Genome-wide analysis of drug resistance and virulence of uropathogenic Escherichia coli / 中华微生物学和免疫学杂志

ABSTRACT

Objective:To investigate the drug resistance and pathogenic mechanism of a uropathogenic Escherichia coli (UPEC) strain UPEC132 at the genome-wide level. Methods:The susceptibility of UPEC132 strain to 16 antimicrobial agents was determined by minimum inhibitory concentration (MIC) assay. The UPEC132 strain was genotyped by multilocus sequence typing (MLST). The three-generation sequencing platform was used to sequence and assemble the whole genome of the UPEC132 strain. Drug resistance and virulence gene function annotations were predicted by Prodigal software and screened by using genome database. Genome sequences of the UPEC132 strain and 23 other UPEC strains collected from GenBank were phylogenetically analyzed, and a phylogenetic tree was constructed by RAxML software.Results:The UPEC132 strain was resistant to ampicillin, ampicillin/sulbactam, tetracycline, erythromycin, chloramphenicol and cefazolin. Its genotype was ST10522 by MLST. The whole genome of the UPEC132 strain included one complete genome (chromosome) and two plasmid sequences. The sequence sizes of the chromosome and plasmids 1 and 2 were 5 234 468 bp, 117 139 bp and 101 356 bp, and the guanine-cytosine (GC) content was 50.48%, 49.05%, and 54.04%, respectively. There were 4 856, 140 and 116 genes annotated in the chromosome and plasmids 1 and 2, respectively. Drug resistance genes were mainly distributed in the chromosomal genome, mainly including the multidrug resistance efflux pump gene clusters. Only blaTEM-1 and tetG genes were carried in the plasmid 2. Virulence genes were also mainly distributed in the chromosome genome, including nine pilus adhesins, five iron uptake systems and three secretory toxins. Gene clusters encoding Afa and type Ⅳ fimbriae were located on plasmids 1 and 2, respectively. The phylogenetic tree showed that the UPEC132 strain was not in the same branch with either of the 23 UPEC strains. Conclusions:The UPEC132 strain belonged to ST10522, which was a newly named ST type of Escherichia coli and first reported at home and abroad. The genome-wide genetic information of the UPEC132 strain was fully revealed. The multidrug resistance genes and virulence genes carried by the UPEC132 strain were associated with its drug resistance and pathogenicity.