Genetic diversity, virulence factors and drug resistance of Pantoea strains isolated from samples of fresh fruits, vegetables and soil

Journal of Veterinary Research

Volume 69 (2025): Issue 3 (September 2025)

By:

Ewelina Farian

, Katarzyna Kowalczyk

, Teresa Kłapeć

, Jacek Sroka

, Piotr Skowron

, Grzegorz Siebielec

, Tamara Jadczyszyn

, Jolanta Małgorzata Zdybel

, Tomasz Cencek

and Angelina Wójcik-Fatla

Open Access

|Sep 2025

Figures & Tables

Phylogenetic tree based on the partial 16S rRNA gene sequences of Pantoea strains isolated from food and soil

The activity of hydrolytic enzymes of Pantoea strains isolated from food and soil

Primers used in the study for molecular identification and assessment of virulence and drug resistance

	Primer	Target gene	Sequence (5′→3′)	Product size (bp)	Reference
For molecular identification	infB-01_FinfB-02_R	infB	ATYATGGGHCAYGTHGAYCAACKGAGTARTAACGCAGATCCA	1,124	(44)
	PANsp_atpD_FPANsp_atpD_F	atpD	GAGGGTAACGACTTCTACCACCTGTACGGAGGTGATTGAAC	330
	PANAG_infB_FPANAG_infB_R	infB	TGTCCGGCGTGCCGGCTGCCAACGCGAACGTCGTTGT	730
	PANAN_gyrB_FPANAN_gyrB_R	gyrB	GATGACGARGCCATGCTGCGATCTTGCGGTATTCGCCAC	423	(28)
	PANST_rpoB_FPANST rpoB_R	rpoB	CACCGGTGAACTGATTATCGGTCCTGAGGCATCAATGTGT	539
	16S_27F16S907	16S rRNA	AGAGTTTGATCMTGGCTCAGCCCCGTCAATTCMTTTRAGTTT	920
	p27_Fpl525_R	16S rRNA	AGAGTTTGATCMTGGCTCAGAAGGAGGTGWTCCARCC	1,450	(30)
For virulence gene detection	acrA_FacrA_R	acrA	CTCTCAGGCAGCTTAGCCCTAATGCAGAGGTTCAGTTTTGACTGTT	106	(31)
	acrB_FacrB_R	acrB	GGTCGATTCCGTTCTCCGTTACTACCTGGAAGTAAACGTCATTGGT	104	(31)
	hcp_Fhcp_R	hcp	TGTAAACCAGCGCCATCAGTACCGGTAATGCACAGCTGAA	1,301	(22)
	vgrG_FvgrG_R	vgrG	TGAATCCGCTTGCTTCCTGTATATCGCCCATGCGTTCCAT	1,011	(22)
For antimicrobial resistance gene detection	MOXM_FMOXM_RCITM_FCITM_R	MOX-1, MOX-2, CMY-1, CMY-8-CMY-11, LAT-1-LAT-4, CMY-2-CMY-7, BIL-1	GCTGCTCAAGGAGCACAGGATCACATTGACATAGGTGTGGTGCTGGCCAGAACTGACAGGCAAATTTCTCCTGAACGTGGCTGGC	520462
	DHAM_FDHAM_R	DHA-1, DHA-2	AACTTTCACAGGTGTGCTGGGTCCGTACGCATACTGGCTTTGC	405	(37)
	ACCM_FACCM_R	ACC	AACAGCCTCAGCAGCCGGTTATTCGCCGCAATCATCCCTAGC	346
	EBCM_FEBCM_R	MIR-1T, ACT-1	TCGGTAAAGCCGATGTTGCGGCTTCCACTGCGGCTGCCAGTT	302
	FOXM_FFOXM_R	FOX-1-FOX-5b	AACATGGGGTATCAGGGAGATGCAAAGCGCGTAACCGGATTGG	190
	SHV_FSHV_R	SHV	CACTCAAGGATGTATTGTG TTAGCGTTGCCAGTGCTCG	885	(26)
	TEM-1_FTEM-1 R	TEM	AAGCCATACCAAACGACGAGATTGTTGCCGGGAAGCTAGA	108	(27)

Results of biochemical and molecular identification of Pantoea strains isolated from food and soil

