Shigella sonnei (CCUG 68726, NCTC 12984, CECT 4887)

Name: Shigella sonnei (CCUG 68726, NCTC 12984, CECT 4887)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5172

Type strain

Strain Designation I virulent

Culture col. no. CCUG 68726 NCTC 12984 CECT 4887 DSM 5570 ATCC 29930 3 more

NCBI tax ID(s) 624

Special Collections DSMZ CCUG CIP

History DSMZ <- ATCC; ATCC 29930 <- D. J. Brenner; I virulent <- Walter Reed Army Institute of Research (WRAIR); CIP <- 1982, ATCC <- D.J. Brenner, CDC: strain I virulent <- WRAIR, USA

Links

Shigella sonnei I virulent is an aerobe, Gram-negative, rod-shaped human pathogen that has multiple antibiotic resistances.

antibiotic resistance Gram-negative rod-shaped aerobe human pathogen genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 4971

ATCC 29930,CECT 4887,NCTC 12984,DSM 5570,CIP 82.49,BCRC 15966,CCRC 15966,CCUG 68726

@ref 20215

Last LPSN update 2026-05-29 08:26:06

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Enterobacterales

Family Enterobacteriaceae

Genus Shigella

Species Shigella sonnei

Full scientific name Shigella sonnei (Levine 1920) Weldin 1927 (Approved Lists 1980)

Synonyms (1)

"Bacterium sonnei"

BacDive ID	Other strains from **Shigella sonnei** (26)	Type strain
5173	S. sonnei DSM 25715, NCCP 11768
134552	S. sonnei 46, CIP 106203
134775	S. sonnei CIP 63.10
135403	S. sonnei Cabrera, CIP 51.1
135521	S. sonnei CIP 55.56
135531	S. sonnei CNRSS 99 9844, CIP 106345
135645	S. sonnei Descamps, CIP 66.4
136002	S. sonnei St9, CIP 51.44
136283	S. sonnei 1120-66, CIP 104223, ATCC 25931, CCUG 32351, ...
136427	S. sonnei CNRSS 99 9842, CIP 106346
136441	S. sonnei CNRSS 99 9901, CIP 106347
136526	S. sonnei 545/78, CIP 106470
136595	S. sonnei CIP 67.63
139310	S. sonnei 47, M200, CIP 106204
139677	S. sonnei CIP 52.55
141994	S. sonnei CCUG 9567, NCTC 9774
143437	S. sonnei CCUG 19136
144650	S. sonnei CCUG 26076
144829	S. sonnei CCUG 26684
144877	S. sonnei CCUG 26943
147883	S. sonnei CCUG 34429
148599	S. sonnei CCUG 35690
149522	S. sonnei CCUG 37894
150759	S. sonnei CCUG 42208
152208	S. sonnei CCUG 46081
156599	S. sonnei CCUG 63282

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility	Confidence
122678	negative	rod-shaped
125438	negative			99.75

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
2226	NUTRIENT AGAR (DSMZ Medium 1)	Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
41757	MEDIUM 3 - Columbia agar		Columbia agar (39.000 g);distilled water (1000.000 ml)
2226	TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)	Medium recipe at MediaDive	Name: 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
2226	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
122678	CIP Medium 3	Medium recipe at CIP
122678	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
2226	positive	growth	37
41757	positive	growth	30
63516	positive	growth	30
122678	positive	growth	10-41
122678	negative	growth	5

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
63516	aerobe
122678	facultative anaerobe

Antibiotic susceptibility testing

	Test 1
@ref	2226
Medium	Mueller-Hinton Agar
Manual annotation	1
	Inhibition zone diameter in mm
Amikacin 30µg (disc)	22
Ampicillin 10µg (disc)	22
Aztreonam 30µg (disc)	38
Bacitracin 10Unit	0
Cefalotin 30µg (disc)	22
Cefazolin 30µg (disc)	30
Cefotaxime 30µg (disc)	40
Ceftriaxone 30µg (disc)	38
Chloramphenicol 30µg (disc)	30-32
Clindamycin 10µg (disc)	0
Colistin 10µg (disc)	14
Doxycycline 30µg (disc)	10
Erythromycin 15µg (disc)	10
Fosfomycin 50µg (disc)	34
Gentamicin 10µg (disc)	20
Imipenem 10µg (disc)	34
Kanamycin 30µg (disc)	22
Lincomycin 15µg (disc)	0
Linezolid 10µg (disc)	0
Mezlocillin 30µg (disc)	26
Moxifloxacin 5µg (disc)	32
Neomycin 30µg (disc)	18
Nitrofurantoin 100µg (disc)	24-26
Norfloxacin 10µg (disc)	36-38
Nystatin 100Unit	6
Ofloxacin 5µg (disc)	34
Oxacillin 5µg (disc)	0
Penicillin G 6µg (disc)	0
Pipemidic acid 20µg (disc)	28
Piperacillin/Tazobactam 40µg (disc)	26
Polymyxin B 300Unit	14
Quinupristin/Dalfopristin 15µg (disc)	8
Teicoplanin 30µg (disc)	0
Tetracycline 30µg (disc)	6
Ticarcillin 75µg (disc)	32
Vancomycin 30µg (disc)	0

