Objective To study the antimicrobial resistance and virulence mechanism of two foodborne CTX-M-55 type extended-spectrum β-lactamase (ESBL)-producing Escherichia coli strains based on whole genome sequences. MethodsThe antimicrobial susceptibility testing of two CTX-M-55 type ESBL-producing Escherichia coli isolates (EC001 and EC002) that were collected from foodborne pathogen surveillance system in 2011 was conducted by antimicrobial susceptibility test and PCR. Then two strains were sequenced using the Illunima Hiseq 2000 platform. Based on the assembled genome sequences of two strains, the annotation of sequence type, plasmid replicon type, serotype, and antimicrobial resistance/virulence genes was performed using BioNumerics software. Results The two strains were identified to be ESBL-producing and fluoroquinolone-resistant. The genomic analysis result showed that strains EC001 and EC002 were ST21 and ST342, respectively, and serotyped to be enteropathogenic Escherichia coli (EPEC) O119∶H8. The plasmid of EC001 belonged to 5 incompatible groups includingIncFII, IncX1, IncY, Col156, and IncI2, and that of EC002 belonged to 2 incompatible groups including IncFII and IncX1. Notably, both strains harbored 2 types of ESBL-encoding genes blaCTX-M-55 and blaTEM-141. Additionally, the multi-antimicrobial resistance genes sul2/3, tet(A)(B), dfrA12, strA/B, aph(3′)-IIa, cml/cmlA1, floR, and oqxA/B were identified on the genome of strain EC001, while fosA and qnrS1 were identified on the genome of strain EC002. Compared with the genome of Escherichia coli K12_1655, two mutations were found at the 83^th (S83L) and 87^th (D87H) codons of gyrA, and one mutation was found at the 80^th (S80I) codon of parC in QRDRs of strain EC001. Noteworthy, 3 mutations were found at the 73^th (D73Y), 185^th (M185T) and 225^th (S225T) codons of pmrE in the chromosome of strain EC001, which might be responsible for its resistance to colistin. The virulence gene prediction result showed that both strains harbored classical locus of enterocyte and effacement (LEE) genes esc, esp, eaeA and tir, while EC001 contained iss gene which could increase serum survival capacity of this bacterium. Conclusion To our best knowledge, we applied whole genome sequencing in annotation of the resistance and virulence mechanism of two CTX-M-55-type ESBL-producing Escherichia coli strains in China. The data in this study will shed light on antimicrobial resistance and virulence mechanisms of Escherichia coli,and finally help prevent and control the contamination of this foodborne pathogen.