Shigella flexneri (DSM 4782, ATCC 29903, KCTC 22192)

Name: Shigella flexneri (DSM 4782, ATCC 29903, KCTC 22192)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5171

Type strain

Strain Designation 24570

Culture col. no. DSM 4782 ATCC 29903 KCTC 22192 WDCM 00125 CCUG 56439 6 more

NCBI tax ID(s) 623

Special Collections DSMZ CCUG KCTC CIP

History <- ATCC; ATCC 29903 <- D. J. Brenner; 24570 <- DSM <- ATCC <- DJ Brenner, 24570 CIP <- 1982, ATCC <- D.J. Brenner, CDC: strain 24570

Links

Shigella flexneri 24570 is an aerobe, Gram-negative human pathogen that has multiple antibiotic resistances.

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

Name and taxonomic classification

SI-ID 44862

KCTC:22192,ATCC 29903,DSM 4782,BCRC 13984,CCRC 13984,VTT E-082767,CCUG 56439,CECT 8175,CIP 82.48

@ref 20215

Last LPSN update 2026-02-09 11:18:54

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Enterobacterales

Family Enterobacteriaceae

Genus Shigella

Species Shigella flexneri

Full scientific name Shigella flexneri Castellani and Chalmers 1919 (Approved Lists 1980)

BacDive ID	Other strains from **Shigella flexneri** (47)	Type strain
134486	S. flexneri Boyd 88, CIP 54.41
134492	S. flexneri Trebuchon, CIP 55.19
134549	S. flexneri 14, M52, CIP 106171
134551	S. flexneri 42, M184, CIP 106199
134806	S. flexneri Bagdad 30/66, CIP 67.61
134963	S. flexneri 112540, CIP 107169
135204	S. flexneri 52, M231, CIP 106209
135205	S. flexneri M232, 53, CIP 106210
135206	S. flexneri 54, CIP 106211
135583	S. flexneri 52261, CIP 56.13
135925	S. flexneri 45, M195, CIP 106202, NCTC 3083
135970	S. flexneri Boyd 203, CIP 52.37
135971	S. flexneri Mulatta 103 Z, CIP 52.43, NCTC 8336
136212	S. flexneri 53125, CIP 53.3
136461	S. flexneri 935, CIP 54.58
137152	S. flexneri 24 D, CIP 52.36
137186	S. flexneri Ratcliffe, CIP 52.24
137190	S. flexneri CIP 52.46
137262	S. flexneri 3591-52, CCUG 32079, CIP 104222, ATCC 12022, ...
137306	S. flexneri Z Withington, CIP 54.40, NCTC 7
138629	S. flexneri 26 D, CIP 52.38
138828	S. flexneri 164, CIP 56.19
139147	S. flexneri Ledingham, CIP 52.35
139151	S. flexneri Boyd 102, CIP 52.40
139153	S. flexneri 145-48, CIP 52.44
139198	S. flexneri Zaboli, CIP 52.25, CIP 52.47
139289	S. flexneri 7, M32, CIP 106164
139295	S. flexneri 44, M190, CIP 106201
139301	S. flexneri M148, 30, CIP 106187
139304	S. flexneri 92, CIP 106192
139305	S. flexneri 36, M174, CIP 106193
139309	S. flexneri M181, 40, CIP 106197
139327	S. flexneri 80, CIP 106236
139471	S. flexneri 2457T, CIP 107659, ATCC 700930
141993	S. flexneri CCUG 9566, NCTC 1
143797	S. flexneri CCUG 21251
143807	S. flexneri CCUG 21270
145724	S. flexneri CCUG 29412
145725	S. flexneri CCUG 29413
145727	S. flexneri CCUG 29415
145728	S. flexneri CCUG 29416
149518	S. flexneri CCUG 37890
149526	S. flexneri CCUG 37906
150071	S. flexneri CCUG 38947
150141	S. flexneri CCUG 39080
151363	S. flexneri CCUG 43875
155003	S. flexneri CCUG 56027

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
67771	negative
119397	negative	rod-shaped
125438	negative		99.694

