摘要

全基因组测序（WGS）已成为公共卫生监测和爆发检测的快速且经济实惠的工具。在这项研究中，我们使用IlluminiaMiSeq®对2015年从零售家禽肉获得的589株弯曲杆菌分离株进行测序，作为国家抗菌素耐药监测系统（NARMS）的一部分。 WGS数据被用于鉴定弯曲杆菌种并比较抗性基因型和表型之间的一致性。 WGS使用gyrA序列信息准确鉴定了386个空肠弯曲杆菌和203个大肠杆菌。将10个抗性基因，包括tetO，blaOXA-61，aph（2“） - Ic，aph（2”） - If，aph（2“） - Ig，aph（3'） - 通过WGS分析确定aardE，aph（3“） - VIIa和Inu（C）加上管家基因中的突变（位置86处的gyrA，位置2074和2075处的23S rRNA）。总体而言，对给定药物的表型抗性与已知抗性基因的存在具有高度一致性。环丙沙星，萘啶酸，庆大霉素，阿奇霉素和氟苯尼考的抗药性和易感表型与基因型之间的一致性为100％。四环素，克林霉素和泰利霉素观察到一些差异。抗性表型与基因型的一致性为67.9％〜100％;而易感表型和基因型的一致性范围为98.0％〜99.6％。我们的研究表明WGS可以正确识别弯曲杆菌种类并以高度的准确度预测抗微生物药物耐药性。

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 589 Campylobacter isolates obtained in 2015 from retail poultry meats as part of the National Antimicrobial Resistance Monitoring System (NARMS). WGS data were used to identify the Campylobacter species and to compare the concordance between resistance genotypes and phenotypes. WGS accurately identified 386 C. jejuni and 203C. coli using gyrA sequence information. Ten resistance genes, including tetO, blaOXA-61, aph(2″)-Ic, aph(2″)-If, aph(2″)-Ig, aph(3’)-III, ant(6)-1a, aadE, aph(3”)-VIIa, and Inu(C), plus mutations in housekeeping genes (gyrA at 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 identify Campylobacterspecies and predict antimicrobial resistance with a high degree of accuracy.

https://www.sciencedirect.com/science/article/pii/S0740002017308857