Zhao S, Tyson G H, Chen Y, Li C, Mukherjee S, Young S, Lam C, Folster J P, Whichard J M, McDermott P F
Division of Animal and Food Microbiology Office of Research, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA
Division of Animal and Food Microbiology Office of Research, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA.
Appl Environ Microbiol. 2015 Oct 30;82(2):459-66. doi: 10.1128/AEM.02873-15. Print 2016 Jan 15.
The objectives of this study were to identify antimicrobial resistance genotypes for Campylobacter and to evaluate the correlation between resistance phenotypes and genotypes using in vitro antimicrobial susceptibility testing and whole-genome sequencing (WGS). A total of 114 Campylobacter species isolates (82 C. coli and 32 C. jejuni) obtained from 2000 to 2013 from humans, retail meats, and cecal samples from food production animals in the United States as part of the National Antimicrobial Resistance Monitoring System were selected for study. Resistance phenotypes were determined using broth microdilution of nine antimicrobials. Genomic DNA was sequenced using the Illumina MiSeq platform, and resistance genotypes were identified using assembled WGS sequences through blastx analysis. Eighteen resistance genes, including tet(O), blaOXA-61, catA, lnu(C), aph(2″)-Ib, aph(2″)-Ic, aph(2')-If, aph(2″)-Ig, aph(2″)-Ih, aac(6')-Ie-aph(2″)-Ia, aac(6')-Ie-aph(2″)-If, aac(6')-Im, aadE, sat4, ant(6'), aad9, aph(3')-Ic, and aph(3')-IIIa, and mutations in two housekeeping genes (gyrA and 23S rRNA) were identified. There was a high degree of correlation between phenotypic resistance to a given drug and the presence of one or more corresponding resistance genes. Phenotypic and genotypic correlation was 100% for tetracycline, ciprofloxacin/nalidixic acid, and erythromycin, and correlations ranged from 95.4% to 98.7% for gentamicin, azithromycin, clindamycin, and telithromycin. All isolates were susceptible to florfenicol, and no genes associated with florfenicol resistance were detected. There was a strong correlation (99.2%) between resistance genotypes and phenotypes, suggesting that WGS is a reliable indicator of resistance to the nine antimicrobial agents assayed in this study. WGS has the potential to be a powerful tool for antimicrobial resistance surveillance programs.
本研究的目的是鉴定弯曲杆菌的抗菌药物耐药基因型，并通过体外抗菌药物敏感性试验和全基因组测序（WGS）评估耐药表型与基因型之间的相关性。作为国家抗菌药物耐药监测系统的一部分，从2000年至2013年从美国的人类、零售肉类以及食品生产动物的盲肠样本中获得了总共114株弯曲杆菌属菌株（82株大肠弯曲杆菌和32株空肠弯曲杆菌）用于研究。使用九种抗菌药物的肉汤微量稀释法测定耐药表型。使用Illumina MiSeq平台对基因组DNA进行测序，并通过blastx分析使用组装的WGS序列鉴定耐药基因型。鉴定出18个耐药基因，包括tet(O)、blaOXA-61、catA、lnu(C)、aph(2″)-Ib、aph(2″)-Ic、aph(2')-If、aph(2″)-Ig、aph(2″)-Ih、aac(6')-Ie-aph(2″)-Ia、aac(6')-Ie-aph(2″)-If、aac(6')-Im、aadE、sat4、ant(6')、aad9、aph(3')-Ic和aph(3')-IIIa，以及两个管家基因（gyrA和23S rRNA）中的突变。对给定药物的表型耐药性与一个或多个相应耐药基因的存在之间存在高度相关性。四环素、环丙沙星/萘啶酸和红霉素的表型与基因型相关性为100%，庆大霉素、阿奇霉素、克林霉素和泰利霉素的相关性在95.4%至98.7%之间。所有分离株对氟苯尼考敏感，未检测到与氟苯尼考耐药相关的基因。耐药基因型与表型之间存在很强的相关性（99.2%），这表明WGS是本研究中所检测的九种抗菌药物耐药性的可靠指标。WGS有潜力成为抗菌药物耐药监测计划的强大工具。
