摘要
      鸭疫里氏杆菌是水禽的一种重要病原体，通常具有多药耐药性。本研究评估了鸭疫里默氏菌抗生素耐药性和抗生素耐药性基因（ARGs）的现状，比较了不同检测方法的结果，并评价了一种研究鸭疫里默氏菌抗生素耐药与ARGs之间关系的新方法。在本研究中，从几个农场的鸭子身上分离到51株鸭疫里默氏菌，评估了它们对28种抗生素的耐药性，并对分离株进行了全基因组测序。对鸭疫里默氏菌携带的ARGs数量进行了预测、比较和分析，并评估了ARGs与抗生素耐药性表型之间的一致性。评估了全基因组框架图测序和组装过程中抗性基因丢失的可能性，并对一种新的ARG检测方法进行了初步测试。51株鸭疫里默氏菌具有多药耐药性（MDR），对氨基糖苷类、甲氧苄啶类、林可酰胺类、多肽类和大环内酯类具有高水平的耐药性。基于51株菌株的全基因组框架图，使用ABRITE软件的3个本地数据库和CARD网站的1个在线数据库来检测ARGs，平均每个分离株鉴定出4至5个ARGs。尽管检测结果因使用的数据库而异，但总体性能是一致的。在线网站检测到的ARG类型比ABRITE软件更多。评估了ARGs与抗生素耐药性表型之间的相关性，并确定ermF基因可能是调节鸭疫里氏杆菌大环内酯类耐药性的关键ARGs。研究和检测鸭疫里默氏菌ARGs的方法简便、快速，具有很强的准确性和针对性。本文报道的ARGs检测方法结合了PCR和基因组检测的优势，可以大大减少工作量，更准确地检测ARGs。
Abstract
Riemerella anatipestifer is an important pathogen in waterfowl, and is generally multidrug resistant. This study assessed the current status of Riemerella anatipestifer antibiotic resistance and antibiotic-resistance genes (ARGs), compared the results of different detection methods, and evaluated a new method of studying the association between antibiotic resistance and ARGs in Riemerella anatipestifer. In this study, 51 strains of Riemerella anatipestifer were isolated from ducks on several farms, their resistance to 28 antibiotics was assessed, and the isolates were subjected to whole-genome sequencing. The number of ARGs carried by Riemerella anatipestifer was predicted, compared, and analyzed, and the consistency between ARGs and antibiotic-resistance phenotypes was assessed. The potential for loss of resistance genes during the sequencing and assembly of genome-wide framework map was assessed, and a new ARG detection method was pilot tested. The 51 strains of Riemerella anatipestifer were multidrug resistant (MDR) and had high level of resistance to aminoglycosides, trimethoprim, lincosamides, polypeptides, and macrolides. Based on the genome-wide framework map of the 51 strains, 3 local databases of ABRicate software and 1 online database of CARD website were used to detect ARGs, and a mean of 4 to 5 ARGs were identified per isolate. Although the detection results differed according to the database used, the general performance was consistent. The online website detected more types of ARGs than the ABRicate software. The association between ARGs and antibiotic-resistance phenotypes was assessed, and the ermF gene was identified as a possible key ARGs regulating macrolide resistance of Riemerella anatipestifer. The method used to investigate and detect Riemerella anatipestifer ARGs was convenient and rapid, and had strong accuracy and pertinence. The ARGs detection method reported here combined the advantages of PCR and genome detection, and could greatly reduce workload and detect ARGs more precisely.

https://www.sciencedirect.com/science/article/pii/S003257912200699X