Strain No.	Sample type	Biochemical identification	Molecular identification						Sequence match
Strain No.	Sample type	Biochemical identification	infB (Panyoea spp.)	infB (P. agglomerans)	gyrB (P. ananatis)	rpoB (P. stewartii)	atpD (Pantoea spp.)	16S (Eubacteria)	Sequence match
1S	strawberry	P. agglomerans	+	+	–	–	+	+	P. agglomerans
2S	raspberry	Pantoea spp.	+	+	–	–	+	+	P. agglomerans
3S	lettuce	Pantoea spp.	+	+	–	–	+	+	P. agglomerans
4S	spinach	P. agglomerans	+	+	–	–	+	+	P. agglomerans
5S	baby spinach	Pantoea spp.	+	+	–	–	+	+	P. agglomerans
6S	arugula	Pantoea spp.	+	+	–	–	+	+	P. agglomerans
7S	onion	P. agglomerans	+	+	–	–	+	+	P. agglomerans
8S	baby spinach	Pantoea spp.	–	–	–	–	+	+	P. eucalypti
9S	iceberg lettuce	Pantoea spp.	+	–	–	–	+	+	P. conspicua
10S	lam’s lettuce	Pantoea spp.	+	+	–	–	+	+	P. agglomerans
11S	soil	Pantoea spp.	+	+	–	–	+	+	P. agglomerans
12S	soil	Pantoea spp.	+	+	–	–	+	+	P. agglomerans
13S	soil	Pantoea spp.	–	+	–	–	+	+	P. agglomerans
14S	soil	Pantoea spp.	+	+	–	–	+	+	P. agglomerans
15S	soil	P. agglomerans	+	+	–	–	+	+	P. agglomerans
16S	soil	Pantoea spp.	+	+	–	–	+	+	P. agglomerans
17S	soil	Pantoea spp.	+	+	–	–	+	+	P. agglomerans
18S	soil	Pantoea spp.	+	+	–	–	+	+	P. agglomerans
19S	soil	Pantoea spp.	+	+	–	–	+	+	P. agglomerans
20S	soil	Pantoea spp.	+	+	–	–	+	+	P. agglomerans
21S	soil	P. agglomerans	+	+	–	–	+	+	P. agglomerans
22S	soil	Pantoea spp.	+	+	–	–	+	+	P. agglomerans
23S	soil	P. agglomerans	+	+	–	–	+	+	P. agglomerans
24S	soil	Pantoea spp.	+	+	–	–	+	+	P. agglomerans
25S	leek	P. ananatis	+	–	+	–	–	+	P. ananatis
26S	radish	P. agglomerans	+	+	–	–	+	+	P. agglomerans
27S	broccoli	Pantoea spp.	–	–	–	–	+	+	P. vagans
28S	soil	Pantoea spp.	+	+	–	–	+	+	P. agglomerans
29S	soil	Pantoea spp.	–	–	–	–	+	+	P. vagans
30S	leek	P. ananatis	+	–	+	–	–	+	Pantoea sp.

Occurrence of virulence and drug resistance genes in Pantoea strains

Species (strain No.)	Sample type	Virulence factor				Drug resistance gene
Species (strain No.)	Sample type	acrA	acrB	vgrG	hcp	TEM	FOX	SHV	MOX	CIT	DHA	ACC	EBC
P. agglomerans (26S)	radish	–	–	+	+	+	+	–	–	–	–	–	–
P. agglomerans (1S)	raspberry	–	–	–	+	+	+	–	–	–	–	–	–
P. agglomerans (6S)	arugula	–	–	–	+	+	+	–	–	–	–	–	–
P. agglomerans (10S)	lamb’s lettuce	–	–	–	+	+	+	–	–	–	–	–	–
P. agglomerans (13S)	soil	–	–	–	+	+	+	–	–	–	–	–	–
P. agglomerans (17S)	soil	–	–	–	+	+	+	–	–	–	–	–	–
P. agglomerans (20S)	soil	–	–	–	+	+	+	–	–	–	–	–	–
P. agglomerans (21S)	soil	–	–	–	+	+	+	–	–	–	–	–	–
P. agglomerans (23S)	soil	–	–	–	+	+	+	–	–	–	–	–	–
P. agglomerans (28S)	soil	–	–	–	+	+	+	–	–	–	–	–	–
P. vagans (29S)	soil	–	–	–	+	+	+	–	–	–	–	–	–
P. agglomerans (22S)	soil	–	–	–	+	+	–	+	–	–	–	–	–
P. agglomerans (3S)	lettuce	–	–	–	+	–	–	–	–	–	–	–	–
P. agglomerans (12S)	soil	–	–	–	+	+	–	–	–	–	–	–	–
P. ananatis (25S)	leek	–	–	–	+	+	–	–	–	–	–	–	–
P. vagans (27S)	broccoli	–	–	–	+	+	–	–	–	–	–	–	–
P. ananatis (30S)	leek	–	–	–	+	+	–	–	–	–	–	–	–
P. agglomerans (4S)	spinach	–	–	–	–	+	+	–	–	–	–	–	–
P. agglomerans (5S)	baby spinach	–	–	–	–	+	+	–	–	–	–	–	–
P. eucalypti (8S)	baby spinach	–	–	–	–	+	+	–	–	–	–	–	–
P. agglomerans (11S)	soil	–	–	–	–	+	+	–	–	–	–	–	–
P. agglomerans (15S)	soil	–	–	–	–	+	+	–	–	–	–	–	–
P. agglomerans (18S)	soil	–	–	–	–	+	+	–	–	–	–	–	–
P. agglomerans (7S)	onion	–	–	–	–	+	–	+	–	–	–	–	–
P. conspicua (9S)	iceberg lettuce	–	–	–	–	+	–	+	–	–	–	–	–
P. agglomerans (2S)	raspberry	–	–	–	–	–	+	–	–	–	–	–	–
P. agglomerans (16S)	soil	–	–	–	–	–	+	–	–	–	–	–	–
P. agglomerans (19S)	soil	–	–	–	–	–	+	–	–	–	–	–	–
P. agglomerans (24S)	soil	–	–	–	–	–	+	–	–	–	–	–	–
P. agglomerans (14S)	soil	–	–	–	–	+	–	–	–	–	–	–	–

