This study used a comparative proteomics approach to distinguish between the two-dimensional electrophoresis profiles of extracellular proteins in Nagasaki and SW114. Protein spots were identified using matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry. The ten proteins unique to Nagasaki were putative adhesin AidA protein, putative extracellular serine protease (autotransporter) (771aa), putative extracellular serine protease (autotransporter) (780aa), protective surface antigen D15, 30S ribosomal protein S2, periplasmic serine protease do/hhoA-like protein, acid phosphatase, membrane protein, protein-disulfide isomerase, and iron ABC transporter substrate-binding protein. Meanwhile, the two proteins unique to SW114 were C4-dicarboxylate ABC transporter substrate-binding protein and peptide ABC transporter substrate-binding protein. Quantitative PCR was used to analyze the mRNA transcript levels of three randomly selected proteins. The afuA, AidA, and ompD15 genes encoding iron ABC transporter substrate-binding protein, putative adhesin AidA protein and protective surface antigen D15 respectively demonstrated significantly higher mRNA transcript levels (39.606, 3.924, and 36.668, respectively) in Nagasaki than in SW114. These observations suggest the levels of differentially expressed proteins were directly proportional to their cellular mRNA levels. Three virulence-related proteins, namely, putative adhesin AidA protein, putative extracellular serine protease (autotransporter) (771aa) and putative extracellular serine protease (autotransporter) (780aa) were identified in Nagasaki. (C) 2014 Elsevier Inc. All rights reserved.