Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland.
Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland.
Infect Genet Evol. 2024 Apr;119:105578. doi: 10.1016/j.meegid.2024.105578. Epub 2024 Feb 27.
Campylobacter is among the most frequent agents of bacterial gastroenteritis in Europe and is primarily linked to the consumption of contaminated food. The aim of this study was to assess genomic diversity and to identify antimicrobial resistance and virulence genes of 155 Campylobacter isolated from broiler carcasses (neck skin samples) in a large-scale Swiss poultry abattoir over a three-year period. Samples originated from broilers from three different types of farming systems (particularly animal-friendly stabling (PAFS), free-range farms, and organic farms). Campylobacter jejuni (n = 127) and Campylobacter coli (n = 28) were analysed using a whole genome sequencing (WGS) approach (MiniSeq; Illumina). Sequence types (STs) were determined in silico from the WGS data and isolates were assigned into complex types (CTs) using the cgMLST SeqSphere+ scheme. Antimicrobial resistance genes were identified using the Resistance Gene Identifier (RGI), and virulence genes were identified using the virulence factor database (VFDB). A high degree of genetic diversity was observed. Many sequence types (C. jejuni ST19, ST21, ST48, ST50, ST122, ST262 and C. coli ST827) occurred more than once and were distributed throughout the study period, irrespective of the year of isolation and of the broiler farming type. Antimicrobial resistance determinants included bla and tet(O) genes, as well as the T86I substitution within GyrA. Virulence genes known to play a role in human Campylobacter infection were identified such as the wlaN, cstIII, neuA1, neuB1, and neuC1. Subtyping of the Campylobacter isolates identified the occurrence of a highly clonal population of C. jejuni ST21 that was isolated throughout the three-year study period from carcasses from farms with geographically different locations and different farming systems. The high rate of genetic diversity observed among broiler carcass isolates is consistent with previous studies. The identification of a persisting highly clonal C. jejuni ST21 subtype suggests that the slaughterhouse may represent an environment in which C. jejuni ST21 may survive, however, the ecological reservoir potentially maintaining this clone remains unknown.
空肠弯曲菌是欧洲最常见的细菌性胃肠炎病原体之一，主要与食用污染食物有关。本研究的目的是评估 155 株空肠弯曲菌的基因组多样性，并鉴定其耐药性和毒力基因，这些菌株均来自瑞士一家大型家禽屠宰场三年内的肉鸡胴体（颈部皮肤样本）。样本来源于来自三种不同养殖系统的肉鸡（特别是动物友好型畜栏（PAFS）、自由放养农场和有机农场）。采用全基因组测序（WGS）方法（MiniSeq；Illumina）分析空肠弯曲菌（n=127）和大肠弯曲菌（n=28）。通过 WGS 数据在计算机中确定序列类型（STs），并使用 cgMLST SeqSphere+ 方案将分离株分配到复合类型（CT）中。使用抗性基因标识符（RGI）鉴定抗生素耐药基因，使用毒力因子数据库（VFDB）鉴定毒力基因。观察到高度的遗传多样性。许多序列类型（空肠弯曲菌 ST19、ST21、ST48、ST50、ST122、ST262 和大肠弯曲菌 ST827）多次出现，并分布在整个研究期间，无论分离年份和肉鸡养殖类型如何。抗生素耐药决定因素包括 bla 和 tet(O) 基因，以及 GyrA 内的 T86I 取代。确定了与人类空肠弯曲菌感染有关的毒力基因，如 wlaN、cstIII、neuA1、neuB1 和 neuC1。空肠弯曲菌分离株的分型确定了在整个三年研究期间从地理位置不同和不同养殖系统的农场的胴体中分离出的高度克隆的空肠弯曲菌 ST21 种群的发生。在肉鸡胴体分离株中观察到的高遗传多样性率与以前的研究一致。持续性高度克隆空肠弯曲菌 ST21 亚型的鉴定表明，屠宰场可能是空肠弯曲菌 ST21 可能存活的环境，然而，潜在维持该克隆的生态库仍然未知。