Reaction mixtures and conditions of PCR reactions performed in the study

Gene(s)	Total volume	PCR reaction mixture	Initial denaturation (temp./duration)	Denaturation, annealing, extension (temp./duration)	Number of cycles	Final extension (temp./duration)
Gene(s)	Total volume	Reagents	Initial denaturation (temp./duration)	Denaturation, annealing, extension (temp./duration)	Number of cycles	Final extension (temp./duration)
infB¹	25 μL	0.3 μL Taq DNA Polymerase (5U/μL)^a2.5 μL 10× PCR buffer with 15 mM MgCl₂^b2.5 μL 2 mM dNTPs^c1 μL 10 pmol of each primer^d2.5 μL DNA template15.2 μL nuclease-free water^e	95°C/5 min	94°C/45 s55°C/1 min72°C/1.5 min	30	72°C/7 min
atpD, infB, gyrB, rpoB, 16S rRNA²	25 μL	0.2 μL Taq DNA Polymerase (5U/μL)2.5 μL 10× PCR buffer with 15 mM MgCl₂2.5 μL 2 mM dNTPs0.5 μL DNA template12.8 μL nuclease-free water	94°C/3 min	94°C/3 min94°C/30 s58°C/30 s72°C/2 min	30	72°C/10 min
16S rRNA¹	50 μL	0.3 μL Taq DNA Polymerase (5U/μL)5 μL 10× PCR buffer with 15 mM MgCl₂5 μL 2 mM dNTPs2 μL 10 pmol of each primer5 μL DNA template30.7 μL nuclease-free water	94°C/2 min	94°C/1 min55°C/1 min72°C/3 min	25	72°C/10 min
acrA or acrB¹	20 μL	0.16 μL Taq DNA Polymerase (5U/μL)2.5 μL 10× PCR buffer with 15 mM MgCl₂2.5 μL 2 mM dNTPs0.5 μL 10 pmol of each primer2 μL DNA template12.34 μL nuclease-free water	95°C/5 min	95°C/30 s 56°C/30 s(acrA) and 55°C/30 s (acrB) 72°C/2 min	30	72°C/10 min
hcp or vgrG¹ESβLgenes¹	25 μL	0.2 μL Taq DNA Polymerase (5U/μL)2.5 μL 10× PCR buffer with 15 mM MgCl₂2.5 μL 2 mM dNTPs1 μL 10 pmol of each primer2 μL DNA template15.8 μL nuclease-free water	95°C/5 min96°C/1 min	95°C/30 s55°C/30 s72°C/2 min94°C/1 min50°C/1 min72°C/2 min	2535	72°C/10 min72°C/10 min
AmpCgenes²	25 μL	0.2 μL Taq DNA Polymerase (5U/μL)2.5 μL 10× PCR buffer with 15 mM MgCl₂2.5 μL 2 mM dNTPs1 μL 10 pmol of each primer2 μL DNA template5.8 μL nuclease-free water	94°C/3 min	94°C/30 s64°C/30 s72°C/1 min	25	72°C/10 min

DOI: https://doi.org/10.2478/jvetres-2025-0047 | Journal eISSN: 2450-8608

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Language: English

Page range: 477 - 488

Submitted on: Jun 10, 2025

Accepted on: Sep 3, 2025

Published on: Sep 13, 2025

Published by: National Veterinary Research Institute in Pulawy

In partnership with: Paradigm Publishing Services

Publication frequency: 4 times per year

Keywords:

ecological niche bacteria,

facultative pathogen,

food,

plant pathogen

Related subjects:

Life sciences,

Molecular biology,

Microbiology and virology,

Life sciences, other,

Medicine,

Veterinary medicine

© 2025 Ewelina Farian, Katarzyna Kowalczyk, Teresa Kłapeć, Jacek Sroka, Piotr Skowron, Grzegorz Siebielec, Tamara Jadczyszyn, Jolanta Małgorzata Zdybel, Tomasz Cencek, Angelina Wójcik-Fatla, published by National Veterinary Research Institute in Pulawy
This work is licensed under the Creative Commons Attribution 4.0 License.

Previous article Volume 69 (2025): Issue 3 (September 2025)

Genetic diversity, virulence factors and drug resistance of Pantoea strains isolated from samples of fresh fruits, vegetables and soil

Figures & Tables

Fig. 1.

Fig. 2.

Primers used in the study for molecular identification and assessment of virulence and drug resistance

Results of biochemical and molecular identification of Pantoea strains isolated from food and soil

Occurrence of virulence and drug resistance genes in Pantoea strains

Reaction mixtures and conditions of PCR reactions performed in the study

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