Table_7_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、家畜与环境中的抗生素耐药性之间存在关联。本研究旨在对尼日利亚埃多州来源的、携带抗生素耐药性的牛源与环境源肠杆菌科（Enterobacteriaceae）分离株进行特征分析。2015年3月至5月期间，研究人员从尼日利亚埃多州3个屠宰场的健康牛只的150份粪便样本中，分离得到共计109株连续的肠杆菌科分离株。同理，研究人员从不同来源的共计100份环境样本中，分离得到43株肠杆菌科分离株。研究采用标准微生物学技术从样本中分离并鉴定上述菌株。分离得到的菌株首先通过Microbact革兰阴性鉴定系统进行预鉴定，随后借助基质辅助激光解吸电离飞行时间（MALDI-TOF）质谱以及核糖体多位点序列分型（rMLST）进行确认。采用柯赫-鲍尔（Kirby-Bauer）法对14种抗生素开展药敏试验。为完成菌株特征分析与耐药决定因子鉴定，研究对部分分离株开展了全基因组测序（WGS）。在109株动物源与43株环境源肠杆菌科分离株中，依据筛选标准分别有18株（占比17%）与8株（占比19%）呈现抗生素耐药性，随后对这些菌株开展了进一步的全基因组测序分析。所有（100%）耐药牛源及环境源肠杆菌科分离株中均检出耐药基因。上述耐药决定因子分别包括β-内酰胺酶基因、氨基糖苷类修饰酶、qnr基因、磺胺类耐药基因、四环素类耐药基因以及甲氧苄啶耐药基因。在18株耐药动物源分离株与8株耐药环境源分离株中，分别有3株（占比17%）与2株（占比25%）为多重耐药（MDR）菌株，其携带的耐药决定因子包括外排泵基因、调控抗生素外排的调控系统以及抗生素靶点改变相关基因。本研究揭示了尼日利亚牛源与环境源肠杆菌科分离株中抗生素耐药性（尤其是多重耐药菌株）的传播情况。动物与环境中此类耐药菌株的存在构成了严重的公共卫生隐患——由这些菌株引发的感染往往难以选择治疗方案，也印证了这一点。据我们所知，本研究是尼日利亚首次针对牛源与环境源肠杆菌科分离株的抗生素耐药性开展的详细基因组特征分析报道。