一株同时携带blaCTX-M-14和blaCTX-M-15基因的多重耐药宋内志贺菌耐药基因及质粒分析

摘要: 目的对1株同时耐头孢菌素和阿奇霉素的多重耐药宋内志贺菌进行全基因组测序分析，明确其携带的耐药基因和质粒特征。方法通过对2011年上海市的60株宋内志贺菌进行抗菌药物敏感性分析，筛选出1株同时耐头孢菌素和阿奇霉素的菌株Sh11sh529，使用二代和纳米孔测序技术获得其基因组序列，分析基因组的耐药基因、质粒、可移动遗传元件等。结果 Sh11sh529基因组中检测到了11个耐药基因以及gyrA基因喹诺酮耐药决定区（QRDR）的突变位点gyrA-S83L，耐药基因包括2种CTX-M型超广谱β内酰胺酶（ESBL）基因bla_CTX-M-14和bla_CTX-M-15，其中bla_CTX-M-14、mphA、aac(3)-IId、dfrA17、aadA5、sul1和qacEdelta基因由1个IncB/O/K/Z型质粒pSh11sh529-2携带，bla_CTX-M-14上游有1个ISEcp1插入子，mphA上游有1个IS26插入子。而bla_CTX-M-15由IncFII型质粒pSh11sh529-3携带，在其上游有1个ISEcp1插入子。该菌株表现出多重耐药性，对头孢菌素类、大环内酯类、氨基糖苷类、磺胺类、青霉素类等5类抗菌药物中的9种耐药。结论应当加强对多重耐药菌株以及同时携带多个类型ESBL菌株的监测和研究，以制定策略减少其流行和传播。
- 宋内志贺菌 /
- 多耐药菌株 /
- 超广谱β内酰胺酶 /
- 质粒 /
- 基因组测序
Abstract: Objective To analyze the whole genome sequencing of a multi-drug resistant Shigella sonnei strain resistant to both cephalosporin and azithromycin and identify the characteristics of its resistance genes and plasmids. Methods A cephalosporin and azithromycin resistant S. sonnei strain (Sh11sh529) was screened by analyzing the antibiotic susceptibility of 60 S. sonnei strains collected from Shanghai in 2011, and genome sequence of the strain was obtained by second-generation sequencing and nanopore sequencing technology. The drug resistance genes, plasmids and genetic mobile elements were analyzed. Results Eleven resistance genes and gyrA-S83L mutation sites in quinolone resistance determining region (QRDR) of gyrA gene were detected in genome of the Sh11sh529 strain. The resistance genes included two extended spectrum β-lactamases (ESBLs) genes bla_CTX-M-14 and bla_CTX-M-15. The bla_CTX-M-14, mphA, aac(3)-IId, dfrA17, aadA5, sul1 and qacEdelta genes were carried by an IncB/O/K/Z plasmid (pSh11sh529-2). There was an ISEcp1 insert in upstream of bla_CTX-M-14, an IS26 insert in upstream of mphA. The bla_CTX-M-15 gene was carried by an IncFII plasmid (pSh11sh529-3), and there was an ISEcp1 insert in upstream of bla_CTX-M-15. The strain was resistant to 9 antibiotics of 5 classes, including cephalosporins, macrolides, aminoglycosides, sulfonamides, and penicillins. Conclusion It is necessary to strengthen the surveillance and research of multi-drug resistant strains and strains carrying multiple types of ESBL for the development of strategies to reduce the prevalence and spread of multi-drug resistant strains.
- Shigella sonnei /
- Multi-drug resistant strain /
- Extended spectrum β-lactamase /
- Plasmid /
- Whole genome sequencing

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图 1 pSh11sh529-2及相似质粒比较圈图

注：红色色块代表耐药基因，橙色代表插入子，紫色为整合子

Figure 1. Circular comparisons image of pSh11sh529-2 and similar plasmids

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图 2 pSh11sh529-3及相似质粒比较圈图

注：红色色块代表耐药基因，橙色代表插入子，灰色为假定蛋白

Figure 2. Circular comparisons image of pSh11sh529-3 and similar plasmid

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图 3 整合子结构图

注：箭头长度与基因长度成比例，箭头方向代表基因的方向

Figure 3. Structure of integrons

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表 1 Sh11sh529的药物敏感性

Table 1. Drug susceptibility of strain Sh11sh529

抗菌药物种类	抗菌药物	MIC （μg/mL）	药物敏感性
氨基糖苷类	妥布霉素	≥16	耐药
	庆大霉素	≥16	耐药
	阿米卡星	≤16	敏感
碳青霉烯类	亚胺培南	≤4	敏感
头孢菌素类	头孢曲松	≥64	耐药
	头孢他啶	16	中等
	头孢西丁	≤8	敏感
	头孢哌酮	≥64	耐药
	头孢吡肟	≤8	敏感
	头孢唑啉	≥32	耐药
氟喹诺酮类	诺氟沙星	≤4	敏感
氟喹诺酮类	左氧氟沙星	≤2	敏感
叶酸通路抑制剂	甲氧苄胺嘧啶/磺胺甲基异恶唑	≥4/76	耐药
大环内酯类	阿奇霉素	≥32	耐药
单环β内酰胺类	氨曲南	16	中等
硝基呋喃	呋喃妥因	≤32	敏感
青霉素类	替卡西林	≥128	耐药
	哌拉西林	≥128	耐药
	氨苄西林	≥32	耐药
氯霉素类	氯霉素	≤8	敏感
四环素类	四环素	≤4	敏感
β-内酰胺类/ β-内酰胺酶抑制剂	替卡西林/克拉维酸	32/264/2	中等
注：MIC. 最小抑菌浓度

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表 2 Sh11sh529携带的主要耐药基因

Table 2. Main resistance genes carried by strain Sh11sh529

序列类型	起始位点	终止位点	耐药基因	匹配度（%）	覆盖度（%）
染色体	1 962 708	1 963 496	aadA1	99.36	100.00
染色体	1 963 554	1 964 078	sat-2	100.00	100.00
染色体	1 964 173	1 964 606	dfrA1	99.62	99.62
pSh11sh529-2	110 933	111 808	bla_CTX-M-14	100.00	100.00
pSh11sh529-2	54 479	55 078	dfrA17	100.00	100.00
pSh11sh529-2	53 560	54 348	aadA5	100.00	100.00
pSh11sh529-2	53 007	53 354	qacEdelta1	100.00	100.00
pSh11sh529-2	52 174	53 013	sul1	100.00	100.00
pSh11sh529-2	47 555	48 415	aac（3）-IId	100.00	100.00
pSh11sh529-2	43 130	44 035	mphA	100.00	100.00
pSh11sh529-3	61 400	62 275	bla_CTX-M-15	100.00	100.00

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