42 0.208 0.78 0.478 0.61 pS88148 etsA Putative type I secretion membrane-fusion protein EtsA 0.49 0.126 0.34 0.211 0.36 0.050 0.31 pS88154   Hypothetical protein 0.47 0.330 4.44 0.163 1.25 0.790 3.00 pS88155 ompT Outer membrane protease (omptin) 0.48 0.178 0.43 0.092 0.42 0.137 0.37 pS88156 hlyF Hemolysin HlyF 1.02

0.981 0.44 0.402 0.72 0.507 0.14 pS88157   Conserved hypothetical protein; putative Mig-14 protein 1.11 0.921 0.47 0.376 0.94 0.942 0.11 S88-1832 gapA d Glyceraldehyde-3-phosphate dehydrogenase 1.70 0.396 0.46 0.254 1.15 3-deazaneplanocin A supplier 0.789 0.90 S88-0266 dinB d DNA polymerase IV 0.69 0.343 2.36 0.131 0.69 0.317 0.90 S88-4457 yjaD d NADH pyrophophatase 0.85 0.586 0.91 0.698 1.26 0.344 1.24 a Fold changes of transcription levels relative to reference condition (growth in LB). Fold change > 4 are in bold print. b p value in Student’s t test for the comparison of the three biological

replicates for each experiment in different growth conditions and the reference condition. p < 0.05 are in bold print. c ORFs present in plasmid pS88 but absent from plasmid pAMM. d Housekeeping genes. Expression of iron uptake systems The concentration of free iron in human urine and serum is low, because iron is sequestered by host selleck molecules [22–24]. E. coli has developed several strategies to acquire iron in such environments. Ten ORFs were upregulated after growth in urine, in serum, and in iron-depleted LB, suggesting they were induced by the low iron concentrations in these media. Five of these 10 ORFs corresponded to iron-uptake and iron-assimilation systems, namely iutA and iucA (aerobactin), iroB (salmochelin) and sitA and sitB (SitABCD iron transport system). These iron-uptake systems have previously been linked to the virulence of ExPEC and APEC [4, 7–9, 24–27]. Mobley et al. also observed upregulation of UPEC iron-acquisition systems such as aerobactin, salmochelin and the SitABCD system in urinary isolates from experimentally infected mice and from women with UTI [14, 16]. Likewise, Li et al. found ioxilan that genes involved in iron acquisition were among the most significantly upregulated genes during growth in chicken

serum of the APEC strain O1 [28], which harbours a plasmid (pAPEC-O1-ColBM) closely related to pS88 [3]. Our study represents the first transcriptional analysis of an E. coli plasmid after growth in human serum. Surprisingly, we found that the salmochelin receptor iroN was not upregulated in our ex vivo experiments, and that the transcript level of the aerobactin receptor iutA was markedly lower than that of the siderophore iucA. In contrast the salmochelin receptor iroN was upregulated 28-fold in the isolate from a neonate with UTI. Such discrepancies have been previously described. In the murine UTI model used by Mobley et al.[16], iroN was upregulated but its transcript level was also lower than that of iroB. Moreover, in their transcriptome analysis of E.