Additional file 1 of A molecular epidemiological study on Escherichia coli in young chicks with colibacillosis identified two possible outbreaks across farms

Additional file 1. Metadata linked to each isolate sequenced in this study including flock and sampling data, bacteriological grading, sequencing quality measures, virulence-associated genes identified and accession numbers to ENA. 1The sample ID explains from what flock (first number) and bird (last number) the isolate was sampled. 2The bacterial culture was graded according to purity of growth on three agar plates incubated over night in either normal oxygen pressure, CO2 chamber or anaerobically: grade 1 = pure growth, grade 2 = few colonies of Enterococcus spp. or Proteus spp. were present on the agar, together with an otherwise pure culture of E. coli. Grade 3 = dominating growth of E. coli with sparse to medium growth of either Enterococci spp, Proteus spp. or less growth of a different bacteria, grade 4 = mixed culture: minimum of three different bacteria, where E. coli was not the dominating bacteria. 3The presence of pathological lesions associated with colibacillosis (colisepticaemia) within an individual bird during necropsy, 1 if ≥2 lesions present, 0 if <2 lesions present. 4Each individual bird received a colibacillosis diagnosis (1) if the bird had lesions of colisepticaemia and the bacteriological examination from the individual sample was graded 1-3.

附加文件1. 本研究中所有测序分离株的关联元数据，涵盖鸡群与采样信息、细菌学分级、测序质量指标、已鉴定的毒力相关基因，以及欧洲核苷酸档案库（European Nucleotide Archive, ENA）的登录号。
1 样本ID可表明该分离株的采源：首位数字对应鸡群编号，末位数字对应家禽个体编号。
2 细菌培养分级依据3个琼脂平板的过夜生长纯度进行判定，培养条件涵盖常压、CO₂培养箱及厌氧环境：1级为纯培养生长；2级为平板上存在少量肠球菌属（Enterococcus spp.）或变形杆菌属（Proteus spp.）菌落，其余为纯大肠杆菌（E. coli）培养物；3级为大肠杆菌占主导生长，同时伴稀疏至中等量的肠球菌属、变形杆菌属或其他异种细菌生长；4级为混合培养：至少存在3种不同细菌，且大肠杆菌并非优势菌群。
3 尸检时可观察到个体家禽与大肠杆菌病（colibacillosis，即大肠杆菌败血症(colisepticaemia)）相关的病理损伤：若检出≥2处损伤则记为1，若检出<2处损伤则记为0。
4 若个体家禽存在大肠杆菌败血症病变，且对应样本的细菌学检查分级为1~3级，则判定该家禽为大肠杆菌病阳性（记为1），否则记为0。