摘要
目标
本研究的目的是描述12个编码抗微生物耐药性基因（ARGs）的大肠杆菌分离株的基因组序列，这些分离株是从复合乳制品动物粪便样本中分离出来的。
方法
这些分离株是在2013年至2014年间从一项评估美国宾夕法尼亚州乳制品经营是否存在耐药性的大型研究中回收的。在Illumina NextSeq 500平台上对基因组草案进行测序，并使用SPAdes进行组装。
后果
总共鉴定出69个ARG，这些ARG被分为20个独特的基因，对8类抗菌药物产生耐药性。按照检测频率降低的顺序，这些类别为氨基糖苷类、四环素类、磺酰胺类、β-内酰胺类、酚类、甲氧苄啶类、磷霉素类和大环内酯类林可酰胺链脲菌素B（MLS）。在抗性分离株中，鉴定出11种序列类型（ST），其中ST86检测了两次。尽管没有在体内评估致病性，但多个基因组编码了与严重胃肠道和肠外感染有关的毒力因子，包括一个志贺产毒分离株。
结论
这项研究的结果表明，乳制品动物粪便中存在抗微生物耐药性大肠杆菌，编码与严重人类感染有关的毒力因子。
ABSTRACT
Objectives
The aim of this study was to describe the genome sequences of 12 Escherichia coli isolates that encode antimicrobial resistance genes (ARGs) and were isolated from composite dairy animal faecal samples.

Methods
The isolates were recovered between 2013 and 2014 from a larger study evaluating the presence of resistance on dairy operations in Pennsylvania, USA. The draft genomes were sequenced on an Illumina NextSeq 500 platform and were assembled using SPAdes.

Results
In total, 69 ARGs were identified, and these were categorized into 20 unique genes conferring resistance to eight classes of antimicrobials. In order of decreasing frequency of detection, these classes were aminoglycosides, tetracyclines, sulphonamides, β-lactams, phenicols, trimethoprim, fosfomycin, and macrolide-lincosamide-streptogramin B (MLS). Among the resistant isolates, 11 sequence types (ST) were identified, with ST86 detected twice. Although pathogenicity was not evaluated in vivo, multiple genomes encoded virulence factors involved in severe gastrointestinal and extraintestinal infections, including a single Shiga-toxigenic isolate.

Conclusion
The results of this study demonstrate the presence of antimicrobial-resistant E. coli in dairy animal faeces encoding virulence factors involved in severe human infections.

https://www.sciencedirect.com/science/article/pii/S2213716522000832