Spore formation

@ref	Spore formation	Confidence
125439		92.88

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68368	27613 ChEBI	amygdalin	-	fermentation	from API 20E
122678	16947 ChEBI	citrate	-	carbon source
68368	16947 ChEBI	citrate	-	assimilation	from API 20E
68368	17634 ChEBI	D-glucose	+	fermentation	from API 20E
68368	16899 ChEBI	D-mannitol	+	fermentation	from API 20E
68368	5291 ChEBI	gelatin	-	hydrolysis	from API 20E
122678	17234 ChEBI	glucose	+	fermentation
122678	17234 ChEBI	glucose	+	degradation
68368	30849 ChEBI	L-arabinose	+	fermentation	from API 20E
68368	62345 ChEBI	L-rhamnose	+	fermentation	from API 20E
122678	17716 ChEBI	lactose	-	fermentation
68368	25094 ChEBI	lysine	-	degradation	from API 20E
122678	15792 ChEBI	malonate	-	assimilation
122678	29864 ChEBI	mannitol	+	fermentation
68368	28053 ChEBI	melibiose	-	fermentation	from API 20E
68368	17268 ChEBI	myo-inositol	-	fermentation	from API 20E
122678	17632 ChEBI	nitrate	+	reduction
122678	16301 ChEBI	nitrite	+	reduction
68368	18257 ChEBI	ornithine	+	degradation	from API 20E
122678	132112 ChEBI	sodium thiosulfate	-	builds gas from
68368	30911 ChEBI	sorbitol	-	fermentation	from API 20E
68368	17992 ChEBI	sucrose	-	fermentation	from API 20E
68368	27897 ChEBI	tryptophan	-	energy source	from API 20E
68368	16199 ChEBI	urea	-	hydrolysis	from API 20E

Antibiotic resistance

@ref	ChEBI	Metabolite	Resistance conc.
122678		0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
2226	28669	Bacitracin	10 Unit	from Antibiotic test
2226	3745	Clindamycin	10 µg (disc)	from Antibiotic test
2226	6472	Lincomycin	15 µg (disc)	from Antibiotic test
2226	63607	Linezolid	10 µg (disc)	from Antibiotic test
2226	7809	Oxacillin	5 µg (disc)	from Antibiotic test
2226	18208	Penicillin G	6 µg (disc)	from Antibiotic test
2226	29687	Teicoplanin	30 µg (disc)	from Antibiotic test
2226	28001	Vancomycin	30 µg (disc)	from Antibiotic test

Metabolite production

@ref	Chebi-ID	Metabolite
68368	16136 ChEBI	hydrogen sulfide	from API 20E
122678	35581 ChEBI	indole
68368	35581 ChEBI	indole	from API 20E

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test	Voges-proskauer-test	Methylred-test
122678	15688 ChEBI	acetoin		-
122678	17234 ChEBI	glucose			+
68368	35581 ChEBI	indole	-			from API 20E

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
122678	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	+	3.2.1.23	from API zym
122678	beta-galactosidase	+	3.2.1.23
68368	beta-galactosidase	+	3.2.1.23	from API 20E
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
122678	catalase	+	1.11.1.6
68382	cystine arylamidase	+	3.4.11.3	from API zym
68368	cytochrome oxidase	-	1.9.3.1	from API 20E
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	-		from API zym
122678	gelatinase	-
68368	gelatinase	-		from API 20E
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
122678	lysine decarboxylase	-	4.1.1.18
68368	lysine decarboxylase	-	4.1.1.18	from API 20E
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
122678	ornithine decarboxylase	+	4.1.1.17
68368	ornithine decarboxylase	+	4.1.1.17	from API 20E
122678	oxidase	-
68382	trypsin	+	3.4.21.4	from API zym
122678	tryptophan deaminase	-
68368	tryptophan deaminase	-	4.1.99.1	from API 20E
122678	urease	-	3.5.1.5
68368	urease	-	3.5.1.5	from API 20E
68382	valine arylamidase	+		from API zym

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
2226	+	+/-	-	+	-	-	-	-	-	-	-	+	+	-	-	+	-	-	-	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.
2226	+	+/-	-	+	-	-	-	-	-	+	-	+	+	-	-	+	-	-	-	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.
2226	+	-	-	+	-	-	-	-	-	+	-	+	+	-	-	+	-	-	-	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
122678	-	+	+	-	-	+	+	+	+	-	+	+	-	+	-	+	-	-	-	-

