Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States of America.
Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, United States of America.
PLoS One. 2022 Mar 17;17(3):e0265445. doi: 10.1371/journal.pone.0265445. eCollection 2022.
Food animals are known reservoirs of multidrug-resistant (MDR) Escherichia coli, but information regarding the factors influencing colonization by these organisms is lacking. Here we report the genomic analysis of 66 MDR E. coli isolates from non-redundant veal calf fecal samples. Genes conferring resistance to aminoglycosides, β-lactams, sulfonamides, and tetracyclines were the most frequent antimicrobial resistance genes (ARGs) detected and included those that confer resistance to clinically significant antibiotics (blaCMY-2, blaCTX-M, mph(A), erm(B), aac(6')Ib-cr, and qnrS1). Co-occurrence analyses indicated that multiple ARGs significantly co-occurred with each other, and with metal and biocide resistance genes (MRGs and BRGs). Genomic analysis also indicated that the MDR E. coli isolated from veal calves were highly diverse. The most frequently detected genotype was phylogroup A-ST Cplx 10. A high percentage of isolates (50%) were identified as sequence types that are the causative agents of extra-intestinal infections (ExPECs), such as ST69, ST410, ST117, ST88, ST617, ST648, ST10, ST58, and ST167, and an appreciable number of these isolates encoded virulence factors involved in the colonization and infection of the human urinary tract. There was a significant difference in the presence of multiple accessory virulence factors (VFs) between MDR and susceptible strains. VFs associated with enterohemorrhagic infections, such as stx, tir, and eae, were more likely to be harbored by antimicrobial-susceptible strains, while factors associated with extraintestinal infections such as the sit system, aerobactin, and pap fimbriae genes were more likely to be encoded in resistant strains. A comparative analysis of SNPs between strains indicated that several closely related strains were recovered from animals on different farms indicating the potential for resistant strains to circulate among farms. These results indicate that veal calves are a reservoir for a diverse group of MDR E. coli that harbor various resistance genes and virulence factors associated with human infections. Evidence of co-occurrence of ARGs with MRGs, BRGs, and iron-scavenging genes (sit and aerobactin) may lead to management strategies for reducing colonization of resistant bacteria in the calf gut.
食源性动物是多药耐药（MDR）大肠杆菌的已知储层，但关于影响这些生物体定植的因素的信息尚不清楚。在这里，我们报告了来自非冗余犊牛粪便样本的 66 株 MDR 大肠杆菌分离株的基因组分析。检测到的赋予抗氨基糖苷类、β-内酰胺类、磺胺类和四环素类药物的抗性的基因是最常见的抗生素耐药基因（ARGs），其中包括那些赋予临床重要抗生素（blaCMY-2、blaCTX-M、mph(A)、erm(B)、aac(6')Ib-cr 和 qnrS1）耐药性的基因。共现分析表明，多个 ARGs 彼此之间以及与金属和杀生物剂耐药基因（MRGs 和 BRGs）显著共现。基因组分析还表明，从犊牛中分离出的 MDR 大肠杆菌具有高度多样性。最常检测到的基因型是 A-ST Cplx 10 phylogroup。相当一部分（50%）分离株被鉴定为肠外感染（ExPECs）的病原体，如 ST69、ST410、ST117、ST88、ST617、ST648、ST10、ST58 和 ST167，这些分离株中有相当数量编码了与人类尿路感染的定植和感染有关的毒力因子。在 MDR 和敏感菌株之间存在多种辅助毒力因子（VFs）的存在存在显著差异。与肠出血性感染相关的 VFs，如 stx、tir 和 eae，更有可能存在于对抗菌药物敏感的菌株中，而与肠外感染相关的因子，如 sit 系统、aerobactin 和 pap 菌毛基因，更有可能存在于耐药菌株中编码。对菌株之间 SNP 的比较分析表明，从不同农场的动物中回收了一些密切相关的菌株，表明耐药菌株有可能在农场之间传播。这些结果表明，犊牛是一组多样化的 MDR 大肠杆菌的储层，这些大肠杆菌携带与人类感染相关的各种耐药基因和毒力因子。ARGs 与 MRGs、BRGs 和铁摄取基因（sit 和 aerobactin）的共存证据可能导致减少犊牛肠道中耐药菌定植的管理策略。
