Supplementary Table 1. Oligonucleotide primers used in this study.

Name / Sequence
16S5’for / TGAAGAGTTTGATCATGGC
16S5’rev / ATCCGATAGTGCAAGGTCC
16S3’for / ACTCGACTCCATGAAGTCG
16S3’rev / TAAGGAGGTGATCCAACC
5Sfor / TGCTTGGCGGCCATAGCG
5Srev / ATGCTTGGCAGTTCCCTA
23Sins-for / CCATCACTCAAGTGCCTC
23Sins-rev / TCCTCAAATGTCCCGCTT
23S5’for / GGTTAAGCGAATAAGCGT
23S5’rev / TGAGATGTTTCAGTTCTCC
23S3’for / TGGTGTTCGGGTTGTCAT
23S3’rev / AGGTTAAGCCTCACGGTTC

Supplementary Table 2. P. mirabilis genes involved in LPS or Enterobacterial common antigen biosynthesis.

Gene # / Name / Description
PMI0275 / arnT / putative 4-amino-4-deoxy-L-arabinose transferase (lipid A modification)
PMI0718 / msbA / lipid A export ATP-binding/permease protein
PMI0719 / lpxK / tetraacyldisaccharide 4'-kinase (Lipid A 4'-kinase)
PMI0722 / kdsB / 3-deoxy-manno-octulosonate cytidylyltransferase (CMP-KDO synthetase)
PMI1047 / arnT / undecaprenyl phosphate-alpha-4-amino-4-deoxy-l-arabinose arabinosyl transferase
PMI1090 / kdsA / 2-dehydro-3-deoxyphosphooctulonate aldolase (KDO 8-P synthase)
PMI1154 / msbB; / lipid A biosynthesis (KDO)2-(lauroyl)-lipid IVA acyltransferase
PMI1490 / galU / UTP--glucose-1-phosphate uridylyltransferase
PMI1595 / pagP / putative antimicrobial peptide resistance and lipid A acylation protein
PMI1686 / htrB/waaM / lipid A biosynthesis lauroyl acyltransferase
PMI1951 / galE / UDP-glucose 4-epimerase
PMI2064 / lpxC / UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
PMI2160 / lpxH / UDP-2,3-diacylglucosamine hydrolase
PMI2182 / wzz / O-antigen chain length determinant
PMI2272 / lpxB / lipid-A-disaccharide synthase
PMI2273 / lpxA / acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
PMI2275 / lpxD / UDP-3-o-[3-hydroxymyristoyl] glucosamine N-acyltransferase
PMI2358 / rfaE/hldE/
waaE / bifunctional protein HldE [includes: D-beta-D-heptose 7-phosphate kinase and D-beta-D-heptose 1-phosphate adenosyltransferase]
PMI2754 / pgi / glucose-6-phosphate isomerase
PMI2971 / putative surface polysaccharide modification acyltransferase
PMI3160 / glycosyl transferase; looks like rfaF ADP-heptose--LPS heptosyltransferase II
PMI3163 / rfaL / O-antigen ligase
PMI3165 / coaD / phosphopantetheine adenylyltransferase (CMP-deoxy-D-manno-octulosonate-lipid A transferase)
PMI3166 / waaE / lipopolysaccharide core biosynthesis glycosyl transferase
PMI3167 / waaA / KDO transferase
PMI3168 / waaQ/rfaQ / lipopolysaccharide core biosynthesis glycosyl transferase
PMI3169 / wabG / lipopolysaccharide core biosynthesis glycosyl transferase
PMI3170 / wabH / lipopolysaccharide core biosynthesis glycosyl transferase
PMI3171 / lipopolysaccharide core biosynthesis protein
PMI3172 / lipopolysaccharide core biosynthesis glycosyl transferase
PMI3173 / glycosyltransferase
PMI1374 / waaC/rfaC / lipopolysaccharide heptosyltransferase 1
PMI3175 / waaF/rfaF / ADP-heptose--LPS heptosyltransferase II
PMI3176 / waaD/rfaD/hldD / ADP-L-glycero-D-manno-heptose-6-epimerase
PMI3187 / putative methyltransferase
PMI3188 / wbnF / nucleotide sugar epimerase
PMI3192 / wzy / O antigen polysaccharide unit polymerase
PMI3193 / putative O antigen biosynthesis protein
PMI3194 / flippase; maybe involved in LPS-biosynthesis
PMI3197 / putative O antigen biosynthesis protein
PMI3317 / wzzE / lipopolysaccharide biosynthesis protein
PMI3322 / rffC / lipopolysaccharide biosynthesis acetyltransferase
PMI3323 / rffA / lipopolysaccharide biosynthesis aminotransferase
PMI3324 / wzxE / O-antigen translocase (flippase)
PMI3652 / kdsC / 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase

Enterobacterial common antigen.

PMI3316 / wecA/rfe / undecaprenyl-phosphate alpha-N-acetylglucosaminyl 1-phosphate transferase
PMI3318 / rffE / UDP-N-acetylglucosamine 2-epimerase
PMI3319 / rffD / UDP-N-acetylmannosamine dehydrogenase
PMI3320 / rffG / dTDP-D-glucose-4,6-dihydratase
PMI3321 / rffH / glucose-1-phosphate thimidyltransferase
PMI3325 / rffT/wecF / 4-alpha-L-fucosyltranserase
PMI3326 / wzyE/wecF / putative ECA polymerase
PMI3327 / rffM/wecG / probable UDP-N-acetyl-D-mannosaminuronic acid transferase

Supplementary Table 3. Multidrug efflux genes.

Gene # / Gene / Description
PMI0124-0125 / mdlAB / Putative efflux ABC transporter
PMI0131-0133 / acrBAR / Multidrug efflux and repressor
PMI0272 / Possible antibiotic resistance efflux pump component
PMI1029 / marC / Multiple antibiotic resistance protein
PMI1043-1045 / arnBCA / Polymyxin resistance
PMI1099 / mdtH / Multidrug resistance protein
PMI1158-1159 / mdtJI / Multidrug resistance proteins
PMI1246 / Possible carbapenem resistance, CpmG-like
PMI1254 / Putative methylenomycin A resistance protein
PMI1261 / mdtL / Multidrug resistance protein
PMI1264-1265 / Putative multidrug resistance proteins
PMI1401 / Putative drug resistance protein
PMI1404 / mdtK / Multidrug resistance protein
PMI1585-1587 / mdtABC / Multidrug resistance proteins
PMI1687 / mdtG / Multidrug resistance protein
PMI2710 / Putative multidrug resistance protein
PMI3209 / emrD / Multidrug resistance protein D
PMI3598-3599 / Multidrug efflux pump
PMI3611 / Putative drug resistance protein
PMI3673 / Putative albA albicidin resistance protein

Supplementary Table 4. Two-component regulator systems.

Gene # / Name / Regulated system
PMI0051-52 / phoBR / Phosphate regulon
PMI0192-93 / uhpBA / Putative hexosephosphate transport
PMI0884-85 / phoQP / Mg2+/starvation/stress
PMI1226-27 / kdpED / Potassium transport/osmotic stress
PMI1588-89 / baeSR / Antibiotic resistance/solvent stress
PMI1684-85 / ttrSR / Tetrathionate reductase complex
PMI1696-97 / rssBA / Swarming motility
PMI1729-31 / rsbA-rcsBC / Capsular synthesis/swarming motility
PMI1872, 1874 / Unknown
PMI2405-06 / pgtAB / Phosphoglycerate transport system
PMI2883-84 / ntrB-glnG / Nitrogen regulation
PMI2891-92 / ompR-envZ / Osmolarity
PMI3198-99 / cpxAR / Envelope stress
PMI3430-31 / Unknown
PMI3568-69 / narLX / Nitrate/nitrite
PMI3678/PMI3719 / arcBA / Aerobic respiration control