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
122678	not determinedn.d.	+	+	+	+	+	-	+	-	+	+	+	-	-	+	+	-	-	-	-	+	+	-	-	+	+	-	-	-	-	-	-	+	-	+	-	-	-	-	-	-	-	-	-	-	+	-	-	-	+	+	-	-	-	-	+	+	-	-	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	+	-	+	-	-	-	+	+	-	+	-	-	-	+	-	-	+	+	+	+	-	+	-	-	-	+

Isolation, sampling and environmental information

Taxonmaps

69479

Global distribution of 16S sequence FR870445 (>99% sequence identity) for Enterobacteriaceae from Microbeatlas

Aquatic Samples	5613
Soil Samples	2111
Animal Samples	88071
Plant Samples	1835
Total Samples	97630

Interaction and safety

Risk assessment

@ref	Pathogenicity human	Pathogenicity animal	Biosafety level	Biosafety level comment
2226			2	Risk group (German classification) According to TRBA 466
122678			2	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM295039v1 assembly for Shigella sonnei ATCC 29930	complete	GCA_002950395	624.1345	2872158770	624	97.31
66792	57940_C01 assembly for Shigella sonnei NCTC12984	contig	GCA_900457155	624.1595	8118001194	624	76.36

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Shigella sonnei partial 16S rRNA gene, type strain CECT 4887T	FR870445	1530	624
124043	Shigella sonnei strain CECT 4887 16S ribosomal RNA gene, partial sequence.	PP859296	403	624
124043	Shigella sonnei strain CECT 4887 16S ribosomal RNA gene, partial sequence.	PP859381	1221	624
124043	Shigella sonnei strain CECT 4887 16S ribosomal RNA gene, partial sequence.	MK185059	586	624

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM295039v1 assembly for Shigella sonnei ATCC 29930
BV-BRC: 624.1345

