Shigella sonnei (CIP 104223, ATCC 25931, CCUG 32351)

Name: Shigella sonnei (CIP 104223, ATCC 25931, CCUG 32351)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 136283

Type strain

Strain Designation 1120-66

Culture col. no. CIP 104223 ATCC 25931 CCUG 32351 NCDC 1120-66 1120-66

NCBI tax ID(s) 624

Special Collections CCUG CIP

Links

Shigella sonnei 1120-66 is a facultative anaerobe, mesophilic, Gram-negative prokaryote that was isolated from Human feces.

Gram-negative rod-shaped facultative anaerobe mesophilic genome sequence

Name and taxonomic classification

SI-ID 305279

LMG 10473,ATCC 25931,CIP 104223,CCUG 32351,CECT 4631,KCTC 2518,BCRC 15965,CCRC 15965

@ref 20215

Last LPSN update 2025-12-16 10:02:32

Domain Pseudomonadati

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
5172	S. sonnei I virulent, CCUG 68726, NCTC 12984, CECT ... (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
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
125438	negative			99.75
35641	negative	rod-shaped

Culture and growth conditions

Culture medium

@ref	Name	Composition	Medium link
35641	MEDIUM 3 - Columbia agar	Columbia agar (39.000 g);distilled water (1000.000 ml)
35641	CIP Medium 3		Medium recipe at CIP
35641	CIP Medium 72		Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
35641	positive	growth	30	mesophilic
35641	positive	growth	10-41
35641	negative	growth	5

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
35641	facultative anaerobe
125439	obligate aerobe	95.1

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68368	29016 ChEBI	arginine	-	hydrolysis	from API 20E
35641	16947 ChEBI	citrate	-	carbon source
68368	16947 ChEBI	citrate	-	assimilation	from API 20E
68368	17634 ChEBI	D-glucose	-	fermentation	from API 20E
68368	5291 ChEBI	gelatin	-	hydrolysis	from API 20E
35641	17234 ChEBI	glucose	+	fermentation
35641	17234 ChEBI	glucose	+	degradation
68368	62345 ChEBI	L-rhamnose	-	fermentation	from API 20E
35641	17716 ChEBI	lactose	-	fermentation
68368	25094 ChEBI	lysine	-	degradation	from API 20E
35641	15792 ChEBI	malonate	-	assimilation
35641	29864 ChEBI	mannitol	-	fermentation
68368	28053 ChEBI	melibiose	-	fermentation	from API 20E
68368	17268 ChEBI	myo-inositol	-	fermentation	from API 20E
35641	17632 ChEBI	nitrate	+	reduction
35641	16301 ChEBI	nitrite	+	reduction
68368	18257 ChEBI	ornithine	-	degradation	from API 20E
35641	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	Metabolite	Is antibiotic	Is sensitive	Is resistant
35641	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite
68368	15688 ChEBI	acetoin	from API 20E
68368	17997 ChEBI	dinitrogen	from API 20E
68368	16136 ChEBI	hydrogen sulfide	from API 20E
35641	35581 ChEBI	indole
68368	35581 ChEBI	indole	from API 20E

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test	Indole test
35641	15688 ChEBI	acetoin	-
68368	15688 ChEBI	acetoin	-			from API 20E
35641	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
35641	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
68368	arginine dihydrolase	-	3.5.3.6	from API 20E
35641	beta-galactosidase	+	3.2.1.23
68382	beta-galactosidase	+	3.2.1.23	from API zym
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
35641	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	-		from API zym
35641	gelatinase	-
68368	gelatinase	-		from API 20E
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
35641	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
35641	ornithine decarboxylase	+	4.1.1.17
68368	ornithine decarboxylase	-	4.1.1.17	from API 20E
35641	oxidase	-
35641	phenylalanine ammonia-lyase	-	4.3.1.24
68382	trypsin	-	3.4.21.4	from API zym
35641	tryptophan deaminase	-
68368	tryptophan deaminase	-	4.1.99.1	from API 20E
35641	urease	-	3.5.1.5
68368	urease	-	3.5.1.5	from API 20E
68382	valine arylamidase	+		from API zym

Fatty acid profile

Metadata FA analysis

@ref

50969

Fatty acid	Percentage	ECL
C16:1 ω7c	23.1	15.819
C16:0	20.4	16
C18:1 ω7c /12t/9t	17.7	17.824
C15:0	10.4	15
C14:0	6.2	14
C14:0 3OH/C16:1 ISO I	5.5	15.485
C17:0 CYCLO	4.2	16.888
C12:0	3.4	12
C17:0	2.1	17
C13:0	1.8	13
C13:0 3OH/C15:1 i I/H	1.5	14.469
C12:0 ALDE ?	1.2	10.915
C17:1 ω8c	1	16.792
C15:1 ω8c	0.8	14.792
C18:2 ω6,9c/C18:0 ANTE	0.8	17.724

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
35641	-	-	-	-	-	-	-	-	-	-	-	-	not determinedn.d.	-	-	-	-	-	not determinedn.d.	not determinedn.d.	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
35641	-	+	+	-	-	+	+	-	-	-	+	+	-	+	+	+	-	-	-	-

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
35641	not determinedn.d.	+	+	+	+	+	-	+	+	+	+	+	-	-	+	+	-	-	-	-	+	+	-	-	+	+	-	-	-	-	-	-	+	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	+	-	-	-	-	-	+	-	-	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	+	+	-	-	-	-	-	-	-	-	+	+	+	+	-	+	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Human	-
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)

Isolation

@ref	Sample type	Sampling date	Isolation date
50969	Human feces	1966
35641	Human, Feces		1966

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
35641	2	Risk group (French classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	NCBI tax ID	Score
124043	ASM2287006v1 assembly for Shigella sonnei PartP-Ssonnei-RM8376	complete	GCA_022870065	624.3918	624	96.81
124043	ASM637044v1 assembly for Shigella sonnei FDAARGOS_776	contig	GCA_006370445	624.1857	624	75.75

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Shigella sonnei strain FDAARGOS_776
PATRIC: 624.1857

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	85.90	no
125439	motility	BacteriaNetⓘ	yes	55.70	no
125439	gram_stain	BacteriaNetⓘ	negative	86.00	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 sonnei strain FDAARGOS_776 strain Not applicable
PATRIC: 624.1857