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
36625	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
1822	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
1822	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
119397	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
1822	positive	growth	37
36625	positive	growth	30
60957	positive	growth	30
67771	positive	growth	37
119397	positive	growth	30-41
119397	negative	growth	5
119397	negative	growth	10

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
60957	aerobe
67771	aerobe
119397	facultative anaerobe
125439	obligate aerobe	95.1

Antibiotic susceptibility testing

	Test 1	Test 2	Test 3	Test 4
@ref	1822	1822	1822	1822
Medium	Mueller-Hinton Agar	Mueller Hinton	Mueller-Hinton Agar	Müller-Hinton Agar
Manual annotation	1	1	1	1
	Inhibition zone diameter in mm	Inhibition zone diameter in mm	Inhibition zone diameter in mm	Inhibition zone diameter in mm
Amikacin 30µg (disc)	22	20-22	20-22	20-22
Ampicillin 10µg (disc)	24	24-26	24	28
Aztreonam 30µg (disc)	38-40	38	36	38
Bacitracin 10Unit	0	0	0	n.d.
Cefalotin 30µg (disc)	24	24	22	n.d.
Cefazolin 30µg (disc)	30-32	28-30	26-28	n.d.
Cefiderocol 30µg (disc)	n.d.	n.d.	n.d.	28
Cefotaxime 30µg (disc)	40	40	38	40
Ceftazidime 10µg (disc)	n.d.	n.d.	n.d.	32-34
Ceftriaxone 30µg (disc)	40	36	34-36	38
Chloramphenicol 30µg (disc)	34	34-36	32	34-36
Ciprofloxacin 5µg (disc)	n.d.	n.d.	n.d.	40
Clindamycin 10µg (disc)	0	0	0	0
Colistin 10µg (disc)	16	16	16	n.d.
Colistin sulphate 10µg (disc)	n.d.	n.d.	n.d.	16
Doxycycline 30µg (disc)	26-28	28	26-28	n.d.
Erythromycin 15µg (disc)	12-14	16	10	10
Fosfomycin 50µg (disc)	34	30	38	28-30
Gentamicin 30µg (disc)	n.d.	n.d.	n.d.	18
Gentamycin 10µg (disc)				n.d.
Imipenem 10µg (disc)	34-36	36-38	32-34	32-34
Kanamycin 30µg (disc)	32	22	20	22
Levofloxacin 5µg (disc)	n.d.	n.d.	n.d.	38
Lincomycin 15µg (disc)	0	0	0	n.d.
Linezolid 10µg (disc)	0	10	10	10-12
Meropenem 10µg (disc)	n.d.	n.d.	n.d.	40
Mezlocillin 30µg (disc)	30	28-30	28	n.d.
Moxifloxacin 5µg (disc)	32-34	36-38	34	32-34
Neomycin 30µg (disc)	18-20	18-20	18	n.d.
Nitrofurantoin 100µg (disc)	28	24-26	26	26
Norfloxacin 10µg (disc)	34	40	36	n.d.
Nystatin 100Unit	0	0	0	n.d.
Ofloxacin 5µg (disc)	34	38	34-36	34
Oxacillin 5µg (disc)	0	0	0	0
Penicillin G 6µg (disc)	8-10	6-8	8	6
Pipemidic acid 20µg (disc)	30	30-32	28	n.d.
Piperacillin/Tazobactam 40µg (disc)	30	30	30	n.d.
Piperacillin/Tazobactam 110µg (disc)	n.d.	n.d.	n.d.	32-34
Polymyxin B 300Unit	16	18	16	16
Quinupristin/Dalfopristin 15µg (disc)	0	6	8	0
Rifampicin 5µg (disc)	n.d.	n.d.	n.d.	8
Teicoplanin 30µg (disc)	0	0	0	0
Tetracycline 30µg (disc)	30	30	30	30
Ticarcillin 75µg (disc)	32	30	32	34-36
Tigecycline 15µg (disc)	n.d.	n.d.	n.d.	28-30
Trimethoprim-sulfamethoxazole (1:19) 10µg (disc)	n.d.	n.d.	n.d.	30
Vancomycin 30µg (disc)	0	0	6	8

