Whole-genome sequencing of clarithromycin resistant Helicobacter pylori characterizes unidentified variants of multidrug resistant efflux pump genes

Iwamoto, Akira; Tanahashi, Toshihito; Okada, Rina; Yoshida, Yukio; Kikuchi, Kaoru; Keida, Yoshihide; Murakami, Yoshiki; Yang, Lin; Yamamoto, Koji; Nishiumi, Shin; Yoshida, Masaru; Azuma, Takeshi

doi:10.1186/1757-4749-6-27

Gut Pathogens

Table 6 SNVs of hp0605-hp0607 cluster in 12 CLR-resistant H. pylori

From: Whole-genome sequencing of clarithromycin resistant Helicobacter pylori characterizes unidentified variants of multidrug resistant efflux pump genes

	Locus tag	HP0605 (NP_207400.1)
	Annotation	hypothetical protein
	Coding sequence	c.530A > C		c.546A > G		c.804 T > C		c.1365 T > C
	Amino acid	p.Asn177Thr		No		No		No
	Nucleotide position^a	641828		641844		642102		642663
Strain		Count reads/Total reads	Frequency (%)	Count reads/Total reads	Frequency (%)	Count reads/Total reads	Frequency (%)	Count reads/Total reads	Frequency (%)
S1		179/180	99.4	181/181	100	140/141	99.3	107/107	100
S2		373/373	100	392/394	99.5	319/320	99.7	295/295	100
S4		212/213	99.5	219/221	99.1	212/214	99.1	204/205	99.5
S8		507/508	99.8	530/532	99.6	478/479	99.8	503/506	99.4
S13		218/218	100	225/225	100	169/170	99.4	179/179	100
S16		343/343	100	371/371	100	325/325	100	312/313	99.7
S17		266/266	100	306/306	100	185/186	99.5	246/246	100
S22		328/328	100	348/348	100	299/299	100	287/289	99.3
S23		-		-		-		-
S26		341/341	100	368/368	100	321/321	100	310/311	99.7
174		123/123	100	124/124	100	114/114	100	151/151	100
194		305/306	99.7	324/324	100	341/343	99.4	231/232	99.6
	Locus tag	HP0606 (NP_207401.1)
	Annotation	membrane fusion protein MtrC
	Coding sequence	c.99 T > C		c.105A > G		c.192A > G
	Amino acid	No		No		No
	Nucleotide position	642841		642847		642934
Strain		Count reads/Total reads	Frequency (%)	Count reads/Total reads	Frequency (%)	Count reads/Total reads	Frequency (%)
S1		140/140	100	129/129	100	139/140	99.3
S2		340/340	100	324/324	100	383/385	99.5
S4		194/194	100	192/193	99.5	221/223	99.1
S8		496/498	99.6	472/473	99.8	505/506	99.8
S13		203/203	100	194/194	100	-
S16		329/331	99.4	316/317	99.7	335/335	100
S17		233/233	100	230/230	100	272/273	99.6
S22		295/295	100	285/285	100	320/322	99.4
S23		109/109	100	105/105	100	110/110	100
S26		323/325	99.4	311/312	99.7	331/331	100
174		137/138	99.3	126/127	99.2	137/138	99.3
194		-		-		299/301	99.3
	Locus tag	HP0607 (NP_207402.1)
	Annotation	acriflavine resistance protein AcrB
	Coding sequence	c.1341T>C		c.39A>G
	Amino acid	No		No
	Nucleotide position	644800		643498
Strain		Count reads/Total reads	Frequency (%)	Count reads/Total reads	Frequency (%)
S1		159/160	99.4	123/124	99.2
S2		345/347	99.4	280/280	100
S4		284/286	99.3	182/182	100
S8		585/586	99.8	431/432	99.8
S13		227/228	99.6	164/164	100
S16		425/425	100	295/295	100
S17		317/317	100	198/198	100
S22		346/347	99.7	273/275	99.3
S23		104/104	100	106/106	100
S26		419/419	100	295/295	100
174		113/113	100	-
194		-		342/344	99.4

^aNucelotide position was based on NC_000915.

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ISSN: 1757-4749

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