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.75	no
125438	anaerobic	anaerobicⓘ	no	95.54	no
125438	spore-forming	spore-formingⓘ	no	86.95	no
125438	aerobic	aerobicⓘ	no	68.09	yes
125438	thermophilic	thermophileⓘ	no	98.50	yes
125438	flagellated	motile2+ⓘ	yes	76.80	no

Literature

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Phylogeny	Selection and validation of a multilocus variable-number tandem-repeat analysis panel for typing Shigella spp.	Gorge O, Lopez S, Hilaire V, Lisanti O, Ramisse V, Vergnaud G.	J Clin Microbiol	10.1128/jcm.02027-07	2008
	Phytochemical analysis and green synthesis of silver nanoparticles using Centella asiatica leaf and stem extracts: An investigation of antibacterial activity.	Sharma K, Bhusal M, Magar AB, Pathak I, Shrestha LK, Sharma KR.	PLoS One	10.1371/journal.pone.0321172	2025
	HPLC-ESI-HRMS/MS-Based Metabolite Profiling and Bioactivity Assessment of Catharanthus roseus	Joshi S, Huo C, Budhathoki R, Gurung A, Bhattarai S, Sharma K, Kim K, Parajuli N.	Plants (Basel)		2025
	Antibacterial Activity and Possible Mechanism of Litsea cubeba Essential Oil Against Shigella sonnei and Its Application in Lettuce.	Bai X, Chen T, Liu X, Liu Z, Ma R, Su R, Li X, Lu X, Xia X, Shi C.	Foodborne Pathog Dis	10.1089/fpd.2022.0084	2023
	Inhibitory efficacy, production dynamics, and characterization of postbiotics of lactic acid bacteria.	Rahman MM, Sazili AQ, Ahmad SA, Khalil KA, Ismail-Fitry MR, Sarker MSK.	BMC Microbiol	10.1186/s12866-025-04123-z	2025
	Genome Mining Reveals a Sactipeptide Biosynthetic Cluster in Staphylococcus pseudintermedius.	Elsakhawy OK, Abouelkhair MA.	Vet Sci	10.3390/vetsci12070635	2025
	Flavonoids Identified in Terminalia spp. Inhibit Gastrointestinal Pathogens and Potentiate Conventional Antibiotics via Efflux Pump Inhibition.	Zai MJ, Cheesman MJ, Cock IE.	Molecules	10.3390/molecules30112300	2025
	REGECEL (an Oxidized Regenerated Cellulose) Provides Superior Bioactivity Effect on Microorganisms.	Alhetheel AF, Alrfaei BM, Mujamammi AH, Hakami JA, Alshuhri AA.	Infect Drug Resist	10.2147/idr.s454539	2024
	Molecular Characterization of Some Bacillus Species from Vegetables and Evaluation of Their Antimicrobial and Antibiotic Potency.	Koilybayeva M, Shynykul Z, Ustenova G, Abzaliyeva S, Alimzhanova M, Amirkhanova A, Turgumbayeva A, Mustafina K, Yeleken G, Raganina K, Kapsalyamova E.	Molecules	10.3390/molecules28073210	2023
	Screening, isolation, identification and evaluation of bacteria with probiotic potential from traditional palmyra palm nectar.	Kanimozhi R, Sangavi R, Malligarjunan N, Gowrishankar S.	Front Cell Infect Microbiol	10.3389/fcimb.2025.1685639	2025
	Antibacterial Activity and Mechanism of Linalool against Shigella sonnei and Its Application in Lettuce.	Su R, Guo P, Zhang Z, Wang J, Guo X, Guo D, Wang Y, Lu X, Shi C.	Foods	10.3390/foods11203160	2022
	Plant-mediated synthesis of zinc oxide (ZnO) nanoparticles using Alnus nepalensis D. Don for biological applications.	Jaishi DR, Ojha I, Bhattarai G, Baraili R, Pathak I, Ojha DR, Shrestha DK, Sharma KR.	Heliyon	10.1016/j.heliyon.2024.e39255	2024
	Exploring the mechanisms by which camel lactoferrin can kill Salmonella enterica serovar typhimurium and Shigella sonnei.	Almehdar HA, Abd El-Baky N, Mattar EH, Albiheyri R, Bamagoos A, Aljaddawi A, Uversky VN, Redwan EM.	PeerJ	10.7717/peerj.14809	2023
	Phytochemical Analysis and Antimicrobial Activity of Terminalia bellirica (Gaertn.) Roxb. and Terminalia chebula Retz. Fruit Extracts Against Gastrointestinal Pathogens: Enhancing Antibiotic Efficacy.	Tiwana G, Cock IE, Cheesman MJ.	Microorganisms	10.3390/microorganisms12122664	2024
Pathogenicity	A-to-I mRNA editing in bacteria can affect protein sequence, disulfide bond formation, and function.	Didi L, Fargeon O, Aspit L, Elias E, Braverman D, Melamed D, Keidar-Friedman D, Sorek N, Raz O, Tamir SO, Zarivach R, Sal-Man N, Dahan O, Pilpel Y, Bar Yaacov D.	Nucleic Acids Res	10.1093/nar/gkaf584	2025
	Plant assisted synthesis of silver nanoparticles using Persicaria perfoliata (L.) for antioxidant, antibacterial, and anticancer properties.	Shrestha DK, Jaishi DR, Ojha I, Ojha DR, Pathak I, Magar AB, Parajuli N, Sharma KR.	Heliyon	10.1016/j.heliyon.2024.e40543	2024
Phylogeny	Metabolic Comparison and Molecular Networking of Antimicrobials in Streptomyces Species.	Thapa BB, Huo C, Budhathoki R, Chaudhary P, Joshi S, Poudel PB, Magar RT, Parajuli N, Kim KH, Sohng JK.	Int J Mol Sci	10.3390/ijms25084193	2024
	Proteomics reveals energy limitation and amino acid consumption as antibacterial mechanism of linalool against Shigella sonnei and its application in fresh beef preservation.	He R, Chen H, Wu H, Liu J, Chen W, Zhang M, Chen W, Zhong Q.	Food Chem X	10.1016/j.fochx.2023.100837	2023
	Protein-Protein Interactions as Promising Molecular Targets for Novel Antimicrobials Aimed at Gram-Negative Bacteria.	Maj P, Trylska J.	Int J Mol Sci	10.3390/ijms262210861	2025