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68368	27613 ChEBI	amygdalin	-	fermentation	from API 20E
68374	29016 ChEBI	arginine	-	hydrolysis	from API ID32E
68368	29016 ChEBI	arginine	-	hydrolysis	from API 20E
68374	17057 ChEBI	cellobiose	-	builds acid from	from API ID32E
119397	16947 ChEBI	citrate	-	carbon source
68368	16947 ChEBI	citrate	-	assimilation	from API 20E
68374	18333 ChEBI	D-arabitol	-	builds acid from	from API ID32E
68374	18024 ChEBI	D-galacturonic acid	+	builds acid from	from API ID32E
68374	17634 ChEBI	D-glucose	-	builds acid from	from API ID32E
68368	17634 ChEBI	D-glucose	+	fermentation	from API 20E
68374	16899 ChEBI	D-mannitol	-	builds acid from	from API ID32E
68368	16899 ChEBI	D-mannitol	+	fermentation	from API 20E
68368	5291 ChEBI	gelatin	-	hydrolysis	from API 20E
119397	17234 ChEBI	glucose	+	fermentation
119397	17234 ChEBI	glucose	+	degradation
68374	30849 ChEBI	L-arabinose	-	builds acid from	from API ID32E
68368	30849 ChEBI	L-arabinose	+	fermentation	from API 20E
68374	18403 ChEBI	L-arabitol	-	builds acid from	from API ID32E
68374	62345 ChEBI	L-rhamnose	-	builds acid from	from API ID32E
68368	62345 ChEBI	L-rhamnose	-	fermentation	from API 20E
119397	17716 ChEBI	lactose	-	fermentation
68374	25094 ChEBI	lysine	-	degradation	from API ID32E
68368	25094 ChEBI	lysine	-	degradation	from API 20E
68374	15792 ChEBI	malonate	-	assimilation	from API ID32E
119397	15792 ChEBI	malonate	-	assimilation
68374	17306 ChEBI	maltose	-	builds acid from	from API ID32E
119397	29864 ChEBI	mannitol	+	fermentation
68368	28053 ChEBI	melibiose	+	fermentation	from API 20E
68374	17268 ChEBI	myo-inositol	-	builds acid from	from API ID32E
68368	17268 ChEBI	myo-inositol	-	fermentation	from API 20E
119397	17632 ChEBI	nitrate	+	reduction
119397	16301 ChEBI	nitrite	+	reduction
68374	18257 ChEBI	ornithine	-	degradation	from API ID32E
68368	18257 ChEBI	ornithine	-	degradation	from API 20E
68374	18394 ChEBI	palatinose	-	builds acid from	from API ID32E
68374		Potassium 5-ketogluconate	-	builds acid from	from API ID32E
68374	15963 ChEBI	ribitol	-	builds acid from	from API ID32E
119397	132112 ChEBI	sodium thiosulfate	-	builds gas from
68374	30911 ChEBI	sorbitol	-	builds acid from	from API ID32E
68368	30911 ChEBI	sorbitol	-	fermentation	from API 20E
68374	17992 ChEBI	sucrose	-	builds acid from	from API ID32E
68374	27082 ChEBI	trehalose	-	builds acid from	from API ID32E
68374	27897 ChEBI	tryptophan	+	energy source	from API ID32E
68368	27897 ChEBI	tryptophan	+	energy source	from API 20E
68374	16199 ChEBI	urea	-	hydrolysis	from API ID32E
68368	16199 ChEBI	urea	-	hydrolysis	from API 20E

Antibiotic resistance

@ref	ChEBI	Metabolite	Resistance conc.
119397		0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
1822	28669	Bacitracin	10 Unit	from Antibiotic test
1822	3745	Clindamycin	10 µg (disc)	from Antibiotic test
1822	6472	Lincomycin	15 µg (disc)	from Antibiotic test
1822	7660	Nystatin	100 Unit	from Antibiotic test
1822	7809	Oxacillin	5 µg (disc)	from Antibiotic test
1822	29687	Teicoplanin	30 µg (disc)	from Antibiotic test

Metabolite production

@ref	Chebi-ID	Metabolite
68368	16136 ChEBI	hydrogen sulfide	from API 20E
119397	35581 ChEBI	indole
68368	35581 ChEBI	indole	from API 20E
68374	35581 ChEBI	indole	from API ID32E

