https://scholars.lib.ntu.edu.tw/handle/123456789/605968
標題: | Comparison of Reference‐Based Assembly and De Novo Assembly for Bacterial Plasmid Reconstruction and AMR Gene Localization in Salmonella enterica Serovar Schwarzengrund Isolates | 作者: | Li, I-Chen Yu, Gine-Ye Huang, Jing-Fang Chen, Zeng-Weng CHUNG-HSI CHOU |
關鍵字: | Antimicrobial resistance genes;De novo assembly;Plasmids;Reference?based assembly;Salmonella enterica serovar Schwarzengrund | 公開日期: | 2022 | 卷: | 10 | 期: | 2 | 來源出版物: | Microorganisms | 摘要: | It is well established that plasmids carrying multiple antimicrobial resistance (AMR) genes can be easily transferred among bacterial isolates by horizontal gene transfer. Previous studies have shown that a combination of short? and long?read approaches is effective in reconstructing accurate plasmids. However, high?quality Illumina short reads mapped onto the long reads in the context of an AMR hybrid monitoring strategy have not yet been explored. Hence, this study aimed to improve the reconstruction of plasmids, including the localization of AMR genes, using the abovedescribed parameters on whole?genome sequencing (WGS) results. To the best of our knowledge, this study is the first to use S1 nuclease pulsed?field gel electrophoresis (S1?PFGE) to confirm the number and sizes of plasmids detected by in silico?based predictions in Salmonella strains. Our results showed that de novo assembly did not detect the number of bacterial plasmids more accurately than reference?based assembly did. As this new hybrid mapping strategy surpassed de novo assembly in bacterial reconstruction, it was further used to identify the presence and genomic location of AMR genes among three Salmonella enterica serovar Schwarzengrund isolates. The AMR genes identified in the bacterial chromosome among the three Salmonella enterica serovar Schwarzengrund isolates included: AAC(3)?IV, AAC(6′)?Iy, aadA2, APH(4)?Ia, cmlA1, golS, mdsA, mdsB, mdsC, mdtK, qacH, sdiA, sul2, sul3, and TEM?1 genes. Moreover, the presence of TEM?1, AAC(3)?IV, aadA2, APH(4)?Ia, cmlA1, dfrA12, floR, sul1, sul3, and tet(A) genes found within three IncFIB plasmids and one IncX1 plasmid highlight their possible transmission into the environment, which is a public health risk. In conclusion, the generated data using this new hybrid mapping strategy will contribute to the improvement of AMR monitoring and support the risk assessment of AMR dissemination. ? 2022 by the authors. Licensee MDPI, Basel, Switzerland. |
URI: | https://www.scopus.com/inward/record.uri?eid=2-s2.0-85123070002&doi=10.3390%2fmicroorganisms10020227&partnerID=40&md5=06860f1962b4fc72733d29ac6fb92afe https://scholars.lib.ntu.edu.tw/handle/123456789/605968 |
ISSN: | 20762607 | DOI: | 10.3390/microorganisms10020227 |
顯示於: | 獸醫學系 |
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