Tree M, Lam T J G M, McDougall S, Beggs D S, Robertson I D, Barnes A L, Chopra A, Ram R, Stockman C A, Kent T C, Aleri J W
School of Veterinary Medicine, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA 6150, Australia.
GD Animal Health, Deventer, and Faculty of Veterinary Medicine Utrecht University, 3584 CS Utrecht, the Netherlands.
J Dairy Sci. 2025 Jan;108(1):803-820. doi: 10.3168/jds.2024-25157. Epub 2024 Oct 5.
This study aimed to determine the prevalence of antimicrobial resistance (AMR) in commensal Escherichia coli from healthy lactating cows and calves in the Mediterranean pasture-based feeding dairy system of Western Australia (WA). Fecal samples were collected from healthy adult lactating cows and healthy calves from dairy farms in WA. Presumptive commensal E. coli was isolated from these samples and confirmed using matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry. Broth microdilution was used to assess the prevalence and the phenotypic AMR profiles of the E. coli isolates to 8 antimicrobial agents of dairy industry and human importance. The minimum inhibitory concentration for each isolate was interpreted using the epidemiologic cutoff (ECOFF) and Clinical and Laboratory Standards Institute breakpoints. Genomic characterization provided multilocus sequence types and AMR genes for a selection of isolates categorized as nonwild type (NWT) by ECOFF values for the combination of ampicillin, trimethoprim-sulfamethoxazole, and tetracycline. From a total of 1,117 fecal samples (633 adult, 484 calf) collected across 26 randomly selected farms, 891 commensal E. coli isolates were recovered (541 adult, 350 calf). Commensal E. coli classified as NWT was highest for ampicillin for both adult (68.8%; 95% CI [64.7, 72.7]) and calf feces (67.1%; 95% CI [62.0, 72.0]). A large proportion of tetracycline NWT and trimethoprim-sulfamethoxazole NWT organisms were also identified from calf feces, being 44.0% (95% CI [38.7, 49.4]) and 24.6% (95% CI [20.2, 29.4]), respectively. Clinical resistance prevalence was low, being higher for calves than for adult feces for ampicillin (adult: 7.8%, 95% CI [5.7, 10.3]; calf: 30.0%, 95% CI [25.2, 35.1]), tetracycline (adult: 6.3%, 95% CI [4.4, 8.7]; calf: 40.3%, 95% CI [35.1, 45.6]), and trimethoprim-sulfamethoxazole (adult: 2.6%, 95% CI [1.4, 4.3]; calf: 22.0%, 95% CI [17.7, 26.7]). Commensal E. coli originating from calf feces was significantly higher in NWT prevalence compared with adult feces for ciprofloxacin, gentamicin, tetracycline, and trimethoprim-sulfamethoxazole. The overall number of antimicrobials an isolate was classified as NWT toward varied among farms and was significantly higher for isolates originating from calf rather than adult feces. The strain type and sampling source of the commensal E. coli investigated were both associated with the commonality of the resultant resistance genome. Clinical resistance and NWT classification were highest for ampicillin, tetracycline, and trimethoprim-sulfamethoxazole, all antimicrobials commonly used in the treatment of dairy cattle in Australia. Although highly variable across farms, commensal E. coli isolated from healthy dairy calf feces had significantly higher NWT and multidrug resistance (MDR) prevalence compared with feces from healthy adult lactating dairy cows. The resistant genome identified in MDR isolates, although not always consistent with the phenotype, included QnrS1 and genes encoding AmpC β-lactamase and aminoglycoside phosphotransferase.
本研究旨在确定西澳大利亚州（WA）基于地中海牧场饲养的奶牛养殖系统中，健康泌乳奶牛和犊牛共生大肠杆菌的抗菌药物耐药性（AMR）流行情况。从WA的奶牛场采集了健康成年泌乳奶牛和健康犊牛的粪便样本。从这些样本中分离出疑似共生大肠杆菌，并使用基质辅助激光解吸/电离飞行时间质谱进行确认。采用肉汤微量稀释法评估大肠杆菌分离株对8种对乳制品行业和人类具有重要意义的抗菌药物的流行情况和表型AMR谱。使用流行病学临界值（ECOFF）和临床与实验室标准协会的断点来解释每种分离株的最低抑菌浓度。基因组特征分析为根据氨苄西林、甲氧苄啶 - 磺胺甲恶唑和四环素组合的ECOFF值分类为非野生型（NWT）的部分分离株提供了多位点序列类型和AMR基因。在随机选择的26个农场共采集了1117份粪便样本（633份成年奶牛，484份犊牛），从中分离出891株共生大肠杆菌（541株成年奶牛，350株犊牛）。对于成年奶牛（68.8%；95%置信区间[64.7, 72.7]）和犊牛粪便（67.1%；95%置信区间[62.0, 72.0]），分类为NWT的共生大肠杆菌中氨苄西林耐药率最高。从犊牛粪便中还鉴定出很大比例的四环素NWT和甲氧苄啶 - 磺胺甲恶唑NWT菌株，分别为44.0%（95%置信区间[38.7, 49.4]）和24.6%（95%置信区间[20.2, 29.4]）。临床耐药率较低，氨苄西林方面犊牛高于成年奶牛粪便（成年奶牛：7.8%，95%置信区间[5.7, 10.3]；犊牛：30.0%，95%置信区间[25.2, 35.1]），四环素方面（成年奶牛：6.3%，95%置信区间[4.4, 8.7]；犊牛：40.3%，95%置信区间[35.1, 45.6]），甲氧苄啶 - 磺胺甲恶唑方面（成年奶牛：2.6%，95%置信区间[1.4, 4.3]；犊牛：22.0%，95%置信区间[17.7, 26.7]）。对于环丙沙星、庆大霉素、四环素和甲氧苄啶 - 磺胺甲恶唑，源自犊牛粪便的共生大肠杆菌NWT流行率显著高于成年奶牛粪便。分离株被分类为NWT的抗菌药物总数在不同农场之间有所不同，源自犊牛而非成年奶牛粪便的分离株显著更高。所研究的共生大肠杆菌的菌株类型和采样来源均与所得耐药基因组的共性相关。氨苄西林、四环素和甲氧苄啶 - 磺胺甲恶唑的临床耐药和NWT分类最高，这些都是澳大利亚奶牛治疗中常用的抗菌药物。尽管不同农场之间差异很大，但与健康成年泌乳奶牛的粪便相比，从健康奶牛犊粪便中分离出的共生大肠杆菌具有显著更高的NWT和多重耐药（MDR）流行率。在MDR分离株中鉴定出的耐药基因组，尽管并不总是与表型一致，但包括QnrS1以及编码AmpCβ - 内酰胺酶和氨基糖苷磷酸转移酶的基因。
