabolism	A metabolomics pipeline for the mechanistic interrogation of the gut microbiome.	Han S, Van Treuren W, Fischer CR, Merrill BD, DeFelice BC, Sanchez JM, Higginbottom SK, Guthrie L, Fall LA, Dodd D, Fischbach MA, Sonnenburg JL.	Nature	10.1038/s41586-021-03707-9	2021
Genetics	Dynamics of bla_KPC-2 Dissemination from Non-CG258 Klebsiella pneumoniae to Other Enterobacterales via IncN Plasmids in an Area of High Endemicity.	Rada AM, De La Cadena E, Agudelo C, Capataz C, Orozco N, Pallares C, Dinh AQ, Panesso D, Rios R, Diaz L, Correa A, Hanson BM, Villegas MV, Arias CA, Restrepo E.	Antimicrob Agents Chemother	10.1128/aac.01743-20	2020
	Dissecting the role of the human microbiome in COVID-19 via metagenome-assembled genomes.	Ke S, Weiss ST, Liu YY.	Nat Commun	10.1038/s41467-022-32991-w	2022
	Genomic Epidemiology Insights on NDM-Producing Pathogens Revealed the Pivotal Role of Plasmids on bla_NDM Transmission.	Dong H, Li Y, Cheng J, Xia Z, Liu W, Yan T, Chen F, Wang Z, Li R, Shi J, Qin S.	Microbiol Spectr	10.1128/spectrum.02156-21	2022
Pathogenicity	Commensal Hafnia alvei strain reduces food intake and fat mass in obese mice-a new potential probiotic for appetite and body weight management.	Legrand R, Lucas N, Dominique M, Azhar S, Deroissart C, Le Solliec MA, Rondeaux J, Nobis S, Guerin C, Leon F, do Rego JC, Pons N, Le Chatelier E, Ehrlich SD, Lambert G, Dechelotte P, Fetissov SO.	Int J Obes (Lond)	10.1038/s41366-019-0515-9	2020
Pathogenicity	Human gut microbiota stimulate defined innate immune responses that vary from phylum to strain.	Spindler MP, Siu S, Mogno I, Li Z, Yang C, Mehandru S, Britton GJ, Faith JJ.	Cell Host Microbe	10.1016/j.chom.2022.08.009	2022
Pathogenicity	The Number and Type of Chaperone-Usher Fimbriae Reflect Phylogenetic Clade Rather than Host Range in Salmonella.	Cheng RA, Orsi RH, Wiedmann M.	mSystems	10.1128/msystems.00115-22	2022
	Inter-species geographic signatures for tracing horizontal gene transfer and long-term persistence of carbapenem resistance.	Salamzade R, Manson AL, Walker BJ, Brennan-Krohn T, Worby CJ, Ma P, He LL, Shea TP, Qu J, Chapman SB, Howe W, Young SK, Wurster JI, Delaney ML, Kanjilal S, Onderdonk AB, Bittencourt CE, Gussin GM, Kim D, Peterson EM, Ferraro MJ, Hooper DC, Shenoy ES, Cuomo CA, Cosimi LA, Huang SS, Kirby JE, Pierce VM, Bhattacharyya RP, Earl AM.	Genome Med	10.1186/s13073-022-01040-y	2022
	Precise Species Identification for Enterobacter: a Genome Sequence-Based Study with Reporting of Two Novel Species, Enterobacter quasiroggenkampii sp. nov. and Enterobacter quasimori sp. nov.	Wu W, Feng Y, Zong Z.	mSystems	10.1128/msystems.00527-20	2020
Phylogeny	Citrobacter portucalensis sp. nov., isolated from an aquatic sample.	Ribeiro TG, Goncalves BR, da Silva MS, Novais A, Machado E, Carrico JA, Peixe L	Int J Syst Evol Microbiol	10.1099/ijsem.0.002154	2017

References

#20215	Parte, 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 DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#43033	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 104542
#43514	Teresa Gonçalves Ribeiro, Bruno Ribeiro Gonçalves, Mickael Santos da Silva, Ângela Novais, Elisabete Machado, Joao Andre Carriço, Luísa Peixe: Citrobacter portucalensis sp. nov., isolated from an aquatic sample. IJSEM 67: 3513 - 3517 2017 ( DOI 10.1099/ijsem.0.002154 , PubMed 28857032 )
#66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .
#68368	Automatically annotated from API 20E .
#121947	Collection of Institut Pasteur ; Curators of the CIP; CIP 111602
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Citrobacter portucalensis (DSM 104542, CECT 9236, A60)

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