泛耐药鲍氏不动杆菌流行株全基因组与特定基因分析

Whole genome and specific genes in epidemic pandrug-resistant Acinetobacter baumannii strains

目的调查一株泛耐药鲍氏不动杆菌流行株的遗传学背景,为耐药菌的快速诊断提供参考。方法泛耐药鲍氏不动杆菌WA2859分离自2010年3月住院患者痰液标本,作gyrA与parC基因测序、BLASTn比对确认为鲍氏不动杆菌,采用Illumina HiSeq与Ion Torrent PGM两种大规模并行测序仪进行全基因组分析,再进行人工测序补缺口,并进行了特定基因分析(包含β-内酰胺类、氨基糖苷类抗菌药物获得耐药基因,ISaba1-blaADC、ISaba1-blaOXA-23连锁检测)。结果泛耐药鲍氏不动杆菌WA2859株全基因组测序未获完整序列,得到一条推定的染色体序列,长3 887 116bp(内含两个缺口);推定的质粒序列,长260513bp(内含9个缺口);特定基因检出blaTEM、blaADC、blaOXA-23β-内酰胺类抗菌药物获得耐药基因和aac(6′)-Ⅰb、ant(3′)-Ⅰ、ant(2″)-Ⅰ、aph(3′)-Ⅰ氨基糖苷类抗菌药物获得耐药基因,并且ISaba1-blaADC、ISaba1-blaOXA-23连锁检测均阳性。结论特定基因检测与全基因组测序互为补充,对特定基因检测结果作样本聚类分析并可得到菌株亲缘关系结果,可对临床分离的耐药细菌作快速诊断和分子流行病学研究。

OBJECTIVE To investigate genetic background of a pandrug‐resistant Acinetobacter baumannii so as to provide guidance for rapid identification of drug‐resistant strains .METHODS The pandrug‐resistant A .baumannii WA2859 was isolated from the sputum specimens of a hospitalized patient in Mar 2010 ,the A .baumannii strain was conformed through the sequencing of gyrA and parC genes as well as comparison of BLASTn ,the whole ge‐nome was analyzed by using two large‐scale parallel sequencers Illumina HiSeq and Ion Torrent PGM ,and PCR was performed to fill gaps .Furthermore ,the specific genes were analyzed （including resistance genes to beta‐lac‐tams and aminoglycosides ,linkage detection of ISaba1‐blaADC and ISaba1‐blaOXA‐23） .RESULTS Complete graph could not be sequenced by whole genome sequencing ,a putative chromosome sequence （2 gaps inside） was 3887116bp ,a putative plasmid sequence （9 gaps inside） was 260513 bp .The specific genes ,including blaTEM , blaADC ,blaOXA‐23 ,aac（6＇）‐Ⅰb ,ant（3＇）‐Ⅰ ,and ant（2＆quot;）‐Ⅰ ,aph（3＇）‐Ⅰ ,were positive ,and linkage detection was positive for ISaba1‐blaADC and ISaba1‐blaOXA‐23 .CONCLUSION The specific genes are the complement of the whole genome sequencing ,and they are used to perform sample cluster analysis to investigate the phylogenetic relationship among strains and are used to rapidly identify clinical isolates of drug‐resistant strains and study the molecular epidemiology .