Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, Philippines.
These authors contributed equally to this work.
Western Pac Surveill Response J. 2021 Apr 28;12(2):4-18. doi: 10.5365/wpsar.2020.11.1.006. eCollection 2021 Apr-Jun.
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 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 . Concordance between phenotypic and genotypic resistance was 93.27% overall for six antibiotics in three classes, but varied among aminoglycosides. The population of 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 ), with differences in gene composition and synteny from the 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.
是一种机会性病原体，常导致治疗耐药的医院获得性感染。抗菌药物耐药率（AMR）不断上升，同时多重耐药（MDR）和可能广泛耐药（XDR）感染的发生率也在上升。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 年至 2014 年期间在菲律宾采集的 176 株分离株进行了全基因组测序；推导了多位点序列型（MLST）、AMR 决定因素的存在以及分离株之间的亲缘关系；并确定了表型和基因型耐药之间的一致性。碳青霉烯类耐药与 OprD 孔蛋白功能丧失和获得金属β-内酰胺酶（MBL）基因有关。在 3 类 6 种抗生素中，表型和基因型耐药之间的一致性总体为 93.27%，但氨基糖苷类之间存在差异。的种群多样，属于 MLSTs ST235、ST244、ST309 和 ST773 的 XDR 基因组存在克隆扩张。我们发现一个医院中主要克隆 ST235 的持续存在或重新引入的证据，以及医院之间的转移。大多数 ST235 基因组与全球基因组形成一个独特的谱系，因此有可能它们是菲律宾特有的。此外，对一个代表的 XDR ST235 分离株的长读测序确定了一个携带多种耐药基因（包括）的整合子，其基因组成和基因排列与以前描述的类 1 整合子不同。该调查填补了西太平洋地区基因组数据的空白，将有助于正在进行的监测；它还强调了遏制 ST235 在菲律宾内部传播的重要性。