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test	Voges-proskauer-test	Methylred-test
119397	15688 ChEBI	acetoin		-
119397	17234 ChEBI	glucose			+
68374	35581 ChEBI	indole	+			from API ID32E
68368	35581 ChEBI	indole	+			from API 20E

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
119397	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
68374	alpha-galactosidase	+	3.2.1.22	from API ID32E
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68374	alpha-glucosidase	+	3.2.1.20	from API ID32E
68374	alpha-maltosidase	-		from API ID32E
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68374	arginine dihydrolase	-	3.5.3.6	from API ID32E
68368	arginine dihydrolase	-	3.5.3.6	from API 20E
68382	beta-galactosidase	-	3.2.1.23	from API zym
119397	beta-galactosidase	-	3.2.1.23
68374	beta-galactosidase	-	3.2.1.23	from API ID32E
68368	beta-galactosidase	-	3.2.1.23	from API 20E
68382	beta-glucosidase	-	3.2.1.21	from API zym
68374	beta-glucosidase	-	3.2.1.21	from API ID32E
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68374	beta-glucuronidase	-	3.2.1.31	from API ID32E
119397	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
119397	gelatinase	-
68368	gelatinase	-		from API 20E
68374	L-aspartate arylamidase	-	3.4.11.21	from API ID32E
68382	leucine arylamidase	+	3.4.11.1	from API zym
68374	lipase	-		from API ID32E
68382	lipase (C 14)	-		from API zym
119397	lysine decarboxylase	-	4.1.1.18
68374	lysine decarboxylase	-	4.1.1.18	from API ID32E
68368	lysine decarboxylase	-	4.1.1.18	from API 20E
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68374	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API ID32E
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
119397	ornithine decarboxylase	-	4.1.1.17
68374	ornithine decarboxylase	-	4.1.1.17	from API ID32E
68368	ornithine decarboxylase	-	4.1.1.17	from API 20E
119397	oxidase	-
119397	phenylalanine ammonia-lyase	-	4.3.1.24
68382	trypsin	+	3.4.21.4	from API zym
119397	tryptophan deaminase	-
68368	tryptophan deaminase	-	4.1.99.1	from API 20E
119397	urease	-	3.5.1.5
68374	urease	-	3.5.1.5	from API ID32E
68368	urease	-	3.5.1.5	from API 20E
68382	valine arylamidase	+		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	L-lactaldehyde degradation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	aerobactin biosynthesis	100	1 of 1
66794	4-hydroxyphenylacetate degradation	100	10 of 10
66794	ppGpp biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	taurine degradation	100	1 of 1
66794	adipate degradation	100	2 of 2
66794	suberin monomers biosynthesis	100	2 of 2
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	starch degradation	100	10 of 10
66794	biotin biosynthesis	100	4 of 4
66794	sulfopterin metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	acetate fermentation	100	4 of 4
66794	enterobactin biosynthesis	100	3 of 3
66794	tetrahydrofolate metabolism	100	14 of 14
66794	folate polyglutamylation	100	1 of 1
66794	ubiquinone biosynthesis	100	7 of 7
66794	sulfoquinovose degradation	100	3 of 3
66794	gluconeogenesis	100	8 of 8
66794	vitamin K metabolism	100	5 of 5
66794	palmitate biosynthesis	95.45	21 of 22
66794	NAD metabolism	94.44	17 of 18
66794	heme metabolism	92.86	13 of 14
66794	glutathione metabolism	92.86	13 of 14
66794	photosynthesis	92.86	13 of 14
66794	vitamin B6 metabolism	90.91	10 of 11
66794	pentose phosphate pathway	90.91	10 of 11
66794	Entner Doudoroff pathway	90	9 of 10
66794	threonine metabolism	90	9 of 10
66794	valine metabolism	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	degradation of sugar alcohols	87.5	14 of 16
66794	isoleucine metabolism	87.5	7 of 8
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	vitamin B1 metabolism	84.62	11 of 13
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	purine metabolism	82.98	78 of 94
66794	gallate degradation	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	glycogen metabolism	80	4 of 5
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	pyrimidine metabolism	80	36 of 45
66794	alanine metabolism	79.31	23 of 29
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	citric acid cycle	78.57	11 of 14
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	urea cycle	76.92	10 of 13
66794	glycogen biosynthesis	75	3 of 4
66794	lactate fermentation	75	3 of 4
66794	dTDPLrhamnose biosynthesis	75	6 of 8
66794	CMP-KDO biosynthesis	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	flavin biosynthesis	73.33	11 of 15
66794	oxidative phosphorylation	72.53	66 of 91
66794	degradation of sugar acids	72	18 of 25
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	lipid metabolism	70.97	22 of 31
66794	glycolysis	70.59	12 of 17
66794	leucine metabolism	69.23	9 of 13
66794	non-pathway related	68.42	26 of 38
66794	degradation of pentoses	67.86	19 of 28
66794	allantoin degradation	66.67	6 of 9
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	cyanate degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	methane metabolism	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	tryptophan metabolism	65.79	25 of 38
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	proline metabolism	63.64	7 of 11
66794	ketogluconate metabolism	62.5	5 of 8
66794	methionine metabolism	61.54	16 of 26
66794	degradation of hexoses	61.11	11 of 18
66794	hydrogen production	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	propanol degradation	57.14	4 of 7
66794	cysteine metabolism	55.56	10 of 18
66794	nitrate assimilation	55.56	5 of 9
66794	phenol degradation	55	11 of 20
66794	arginine metabolism	54.17	13 of 24
66794	sulfate reduction	53.85	7 of 13
66794	3-phenylpropionate degradation	53.33	8 of 15
66794	lysine metabolism	52.38	22 of 42
66794	histidine metabolism	51.72	15 of 29
66794	carnitine metabolism	50	4 of 8
66794	myo-inositol biosynthesis	50	5 of 10
66794	toluene degradation	50	2 of 4
66794	pantothenate biosynthesis	50	3 of 6
66794	ribulose monophosphate pathway	50	1 of 2
66794	propionate fermentation	50	5 of 10
66794	quinate degradation	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	tyrosine metabolism	50	7 of 14
66794	polyamine pathway	47.83	11 of 23
66794	ascorbate metabolism	45.45	10 of 22
66794	d-xylose degradation	45.45	5 of 11
66794	metabolism of disaccharids	45.45	5 of 11
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	glycine metabolism	40	4 of 10
66794	3-chlorocatechol degradation	40	2 of 5
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	methanogenesis from CO2	33.33	4 of 12
66794	sphingosine metabolism	33.33	2 of 6
66794	vitamin B12 metabolism	32.35	11 of 34
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	arachidonic acid metabolism	27.78	5 of 18
66794	cyclohexanol degradation	25	1 of 4

