Genotyping and antibiotic resistance properties of Helicobacter pylori strains isolated from human and animal gastric biopsies

Figures & data

Table 1 PCR primers and PCR conditions used for genotypes of H. pylori strains in this study

Genes^*	Primer sequence (5'-3')^*	Size of product (bp)^*	Annealing
sla	F: CTCTCGCTTTAGTAGGAGC R: CTGCTTGAATGCGCCAAAC	213	64
slb	F: AGCGCCATACCGCAAGAG R: CTGCTTGAATGCGCCAAAC	187	64
slc	F: CTCTCGCTTTAGTGGGGYT R: CTGCTTGAATGCGCCAAAC	213	64
s2	F: GCTAACACGCCAAATGATCC0 R: CTGCTTGAATGCGCCAAAC	199	64
mla	F: GGTCAAAATGCGGTCATGG R: CCATTGGTACCTGTAGAAAC	290	65
mlb	F: GGCCCCAATGCAGTCATGGA R: GCTGTTAGTGCCTAAAGAAGCAT	291	65
m2	F: GGAGCCCCAGGAAACATTG R: CATAACTAGCGCCTTGCA	352	62
cagA	F: GATAACAGCCAAGCTTTTGAGG R: CTGCAAAAGATTGTTTGGCAGA	300	56
iceAl	F: GTGTTTTTAACCAAAGTATC R: CTATAGCCASTYTCTTTGCA	247	56
iceA2	F: GTTGGGTATATCACAATTTAT R: TTRCCCTAIIIICTAGTAGGT	299/334	53
oipA	F: GTTTTTGATGCATGGGATTT R:GTGCATCTCTTATGGCTTT	401	55
cagE	F: TTGAAAACTTCAAGGATAGGATAGAGC R: GCCTAGCGTAATATCACCATTACCC	508	54
BabA2	F: CCAAACGAAACAAAAAGCGT R: GCTTGTGTAAAAGCCGTCGT	271	55

Notes: *Table adapted from Ranjbar R, Khamesipour F, Jonaidi-Jafari N, Rahimi E. Helicobacter pylori in bottled mineral water: genotyping and antimicrobial resistance properties. BMC Microbiol. 2016;16:1–10. © Ranjbar et al 2016.⁴⁶

Figure 1 Prevalence of H. pylori infection determined by diagnostic tests.

Table 2 Prevalence of H. pylori infection in patients (adult humans and children)

Type of samples (no. of positive)	Prevalence of H. pylori(%)
	Gastric ulcers	Duodenal ulcers	Gastric cancer	Chronic gastritis	Chronic cancer
Adult humans (507)	71 (10.1)	107 (15.2)	4 (0.62)	659 (94.1)	16 (2.2)
Children (19)	2 (10.5)	3 (15.7)	0 (0.0)	17 (89.4)	6 (31.5)

Table 3 Antibiotic resistance profile of H. pylori isolates of samples

Type of samples (no. of positive)	Antibiotic resistance pattern (%)
	AMI0	Met5	ER5	CIR2	AMXIO	Cet30	TRP25	FZLI	MOX5	TIN4	CIP5
Cows (6)	5 (83.3)	4 (66.6)	4 (66.6)	4 (66.6)	4 (66.6)	1 (16.6)	4 (66.6)	2 (33.3)	1 (16.6)	3 (50.0)	3 (50.0)
Sheep(105)	72 (68.5)	62 (59)	58 (55.2)	65 (61.9)	48 (45.7)	27 (25.7)	64 (60.9)	37 (35.2)	22 (20.9)	42 (40.0)	51 (48.5)
Goats (1)	1 (100)	1 (100)	1 (100)	1 (100)	1 (100)	0 (0.0)	1 (100)	0 (0.0)	0 (0.0)	1 (100)	1 (100)
Adults (507)	380 (74.9)	314(61.9)	308 (60.7)	321 (63.3)	318 (62.7)	127 (25.0)	315 (62.1)	137 (27.0)	121 (23.8)	252 (49.7)	248 (48.9)
Children (19)	17 (89.4)	12 (63.1)	13 (68.4)	14 (73.6)	13 (68.4)	2 (10.5)	1 1 (57.8)	4 (21.0)	2 (10.5)	9 (47.3)	9 (47.3)
Total (638)	475 (74.4)	393 (61.5)	384 (60.1)	405 (63.4)	384 (60.1)	157 (24.6)	395 (61.9)	180 (28.2)	146 (22.8)	307(48.1)	312 (48.9)

Abbreviations: AM10, ampicillin (10 µg); Met5, metronidazole (5 µg); ER5, erythromycin (5 µg); CLR2, clarithromycin (2 µg); AMX10, amoxicillin (10 µg); Lev5, levofloxacin (5 µg); Cef30, cefsulodin (30 µg); TRP25, trimethoprim (25 µg); FZL1, furazolidone (1 µg); Mox5, moxifloxacin (5 µg); Tin, tinidazole (prepared from pure powders, Sigma-Aldrich Co, 5 µg); CIP5, ciprofloxacin (5 µg).

Table 4 Total distribution of various genotypes in H. pylori strains of positive samples

Type of samples (no. of positive)	Antibiotic resistance pattern (%)
	CogE	CagA	IceAl	lceA2	OipA	BabA2	VacAs1a	VacAs1b	VacAs1c	VacAs2	VacAm1a	VacAm1b	VacAm2
Cows (6)	3 (50.0)	5 (83.3)	3(50)	3 (50.0)	1 (16.6)	2 (33.3)	6 (100)	2 (33.3)	0 (0.0)	2 (33.3)	2 (33.3)	0 (0.0)	5 (83.3)
Sheep (105)	54 (51.4)	88 (83.8)	48 (45.7)	48 (45.7)	1 1 (10.4)	17(16.1)	51 (48.5)	39 (37.1)	0 (0.0)	14(13.3)	46 (43.8)	0 (0.0)	22 (20.9)
Goats (1)	1 (100)	1 (100)	1 (100)	1 (100)	0 (0.0)	0 (0.0)	1 (100)	0 (0.0)	0 (0.0)	0 (0.0)	1 (100)	0 (0.0)	1 (100)
Adults (507)	243 (47.9)	446 (87.9)	238 (46.9)	238 (46.9)	82 (16.1)	152 (29.9)	251 (49.5)	68 (13.4)	106 (20.9)	74 (14.5)	168 (33.1)	42 (8.2)	312(61.5)
Children (19)	9 (47.3)	17 (89.4)	10 (52.6)	10 (52.6)	3(15.7)	4 (21.0)	9 (47.3)	3(15.7)	2 (10.5)	2 (10.5)	2 (10.5)	0 (0.0)	17(17.0)
Total (638)	310 (48.5)	541 (84.7)	300 (47.0)	300 (47.0)	97(15.2)	175 (27.4)	318 (49.8)	1 12 (17.5)	108 (16.9)	92 (14.4)	219 (34.3)	42 (6.5)	357 (55.9)