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	85.84	no
125439	gram_stain	BacteriaNetⓘ	negative	65.06	no
125439	motility	BacteriaNetⓘ	yes	40.96	no
125439	spore_formation	BacteriaNetⓘ	no	92.88	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Shigella sonnei ATCC 29930
NCBI: GCA_002950395.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.75	no
125438	anaerobic	anaerobicⓘ	no	95.04	yes
125438	aerobic	aerobicⓘ	no	67.75	no
125438	spore-forming	spore-formingⓘ	no	87.45	no
125438	thermophilic	thermophileⓘ	no	98.50	yes
125438	flagellated	motile2+ⓘ	yes	76.80	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Laboratory evaluation of the broad-spectrum antibacterial efficacy of a low-irradiance visible 405-nm light system for surface-simulated decontamination.	Sinclair LG, Dougall LR, Ilieva Z, McKenzie K, Anderson JG, MacGregor SJ, Maclean M.	Health Technol (Berl)	10.1007/s12553-023-00761-3	2023
	Bacteriophage-based nano-biosensors for the fast impedimetric determination of pathogens in food samples.	Abdelhamied N, Abdelrahman F, El-Shibiny A, Hassan RYA.	Sci Rep	10.1038/s41598-023-30520-3	2023
	A case report of black swan (Cygnus atratus) died from gastric perforation and secondary infection resulting from ingestion of cloth-like foreign material.	Jiao X, Wang H, Yan Y, Codjia CR, Wang X.	Front Vet Sci	10.3389/fvets.2025.1608317	2025
Genetics	Functional Enrichment and Sequence-Based Discovery Identify Promiscuous and Efficient Poly Lactic Acid Degrading Enzymes.	Stojanovski G, Bawn M, Locks A, Ambrose-Dempster E, Ward JM, Jeffries JWE, Hailes HC.	Environ Sci Technol	10.1021/acs.est.4c07279	2025
	First Detection of Carbapenem-Resistant Escherichia fergusonii Strains Harbouring Beta-Lactamase Genes from Clinical Samples.	Adesina T, Nwinyi O, De N, Akinnola O, Omonigbehin E.	Pathogens	10.3390/pathogens8040164	2019
Phylogeny	Molecular Characterization of Bacteria, Detection of Enterotoxin Genes, and Screening of Antibiotic Susceptibility Patterns in Traditionally Processed Meat Products of Sikkim, India.	Bhutia MO, Thapa N, Tamang JP.	Front Microbiol	10.3389/fmicb.2020.599606	2020
	Characterization, Bioactivity and Application of Chitosan-Based Nanoparticles in a Food Emulsion Model.	Oliveira Lima K, Barreto Pinilla CM, Aleman A, Lopez-Caballero ME, Gomez-Guillen MC, Montero P, Prentice C.	Polymers (Basel)	10.3390/polym13193331	2021
Pathogenicity	Diversity and Local Coadaptation of Escherichia coli and Coliphages From Small Ruminants.	Molina F, Simancas A, Tabla R, Gomez A, Roa I, Rebollo JE.	Front Microbiol	10.3389/fmicb.2020.564522	2020
Phylogeny	In Situ Profiling of the Three Dominant Phyla Within the Human Gut Using TaqMan PCR for Pre-Hospital Diagnosis of Gut Dysbiosis.	Jo YJ, Tagele SB, Pham HQ, Jung Y, Ibal JC, Choi S, Kang GU, Park S, Kang Y, Kim S, Koh H, Shin JH.	Int J Mol Sci	10.3390/ijms21061916	2020
	Contamination analysis of Arctic ice samples as planetary field analogs and implications for future life-detection missions to Europa and Enceladus.	Coelho LF, Blais MA, Matveev A, Keller-Costa T, Vincent WF, Costa R, Martins Z, Canario J.	Sci Rep	10.1038/s41598-022-16370-5	2022
Pathogenicity	A New Pipeline for Designing Phage Cocktails Based on Phage-Bacteria Infection Networks.	Molina F, Simancas A, Ramirez M, Tabla R, Roa I, Rebollo JE.	Front Microbiol	10.3389/fmicb.2021.564532	2021
	In vitro investigation of Mangifera indica L. peel extracts: antibacterial, antioxidant, and docking studies.	El-Sayed SM, Abd-Elhalim BT, El-Dougdoug KA, Gamal RF, El-Bana GG, Mohamed NNI.	AMB Express	10.1186/s13568-025-01882-w	2025
	Antimicrobial, antibiofilm, and antiviral investigations using egyptian phoenix dactylifera L. pits extract.	Gomaa HH, Amin DY, Ahmed AR, Ismail NA, El Dougdoug KA, Abd-Elhalim BT.	AMB Express	10.1186/s13568-024-01695-3	2024
	Biosynthesis and characterization of silver nanoparticles from Punica granatum (pomegranate) peel waste and its application to inhibit foodborne pathogens.	Farouk SM, Abu-Hussien SH, Abd-Elhalim BT, Mohamed RM, Arabe NM, Hussain AAT, Mostafa ME, Hemdan B, El-Sayed SM, Bakry A, Ebeed NM, Salah M, Elhariry H, Galal A.	Sci Rep	10.1038/s41598-023-46355-x	2023