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	Gas Chromatography-Mass Spectrometry Profiling of Volatile Metabolites Produced by Some Bacillus spp. and Evaluation of Their Antibacterial and Antibiotic Activities.	Koilybayeva M, Shynykul Z, Ustenova G, Waleron K, Jonca J, Mustafina K, Amirkhanova A, Koloskova Y, Bayaliyeva R, Akhayeva T, Alimzhanova M, Turgumbayeva A, Kurmangaliyeva G, Kantureyeva A, Batyrbayeva D, Alibayeva Z.	Molecules	10.3390/molecules28227556	2023
	Green-synthesized cardamom-modified iron oxide nanoparticles with potent antibacterial, antioxidant, anti-inflammatory, and anticancer activities.	Gupta SBR, Paul S, Momin MA, Hasan MF, Akhtar-E-Ekram M, Uddin MS, Hasan T, Saleh MA, Zaman S.	RSC Adv	10.1039/d5ra06699a	2025
	Essential Oil Analysis and Antimicrobial Evaluation of Three Aromatic Plant Species Growing in Saudi Arabia.	El-Said H, Ashgar SS, Bader A, AlQathama A, Halwani M, Ascrizzi R, Flamini G.	Molecules	10.3390/molecules26040959	2021
	Screening of Antioxidant and Antimicrobial Activity of Micromeria fruticosa serpyllifolia Volatile Oils: A Comparative Study of Plants Collected from Different Regions of West Bank, Palestine.	Salameh N, Shraim N, Jaradat N, El Masri M, Adwan L, K'aibni S, Alkowni R, Radwan A, AbuAlhasan M.	Biomed Res Int	10.1155/2020/4851879	2020
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	Antibacterial, Antifungal, and Cytotoxic Effects of Endophytic Streptomyces Species Isolated from the Himalayan Regions of Nepal and Their Metabolite Study.	Yadav RP, Huo C, Budhathoki R, Budthapa P, Bhattarai BR, Rana M, Kim KH, Parajuli N.	Biomedicines	10.3390/biomedicines12102192	2024
	Evaluation of Antimicrobial Activity of Triphala Constituents and Nanoformulation.	Omran Z, Bader A, Porta A, Vandamme T, Anton N, Alehaideb Z, El-Said H, Faidah H, Essa A, Vassallo A, Halwani M.	Evid Based Complement Alternat Med	10.1155/2020/6976973	2020
Genetics	Genomic Drivers of Multidrug-Resistant Shigella Affecting Vulnerable Patient Populations in the United States and Abroad.	Worley JN, Javkar K, Hoffmann M, Hysell K, Garcia-Williams A, Tagg K, Kanjilal S, Strain E, Pop M, Allard M, Francois Watkins L, Bry L.	mBio	10.1128/mbio.03188-20	2021
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	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
	Sequence-Specific Electrochemical Genosensor for Rapid Detection of bla_OXA-51-like Gene in Acinetobacter baumannii.	Kanapathy S, Obande GA, Chuah C, Shueb RH, Yean CY, Banga Singh KK.	Microorganisms	10.3390/microorganisms10071413	2022
	Effects of Synbiotic Lacticaseibacillus paracasei, Bifidobacterium breve, and Prebiotics on the Growth Stimulation of Beneficial Gut Microbiota.	Kaewarsar E, Chaiyasut C, Lailerd N, Makhamrueang N, Peerajan S, Sirilun S.	Foods	10.3390/foods12203847	2023
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	Identification of Antibacterial Peptide Candidates Encrypted in Stress-Related and Metabolic Saccharomyces cerevisiae Proteins.	Santos MFDS, Freitas CS, Verissimo da Costa GC, Pereira PR, Paschoalin VMF.	Pharmaceuticals (Basel)	10.3390/ph15020163	2022
	Antibacterial and Antioxidant Activities, Toxicity, and Physicochemical Properties of Crassocephalum montuosum (S Moore) Milne-Redh and Crassocephalum picridifolium (DC) S Moore.	Valentin BC, Salvius BA, Jean Baptiste LS.	Adv Pharmacol Pharm Sci	10.1155/adpp/9954073	2024
	Characterization of Functional B-Cell Epitopes at the Amino Terminus of Shigella Invasion Plasmid Antigen B (IpaB).	Li S, Han X, Upadhyay I, Zhang W.	Appl Environ Microbiol	10.1128/aem.00384-22	2022
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	PlyKp104, a Novel Phage Lysin for the Treatment of Klebsiella pneumoniae, Pseudomonas aeruginosa, and Other Gram-Negative ESKAPE Pathogens.	Euler CW, Raz A, Hernandez A, Serrano A, Xu S, Andersson M, Zou G, Zhang Y, Fischetti VA, Li J.	Antimicrob Agents Chemother	10.1128/aac.01519-22	2023
	Detection of Listeria monocytogenes in Food Using the Proofman-LMTIA Assay.	Song C, Wang B, Wang Y, Liu J, Wang D.	Molecules	10.3390/molecules28145457	2023
	Comparison of Gold Biosensor Combined with Light Microscope Imaging System with ELISA for Detecting Salmonella in Chicken after Exposure to Simulated Chilling Condition.	Park MK.	J Microbiol Biotechnol	10.4014/jmb.2212.12011	2023
	Mesoporous Silica Nanoparticles-Enhanced Microarray Technology for Highly Sensitive Simultaneous Detection of Multiplex Foodborne Pathogens.	Hormsombut T, Mekjinda N, Kalasin S, Surareungchai W, Rijiravanich P.	ACS Appl Bio Mater	10.1021/acsabm.4c00005	2024