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
1822	-	-	-	-	-	-	-	-	+	-	-	+	+	-	-	-	-	+	-	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.
1822	-	-	-	-	-	-	-	-	+	-	-	+	+	-	-	-	+	+	-	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.
1822	-	-	-	-	-	-	-	-	+	+	-	+	+	-	-	-	-	+	-	+	-	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
119397	-	+	-	-	-	+	+	-	+	-	+	+	-	-	-	+	-	-	-	-

API ID32E

@ref	ODC	ADH (Arg)	LDC (Lys)	URE	LARL	GAT	5KG	LipaseLIP	Phenol red (Acidification)RP	beta GLU	MAN	MAL	ADO	PLE	beta GUR	MNT	IND	N-Acetyl-beta-Glucosaminidasebeta NAG	beta GAL	GLU	SAC	LARA	DARL	alpha GLU	alpha GAL	TRE	RHA	INO	CEL	SOR	alpha-MaltosidasealphaMAL	L-aspartic acid arylamidaseAspA
60957	-	-	-	-	-	+	-	-	+	-	-	-	-	-	-	-	+	-	-	-	-	-	-	+	+	-	-	-	-	-	-	-

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
119397	not determinedn.d.	+	+	+	+	+	-	+	-	+	+	+	-	-	-	+	-	-	-	-	-	+	-	-	-	+	-	-	-	-	-	-	+	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	+	+	-	-	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	+	+	-	-	-	-	-	+	-	-	-	-	-	-	+	-	-	-	-	-

