PointFinder: a novel web tool for WGS-based detection of antimicrobial resistance associated with chromosomal point mutations in bacterial pathogens.
PointFinder: a novel web tool for WGS-based detection of antimicrobial resistance associated with chromosomal point mutations in bacterial pathogens.
复制标题
DOI：
10.1093/jac/dkx217
复制
发表时间：
2017-10-01
期刊：
影响因子：
--
通讯作者：
Aarestrup FM
中科院分区：
文献类型：
--
作者：
Zankari E;Allesøe R;Joensen KG;Cavaco LM;Lund O;Aarestrup FM
抗生素耐药性是一个主要的健康问题，因为曾经非常有效的药物不再能治愈细菌感染。WGS先前已被证明是检测水平获得的抗菌素耐药基因的替代方法。然而，仍然缺乏合适的生物信息学方法，可以提供容易解释的，准确和快速的结果与染色体点突变相关的抗生素耐药性。对150株分离株进行了表型抗菌药物敏感性试验，涵盖3种不同的细菌：肠道沙门氏菌、大肠杆菌和空肠弯曲菌。使用网络服务器Rescue-2.1鉴定获得性抗菌素耐药基因，并使用两种方法，即新型Pointlance（使用BLAST）和内部方法（原始WGS读数作图）鉴定染色体点突变。结果与表型抗菌药物敏感性测试结果进行了比较。共有685个不同的表型检测与染色体耐药性喹诺酮类，多粘菌素，利福平，大环内酯类和四环素类导致98.4%的一致性。观察到11例测试和预测敏感性之间的不一致：2例C。空肠分离株具有表型氟喹诺酮耐药，2株具有表型红霉素耐药，5株大肠杆菌素敏感。当用Velvet组装时，检测到pmrB V161 G突变的大肠杆菌分离株，但当使用SPAdes或定位读数时，则没有。PointFinder被证明是一种用户友好的网络工具，用于检测与抗菌药物耐药性相关的染色体点突变，其表型和预测的抗菌药物敏感性之间具有高度一致性。
Antibiotic resistance is a major health problem, as drugs that were once highly effective no longer cure bacterial infections. WGS has previously been shown to be an alternative method for detecting horizontally acquired antimicrobial resistance genes. However, suitable bioinformatics methods that can provide easily interpretable, accurate and fast results for antimicrobial resistance associated with chromosomal point mutations are still lacking. Phenotypic antimicrobial susceptibility tests were performed on 150 isolates covering three different bacterial species: Salmonella enterica, Escherichia coli and Campylobacter jejuni. The web-server ResFinder-2.1 was used to identify acquired antimicrobial resistance genes and two methods, the novel PointFinder (using BLAST) and an in-house method (mapping of raw WGS reads), were used to identify chromosomal point mutations. Results were compared with phenotypic antimicrobial susceptibility testing results. A total of 685 different phenotypic tests associated with chromosomal resistance to quinolones, polymyxin, rifampicin, macrolides and tetracyclines resulted in 98.4% concordance. Eleven cases of disagreement between tested and predicted susceptibility were observed: two C. jejuni isolates with phenotypic fluoroquinolone resistance and two with phenotypic erythromycin resistance and five colistin-susceptible E. coli isolates with a detected pmrB V161G mutation when assembled with Velvet, but not when using SPAdes or when mapping the reads. PointFinder proved, with high concordance between phenotypic and predicted antimicrobial susceptibility, to be a user-friendly web tool for detection of chromosomal point mutations associated with antimicrobial resistance.
登录
查看更多内容
影响因子：
2.6
作者：
Cavaco, Lina Maria;Frimodt-Moller, Niels;Aarestrup, Frank Moller
通讯作者：
Aarestrup, Frank Moller
影响因子：
16.6
作者：
Bradley P;Gordon NC;Walker TM;Dunn L;Heys S;Huang B;Earle S;Pankhurst LJ;Anson L;de Cesare M;Piazza P;Votintseva AA;Golubchik T;Wilson DJ;Wyllie DH;Diel R;Niemann S;Feuerriegel S;Kohl TA;Ismail N;Omar SV;Smith EG;Buck D;McVean G;Walker AS;Peto TE;Crook DW;Iqbal Z
通讯作者：
Iqbal Z
影响因子：
14.9
作者：
SIGMUND, CD;ETTAYEBI, M;MORGAN, EA
通讯作者：
MORGAN, EA
影响因子：
9.4
作者：
Joensen, Katrine Grimstrup;Scheutz, Flemming;Aarestrup, Frank M.
通讯作者：
Aarestrup, Frank M.
影响因子：
3.9
作者：
MAKOSKY, PC;DAHLBERG, AE
通讯作者：
DAHLBERG, AE