oxacillin敏感的meca阳性金黄色葡萄球菌ST59的基因组特征

Vladimir V. Gostev, O.S. Sulian, P.A. Pavlova, E.V. Nesterova, O.S. Kalinogorskaya, P.S. Chulkova, N.N. Trofimova, V.A. Ageevets, I.V. Ageevets, Sergey V. Sidorenko
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By employing the broth serial dilution and VITEK, the isolates’ phenotypic susceptibility to oxacillin was determined. The cefoxitin inhibition zones ranged from 17 to 22 mm. All isolates showed a penicillinclavulanate MIC ≤ 0.5 µg/mL. Isolates obtained from carriers belonged to the ST59-t1950-SCCmec Vb (seb+) genotype whereas the isolate obtained from SSTI belonged to the ST59-t437-SCCmec Vb (seb/ lukF/lukS+) genotype. Nucleotide position -33 (C/T) of mecA promoter and mutations in PBP2a (S225R + E246G) were present in all isolates. Based on phylogenetic analysis and Bayesian clustering the ST59 genomes were divided into four clusters and all Russian genomes belonged to the East Asian ST59 sublineage. The PVL toxin was present in the genomes of the first cluster of the East Asian ST59 sublineage. Pairwise comparisons of nucleotide substitutions among the genomes of Russian isolates showed a high similarity: median 13, interquartile range 8–18. All ST59 clusters were characterized by the presence of enterotoxin B, as well as mutations in PBP2a (S225R and E246G) and the promoter regions of the mecA gene (-7 G/A or -33 C/T). The genomes of the Russian isolates differed from the globally spread ST59 by specific mutations at the following loci (relative to the reference genome of S. aureus M013TW): lactose catabolism regulator RS03495 (N168D), ribosomal protein L28 (V47A), putative glyoxalase RS07825 (V42A), and the hypothetical protein RS13235 (K32E). Conclusions. Russian MRSA-ST59 isolates belong to the East Asian sublineage and are characterized by the presence of the enterotoxin B gene. Oxacillin susceptibility and borderline resistance to cefoxitin are specific characteristics of MRSA-ST59. OS-MRSA phenotypes have a risk of improper sensitivity testing leading to ineffective antibiotic treatment. 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引用次数: 0

摘要

目标。目的对圣彼得堡分离的oxacillin敏感的meca阳性金黄色葡萄球菌ST59进行基因组鉴定。材料与方法。9株oxacillin敏感meca阳性的ST59金黄色葡萄球菌分离株(OS-MRSA)纳入研究。分离株来自2018-2019年圣彼得堡金黄色葡萄球菌鼻筛查期间未出现葡萄球菌感染临床体征的儿童。1株分离株来自1例皮肤和软组织感染(SSTI)的成人患者。进行抗生素药敏和全基因组测序。分析包括开放获取数据库中的242个金黄色葡萄球菌ST59基因组。结果。采用肉汤系列稀释法和VITEK法测定了分离株对oxacillin的表型敏感性。头孢西丁的抑制区范围为17 ~ 22 mm。所有分离株的MIC≤0.5µg/mL。从载体分离得到的分离株为ST59-t1950-SCCmec Vb (seb+)基因型,从SSTI分离得到的分离株为ST59-t437-SCCmec Vb (seb/ lukF/lukS+)基因型。mecA启动子核苷酸位置-33 (C/T)和PBP2a (S225R + E246G)突变在所有分离株中均存在。基于系统发育分析和贝叶斯聚类,将俄罗斯人的ST59基因组划分为4个聚类,所有俄罗斯人的基因组都属于东亚ST59亚系。PVL毒素存在于东亚ST59亚谱系第一簇的基因组中。俄罗斯分离株基因组间核苷酸替换的两两比较显示高度相似:中位数为13,四分位数范围为8-18。所有ST59簇的特征都是存在肠毒素B,以及PBP2a (S225R和E246G)和mecA基因启动子区域(-7 G/A或-33 C/T)的突变。俄罗斯分离株的基因组与全球传播的ST59的不同之处是:乳糖分解代谢调节因子RS03495 (N168D)、核糖体蛋白L28 (V47A)、假定的乙醛酶RS07825 (V42A)和假定的蛋白RS13235 (K32E)位点发生了特异性突变(相对于金黄色葡萄球菌M013TW的参考基因组)。结论。俄罗斯MRSA-ST59分离株属于东亚亚谱系,其特征是存在肠毒素B基因。Oxacillin敏感性和对头孢西丁的边缘性耐药是MRSA-ST59的特异性特征。OS-MRSA表型存在敏感性检测不当导致抗生素治疗无效的风险。检测mecA基因是鉴别MSSA与MRSA最准确的方法。
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Genomic characterization of oxacillin-susceptible mecA-positive Staphylococcus aureus ST59
Objective. To characterize the genomes of oxacillin-susceptible mecA-positive Staphylococcus aureus ST59 isolated in St. Petersburg. Materials and Methods. Nine oxacillin-susceptible mecA-positive of S. aureus isolates (OS-MRSA) of ST59 were included in the study. The isolates were obtained from children who showed no clinical signs of staphylococcal infections during nasal screening of S. aureus in St. Petersburg in 2018–2019. One isolate was obtained from an adult patient with skin and soft tissue infection (SSTI). The susceptibility to antibiotics and whole genome sequencing were performed. The analysis included 242 genomes of S. aureus ST59 from open access databases. Results. By employing the broth serial dilution and VITEK, the isolates’ phenotypic susceptibility to oxacillin was determined. The cefoxitin inhibition zones ranged from 17 to 22 mm. All isolates showed a penicillinclavulanate MIC ≤ 0.5 µg/mL. Isolates obtained from carriers belonged to the ST59-t1950-SCCmec Vb (seb+) genotype whereas the isolate obtained from SSTI belonged to the ST59-t437-SCCmec Vb (seb/ lukF/lukS+) genotype. Nucleotide position -33 (C/T) of mecA promoter and mutations in PBP2a (S225R + E246G) were present in all isolates. Based on phylogenetic analysis and Bayesian clustering the ST59 genomes were divided into four clusters and all Russian genomes belonged to the East Asian ST59 sublineage. The PVL toxin was present in the genomes of the first cluster of the East Asian ST59 sublineage. Pairwise comparisons of nucleotide substitutions among the genomes of Russian isolates showed a high similarity: median 13, interquartile range 8–18. All ST59 clusters were characterized by the presence of enterotoxin B, as well as mutations in PBP2a (S225R and E246G) and the promoter regions of the mecA gene (-7 G/A or -33 C/T). The genomes of the Russian isolates differed from the globally spread ST59 by specific mutations at the following loci (relative to the reference genome of S. aureus M013TW): lactose catabolism regulator RS03495 (N168D), ribosomal protein L28 (V47A), putative glyoxalase RS07825 (V42A), and the hypothetical protein RS13235 (K32E). Conclusions. Russian MRSA-ST59 isolates belong to the East Asian sublineage and are characterized by the presence of the enterotoxin B gene. Oxacillin susceptibility and borderline resistance to cefoxitin are specific characteristics of MRSA-ST59. OS-MRSA phenotypes have a risk of improper sensitivity testing leading to ineffective antibiotic treatment. Detection of mecA gene is the most accurate method for differentiating between MSSA and MRSA.
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