	Compatibility and antimicrobial activity of silver nanoparticles synthesized using Lycopersicon esculentum peels.	Ali E, Abu-Hussien SH, Hesham E, Ahmed S, Mostafa H, Gamal A, El-Sayed SM, Hemdan B, Bakry A, Ebeed NM, Elhariry H, Galal A, Abd-Elhalim BT.	AMB Express	10.1186/s13568-024-01774-5	2024
	Optimization, characterization and biosafety of carotenoids produced from whey using Micrococcus luteus.	Hegazy AA, Abu-Hussien SH, Elsenosy NK, El-Sayed SM, Abo El-Naga MY.	BMC Biotechnol	10.1186/s12896-024-00899-6	2024
	Copper nanoparticles biosynthesis by Stevia rebaudiana extract: biocompatibility and antimicrobial application.	Abdelhai MF, Shabaan RH, Kamal NM, Elemary EA, Abd-Elhalim BT, Hassan EA.	AMB Express	10.1186/s13568-024-01707-2	2024
	Utilization of biosynthesized silver nanoparticles from Agaricus bisporus extract for food safety application: synthesis, characterization, antimicrobial efficacy, and toxicological assessment.	Amr M, Abu-Hussien SH, Ismail R, Aboubakr A, Wael R, Yasser M, Hemdan B, El-Sayed SM, Bakry A, Ebeed NM, Elhariry H, Galal A, Abd-Elhalim BT.	Sci Rep	10.1038/s41598-023-42103-3	2023
	Evaluation of the Antidiarrheal and Antioxidant Effects of Some Chewing Sticks Commonly Used for Oral Hygiene in Ghana.	Essuman EK, Boakye AA, Tettey CO, Hunkpe G, Kortei NK, Kwansa-Bentum H, Waikhom SD, Aninagyei E.	Evid Based Complement Alternat Med	10.1155/2021/7270250	2021
	Antiseptic quaternary ammonium compound tolerance by gram-negative bacteria can be rapidly detected using an impermeant fluorescent dye-based assay.	Gregorchuk BSJ, Reimer SL, Beniac DR, Hiebert SL, Booth TF, Wuzinski M, Funk BE, Milner KA, Cartwright NH, Doucet AN, Mulvey MR, Khajehpour M, Zhanel GG, Bay DC.	Sci Rep	10.1038/s41598-020-77446-8	2020
	Characterization and application of tannase and gallic acid produced by co-fungi of Aspergillus niger and Trichoderma viride utilizing agro-residues substrates.	Ahmed AI, Abou-Taleb KAA, Abd-Elhalim BT.	Sci Rep	10.1038/s41598-023-43955-5	2023
	Enhancing durability and sustainable preservation of Egyptian stone monuments using metabolites produced by Streptomyces exfoliatus.	Abd-Elhalim BT, Hemdan BA, El-Sayed SM, Ahmed MA, Maan SA, Abu-Hussien SH.	Sci Rep	10.1038/s41598-023-36542-1	2023
	Chicken Skin Decontamination of Thermotolerant Campylobacter spp. and Hygiene Indicator Escherichia coli Assessed by Viability Real-Time PCR.	Wulsten IF, Thieck M, Gohler A, Schuh E, Stingl K.	Pathogens	10.3390/pathogens11060706	2022
Phylogeny	Simultaneous detection and differentiation of Escherichia coli populations from environmental freshwaters by means of sequence variations in a fragment of the beta-D-glucuronidase gene.	Farnleitner AH, Kreuzinger N, Kavka GG, Grillenberger S, Rath J, Mach RL.	Appl Environ Microbiol	10.1128/aem.66.4.1340-1346.2000	2000
	Photocatalytic Degradation of Coomassie Brilliant Blue R-250 and Antimicrobial Activities of Iron Oxide Nanoparticles Synthesized by Aspergillus flavus.	Elkhouli RR, ElBaghdady KZ, Khalil MMH, Mohamed SS.	Curr Microbiol	10.1007/s00284-025-04299-7	2025
Pathogenicity	Shigella sonnei and Shigella flexneri infection in Caenorhabditis elegans led to species-specific regulatory responses in the host and pathogen.	Wong BC, Tan HS.	Microb Genom	10.1099/mgen.0.001339	2025
	In vitro evaluation the spectrum of antibacterial activity of botanical extracts and activity enhancement with outer membrane permeabilizers.	Gregory C, Langland J.	BMC Complement Med Ther	10.1186/s12906-025-05147-8	2025
Phylogeny	Epidemiological Characteristics, Antibiotic Resistance Patterns and Genomic Analysis of Shigella Isolated in Pudong, Shanghai During 2013-2024.	Zhang Y, Wang X, Liang Y, Wang W, Huang H, Yang B, Zhang A, Zhuang Y, Chen M, Feng J, Zhao B.	Antibiotics (Basel)	10.3390/antibiotics14111091	2025
	Physicochemical properties and antimicrobial activities of MytiLec-1, a member from the mytilectin family of mussels.	Hossain MM, Rajia S, Ohkawa M, Yoshimoto S, Fujii Y, Kawsar SMA, Ozeki Y, Hasan I.	Int J Biol Macromol	10.1016/j.ijbiomac.2023.127628	2023
	Topoisomerase inhibitory activity of ethanolic extracts from botanicals Coptis chinensis and Salvia officinalis.	Ingersoll W, Trapp S, Turner T, Ruiz G, Langland J.	J Med Microbiol	10.1099/jmm.0.002024	2025
