Data_Sheet_1_The Use of a Combined Bioinformatics Approach to Locate Antibiotic Resistance Genes on Plasmids From Whole Genome Sequences of Salmonella enterica Serovars From Humans in Ghana.pdf

In the current study, we identified plasmids carrying antimicrobial resistance genes in draft whole genome sequences of 16 selected Salmonella enterica isolates representing six different serovars from humans in Ghana. The plasmids and the location of resistance genes in the genomes were predicted using a combination of PlasmidFinder, ResFinder, plasmidSPAdes and BLAST genomic analysis tools. Subsequently, S1-PFGE was employed for analysis of plasmid profiles. Whole genome sequencing confirmed the presence of antimicrobial resistance genes in Salmonella isolates showing multidrug resistance phenotypically. ESBL, either blaTEM52−B or blaCTX−M15 were present in two cephalosporin resistant isolates of S. Virchow and S. Poona, respectively. The systematic genome analysis revealed the presence of different plasmids in different serovars, with or without insertion of antimicrobial resistance genes. In S. Enteritidis, resistance genes were carried predominantly on plasmids of IncN type, in S. Typhimurium on plasmids of IncFII(S)/IncFIB(S)/IncQ1 type. In S. Virchow and in S. Poona, resistance genes were detected on plasmids of IncX1 and TrfA/IncHI2/IncHI2A type, respectively. The latter two plasmids were described for the first time in these serovars. The combination of genomic analytical tools allowed nearly full mapping of the resistance plasmids in all Salmonella strains analyzed. The results suggest that the improved analytical approach used in the current study may be used to identify plasmids that are specifically associated with resistance phenotypes in whole genome sequences. Such knowledge would allow the development of rapid multidrug resistance tracking tools in Salmonella populations using WGS.

本研究中，我们从加纳人类宿主来源的、涵盖6种不同血清型的16株经筛选的肠炎沙门氏菌（Salmonella enterica）分离株的全基因组草图序列（draft whole genome sequences）中，鉴定出携带抗菌耐药基因的质粒。本研究结合使用质粒识别工具（PlasmidFinder）、耐药基因识别工具（ResFinder）、plasmidSPAdes以及BLAST（基本局部比对搜索工具）基因组分析工具，对质粒及耐药基因在基因组中的定位进行预测。随后，我们采用S1脉冲场凝胶电泳（S1-PFGE）对质粒图谱开展分析。全基因组测序结果证实，表型呈现多重耐药的沙门氏菌分离株中确实存在抗菌耐药基因。超广谱β-内酰胺酶（Extended-Spectrum β-Lactamases，ESBL）中，blaTEM-52B与blaCTX-M-15分别存在于对头孢菌素耐药的维希血清型沙门氏菌（S.Virchow）和浦那血清型沙门氏菌（S.Poona）分离株中。系统性基因组分析显示，不同血清型沙门氏菌携带不同类型的质粒，部分质粒携带有抗菌耐药基因，部分则无相关耐药基因携带。在肠炎血清型沙门氏菌（S.Enteritidis）中，耐药基因主要由IncN型质粒携带；在鼠伤寒血清型沙门氏菌（S.Typhimurium）中，耐药基因则由IncFII(S)/IncFIB(S)/IncQ1型质粒携带。在维希血清型沙门氏菌（S.Virchow）和浦那血清型沙门氏菌（S.Poona）中，耐药基因分别由IncX1型和TrfA/IncHI2/IncHI2A型质粒携带。上述两种质粒为首次在这两种血清型中被报道。本次采用的多基因组分析工具组合，可实现对所有受试沙门氏菌菌株的耐药质粒近乎完整的图谱绘制。本研究结果表明，此次使用的优化分析方法可用于在全基因组序列中鉴定与耐药表型特异性相关的质粒。基于此类研究成果，可开发利用全基因组测序（Whole Genome Sequencing，WGS）技术快速追踪沙门氏菌种群中多重耐药性的工具。