	Prevalence and determinants of faecal carriage of carbapenem- and third-generation cephalosporin-resistant Enterobacterales: a cross-sectional household survey in northern Vietnam.	van Wijk M, Tran HH, Vu BNT, Tacoli C, Nguyen TCT, Pham QD, Nguyen THT, Nguyen TT, Nguyen HAT, Trinh TS, Pham TD, Tran HKT, Vu DTV, Dang DA, Tran TD, Nguyen DT, van Doorn HR, Kesteman T, Lewycka S.	Lancet Reg Health West Pac	10.1016/j.lanwpc.2024.101281	2025
	Isolation, identification and potential probiotic characterization of lactic acid bacteria from Thai traditional fermented food.	Suwannaphan S.	AIMS Microbiol	10.3934/microbiol.2021026	2021
	LC-HRMS Profiling and Antidiabetic, Antioxidant, and Antibacterial Activities of Acacia catechu (L.f.) Willd.	Aryal B, Adhikari B, Aryal N, Bhattarai BR, Khadayat K, Parajuli N.	Biomed Res Int	10.1155/2021/7588711	2021
	Biosolids as a Source of Antibiotic Resistance Plasmids for Commensal and Pathogenic Bacteria.	Law A, Solano O, Brown CJ, Hunter SS, Fagnan M, Top EM, Stalder T.	Front Microbiol	10.3389/fmicb.2021.606409	2021
	Effect of O-Antigen Chain Length Regulation on the Immunogenicity of Shigella and Salmonella Generalized Modules for Membrane Antigens (GMMA).	Gasperini G, Raso MM, Arato V, Aruta MG, Cescutti P, Necchi F, Micoli F.	Int J Mol Sci	10.3390/ijms22031309	2021
	Volatile Compounds and Antioxidant and Antimicrobial Activities of Selected Citrus Essential Oils Originated from Nepal.	Bhandari DP, Poudel DK, Satyal P, Khadayat K, Dhami S, Aryal D, Chaudhary P, Ghimire A, Parajuli N.	Molecules	10.3390/molecules26216683	2021
	A Combination of Novel Nucleic Acid Cross-Linking Dye and Recombinase-Aided Amplification for the Rapid Detection of Viable Salmonella in Milk.	Feng X, Zhou D, Gan B, Xie G, Xu H.	Foods	10.3390/foods11152375	2022
	Can Nature Overcome Invasive Gastrointestinal Infections?	Duda-Madej A, Viscardi S, Stecko J, Szymanska N, Topola E, Pacyga K, Szandruk-Bender M.	Int J Mol Sci	10.3390/ijms26125795	2025
	Antimicrobial activities of leptospermone isolated from Leptospermum scoparium seeds and structure-activity relationships of its derivatives against foodborne bacteria.	Jeong EY, Lee MJ, Lee HS.	Food Sci Biotechnol	10.1007/s10068-018-0391-4	2018
Metabolism	Antimicrobial activity of Anonna mucosa (Jacq.) grown in vivo and obtained by in vitroculture.	Barboza TJ, Ferreira AF, Ignacio AC, Albarello N.	Braz J Microbiol	10.1590/s1517-838246320140468	2015
	Isolation, Molecular Characterization and Probiotic Potential of Lactic Acid Bacteria in Saudi Raw and Fermented Milk.	Bin Masalam MS, Bahieldin A, Alharbi MG, Al-Masaudi S, Al-Jaouni SK, Harakeh SM, Al-Hindi RR.	Evid Based Complement Alternat Med	10.1155/2018/7970463	2018
	Occurrence of Diarrheagenic Pathogens and Their Coinfection Profiles in Diarrheic Under Five Children and Tracked Human Contacts in Urban and Rural Settings of Eastern Ethiopia.	Belina D, Gobena T, Kebede A, Chimdessa M, Hailu Y, Hald T.	Microbiol Insights	10.1177/11786361231196527	2023
	The Impact of Silver Nanoparticles Produced by Bacillus pumilus As Antimicrobial and Nematicide.	Mahmoud WM, Abdelmoneim TS, Elazzazy AM.	Front Microbiol	10.3389/fmicb.2016.01746	2016
	Design of a Bacteriophage Cocktail Active against Shigella Species and Testing of Its Therapeutic Potential in Galleria mellonella.	Filippov AA, Su W, Sergueev KV, Kevorkian RT, Snesrud EC, Srijan A, He Y, Fouts DE, Lurchachaiwong W, McGann PT, Ellison DW, Swierczewski BE, Nikolich MP.	Antibiotics (Basel)	10.3390/antibiotics11111659	2022
	Probiotics as an Alternative to Antibiotics: Genomic and Physiological Characterization of Aerobic Spore Formers from the Human Intestine.	Vittoria M, Saggese A, Isticato R, Baccigalupi L, Ricca E.	Microorganisms	10.3390/microorganisms11081978	2023
	The Therapeutic Properties of Plants Used Traditionally to Treat Gastrointestinal Disorders on Groote Eylandt, Australia.	Mazerand C, Cock IE.	Evid Based Complement Alternat Med	10.1155/2020/2438491	2020
	Structure-activity relationship of benzophenanthridine alkaloids from Zanthoxylum rhoifolium having antimicrobial activity.	Tavares Lde C, Zanon G, Weber AD, Neto AT, Mostardeiro CP, Da Cruz IB, Oliveira RM, Ilha V, Dalcol II, Morel AF.	PLoS One	10.1371/journal.pone.0097000	2014
	Glechoma curviflora Volatile Oil from Palestine: Chemical Composition and Neuroprotective, Antimicrobial, and Cyclooxygenase Inhibitory Activities.	Al-Maharik N, Jaradat N, Qneibi M, Abualhasan MN, Emwas N.	Evid Based Complement Alternat Med	10.1155/2020/4195272	2020
	Antimicrobial activities of active component isolated from Lawsonia inermis leaves and structure-activity relationships of its analogues against food-borne bacteria.	Yang JY, Lee HS.	J Food Sci Technol	10.1007/s13197-013-1245-y	2015
	From by-products to new application opportunities: the enhancement of the leaves deriving from the fruit plants for new potential healthy products.	Regolo L, Giampieri F, Battino M, Armas Diaz Y, Mezzetti B, Elexpuru-Zabaleta M, Mazas C, Tutusaus K, Mazzoni L.	Front Nutr	10.3389/fnut.2024.1083759	2024
