摘要
      弗氏柠檬酸杆菌是医院感染的常见来源，也是腹泻疾病的常见原因，近年来，它对各种抗菌药物的耐药性也越来越强。在本研究中，我们筛选并鉴定了从一只驯养病鸭中获得的耐多药弗氏梭菌分离株，以更好地了解该分离株的遗传多样性、分子流行病学以及与抗微生物耐药性基因（ARGs）和毒力因子基因（VFGs）相关的潜在因素。采用培养、染色、生化、聚合酶链式反应和基质辅助激光解吸/电离飞行时间法分离弗氏梭菌BAU_TM8菌株。菌株的MDR特性通过圆盘扩散试验确定。弗氏梭菌BAU_TM8的完整基因组序列使用Illumina NextSeq2000平台进行。使用几个开源数据库鉴定了弗氏C.freundii BAU_TM8菌株的ARGs、VFGs和基因组功能特征。该菌株的序列类型为ST669，致病性指数为0.919，为强毒株。通过系统发育分析，该菌株与从美国和中国的人类和环境样本中分离的两个菌株密切相关，尽管地理距离很大。弗氏C.freundii BAU_TM8菌株由40个AGR组成，编码对19种抗菌类别的耐药性，与分离物的表型特性显示出约85%的相似性。此外，毒力因子数据库在该菌株中检测到66个VFG。该菌株包含1581个子系统，子系统覆盖率为33%，2275个基因编码氨基酸衍生物、碳水化合物代谢、蛋白质代谢、辅因子、维生素、辅基、色素、呼吸、运动性和趋化性、应激反应、DNA代谢、核苷和核苷酸等。在本研究中检测到的弗氏梭菌BAU_TM8菌株中普遍存在ARGs和VFGs，这突出了人们对人类、动物和环境中抗微生物耐药性的日益关注。
Abstract
Citrobacter freundii is a prevalent source of nosocomial infections and a well-known cause of diarrheal diseases, and in recent years, it has also become increasingly resistant to a variety of antimicrobials. In this study, we screened and characterized a multidrug-resistant (MDR) C. freundii isolate obtained from a domesticated diseased duck to better understand the genetic variety, molecular epidemiology, and underlying factors linked to the antimicrobial resistance genes (ARGs) and virulence factor genes (VFGs) of the isolate. The C. freundii BAU_TM8 strain was isolated using culturing, staining, biochemical, polymerase chain reaction, and Matrix-assisted laser desorption/ionization-time of flight methods. The MDR properties of the strain were determined by a disk diffusion test. The complete genomic sequence of C. freundii BAU_TM8 was performed using the Illumina NextSeq2000 platform. The ARGs, VFGs, and genomic functional characteristics of the C. freundii BAU_TM8 strain were identified using several open-source databases. The sequence types of this strain was ST669, and the pathogenicity index of the strain was 0.919, indicating a highly virulent strain. Using phylogenetic analysis, this strain was closely related to two strains isolated from human and environmental samples in the USA and China, despite huge geographical distance. The C. freundii BAU_TM8 strain consisted of 40 AGRs encoding resistance to 19 antimicrobial categories, showing about 85% similarity with the phenotypic properties of the isolate. Moreover, the virulence factor database detected 66 VFGs in this strain. This strain contained 1581 subsystems, having 33% subsystem coverage and 2275 genes encoding amino acid derivatives, carbohydrate metabolism, protein metabolism, cofactors, vitamins, prosthetic groups, pigments, respiration, motility and chemotaxis, stress response, DNA metabolism, nucleosides and nucleotides, and others. The ubiquitous occurrence of ARGs and VFGs in the C. freundii BAU_TM8 strain detected in this study highlights the growing concern of antimicrobial resistance in humans, animals, and environments.

https://www.researchsquare.com/article/rs-2608165/v1