Genomic Surveillance of Pseudomonas aeruginosa in the Philippines from 2013-2014
Genomic Surveillance of Pseudomonas aeruginosa in the Philippines from 2013-2014
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2013-2014年菲律宾铜绿假单胞菌基因组监测
DOI：
10.1101/2020.03.19.998229
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发表时间：
2020
期刊：
影响因子：
--
通讯作者：
Chilam J
中科院分区：
文献类型：
--
作者：
Chilam J
铜绿假单胞菌是一种机会致病菌，经常引起医院感染的治疗耐药。抗生素耐药性（AMR）的发生率正在增加，多重耐药（MDR）和可能的广泛耐药（XDR）感染的发生率也在增加。我们的目的是描述这种病原体的分子流行病学和AMR机制。我们对2013-2014年在菲律宾收集的176株铜绿假单胞菌分离株进行了全基因组测序;推导了多位点序列类型（MLST）、AMR决定簇的存在和分离株之间的相关性;并确定了表型和基因型耐药之间的一致性。碳青霉烯耐药与OprD孔蛋白功能丧失和金属β-内酰胺酶（MBL）基因blaVIM的获得相关。表型和基因型之间的一致性为93.27%，在三个类别的六种抗生素，但不同的氨基糖苷类。铜绿假单胞菌的群体是多样的，具有属于MLST ST ST 235、ST 244、ST 309和ST 773的XDR基因组的克隆扩增。我们发现证据的持续存在或重新引入的优势克隆ST 235在一家医院，和医院之间的转移。大多数ST 235基因组形成了与全球基因组不同的谱系，因此提高了它们可能是菲律宾独有的可能性。此外，一种代表性XDR ST 235分离株的长读段测序鉴定出携带多个耐药基因（包括blaVIM-2）的整合子，与先前描述的铜绿假单胞菌1类整合子在基因组成和同线性方面存在差异。该调查填补了西太平洋地区基因组数据的差距，将有助于持续监测;它还强调了遏制ST 235在菲律宾传播的重要性。
Pseudomonas aeruginosa is an opportunistic pathogen that often causes nosocomial infections resistant to treatment. Rates of antimicrobial resistance (AMR) are increasing, as are rates of multidrug-resistant (MDR) and possible extensively drug-resistant (XDR) infections. Our objective was to characterize the molecular epidemiology and AMR mechanisms of this pathogen. We sequenced the whole genome for each of 176 P. aeruginosa isolates collected in the Philippines in 2013–2014; derived the multilocus sequence type (MLST), presence of AMR determinants and relatedness between isolates; and determined concordance between phenotypic and genotypic resistance. Carbapenem resistance was associated with loss of function of the OprD porin and acquisition of the metallo-β-lactamase (MBL) gene blaVIM. Concordance between phenotypic and genotypic resistance was 93.27% overall for six antibiotics in three classes, but varied among aminoglycosides. The population of P. aeruginosa was diverse, with clonal expansions of XDR genomes belonging to MLSTs ST235, ST244, ST309 and ST773. We found evidence of persistence or reintroduction of the predominant clone ST235 in one hospital, and of transfer between hospitals. Most of the ST235 genomes formed a distinct lineage from global genomes, thus raising the possibility that they may be unique to the Philippines. In addition, long-read sequencing of one representative XDR ST235 isolate identified an integron carrying multiple resistance genes (including blaVIM-2), with differences in gene composition and synteny from the P. aeruginosa class 1 integrons described previously. The survey bridges the gap in genomic data from the Western Pacific Region and will be useful for ongoing surveillance; it also highlights the importance of curtailing the spread of ST235 within the Philippines.
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影响因子：
6.4
作者：
Pelegrin, Andreu Coello;Saharman, Yulia Rosa;Severin, Juliette A.
通讯作者：
Severin, Juliette A.
影响因子：
2.9
作者：
Juayang AC;Lim JPT;Bonifacio AFV;Lambot AVL;Millan SM;Sevilla VZJN;Sy JKT;Villanueva PJ;Grajales CP;Gallega CT
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影响因子：
3.9
作者：
A. Page;Nishadi H De Silva;Martin Hunt;M. Quail;J. Parkhill;S. Harris;T. Otto;Jacqueline A. Keane
通讯作者：
Jacqueline A. Keane
影响因子：
14.2
作者：
Treepong, P.;Kos, V. N.;Hocquet, D.
通讯作者：
Hocquet, D.