Genomic Surveillance of Methicillin-Resistant Staphylococcus aureus in the Philippines from 2013-2014
Genomic Surveillance of Methicillin-Resistant Staphylococcus aureus in the Philippines from 2013-2014
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2013-2014年菲律宾耐甲氧西林金黄色葡萄球菌基因组监测
DOI：
10.1101/2020.03.19.998401
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发表时间：
2020
期刊：
影响因子：
--
通讯作者：
Masim M
中科院分区：
文献类型：
--
作者：
Masim M
耐甲氧西林金黄色葡萄球菌(MRSA)仍然是全球医院和社区感染的主要原因之一。在菲律宾，自2010年以来，MRSA的比率一直保持在50%以上，但对包括万古霉素在内的其他抗生素的耐药性很低。MRSA的负担可以部分归因于循环克隆的病原体特异性，但对在菲律宾传播的金黄色葡萄球菌克隆知之甚少。我们对2013-2014年间在抗菌素耐药性监测计划中收集的116株金黄色葡萄球菌的全基因组进行了测序。多位点序列类型、SpA类型、SCCmec类型、抗菌素耐药(AMR)决定基因和毒力基因的存在以及分离株之间的亲缘关系都来自于序列数据。同时测定了表型抗性与基因抗性的一致性。菲律宾的MRSA种群由数量有限的基因克隆组成，包括几个国际流行克隆，如CC30-SpA-T019-SCCmec-IV-PVL+、CC5-SCCmec-TypeIV和ST239-Spa-T030-SCCmec-TypeIII。CC30基因组与西南太平洋克隆人有亲缘关系，但形成了一个独特的、多样化的谱系，有证据表明它在全球范围内传播。我们发现，对磺胺甲恶唑/甲氧苄啶的耐药性在不同的位置和基因克隆上是独立获得的，但主要是在患有侵袭性感染的儿科患者中。7类8种抗生素表型耐药与基因耐药的符合率为99.68%。我们已经在菲律宾进行了第一次全面的金黄色葡萄球菌基因组调查，这弥补了西太平洋地区基因组数据的差距，并将构成未来监测的遗传背景。
Methicillin-resistant Staphylococcus aureus (MRSA) remains one of the leading causes of both nosocomial and community infections worldwide. In the Philippines, MRSA rates have remained above 50% since 2010, but resistance to other antibiotics, including vancomycin, is low. The MRSA burden can be partially attributed to pathogen-specific characteristics of the circulating clones, but little was known about the S. aureus clones circulating in the Philippines. We sequenced the whole genomes of 116 S. aureus isolates collected in 2013–2014 within the Antimicrobial Resistance Surveillance Program. The multilocus sequence type, spa type, SCCmec type, presence of antimicrobial resistance (AMR) determinants and virulence genes and relatedness between the isolates were all derived from the sequence data. The concordance between phenotypic and genotypic resistance was also determined. The MRSA population in the Philippines comprised a limited number of genetic clones, including several international epidemic clones, such as CC30-spa-t019-SCCmec-IV-PVL+, CC5-SCCmec-typeIV and ST239-spa-t030-SCCmec-typeIII. The CC30 genomes were related to the South-West Pacific clone but formed a distinct, diverse lineage, with evidence of global dissemination. We showed independent acquisition of resistance to sulfamethoxazole/trimethoprim in various locations and genetic clones but mostly in paediatric patients with invasive infections. The concordance between phenotypic and genotypic resistance was 99.68% overall for eight antibiotics in seven classes. We have made the first comprehensive genomic survey of S. aureus in the Philippines, which bridges the gap in genomic data from the Western Pacific Region and will constitute the genetic background for contextualizing prospective surveillance.
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开放式细菌种群基因组学：BIGSDB软件，pubmlst.org网站及其应用。
影响因子：
--
作者：
Jolley KA;Bray JE;Maiden MCJ
通讯作者：
Maiden MCJ
葡萄球菌“80/81 复合体：流行病学和实验室观察。
影响因子：
6.4
作者：
A. Nahmias;N. Sakurai;Richard Blumberg;Ann Doege;C. Sulzer
通讯作者：
C. Sulzer
影响因子：
7
作者：
Holden MT;Hsu LY;Kurt K;Weinert LA;Mather AE;Harris SR;Strommenger B;Layer F;Witte W;de Lencastre H;Skov R;Westh H;Zemlicková H;Coombs G;Kearns AM;Hill RL;Edgeworth J;Gould I;Gant V;Cooke J;Edwards GF;McAdam PR;Templeton KE;McCann A;Zhou Z;Castillo-Ramírez S;Feil EJ;Hudson LO;Enright MC;Balloux F;Aanensen DM;Spratt BG;Fitzgerald JR;Parkhill J;Achtman M;Bentley SD;Nübel U
通讯作者：
Nübel U
Arias 等人的勘误表，“九个拉丁美洲国家金黄色葡萄球菌菌血症的分子流行病学和系统基因组学前瞻性队列多中心研究”
影响因子：
4.9
作者：
C. Arias;Jinnethe Reyes;L. Carvajal;Sandra L. Rincon;Lorena Díaz;D. Panesso;Gabriel Ibarra;Rafael Ríos;J. Munita;M. Salles;C. Álvarez;J. Labarca;Coralith García;C. Luna;C. Mejía;J. Zurita;M. Guzmán;E. Rodríguez;A. Narechania;Laura J Rojas;P. Planet;G. Weinstock;E. Gotuzzo;C. Seas
通讯作者：
C. Seas
影响因子：
9.4
作者：
McCarthy, Alex J.;Breathnach, Aodhan S.;Lindsay, Jodi A.
通讯作者：
Lindsay, Jodi A.