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首页> 外文期刊>Food microbiology >Use of whole-genome sequencing for Campylobacter surveillance from NARMS retail poultry in the United States in 2015
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Use of whole-genome sequencing for Campylobacter surveillance from NARMS retail poultry in the United States in 2015

机译：2015年，使用全基因组测序对美国NARMS零售家禽的弯曲杆菌进行监测

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Whole genome sequencing (WGS) has become a rapid and affordable tool for public health surveillance and outbreak detection. In this study, we used the Illuminia MiSeq®to sequence 589Campylobacterisolates obtained in 2015 from retail poultry meats as part of the National Antimicrobial Resistance Monitoring System (NARMS). WGS data were used to identify theCampylobacterspecies and to compare the concordance between resistance genotypes and phenotypes. WGS accurately identified386 C. jejuniand 203C. coliusinggyrAsequence information. Ten resistance genes, includingtetO, blaOXA-61, aph(2″)-Ic, aph(2″)-If, aph(2″)-Ig, aph(3’)-III, ant(6)-1a, aadE, aph(3”)-VIIa,andInu(C), plus mutations in housekeeping genes (gyrAat position 86, 23S rRNA at position 2074 and 2075), were identified by WGS analysis. Overall, there was a high concordance between phenotypic resistance to a given drug and the presence of known resistance genes. Concordance between both resistance and susceptible phenotypes and genotype was 100% for ciprofloxacin, nalidixic acid, gentamicin, azithromycin, and florfenicol. A few discrepancies were observed for tetracycline, clindamycin, and telithromycin. The concordance between resistance phenotype and genotype ranged from 67.9% to 100%; whereas, the concordance between susceptible phenotype and genotype ranged from 98.0% to 99.6%. Our study demonstrates that WGS can correctly identifyCampylobacterspecies and predict antimicrobial resistance with a high degree of accuracy.
机译：全基因组测序（WGS）已成为用于公共卫生监视和暴发检测的快速且负担得起的工具。在这项研究中，我们使用IlluminiaMiSeq®测序了2015年从零售家禽肉中获得的589变形杆菌，作为国家抗菌素耐药性监测系统（NARMS）的一部分。 WGS数据用于鉴定弯曲杆菌属物种，并比较耐药基因型和表型之间的一致性。 WGS准确地确定了386 C. jejuniand 203C。 coliusinggyr序列信息。十个抗性基因，包括tetO，blaOXA-61，aph（2″）-Ic，aph（2″）-If，aph（2″）-Ig，aph（3'）-III，ant（6）-1a，aadE ，aph（3”）-VIIa和Inu（C），加上管家基因的突变（gyrAat 86位，23S rRNA 2074和2075位），通过WGS分析鉴定。总体而言，对特定药物的表型耐药性与已知耐药基因的存在高度一致。环丙沙星，萘啶酸，庆大霉素，阿奇霉素和氟苯尼考的​​耐药性和易感表型与基因型之间的一致性为100％。观察到四环素，克林霉素和telithromycin的差异。耐药表型与基因型之间的一致性范围为67.9％至100％。易感表型与基因型之间的一致性为98.0％至99.6％。我们的研究表明，WGS可以正确地识别弯曲杆菌属物种，并可以高度准确地预测抗菌素耐药性。

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