Whole-genome sequencing of clarithromycin resistant Helicobacter pylori characterizes unidentified variants of multidrug resistant efflux pump genes.
Whole-genome sequencing of clarithromycin resistant Helicobacter pylori characterizes unidentified variants of multidrug resistant efflux pump genes.
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DOI：
10.1186/1757-4749-6-27
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发表时间：
2014
期刊：
影响因子：
4.2
通讯作者：
Azuma T
中科院分区：
文献类型：
--
作者：
Iwamoto A;Tanahashi T;Okada R;Yoshida Y;Kikuchi K;Keida Y;Murakami Y;Yang L;Yamamoto K;Nishiumi S;Yoshida M;Azuma T
克拉霉素是根除幽门螺杆菌的关键药物。pylori）感染，并且广泛使用抗幽门螺杆菌导致原发性CLR抗性H.幽门。已知的耐药机制是23 S rRNA基因的A2146 G和A2147 G突变，但缺乏其他遗传机制参与的证据。使用MiSeq平台，对19株临床菌株和参考菌株ATCC 26695进行全基因组测序，以鉴定CLR耐药表型中多药耐药外排泵基因的单核苷酸变体（SNV）。基于ATCC 26695的测序数据，超过100万个测序读段（覆盖率超过50倍）足以检测SNV，但不能检测细菌基因组中的插入缺失。临床分离株的测序读数范围为182万至1080万，平均覆盖范围为90.9至686.3倍，这是检测SNV的可接受标准。利用等位基因特异性PCR的常规方法，在12个临床耐药菌株中检测到23 S rRNA基因的点突变，而在7个临床敏感菌株中未检测到。CLR耐药菌株的所有测序读数在23 S rRNA基因的相同位置处具有G突变。此外，检查了TolC同源物的四个基因簇（hp 0605-hp 0607、hp 0971-hp 0969、hp 1327-hp 1329和hp 1489-hp 1487）的遗传变体，这些基因簇与多药耐药性有关。特异性SNV主要存在于抗性菌株中。TolC同源基因簇参与了H. pylori菌株。全基因组测序产生了新的理解基因型-表型关系。
Clarithromycin (CLR) is the key drug in eradication therapy of Helicobacter pylori (H. pylori) infection, and widespread use of CLR has led to an increase in primary CLR-resistant H. pylori. The known mechanism of CLR resistance has been established in A2146G and A2147G mutations in the 23S rRNA gene, but evidence of the involvement of other genetic mechanisms is lacking. Using the MiSeq platform, whole-genome sequencing of the 19 clinical strains and the reference strain ATCC26695 was performed to identify single nucleotide variants (SNVs) of multi-drug resistant efflux pump genes in the CLR-resistant phenotype. Based on sequencing data of ATCC26695, over one million sequencing reads with over 50-fold coverage were sufficient to detect SNVs, but not indels in the bacterial genome. Sequencing reads of the clinical isolates ranged from 1.82 to 10.8 million, and average coverage ranged from 90.9- to 686.3-fold, which were acceptable criteria for detecting SNVs. Utilizing the conventional approach of allele-specific PCR, point mutations in the 23S rRNA gene were detected in 12 clinical resistant isolates, but not in 7 clinical susceptible isolates. All sequencing reads of CLR-resistant strains had a G mutation in an identical position of the 23S rRNA gene. In addition, genetic variants of four gene clusters (hp0605-hp0607, hp0971-hp0969, hp1327-hp1329, and hp1489-hp1487) of TolC homologues, which have been implicated in multi-drug resistance, were examined. Specific SNVs were dominantly found in resistant strains. Gene clusters of TolC homologues are involved in CLR susceptibility profiles in individual H. pylori strains. Whole-genome sequencing has yielded novel understanding of genotype-phenotype relationships.
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影响因子：
46.9
作者：
通讯作者：
--
DOI：
10.1111/j.1440-1746.2007.04919.x
发表时间：
2007-11-01
影响因子：
4.1
作者：
Furuta, Takahisa;Soya, Yoshihiro;Hishida, Akira
通讯作者：
Hishida, Akira
影响因子：
6.7
作者：
Howden BP;McEvoy CR;Allen DL;Chua K;Gao W;Harrison PF;Bell J;Coombs G;Bennett-Wood V;Porter JL;Robins-Browne R;Davies JK;Seemann T;Stinear TP
通讯作者：
Stinear TP
影响因子：
4.5
作者：
Caselli, M.;Zullo, A.;Gasbarrini, G.
通讯作者：
Gasbarrini, G.
幽门螺杆菌感染
影响因子：
158.5
作者：
McColl, Kenneth E. L.
通讯作者：
McColl, Kenneth E. L.