Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh.
Department of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh.
Braz J Microbiol. 2021 Jun;52(2):989-1004. doi: 10.1007/s42770-021-00441-2. Epub 2021 Feb 16.
Poultry originated Escherichia fergusonii (POEF), an emerging bacterial pathogen, causes a wide range of intestinal and extra-intestinal infections in the poultry industry which incurred significant economic losses worldwide. Chromosomal co-existence of antibiotics and metal resistance genes has recently been the focal point of POEF isolates besides its pathogenic potentials. This study reports the complete genome analysis of POEF strain OTSVEF-60 from the poultry originated samples of Bangladesh. The assembled draft genome of the strain was 4.2 Mbp containing 4503 coding sequences, 120 RNA (rRNA = 34, tRNA = 79, ncRNA = 7), and three intact phage signature regions. Forty-one broad range antibiotic resistance genes (ARGs) including dfrA12, qnrS1, bla, aadA2, tet(A), and sul-2 along with multiple efflux pump genes were detected, which translated to phenotypic resistant patterns of the pathogen to trimethoprim, fluoroquinolones, β-lactams, aminoglycoside, tetracycline, and sulfonamides. Moreover, 22 metal resistance genes were found co-existing within the genome of the POEF strain, and numerous virulence genes (VGs) coding for cit (AB), feo (AB), fep (ABCG), csg (ABCDEFG), fliC, ompA, gadA, ecpD, etc. were also identified throughout the genome. In addition, we detected a class I integron gene cassette harboring dfrA12, ant (3″)-I, and qacEΔ-sul2 genes; 42 copies of insertion sequence (IS) elements; and two CRISPR arrays. The genomic functional analysis predicted several metabolic pathways related to motility, flagellar assembly, epithelial cell invasion, quorum sensing, biofilm formation, and biosynthesis of vitamin, co-factors, and secondary metabolites. We herein for the first time detected multiple ARGs, VGs, mobile genetic elements, and some metabolic functional genes in the complete genome of POEF strain OTSVEF-60, which might be associated with the pathogenesis, spreading of ARGs and VGs, and subsequent treatment failure against this emerging avian pathogen with currently available antimicrobials.
家禽源弗格森埃希氏菌（POEF）是一种新兴的细菌病原体，可引起家禽业广泛的肠道和肠道外感染，给全球造成了巨大的经济损失。除了其致病潜力外，POEF 分离株中抗生素和金属耐药基因的染色体共存最近也成为了焦点。本研究报告了来自孟加拉国家禽源样本的 POEF 菌株 OTSVEF-60 的全基因组分析。该菌株的组装草案基因组为 4.2 Mbp，包含 4503 个编码序列、120 个 RNA（rRNA = 34、tRNA = 79、ncRNA = 7）和三个完整的噬菌体特征区域。检测到 41 种广谱抗生素耐药基因（ARGs），包括 dfrA12、qnrS1、bla、aadA2、tet(A) 和 sul-2，以及多种外排泵基因，这使得该病原体对甲氧苄啶、氟喹诺酮类、β-内酰胺类、氨基糖苷类、四环素类和磺胺类药物产生表型耐药。此外，在 POEF 菌株的基因组中还发现了 22 种金属耐药基因，并且在整个基因组中还发现了许多编码 cit(AB)、feo(AB)、fep(ABCG)、csg(ABCDEFG)、fliC、ompA、gadA、ecpD 等的毒力基因 (VGs)。此外，我们还检测到一个携带 dfrA12、ant(3″)-I 和 qacEΔ-sul2 基因的 I 类整合子基因盒；42 个插入序列 (IS) 元件；和两个 CRISPR 数组。基因组功能分析预测了与运动性、鞭毛组装、上皮细胞入侵、群体感应、生物膜形成以及维生素、辅助因子和次生代谢物生物合成相关的多种代谢途径。我们首次在 POEF 菌株 OTSVEF-60 的全基因组中检测到多种 ARGs、VGs、移动遗传元件和一些代谢功能基因，这些基因可能与该新兴禽源病原体的发病机制、ARGs 和 VGs 的传播以及随后对现有抗生素的治疗失败有关。