Pathogenicity	Applications of Fruit Polyphenols and Their Functionalized Nanoparticles Against Foodborne Bacteria: A Mini Review.	Kumar H, Bhardwaj K, Cruz-Martins N, Nepovimova E, Oleksak P, Dhanjal DS, Bhardwaj S, Singh R, Chopra C, Verma R, Chauhan PP, Kumar D, Kuca K.	Molecules	10.3390/molecules26113447	2021
	Comparative Genomics and Physiological Characterization of Two Aerobic Spore Formers Isolated from Human Ileal Samples.	Saggese A, Giglio R, D'Anzi N, Baccigalupi L, Ricca E.	Int J Mol Sci	10.3390/ijms232314946	2022
	The Lactobacillus as a Probiotic: Focusing on Liver Diseases.	Jeong JJ, Park HJ, Cha MG, Park E, Won SM, Ganesan R, Gupta H, Gebru YA, Sharma SP, Lee SB, Kwon GH, Jeong MK, Min BH, Hyun JY, Eom JA, Yoon SJ, Choi MR, Kim DJ, Suk KT.	Microorganisms	10.3390/microorganisms10020288	2022
	Development of a novel polymerase spiral reaction (PSR) assay for rapid and visual detection of Clostridium perfringens in meat.	Milton AAP, Momin KM, Ghatak S, Priya GB, Angappan M, Das S, Puro K, Sanjukta RK, Shakuntala I, Sen A, Kandpal BK.	Heliyon	10.1016/j.heliyon.2021.e05941	2021
Metabolism	Efficient biosynthesis of a Cecropin A-melittin mutant in Bacillus subtilis WB700.	Ji S, Li W, Baloch AR, Wang M, Li H, Cao B, Zhang H.	Sci Rep	10.1038/srep40587	2017
Enzymology	Development and evaluation of a rapid and sensitive RPA assay for specific detection of Vibrio parahaemolyticus in seafood.	Geng Y, Tan K, Liu L, Sun XX, Zhao B, Wang J.	BMC Microbiol	10.1186/s12866-019-1562-z	2019
Metabolism	Bioprospecting Antimicrobials from Lactiplantibacillus plantarum: Key Factors Underlying Its Probiotic Action.	Rocchetti MT, Russo P, Capozzi V, Drider D, Spano G, Fiocco D.	Int J Mol Sci	10.3390/ijms222112076	2021
	Development of a recombinase polymerase amplification assay with lateral flow dipstick (RPA-LFD) for rapid detection of Shigella spp. and enteroinvasive Escherichia coli.	Bian Z, Liu W, Jin J, Hao Y, Jiang L, Xie Y, Zhang H.	PLoS One	10.1371/journal.pone.0278869	2022
Genetics	Synthesis, Characterization, and Biologic Activity of New Acyl Hydrazides and 1,3,4-Oxadiazole Derivatives.	Zarafu I, Matei L, Bleotu C, Ionita P, Tatibouet A, Paun A, Nicolau I, Hanganu A, Limban C, Nuta DC, Nemes RM, Diaconu CC, Radulescu C.	Molecules	10.3390/molecules25143308	2020
Pathogenicity	Antimicrobial activities of chicken beta-defensin (4 and 10) peptides against pathogenic bacteria and fungi.	Yacoub HA, Elazzazy AM, Abuzinadah OA, Al-Hejin AM, Mahmoud MM, Harakeh SM.	Front Cell Infect Microbiol	10.3389/fcimb.2015.00036	2015
Phylogeny	16S rRNA gene sequencing on a benchtop sequencer: accuracy for identification of clinically important bacteria.	Watts GS, Youens-Clark K, Slepian MJ, Wolk DM, Oshiro MM, Metzger GS, Dhingra D, Cranmer LD, Hurwitz BL.	J Appl Microbiol	10.1111/jam.13590	2017
	Shigella in Brazilian children with acute diarrhoea: prevalence, antimicrobial resistance and virulence genes.	Sousa MA, Mendes EN, Collares GB, Peret-Filho LA, Penna FJ, Magalhaes PP.	Mem Inst Oswaldo Cruz	10.1590/s0074-02762013000100005	2013
Pathogenicity	A thermostable Salmonella phage endolysin, Lys68, with broad bactericidal properties against gram-negative pathogens in presence of weak acids.	Oliveira H, Thiagarajan V, Walmagh M, Sillankorva S, Lavigne R, Neves-Petersen MT, Kluskens LD, Azeredo J.	PLoS One	10.1371/journal.pone.0108376	2014
	A selective antibiotic for Lyme disease.	Leimer N, Wu X, Imai Y, Morrissette M, Pitt N, Favre-Godal Q, Iinishi A, Jain S, Caboni M, Leus IV, Bonifay V, Niles S, Bargabos R, Ghiglieri M, Corsetti R, Krumpoch M, Fox G, Son S, Klepacki D, Polikanov YS, Freliech CA, McCarthy JE, Edmondson DG, Norris SJ, D'Onofrio A, Hu LT, Zgurskaya HI, Lewis K.	Cell	10.1016/j.cell.2021.09.011	2021
	Incidence of Campylobacter concisus and C. ureolyticus in traveler's diarrhea cases and asymptomatic controls in Nepal and Thailand.	Serichantalergs O, Ruekit S, Pandey P, Anuras S, Mason C, Bodhidatta L, Swierczewski B.	Gut Pathog	10.1186/s13099-017-0197-6	2017
	Chemical Composition, Antibacterial Activity, and Antibiotic Potentiation of Boswellia sacra Flueck. Oleoresin Extracts from the Dhofar Region of Oman.	Rashan L, White A, Haulet M, Favelin N, Das P, Cock IE.	Evid Based Complement Alternat Med	10.1155/2021/9918935	2021
Enzymology	Pentaplex PCR assay for detection of hemorrhagic bacteria from stool samples.	Al-Talib H, Latif B, Mohd-Zain Z.	J Clin Microbiol	10.1128/jcm.00891-14	2014
	Inhibitory Effect of Substances Produced by Native Lactococcus lactis Strains of Tropical Fruits towards Food Pathogens.	Tenea GN, Hurtado P, Ortega C.	Prev Nutr Food Sci	10.3746/pnf.2018.23.3.260	2018
Enzymology	Three-hour molecular detection of Campylobacter, Salmonella, Yersinia, and Shigella species in feces with accuracy as high as that of culture.	Cunningham SA, Sloan LM, Nyre LM, Vetter EA, Mandrekar J, Patel R.	J Clin Microbiol	10.1128/jcm.00339-10	2010