	Antibacterial and anticancer activities of three novel lectin-conjugated chitosan nanoparticles.	Soliman MM, El-Shatoury EH, El-Araby MMI.	Appl Microbiol Biotechnol	10.1007/s00253-024-13344-7	2024
	Characterization of Serratia marcescens (OK482790)' prodigiosin along with in vitro and in silico validation for its medicinal bioactivities.	Hamada MA, Mohamed ET.	BMC Microbiol	10.1186/s12866-024-03634-5	2024
	Carbohydrate-Binding Properties and Antimicrobial and Anticancer Potential of a New Lectin from the Phloem Sap of Cucurbita pepo.	Islam MA, Hossain MM, Khanam A, Asaduzzaman AKM, Kabir SR, Ozeki Y, Fujii Y, Hasan I.	Molecules	10.3390/molecules29112531	2024
	Improvement of Alginate Extraction from Brown Seaweed (Laminaria digitata L.) and Valorization of Its Remaining Ethanolic Fraction.	Savic Gajic IM, Savic IM, Ivanovska AM, Vunduk JD, Mihalj IS, Svircev ZB.	Mar Drugs	10.3390/md22060280	2024
	Metabolically-targeted dCas9 expression in bacteria.	Pellegrino GM, Browne TS, Sharath K, Bari KA, Vancuren SJ, Allen-Vercoe E, Gloor GB, Edgell DR.	Nucleic Acids Res	10.1093/nar/gkac1248	2023
Genetics	Multiple Mechanisms Confer Resistance to Azithromycin in Shigella in Bangladesh: a Comprehensive Whole Genome-Based Approach.	Nusrin S, Asad A, Hayat S, Islam B, Begum R, Nabila FH, Islam Z.	Microbiol Spectr	10.1128/spectrum.00741-22	2022
	Interaction of Ziziphus mucronata subsp. mucronata Methanol Extract and First-Line Antibiotics is Synergistic In Vitro through Production of Reactive Oxygen Species.	Olajuyigbe AA, Olajuyigbe OO, Coopoosamy RM.	J Trop Med	10.1155/2020/4087394	2020
Enzymology	Pseudomonas Phage ZCPS1 Endolysin as a Potential Therapeutic Agent.	Abdelrahman F, Gangakhedkar R, Nair G, El-Didamony G, Askora A, Jain V, El-Shibiny A.	Viruses	10.3390/v15020520	2023
	Bacteriophages Isolated From Turkeys Infecting Diverse Salmonella Serovars.	Lu Z, Marchant J, Thompson S, Melgarejo H, Ignatova D, Kopic S, Damaj R, Trejo H, Paramo R, Reed A, Breidt F, Kathariou S.	Front Microbiol	10.3389/fmicb.2022.933751	2022
	Performance of a new molecular assay for the detection of gastrointestinal pathogens.	Gingras BA, Maggiore JA.	Access Microbiol	10.1099/acmi.0.000160	2020
	Green Extraction Approach for Isolation of Bioactive Compounds in Wild Thyme (Thymus serpyllum L.) Herbal Dust-Chemical Profile, Antioxidant and Antimicrobial Activity and Comparison with Conventional Techniques.	Mrkonjic Z, Kaplan M, Milosevic S, Bozovic D, Sknepnek A, Miletic D, Lazarevic Mrkonjic I, Rakic D, Zekovic Z, Pavlic B.	Plants (Basel)	10.3390/plants13060897	2024
Enzymology	Characterization of Two Antimicrobial Peptides from Antarctic Fishes (Notothenia coriiceps and Parachaenichthys charcoti).	Shin SC, Ahn IH, Ahn DH, Lee YM, Lee J, Lee JH, Kim HW, Park H.	PLoS One	10.1371/journal.pone.0170821	2017
	Evaluation of the antibacterial potential of silver nanoparticles synthesized through the interaction of antibiotic and aqueous callus extract of Fagonia indica.	Adil M, Khan T, Aasim M, Khan AA, Ashraf M.	AMB Express	10.1186/s13568-019-0797-2	2019
	Chemical Composition and Antibacterial Activity of Essential Oil of Cosmos bipinnatus Cav. Leaves from South Africa.	Olajuyigbe O, Ashafa A.	Iran J Pharm Res		2014
	Microorganisms of the Intestinal Microbiota of Oncorhynchus Mykiss Produce Antagonistic Substances Against Bacteria Contaminating Food and Causing Disease in Humans.	Lobos O, Barrera A, Padilla C.	Ital J Food Saf	10.4081/ijfs.2017.6240	2017
Pathogenicity	In vitro antibacterial and time-kill evaluation of the Erythrina caffra Thunb. extract against bacteria associated with diarrhoea.	Olajuyigbe OO, Afolayan AJ.	ScientificWorldJournal	10.1100/2012/738314	2012
	Chemical composition, antioxidant activities and antibacterial activities of essential oil from Erythrina caffra Thunb. growing in South Africa.	Wintola OA, Olajuyigbe AA, Afolayan AJ, Coopoosamy RM, Olajuyigbe OO.	Heliyon	10.1016/j.heliyon.2021.e07244	2021
Enzymology	Coriolus versicolor Mushroom Grown on Selenium-Rich Zeolitic Tuff as a Potential Novel Food Supplement.	Matijasevic D, Pantic M, Stanisavljevic N, Jevtic S, Rajic N, Levic S, Levic S, Nedovic V, Niksic M.	Food Technol Biotechnol	10.17113/ftb.60.01.22.7172	2022
Pathogenicity	Evaluation of the antibacterial and antifungal potential of Peltophorum africanum: toxicological effect on human Chang liver cell line.	Okeleye BI, Mkwetshana NT, Ndip RN.	ScientificWorldJournal	10.1155/2013/878735	2013
