El-Adawy Hosny, Hotzel Helmut, García-Soto Silvia, Tomaso Herbert, Hafez Hafez M, Schwarz Stefan, Neubauer Heinrich, Linde Jörg
Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany.
Faculty of Veterinary Medicine, Kafrelsheikh University, Kafr El-Sheikh, Egypt.
Front Vet Sci. 2023 Feb 16;10:1092179. doi: 10.3389/fvets.2023.1092179. eCollection 2023.
(.) is a zoonotic bacterium of public health significance. The present investigation was designed to assess the epidemiology and genetic heterogeneity of recovered from commercial turkey farms in Germany using whole-genome sequencing. The Illumina MiSeq technology was used to sequence 66 isolates obtained between 2010 and 2011 from commercial meat turkey flocks located in ten German federal states. Phenotypic antimicrobial resistance was determined. Phylogeny, resistome, plasmidome and virulome profiles were analyzed using whole-genome sequencing data. Genetic resistance markers were identified with bioinformatics tools (AMRFinder, ResFinder, NCBI and ABRicate) and compared with the phenotypic antimicrobial resistance. The isolates were assigned to 28 different sequence types and 11 clonal complexes. The average pairwise single nucleotide-polymorphisms distance of 14,585 SNPs (range: 0-26,540 SNPs) revealed a high genetic distinction between the isolates. Thirteen virulence-associated genes were identified in isolates. Most of the isolates harbored the genes A (83.3%) and B (78.8%). The N gene associated with the Guillain-Barré syndrome was detected in nine (13.6%) isolates. The genes for resistance to ampicillin ( ), tetracycline [(O)], neomycin [(3')-IIIa], streptomycin () and streptothricin () were detected in isolated using WGS. A gene cluster comprising the genes (3')-IIIa and was present in six isolates. The single point mutation T86I in the housekeeping gene conferring resistance to quinolones was retrieved in 93.6% of phenotypically fluoroquinolone-resistant isolates. Five phenotypically erythromycin-susceptible isolates carried the mutation A103V in the gene for the ribosomal protein L22 inferring macrolide resistance. An assortment of 13 β-lactam resistance genes ( variants) was detected in 58 isolates. Out of 66 sequenced isolates, 28 (42.4%) carried plasmid-borne contigs. Six isolates harbored a pTet-like plasmid-borne contig which carries the (O) gene. This study emphasized the potential of whole-genome sequencing to ameliorate the routine surveillance of . Whole-genome sequencing can predict antimicrobial resistance with a high degree of accuracy. However, resistance gene databases need curation and updates to revoke inaccuracy when using WGS-based analysis pipelines for AMR detection.
（.）是一种具有公共卫生意义的人畜共患病细菌。本研究旨在利用全基因组测序评估从德国商业火鸡养殖场分离出的（.）的流行病学和遗传异质性。使用Illumina MiSeq技术对2010年至2011年间从德国十个联邦州的商业肉用火鸡群中获得的66株（.）分离株进行测序。测定了表型抗菌药物耐药性。利用全基因组测序数据分析了系统发育、耐药基因组、质粒组和毒力组图谱。使用生物信息学工具（AMRFinder、ResFinder、NCBI和ABRicate）鉴定遗传耐药标记，并与表型抗菌药物耐药性进行比较。这些分离株被分为28种不同的序列类型和11个克隆复合体。14585个单核苷酸多态性（范围：0 - 26540个单核苷酸多态性）的平均成对距离显示分离株之间存在高度遗传差异。在（.）分离株中鉴定出13个毒力相关基因。大多数分离株携带基因A（83.3%）和基因B（78.8%）。在9株（13.6%）分离株中检测到与吉兰 - 巴雷综合征相关的N基因。使用全基因组测序在分离株中检测到对氨苄西林（）、四环素[（O）]、新霉素[（3'）-IIIa]、链霉素（）和链丝菌素（）的耐药基因。一个包含基因（3'）-IIIa和的基因簇存在于6株分离株中。在93.6%的表型氟喹诺酮耐药分离株中检测到管家基因中赋予对喹诺酮耐药性的单点突变T86I。5株表型红霉素敏感的分离株在核糖体蛋白L22基因中携带A103V突变，推断具有大环内酯耐药性。在58株（.）分离株中检测到13种β-内酰胺耐药基因（变体）。在66株测序分离株中，28株（42.4%）携带质粒携带的重叠群。6株分离株含有携带（O）基因的类pTet质粒携带的重叠群。本研究强调了全基因组测序在改善（.）常规监测方面的潜力。全基因组测序可以高度准确地预测抗菌药物耐药性。然而，在使用基于全基因组测序的分析流程进行抗菌药物耐药性检测时，耐药基因数据库需要整理和更新以消除不准确之处。