	Silver nanoparticles synthesis mediated by new isolates of Bacillus spp., nanoparticle characterization and their activity against Bean Yellow Mosaic Virus and human pathogens.	Elbeshehy EK, Elazzazy AM, Aggelis G.	Front Microbiol	10.3389/fmicb.2015.00453	2015
	In Silico Analysis of the cadF Gene and Development of a Duplex Polymerase Chain Reaction for Species-Specific Identification of Campylobacter jejuni and Campylobacter coli.	Shams S, Bakhshi B, Tohidi Moghadam T.	Jundishapur J Microbiol	10.5812/jjm.29645	2016
	Characterization of the Three New Kayviruses and Their Lytic Activity Against Multidrug-Resistant Staphylococcus aureus.	Lubowska N, Grygorcewicz B, Kosznik-Kwasnicka K, Zauszkiewicz-Pawlak A, Wegrzyn A, Dolegowska B, Piechowicz L.	Microorganisms	10.3390/microorganisms7100471	2019
Pathogenicity	A new antibiotic selectively kills Gram-negative pathogens.	Imai Y, Meyer KJ, Iinishi A, Favre-Godal Q, Green R, Manuse S, Caboni M, Mori M, Niles S, Ghiglieri M, Honrao C, Ma X, Guo JJ, Makriyannis A, Linares-Otoya L, Bohringer N, Wuisan ZG, Kaur H, Wu R, Mateus A, Typas A, Savitski MM, Espinoza JL, O'Rourke A, Nelson KE, Hiller S, Noinaj N, Schaberle TF, D'Onofrio A, Lewis K.	Nature	10.1038/s41586-019-1791-1	2019
	Probiotic potential of Lactobacillus strains with antimicrobial activity against some human pathogenic strains.	Shokryazdan P, Sieo CC, Kalavathy R, Liang JB, Alitheen NB, Faseleh Jahromi M, Ho YW.	Biomed Res Int	10.1155/2014/927268	2014
	Genistein in 1:1 inclusion complexes with ramified cyclodextrins: theoretical, physicochemical and biological evaluation.	Danciu C, Soica C, Oltean M, Avram S, Borcan F, Csanyi E, Ambrus R, Zupko I, Muntean D, Dehelean CA, Craina M, Popovici RA.	Int J Mol Sci	10.3390/ijms15021962	2014
Enzymology	A pentaplex PCR assay for the rapid detection of methicillin-resistant Staphylococcus aureus and Panton-Valentine Leucocidin.	Al-Talib H, Yean CY, Al-Khateeb A, Hassan H, Singh KK, Al-Jashamy K, Ravichandran M.	BMC Microbiol	10.1186/1471-2180-9-113	2009
Enzymology	Evaluation of microplate immunocapture method for detection of Vibrio cholerae, Salmonella Typhi and Shigella flexneri from food.	Fakruddin M, Hossain MN, Ahmed MM.	BMC Microbiol	10.1186/s12866-017-1099-y	2017
Enzymology	Development of a Flow Cytometry-Based Method for Rapid Detection of Escherichia coli and Shigella Spp. Using an Oligonucleotide Probe.	Xue Y, Wilkes JG, Moskal TJ, Williams AJ, Cooper WM, Nayak R, Rafii F, Buzatu DA.	PLoS One	10.1371/journal.pone.0150038	2016
	Usefulness of ribotyping in a molecular epidemiology study of shigellosis.	Mendoza MC, Martin MC, Gonzalez-Hevia MA.	Epidemiol Infect	10.1017/s0950268800052353	1996
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
Phylogeny	Distribution of indigenous bacterial pathogens and potential pathogens associated with roof-harvested rainwater.	Dobrowsky PH, De Kwaadsteniet M, Cloete TE, Khan W.	Appl Environ Microbiol	10.1128/aem.04130-13	2014
	A Novel Assay for Detection of Methicillin-Resistant Staphylococcus aureus Directly From Clinical Samples.	McClure JA, Conly JM, Obasuyi O, Ward L, Ugarte-Torres A, Louie T, Zhang K.	Front Microbiol	10.3389/fmicb.2020.01295	2020
	Rapid PCR Detection of Mycoplasma hominis, Ureaplasma urealyticum, and Ureaplasma parvum.	Cunningham SA, Mandrekar JN, Rosenblatt JE, Patel R.	Int J Bacteriol	10.1155/2013/168742	2013
	Computational identification of a systemic antibiotic for gram-negative bacteria.	Miller RD, Iinishi A, Modaresi SM, Yoo BK, Curtis TD, Lariviere PJ, Liang L, Son S, Nicolau S, Bargabos R, Morrissette M, Gates MF, Pitt N, Jakob RP, Rath P, Maier T, Malyutin AG, Kaiser JT, Niles S, Karavas B, Ghiglieri M, Bowman SEJ, Rees DC, Hiller S, Lewis K.	Nat Microbiol	10.1038/s41564-022-01227-4	2022
Enzymology	Rapid and sensitive detection of Shiga toxin-producing Escherichia coli from nonenriched stool specimens by real-time PCR in comparison to enzyme immunoassay and culture.	Grys TE, Sloan LM, Rosenblatt JE, Patel R.	J Clin Microbiol	10.1128/jcm.02013-08	2009
Enzymology	Evaluation and implementation of a chromogenic agar medium for salmonella detection in stool in routine laboratory diagnostics.	van Dijk S, Bruins MJ, Ruijs GJ.	J Clin Microbiol	10.1128/jcm.01643-08	2009
Enzymology	Rapid detection and simultaneous genotyping of Cronobacter spp. (formerly Enterobacter sakazakii) in powdered infant formula using real-time PCR and high resolution melting (HRM) analysis.	Cai XQ, Yu HQ, Ruan ZX, Yang LL, Bai JS, Qiu DY, Jian ZH, Xiao YQ, Yang JY, Le TH, Zhu XQ.	PLoS One	10.1371/journal.pone.0067082	2013
Pathogenicity	Bactericidal and antiendotoxic properties of short cationic peptides derived from a snake venom Lys49 phospholipase A2.	Santamaria C, Larios S, Quiros S, Pizarro-Cerda J, Gorvel JP, Lomonte B, Moreno E.	Antimicrob Agents Chemother	10.1128/aac.49.4.1340-1345.2005	2005
