Onyeka Libby Obumneke, Adesiyun Abiodun A, Ismail Arshad, Allam Mushal, Keddy Karen H, Thompson Peter N
Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Onderstepoort 0110, South Africa.
Department of Veterinary Public Health and Preventive Medicine, College of Veterinary Medicine, Michael Okpara University of Agriculture, Umudike 440101, Abia State, Nigeria.
Pathogens. 2024 Aug 29;13(9):732. doi: 10.3390/pathogens13090732.
We used whole genome sequencing (WGS) as an epidemiologic surveillance tool to elucidate the transmission dynamics of Shiga toxin-producing (STEC) strains along the beef production chain in South Africa. Isolates were obtained from a cattle farm, abattoirs and retail outlets. Isolates were analysed using WGS on a MiSeq platform (Illumina, San Diego, CA, USA) and phylogenetic analysis was carried out. Of the 85 isolates, 39% (33) carried the gene and 61% (52) had lost the gene. The prevalence of subtypes was as follows; 55% (18/33), 52% (17/33), 55% (18/33), 27% (9/33), 30% (10/33) and 15% (5/33). Thirty-five different serogenotypes were detected, of which 65% (56) were flagellar H-antigens and 34% (29) were both O-antigens and flagellar H-antigens. We identified 50 different sequence types (STs), and only nine of the isolates were assigned to three different clonal complexes. Core genome phylogenetic analysis revealed genetic relatedness, and isolates clustered mainly according to their STs and serogenotypes regardless of subtypes. This study provides evidence of horizontal transmission and recirculation of STEC strains in Gauteng province and demonstrates that every stage of the beef production chain plays a significant role in STEC entry into the food chain.
我们使用全基因组测序（WGS）作为一种流行病学监测工具，以阐明南非牛肉生产链中产志贺毒素大肠杆菌（STEC）菌株的传播动态。分离株取自一个养牛场、屠宰场和零售店。使用MiSeq平台（美国加利福尼亚州圣地亚哥市Illumina公司）对分离株进行WGS分析，并进行系统发育分析。在85株分离株中，39%（33株）携带该基因，61%（52株）已失去该基因。该亚型的流行情况如下：55%（18/33）、52%（17/33）、55%（18/33）、27%（9/33）、30%（10/33）和15%（5/33）。检测到35种不同的血清型，其中65%（56种）为鞭毛H抗原，34%（29种）为O抗原和鞭毛H抗原。我们鉴定出50种不同的序列类型（STs），只有9株分离株被归入三种不同的克隆复合体。核心基因组系统发育分析揭示了遗传相关性，分离株主要根据其STs和血清型聚类，而不考虑该亚型。本研究提供了STEC菌株在豪登省水平传播和再循环的证据，并表明牛肉生产链的每个阶段在STEC进入食物链中都起着重要作用。
