National Food Institute, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.
J Antimicrob Chemother. 2013 Apr;68(4):771-7. doi: 10.1093/jac/dks496. Epub 2012 Dec 11.
Antimicrobial susceptibility testing of bacterial isolates is essential for clinical diagnosis, to detect emerging problems and to guide empirical treatment. Current phenotypic procedures are sometimes associated with mistakes and may require further genetic testing. Whole-genome sequencing (WGS) may soon be within reach even for routine surveillance and clinical diagnostics. The aim of this study was to evaluate WGS as a routine tool for surveillance of antimicrobial resistance compared with current phenotypic procedures.
Antimicrobial susceptibility tests were performed on 200 isolates originating from Danish pigs, covering four bacterial species. Genomic DNA was purified from all isolates and sequenced as paired-end reads on the Illumina platform. The web servers ResFinder and MLST (www.genomicepidemiology.org) were used to identify acquired antimicrobial resistance genes and MLST types (where MLST stands for multilocus sequence typing). ResFinder results were compared with phenotypic antimicrobial susceptibility testing results using EUCAST epidemiological cut-off values and MLST types.
A total of 3051 different phenotypic tests were performed; 482 led to the categorizing of isolates as resistant and 2569 as susceptible. Seven cases of disagreement between tested and predicted susceptibility were observed, six of which were related to spectinomycin resistance in Escherichia coli. Correlation between MLST type and resistance profiles was only observed in Salmonella Typhimurium, where isolates belonging to sequence type (ST) 34 were more resistant than ST19 isolates.
High concordance (99.74%) between phenotypic and predicted antimicrobial susceptibility was observed. Thus, antimicrobial resistance testing based on WGS is an alternative to conventional phenotypic methods.
细菌分离物的药敏试验对于临床诊断、发现新出现的问题以及指导经验性治疗至关重要。目前的表型检测程序有时会出现错误，可能需要进一步的基因检测。全基因组测序（WGS）可能很快就可以用于常规监测和临床诊断。本研究旨在评估 WGS 作为一种常规工具，与当前的表型检测程序相比，用于监测抗菌药物耐药性。
对来自丹麦猪的 200 株细菌分离物进行了药敏试验，涵盖了四种细菌。从所有分离物中提取基因组 DNA，并在 Illumina 平台上进行了配对末端测序。使用 ResFinder 和 MLST（www.genomicepidemiology.org）网络服务器来识别获得性抗菌药物耐药基因和 MLST 类型（其中 MLST 代表多位点序列分型）。将 ResFinder 结果与基于 EUCAST 流行病学截断值的表型药敏试验结果进行比较，并比较 MLST 类型。
总共进行了 3051 次不同的表型测试；482 次测试导致将分离物归类为耐药，2569 次测试归类为敏感。观察到 7 次测试和预测的药敏结果不一致，其中 6 次与大肠杆菌中的壮观霉素耐药有关。仅在肠炎沙门氏菌中观察到 MLST 类型与耐药谱之间的相关性，其中属于序列型（ST）34 的分离物比 ST19 分离物更耐药。
观察到表型和预测的抗菌药物敏感性之间具有很高的一致性（99.74%）。因此，基于 WGS 的抗菌药物耐药性检测是常规表型方法的替代方法。