Phylogeny	Phylogenetic analysis of Salmonella, Shigella, and Escherichia coli strains on the basis of the gyrB gene sequence.	Fukushima M, Kakinuma K, Kawaguchi R.	J Clin Microbiol	10.1128/jcm.40.8.2779-2785.2002	2002
	Non-Antibiotics Strategies to Control Salmonella Infection in Poultry.	Ruvalcaba-Gomez JM, Villagran Z, Valdez-Alarcon JJ, Martinez-Nunez M, Gomez-Godinez LJ, Ruesga-Gutierrez E, Anaya-Esparza LM, Arteaga-Garibay RI, Villarruel-Lopez A.	Animals (Basel)	10.3390/ani12010102	2022
Phylogeny	Performances of VITEK 2 colorimetric cards for identification of gram-positive and gram-negative bacteria.	Wallet F, Loiez C, Renaux E, Lemaitre N, Courcol RJ.	J Clin Microbiol	10.1128/jcm.43.9.4402-4406.2005	2005
Enzymology	Comparison of five PCR methods for detection of Helicobacter pylori DNA in gastric tissues.	Lu JJ, Perng CL, Shyu RY, Chen CH, Lou Q, Chong SK, Lee CH.	J Clin Microbiol	10.1128/jcm.37.3.772-774.1999	1999
	Evaluation of antibodies reactive with Campylobacter jejuni in Egyptian diarrhea patients.	Ismail TF, Wasfy MO, Oyofo BA, Mansour MM, El-Berry HM, Churilla AM, Eldin SS, Peruski LF.	Clin Diagn Lab Immunol	10.1128/cdli.4.5.536-539.1997	1997
Phylogeny	Streptococcus iniae, a human and animal pathogen: specific identification by the chaperonin 60 gene identification method.	Goh SH, Driedger D, Gillett S, Low DE, Hemmingsen SM, Amos M, Chan D, Lovgren M, Willey BM, Shaw C, Smith JA.	J Clin Microbiol	10.1128/jcm.36.7.2164-2166.1998	1998
Phylogeny	Multiplex PCR for detection of the Vibrio genus and five pathogenic Vibrio species with primer sets designed using comparative genomics.	Kim HJ, Ryu JO, Lee SY, Kim ES, Kim HY.	BMC Microbiol	10.1186/s12866-015-0577-3	2015
Enzymology	Enterohepatic helicobacter in ulcerative colitis: potential pathogenic entities?	Thomson JM, Hansen R, Berry SH, Hope ME, Murray GI, Mukhopadhya I, McLean MH, Shen Z, Fox JG, El-Omar E, Hold GL.	PLoS One	10.1371/journal.pone.0017184	2011
Enzymology	Detection of Campylobacter species and Arcobacter butzleri in stool samples by use of real-time multiplex PCR.	de Boer RF, Ott A, Guren P, van Zanten E, van Belkum A, Kooistra-Smid AM.	J Clin Microbiol	10.1128/jcm.01716-12	2013
Enzymology	Evaluation of the VITEK 2 system for rapid identification of medically relevant gram-negative rods.	Funke G, Monnet D, deBernardis C, von Graevenitz A, Freney J.	J Clin Microbiol	10.1128/jcm.36.7.1948-1952.1998	1998
Pathogenicity	Susceptibility to antibiotics in urinary tract infections in a secondary care setting from 2005-2006 and 2010-2011, in São Paulo, Brazil: data from 11,943 urine cultures.	Miranda EJ, Oliveira GS, Roque FL, Santos SR, Olmos RD, Lotufo PA.	Rev Inst Med Trop Sao Paulo	10.1590/s0036-46652014000400009	2014
Enzymology	Development of a toxR-based loop-mediated isothermal amplification assay for detecting Vibrio parahaemolyticus.	Chen S, Ge B.	BMC Microbiol	10.1186/1471-2180-10-41	2010
Enzymology	Comparison of conventional, nested, and real-time quantitative PCR for diagnosis of scrub typhus.	Kim DM, Park G, Kim HS, Lee JY, Neupane GP, Graves S, Stenos J.	J Clin Microbiol	10.1128/jcm.01216-09	2011
Metabolism	The type VI secretion system encoded in Salmonella pathogenicity island 19 is required for Salmonella enterica serotype Gallinarum survival within infected macrophages.	Blondel CJ, Jimenez JC, Leiva LE, Alvarez SA, Pinto BI, Contreras F, Pezoa D, Santiviago CA, Contreras I.	Infect Immun	10.1128/iai.01165-12	2013
Phylogeny	Detection and identification of Mycobacterium species isolates by DNA microarray.	Fukushima M, Kakinuma K, Hayashi H, Nagai H, Ito K, Kawaguchi R.	J Clin Microbiol	10.1128/jcm.41.6.2605-2615.2003	2003
Phylogeny	Detection and genotyping of Mycobacterium species from clinical isolates and specimens by oligonucleotide array.	Park H, Jang H, Song E, Chang CL, Lee M, Jeong S, Park J, Kang B, Kim C.	J Clin Microbiol	10.1128/jcm.43.4.1782-1788.2005	2005
Metabolism	Rapid detection of viable salmonellae in produce by coupling propidium monoazide with loop-mediated isothermal amplification.	Chen S, Wang F, Beaulieu JC, Stein RE, Ge B.	Appl Environ Microbiol	10.1128/aem.00354-11	2011
Enzymology	tir- and stx-positive Escherichia coli in stream waters in a metropolitan area.	Higgins JA, Belt KT, Karns JS, Russell-Anelli J, Shelton DR.	Appl Environ Microbiol	10.1128/aem.71.5.2511-2519.2005	2005
Enzymology	Direct detection of verotoxin-producing Escherichia coli in stool samples by PCR.	Ramotar K, Waldhart B, Church D, Szumski R, Louie TJ.	J Clin Microbiol	10.1128/jcm.33.3.519-524.1995	1995
Enzymology	Detection of coliform bacteria in water by polymerase chain reaction and gene probes.	Bej AK, Steffan RJ, DiCesare J, Haff L, Atlas RM.	Appl Environ Microbiol	10.1128/aem.56.2.307-314.1990	1990