	Synergistic interactions of methanolic extract of Acacia mearnsii De Wild. with antibiotics against bacteria of clinical relevance.	Olajuyigbe OO, Afolayan AJ.	Int J Mol Sci	10.3390/ijms13078915	2012
	GABA-Producing Natural Dairy Isolate From Artisanal Zlatar Cheese Attenuates Gut Inflammation and Strengthens Gut Epithelial Barrier in vitro.	Sokovic Bajic S, Djokic J, Dinic M, Veljovic K, Golic N, Mihajlovic S, Tolinacki M.	Front Microbiol	10.3389/fmicb.2019.00527	2019
	The antibacterial, phytochemicals and antioxidants evaluation of the root extracts of Hydnora africanaThunb. used as antidysenteric in Eastern Cape Province, South Africa.	Wintola OA, Afolayan AJ.	BMC Complement Altern Med	10.1186/s12906-015-0835-9	2015
Pathogenicity	Evaluation of the effect of different growth media and temperature on the suitability of biofilm formation by Enterobacter cloacae strains isolated from food samples in South Africa.	Nyenje ME, Green E, Ndip RN.	Molecules	10.3390/molecules18089582	2013
Pathogenicity	Medicinal potential of Morella serata (Lam.) Killick (Myricaceae) root extracts: biological and pharmacological activities.	Ashafa AO.	BMC Complement Altern Med	10.1186/1472-6882-13-163	2013
	Phytochemical analysis and antibacterial evaluation of the ethyl acetate extract of the stem bark of Bridelia micrantha.	Adefuye AO, Ndip RN.	Pharmacogn Mag	10.4103/0973-1296.108139	2013
	Development of a Droplet Digital Polymerase Chain Reaction for Rapid and Simultaneous Identification of Common Foodborne Pathogens in Soft Cheese.	Cremonesi P, Cortimiglia C, Picozzi C, Minozzi G, Malvisi M, Luini M, Castiglioni B.	Front Microbiol	10.3389/fmicb.2016.01725	2016
Phylogeny	Specific discrimination of three pathogenic Salmonella enterica subsp. enterica serotypes by carB-based oligonucleotide microarray.	Shin HH, Hwang BH, Seo JH, Cha HJ.	Appl Environ Microbiol	10.1128/aem.02978-13	2014
	Fecal indicators and bacterial pathogens in bottled water from Dhaka, Bangladesh.	Ahmed W, Yusuf R, Hasan I, Ashraf W, Goonetilleke A, Toze S, Gardner T.	Braz J Microbiol	10.1590/s1517-83822013005000026	2013
Metabolism	An inhibitory compound produced by a soil isolate of Rhodococcus has strong activity against the veterinary pathogen R. equi.	Ward AL, Reddyvari P, Borisova R, Shilabin AG, Lampson BC.	PLoS One	10.1371/journal.pone.0209275	2018
	The Antibacterial Activity of Coriolus versicolor Methanol Extract and Its Effect on Ultrastructural Changes of Staphylococcus aureus and Salmonella Enteritidis.	Matijasevic D, Pantic M, Raskovic B, Pavlovic V, Duvnjak D, Sknepnek A, Niksic M.	Front Microbiol	10.3389/fmicb.2016.01226	2016
Phylogeny	Genetic variability and molecular typing of Shigella sonnei strains isolated in Canada.	Preston MA, Borczyk AA.	J Clin Microbiol	10.1128/jcm.32.6.1427-1430.1994	1994
Enzymology	Molecular method for detection of total coliforms in drinking water samples.	Maheux AF, Boudreau DK, Bisson MA, Dion-Dupont V, Bouchard S, Nkuranga M, Bergeron MG, Rodriguez MJ.	Appl Environ Microbiol	10.1128/aem.00546-14	2014
Biotechnology	Validation of the One Broth One Plate for Salmonella Method for Detection of Salmonella Spp. in Select Food and Environmental Samples: AOAC Performance Tested MethodSM 102002.	Alles S, Roman B, Le QN, Kurteu M, Elmerhebi E, Potter C, Mozola M, Thompson W, Bastin B, Donofrio R.	J AOAC Int	10.1093/jaoacint/qsaa149	2021
Enzymology	Occurrence of virulence genes associated with Diarrheagenic pathotypes in Escherichia coli isolates from surface water.	Sidhu JP, Ahmed W, Hodgers L, Toze S.	Appl Environ Microbiol	10.1128/aem.02888-12	2013
Phylogeny	Comparison of three different methods for detection of Shiga toxin-producing Escherichia coli in a tertiary pediatric care center.	Vallieres E, Saint-Jean M, Rallu F.	J Clin Microbiol	10.1128/jcm.02219-12	2013
Phylogeny	Restriction fragment length polymorphisms in rRNA operons for subtyping Shigella sonnei.	Hinojosa-Ahumada M, Swaminathan B, Hunter SB, Cameron DN, Kiehlbauch JA, Wachsmuth IK, Strockbine NA.	J Clin Microbiol	10.1128/jcm.29.11.2380-2384.1991	1991