Isolation, sampling and environmental information

Taxonmaps

69479

Global distribution of 16S sequence X96963 (>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
1822			2	Risk group (German classification) According to TRBA 466
119397			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	ASM295021v1 assembly for Shigella flexneri 2a ATCC 29903	complete	GCA_002950215	42897.55	2859793810	42897	98.28

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	S.flexneri 16S rRNA gene	X96963	1488	623
124043	Shigella flexneri strain ATCC 29903 16S ribosomal RNA gene, partial sequence.	MN527009	491	623
124043	Shigella flexneri strain ATCC 29903 16S ribosomal RNA gene, partial sequence.	MN527276	491	623
124043	Shigella flexneri strain ATCC 29903 16S ribosomal RNA gene, partial sequence.	MN535393	491	623
124043	Shigella flexneri strain ATCC 29903 16S ribosomal RNA gene, partial sequence.	OQ618959	1361	623
124043	Shigella flexneri strain ATCC 29903 16S ribosomal RNA gene, partial sequence.	OQ619001	1354	623
124043	Shigella flexneri strain ATCC 29903 16S ribosomal RNA gene, partial sequence.	OQ619024	1329	623
124043	Shigella flexneri strain ATCC 29903 16S ribosomal RNA gene, partial sequence.	OQ619031	1356	623
124043	Shigella flexneri strain ATCC 29903 16S ribosomal RNA gene, partial sequence.	OQ619032	1232	623
124043	Shigella flexneri strain ATCC 29903 16S ribosomal RNA gene, partial sequence.	OQ619096	1364	623
124043	Shigella flexneri strain ATCC 29903 16S ribosomal RNA gene, partial sequence.	OQ619115	1305	623
124043	Shigella flexneri strain ATCC 29903 16S ribosomal RNA gene, partial sequence.	OR660251	1094	623
124043	Shigella flexneri strain ATCC 29903 16S ribosomal RNA gene, partial sequence.	MK184303	1487	623

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Shigella flexneri 2a strain ATCC 29903
PATRIC: 42897.55

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	76.20	no
125439	motility	BacteriaNetⓘ	yes	59.10	no
125439	gram_stain	BacteriaNetⓘ	negative	70.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	95.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Shigella flexneri 2a ATCC 29903
NCBI: GCA_002950215.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.69	yes
125438	anaerobic	anaerobicⓘ	no	94.66	no
125438	aerobic	aerobicⓘ	no	73.52	no
125438	spore-forming	spore-formingⓘ	no	88.95	no
125438	thermophilic	thermophileⓘ	no	98.00	yes
125438	flagellated	motile2+ⓘ	yes	75.79	no

Literature

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Genetics	Draft Genome Sequence of 24570, the Type Strain of Shigella flexneri.	Baker KS, Parkhill J, Thomson NR	Genome Announc	10.1128/genomeA.00393-15	2015
Pathogenicity	[Mechanism of resistance of Shigella flexneri 2a resistant to new quinolone antibiotics].	Oonaka K, Fukuyama M, Tanaka M, Sato K, Ohnishi K, Ajima I, Murata M	Kansenshogaku Zasshi	10.11150/kansenshogakuzasshi1970.72.365	1998
Genetics	Virulence phenotypes of Shigella flexneri 2a avirulent mutant 24570 can be complemented by the plasmid-coded positive regulator virF gene.	Qi MS, Yoshikura H, Watanabe H	FEMS Microbiol Lett	10.1111/j.1574-6968.1992.tb05264.x	1992
Pathogenicity	[Membrane component of Shigella flexneri and their relationship to bacteria antigenicity and virulence].	Jin L, Su X	Wei Sheng Wu Xue Bao		1990

References

#1822	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 4782
#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 )
#36625	; Curators of the CIP;
#60957	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 56439
#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) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#68368	Automatically annotated from API 20E .
#68374	Automatically annotated from API ID32E .
#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 .
#119397	Collection of Institut Pasteur ; Curators of the CIP; CIP 82.48
#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 flexneri (DSM 4782, ATCC 29903, KCTC 22192)

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