Pathogenicity	Functional characterization and evaluation of in vitro protective efficacy of murine monoclonal antibodies BURK24 and BURK37 against Burkholderia pseudomallei.	Peddayelachagiri BV, Paul S, Makam SS, Urs RM, Kingston JJ, Tuteja U, Sripathy MH, Batra HV.	PLoS One	10.1371/journal.pone.0090930	2014
Phylogeny	Evaluation of the Biolog automated microbial identification system.	Klingler JM, Stowe RP, Obenhuber DC, Groves TO, Mishra SK, Pierson DL.	Appl Environ Microbiol	10.1128/aem.58.6.2089-2092.1992	1992
Pathogenicity	Antibacterial activities of erythromycins A, B, C, and D and some of their derivatives.	Kibwage IO, Hoogmartens J, Roets E, Vanderhaeghe H, Verbist L, Dubost M, Pascal C, Petitjean P, Levol G.	Antimicrob Agents Chemother	10.1128/aac.28.5.630	1985
Enzymology	Adherent and invasive Escherichia coli is associated with granulomatous colitis in boxer dogs.	Simpson KW, Dogan B, Rishniw M, Goldstein RE, Klaessig S, McDonough PL, German AJ, Yates RM, Russell DG, Johnson SE, Berg DE, Harel J, Bruant G, McDonough SP, Schukken YH.	Infect Immun	10.1128/iai.00067-06	2006
Pathogenicity	Cytochalasin-induced actin disruption of polarized enterocytes can augment internalization of bacteria.	Wells CL, van de Westerlo EM, Jechorek RP, Haines HM, Erlandsen SL.	Infect Immun	10.1128/iai.66.6.2410-2419.1998	1998
	Characterization of murine monoclonal antibodies against serogroup B salmonellae and application as serotyping reagents.	Tsang RS, Chan KH, Lau NW, Choi DK, Law DK, Ng MH.	J Clin Microbiol	10.1128/jcm.29.9.1899-1903.1991	1991
	Quantitation of pneumococcal C polysaccharide in sputum samples from patients with presumptive pneumococcal pneumonia by enzyme immunoassay.	Parkinson AJ, Rabiego ME, Sepulveda C, Davidson M, Johnson C.	J Clin Microbiol	10.1128/jcm.30.2.318-322.1992	1992
Phylogeny	Identification of Staphylococcus species and subspecies by the chaperonin 60 gene identification method and reverse checkerboard hybridization.	Goh SH, Santucci Z, Kloos WE, Faltyn M, George CG, Driedger D, Hemmingsen SM.	J Clin Microbiol	10.1128/jcm.35.12.3116-3121.1997	1997
Metabolism	Jenseniin G, a heat-stable bacteriocin produced by Propionibacterium jensenii P126.	Grinstead DA, Barefoot SF.	Appl Environ Microbiol	10.1128/aem.58.1.215-220.1992	1992
Enzymology	Comparison of Crystal Enteric/Nonfermenter system, API 20E system, and Vitek AutoMicrobic system for identification of gram-negative bacilli.	Robinson A, McCarter YS, Tetreault J.	J Clin Microbiol	10.1128/jcm.33.2.364-370.1995	1995
	Rat monoclonal antibodies against Aspergillus galactomannan.	Stynen D, Sarfati J, Goris A, Prevost MC, Lesourd M, Kamphuis H, Darras V, Latge JP.	Infect Immun	10.1128/iai.60.6.2237-2245.1992	1992
	Probiotic Effects and Metabolic Products of Enterococcus faecalis LD33 with Respiration Capacity.	Jiao Y, Yang H, Shigwedha N, Zhang S, Liu F, Zhang L	Foods	10.3390/foods11040606	2022
Phylogeny	Selective Thermotolerant Lactic Acid Bacteria Isolated From Fermented Juice of Epiphytic Lactic Acid Bacteria and Their Effects on Fermentation Quality of Stylo Silages.	Pitiwittayakul N, Bureenok S, Schonewille JT	Front Microbiol	10.3389/fmicb.2021.673946	2021
Pathogenicity	Screening of the Dichloromethane: Methanolic Extract of Centella asiatica for Antibacterial Activities against Salmonella typhi, Escherichia coli, Shigella sonnei, Bacillus subtilis, and Staphylococcus aureus.	Sieberi BM, Omwenga GI, Wambua RK, Samoei JC, Ngugi MP	ScientificWorldJournal	10.1155/2020/6378712	2020
Pathogenicity	Anti-adhesion of probiotic Enterococcus faecium WEFA23 against five pathogens and the beneficial effect of its S-layer proteins against Listeria monocytogenes.	He Y, Xu X, Zhang F, Xu D, Liu Z, Tao X, Wei H	Can J Microbiol	10.1139/cjm-2018-0031	2018
Pathogenicity	Evaluation of probiotic properties of Lactobacillus plantarum WLPL04 isolated from human breast milk.	Jiang M, Zhang F, Wan C, Xiong Y, Shah NP, Wei H, Tao X	J Dairy Sci	10.3168/jds.2015-10434	2016
Pathogenicity	Study of probiotic potential of four wild Lactobacillus rhamnosus strains.	Tuo Y, Zhang W, Zhang L, Ai L, Zhang Y, Han X, Yi H	Anaerobe	10.1016/j.anaerobe.2013.03.007	2013
	Antibacterial Mechanism of Eugenol Against Shigella sonnei and Its Antibacterial Application in Lettuce Juice.	Su R, Bai X, Liu X, Song L, Liu X, Zhan X, Guo D, Wang Y, Chang Y, Shi C	Foodborne Pathog Dis	10.1089/fpd.2022.0046	2022

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 )
#35641	Collection of Institut Pasteur ; Curators of the CIP; CIP 104223
#50969	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 32351
#68368	Automatically annotated from API 20E .
#68382	Automatically annotated from API zym .
#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 (CIP 104223, ATCC 25931, CCUG 32351)

Name and taxonomic classification