Table_1_Genetic Characterization of Antibiotic Resistant Enterobacteriaceae Isolates From Bovine Animals and the Environment in Nigeria.xlsx

There is a link between antibiotic resistance in humans, livestock and the environment. This study was carried out to characterize antibiotic resistant bovine and environmental Enterobacteriaceae isolates from Edo state, Nigeria. A total of 109 consecutive isolates of Enterobacteriaceae were isolated from March–May 2015 from 150 fecal samples of healthy bovine animals from three farms at slaughter in Edo state Nigeria. Similarly, 43 Enterobacteriaceae isolates were also obtained from a total of 100 environmental samples from different sources. Isolates were recovered and identified from samples using standard microbiological techniques. Recovered isolates were pre-identified by the Microbact Gram-Negative identification system and confirmed with Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry and ribosomal multilocus sequence typing (rMLST). Antibiotic susceptibility testing was carried out by Kirby-Bauer method for 14 antibiotics. Whole genome sequencing (WGS) was carried out for isolate characterization and identification of resistance determinants. Out of 109 animal and 43 environmental Enterobacteriaceae isolates, 18 (17%) and 8 (19%) isolates based on selection criteria showed antibiotic resistance and were further investigated by whole genome sequencing (WGS). Resistance genes were detected in all (100%) of the resistant bovine and environmental Enterobacteriaceae isolates. The resistance determinants included β-lactamase genes, aminoglycoside modifying enzymes, qnr genes, sulfonamide, tetracycline and trimethoprim resistance genes, respectively. Out of the 18 and 8 resistant animal and environmental isolates 3 (17%) and 2 (25%) were multidrug resistant (MDR) and had resistance determinants which included efflux genes, regulatory systems modulating antibiotic efflux and antibiotic target alteration genes. Our study shows the dissemination of antibiotic resistance especially MDR strains among Nigerian bovine and environmental Enterobacteriaceae isolates. The presence of these resistant strains in animals and the environment constitute a serious health concern indicated by the difficult treatment options of the infections caused by these organisms. To the best of our knowledge we report the first detailed genomic characterization of antibiotic resistance in bovine and environmental Enterobacteriaceae isolates for Nigeria.

人类、家畜与环境之间的抗生素耐药性存在着密切的联系。本研究旨在对尼日利亚埃多州分离得到的抗生素耐药性牛源和环境肠杆菌科细菌进行特征描述。自2015年3月至5月，共从尼日利亚埃多州三个屠宰场的150份健康牛只粪便样本中分离出109株连续的肠杆菌科细菌。同样，从不同来源的100份环境样本中亦获得了43株肠杆菌科细菌分离株。通过标准微生物学技术从样本中恢复并鉴定了分离株，初步鉴定采用Microbact革兰氏阴性鉴定系统，并通过基质辅助激光解吸电离飞行时间质谱（MALDI-TOF）和核糖体多基因序列分型（rMLST）进行确认。对14种抗生素进行了抗生素敏感性测试。为了分离株的特征描述和耐药决定子的鉴定，进行了全基因组测序（WGS）。在109株动物和43株环境肠杆菌科细菌分离株中，根据选择标准，18株（17%）和8株（19%）分离株表现出抗生素耐药性，并通过全基因组测序（WGS）进行了进一步研究。在所有耐药的牛和环境肠杆菌科细菌分离株中（100%），均检测到耐药基因。耐药决定子包括β-内酰胺酶基因、氨基糖苷类修饰酶、qnr基因、磺胺类、四环素和甲氧苄啶耐药基因等。在18株和8株耐药的动物和环境分离株中，3株（17%）和2株（25%）为多重耐药性（MDR），具有包括外排基因、调节抗生素外排的调节系统以及抗生素靶点改变基因在内的耐药决定子。本研究表明，在尼日利亚的牛和环境肠杆菌科细菌分离株中，特别是多重耐药性菌株的抗生素耐药性正在传播。动物和环境中这些耐药菌株的存在构成了严重的健康问题，这些生物体引起的感染治疗困难，这表明了这一问题的严重性。据我们所知，我们首次报告了尼日利亚牛和环境肠杆菌科细菌分离株抗生素耐药性的详细基因组特征。