Additional file 1: of Comparative genomic analysis of 127 Escherichia coli strains isolated from domestic animals with diarrhea in China
Creators: name: Tang, Fang
name: Wang, Juanfang
name: Li, Dezhi
name: Gao, Song
name: Ren, Jianluan
name: Ma, Liqing
name: Liu, Fei
name: Zhuge, Xiangkai
name: Yan, Genqiang
name: Lu, Yan
name: Dai, Jianjun
Publisher: name: figshare
Year: 2019
Subjects: subject: Biochemistry
subject: Space Science
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Evolutionary Biology
subject: Environmental Sciences not elsewhere classified
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: Table S1. Strains information. Host, collection year, geographical location, sample type, MLST type, O antigen, pathotype, number of scaffolds, and average scaffold size of the 127 isolates used in this study. Table S2. Percentage of strain type. Isolates from this study were compared to putative virulence factor (VF) reference sequences using BLAST, and each putative VF was considered matched with a query sequence if the sequence identity was &gt; 60% and the aligned length coverage was &gt; 50%. The proportion of putative VF in distinct groups was included. Fisher’s exact test was used to determine significant differences of each putative VF between two different groups. P-values were adjusted using Bonferroni correction. Table S3. Putative VF in MG1655. Putative VF detected in the E. coli MG1655 genome. Table S4. Average putative VF numbers of each strain type. This table contains the numbers of putativeVF in each strain and the average numbers of putative VF in the two strain types. Table S5. Percentage of VFs in EAEC strains. Isolates from this study were compared to putative virulence factor (VF) reference sequences using BLAST, and each putative VF was considered matched with a query sequence if the sequence identity was &gt; 60% and the aligned length coverage was &gt; 50%. The proportion of putative VFs in distinct groups is included. Fisher’s exact test was used to determine significant differences in each putative VF between two different groups. P-values were adjusted using Bonferroni correction. Table S6. Percentage of VFs in STEC strains. Isolates from this study were compared to putative virulence factor (VF) reference sequences using BLAST, and each putative VF was considered matched with a query sequence if the sequence identity was &gt; 60% and the aligned length coverage was &gt; 50%. The proportion of putative VFs in distinct groups is included. Fisher’s exact test was used to determine significant differences in each putative VF between two different groups. P-values were adjusted using Bonferroni correction. Table S7. Distribution of VFs in O20 and O8 isolates. Isolates from this study were compared to putative virulence factor (VF) reference sequences using BLAST, and each putative VF was considered matched with a query sequence if the sequence identity was &gt; 60% and the aligned length coverage was &gt; 50%. Table S8. Distribution of putative virulence factors in different O serotypes. Isolates from this study were compared to putative virulence factor (VF) reference sequences using BLAST, and each putative VF was considered matched with a query sequence if the sequence identity was &gt; 60% and the aligned length coverage was &gt; 50%. Table S9. Stx subtype information. This table lists the stx subtypes as well as host, collection year, geographical location, sample type, MLST type, and O antigen of 20 STEC strains in this study. Table S10. Antibiotic resistance of strains. The antibiotic resistance to six drugs (ciprofloxacin, ampicillin, cefotaxime, gentamicin, kanamycin, and doxycycline) of the 127 isolates in this study. Table S11. Reference E. coli genomes. The putative VF reference sequences in this study were collected from the Virulence Factor Database and from previous studies, and the core genes of 199 E.coli genomes in the NCBI GenBank database were then removed. This table contains the name and accession numbers of the 199E.coli genomes. Table S12. Accession numbers of the strains. All genome data from this study were submitted to the NCBI GenBank database. This table contains the accession numbers of the genomes of all 127 E. coli isolates. (PDF 1165 kb)