ICAR-National Institute of Veterinary epidemiology and Disease Informatics (ICAR- NIVEDI), Yelahanka, Bengaluru, 560 064, India.
Department of Biotechnology School of Basic and Applied Sciences, Dayananda Sagar University, Kumaraswamy Layout, Bengaluru, Karnataka, 560078, India.
Mol Biol Rep. 2024 Mar 8;51(1):404. doi: 10.1007/s11033-024-09354-3.
Pathogenic and non-pathogenic strains of Escherichia coli harbouring antibiotic resistance genes (ARGs) from any source (clinical samples, animal settings, or environment) might be transmitted and contribute to the spread and increase of antibiotic resistance in the biosphere. The goal of this study was to investigate the genome to decipher the repertoire of ARGs, virulence genes carried by E. coli strains isolated from livestock, poultry, and their handlers (humans), and then unveil the genetic relatedness between the strains.
Whole genome sequencing was done to investigate the genetic makeup of E. coli isolates (n = 20) [swine (n = 2), cattle (n = 2), sheep (n = 4), poultry (n = 7), and animal handlers (n = 5)] from southern India. The detection of resistome, virulome, biofilm forming genes, mobile genetic elements (MGE), followed by multilocus sequence typing (MLST) and phylogenetic analyses, were performed.
E. coli strains were found to be multi drug resistant, with a resistome encompassing > 20 ARGs, the virulome-17-22 genes, and > 20 key biofilm genes. MGE analysis showed four E. coli isolates (host: poultry, swine and cattle) harbouring composite transposons with ARGs/virulence genes (bla, dfr, qnr/nleB, tir, eae,and esp) with the potential for horizontal transfer. MLST analyses revealed the presence of ST937 and ST3107 in both livestock/poultry and their handlers. Phylogenomic analyses with global E. coli isolates (human/livestock/poultry hosts) showed close relatedness with strains originating from different parts of the world (the United States, China, etc.).
The current study emphasizes the circulation of strains of pathogenic sequence types of clinical importance, carrying a diverse repertoire of genes associated with antibiotic resistance, biofilm formation and virulence properties in animal settings, necessitating immediate mitigation measures to reduce the risk of spread across the biosphere.
来自任何来源（临床样本、动物环境或环境）的携带抗生素耐药基因（ARGs）的致病性和非致病性大肠杆菌菌株可能会传播，并导致抗生素耐药性在生物圈中的传播和增加。本研究的目的是研究基因组以破译大肠杆菌菌株携带的 ARG 和毒力基因库，这些菌株分离自牲畜、家禽及其饲养员（人类），然后揭示菌株之间的遗传关系。
对来自印度南部的 20 株大肠杆菌分离株（猪 2 株、牛 2 株、绵羊 4 株、家禽 7 株和动物饲养员 5 株）进行全基因组测序，以研究其遗传组成。进行了耐药组、毒力组、生物膜形成基因、移动遗传元件（MGE）的检测，随后进行了多位点序列分型（MLST）和系统发育分析。
发现大肠杆菌菌株为多药耐药株，耐药组包含>20 个 ARG、毒力组-17-22 个基因和>20 个关键生物膜基因。MGE 分析显示，4 株大肠杆菌分离株（宿主：家禽、猪和牛）携带含有 ARG/毒力基因（bla、dfr、qnr/nleB、tir、eae 和 esp）的复合转座子，具有潜在的水平转移能力。MLST 分析显示，在牲畜/家禽及其饲养员中存在 ST937 和 ST3107。与来自世界不同地区（美国、中国等）的全球大肠杆菌分离株进行的系统基因组分析显示，它们之间存在密切的亲缘关系。
本研究强调了具有临床重要性的致病性序列类型的菌株在动物环境中循环，携带与抗生素耐药性、生物膜形成和毒力特性相关的基因多样性，需要立即采取缓解措施，以减少在整个生物圈中传播的风险。