Enzymology	Rapid detection, identification, and enumeration of Escherichia coli cells in municipal water by chemiluminescent in situ hybridization.	Stender H, Broomer AJ, Oliveira K, Perry-O'Keefe H, Hyldig-Nielsen JJ, Sage A, Coull J.	Appl Environ Microbiol	10.1128/aem.67.1.142-147.2001	2001
Enzymology	Development of a rapid PCR assay specific for Staphylococcus saprophyticus and application to direct detection from urine samples.	Martineau F, Picard FJ, Menard C, Roy PH, Ouellette M, Bergeron MG.	J Clin Microbiol	10.1128/jcm.38.9.3280-3284.2000	2000
Enzymology	Real-time PCR detection of pathogenic microorganisms in roof-harvested rainwater in Southeast Queensland, Australia.	Ahmed W, Huygens F, Goonetilleke A, Gardner T.	Appl Environ Microbiol	10.1128/aem.00331-08	2008
Enzymology	PCR detection of a newly emerged pandemic Vibrio parahaemolyticus O3:K6 pathogen in pure cultures and seeded waters from the Gulf of Mexico.	Myers ML, Panicker G, Bej AK.	Appl Environ Microbiol	10.1128/aem.69.4.2194-2200.2003	2003
Phylogeny	Development of a PCR assay for identification of staphylococci at genus and species levels.	Martineau F, Picard FJ, Ke D, Paradis S, Roy PH, Ouellette M, Bergeron MG.	J Clin Microbiol	10.1128/jcm.39.7.2541-2547.2001	2001
	PCR amplification of the fimA gene sequence of Salmonella typhimurium, a specific method for detection of Salmonella spp.	Cohen HJ, Mechanda SM, Lin W.	Appl Environ Microbiol	10.1128/aem.62.12.4303-4308.1996	1996
	Analysis of the type 1 pilin gene cluster fim in Salmonella: its distinct evolutionary histories in the 5' and 3' regions.	Boyd EF, Hartl DL.	J Bacteriol	10.1128/jb.181.4.1301-1308.1999	1999
Enzymology	Use of tuf sequences for genus-specific PCR detection and phylogenetic analysis of 28 streptococcal species.	Picard FJ, Ke D, Boudreau DK, Boissinot M, Huletsky A, Richard D, Ouellette M, Roy PH, Bergeron MG.	J Clin Microbiol	10.1128/jcm.42.8.3686-3695.2004	2004
Enzymology	Rapid detection of Vibrio vulnificus in shellfish and Gulf of Mexico water by real-time PCR.	Panicker G, Myers ML, Bej AK.	Appl Environ Microbiol	10.1128/aem.70.1.498-507.2004	2004
	Development of a PCR assay for rapid detection of enterococci.	Ke D, Picard FJ, Martineau F, Menard C, Roy PH, Ouellette M, Bergeron MG.	J Clin Microbiol	10.1128/jcm.37.11.3497-3503.1999	1999
Pathogenicity	New real-time PCR assay for rapid detection of methicillin-resistant Staphylococcus aureus directly from specimens containing a mixture of staphylococci.	Huletsky A, Giroux R, Rossbach V, Gagnon M, Vaillancourt M, Bernier M, Gagnon F, Truchon K, Bastien M, Picard FJ, van Belkum A, Ouellette M, Roy PH, Bergeron MG.	J Clin Microbiol	10.1128/jcm.42.5.1875-1884.2004	2004
Biotechnology	Detection of Salmonella spp. in oysters by PCR.	Bej AK, Mahbubani MH, Boyce MJ, Atlas RM.	Appl Environ Microbiol	10.1128/aem.60.1.368-373.1994	1994
Enzymology	Intergeneric transfer and recombination of the 6-phosphogluconate dehydrogenase gene (gnd) in enteric bacteria.	Nelson K, Selander RK.	Proc Natl Acad Sci U S A	10.1073/pnas.91.21.10227	1994
	The evolution of insertion sequences within enteric bacteria.	Lawrence JG, Ochman H, Hartl DL.	Genetics	10.1093/genetics/131.1.9	1992
	Differential invasiveness & expression of antimicrobial peptides in Shigella serotypes.	Narayan C, Kant V, Mahajan JK, Mohan B, Taneja N.	Indian J Med Res	10.4103/ijmr.ijmr_4864_20	2023
Pathogenicity	Safety assessment and probiotic evaluation of Enterococcus faecium YF5 isolated from sourdough.	Tan Q, Xu H, Aguilar ZP, Peng S, Dong S, Wang B, Li P, Chen T, Xu F, Wei H	J Food Sci	10.1111/1750-3841.12079	2013

References

#2226	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 5570
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#41757	; Curators of the CIP;
#63516	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 68726
#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 .
#68382	Automatically annotated from API zym .
#69479	João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .
#122678	Collection of Institut Pasteur ; Curators of the CIP; CIP 82.49
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#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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Shigella sonnei (CCUG 68726, NCTC 12984, CECT 4887)

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