Table 1.
Resistant strains and mutations conveying phage resistance and outcome of wildtype gene complementations in trans.
| Resistant Isolate | Mutation | Putative gene function | Complementation | |
|---|---|---|---|---|
| Yes | No | |||
| R1 | abcT (A1844T, p.Glu615Val) | ABC transporter | abcT | |
| R1 | actP (A1144G, p.Thr382Ala) | acetate permease | actP | |
| R1 | gtrOC3 (IS4 family insertion) | LPS/ LOS biosynthesis | gtrOC3 | |
| R1 | phoH (1011nt, 103th A loss) | phosphohydrolase | phoH | |
| R1 | decT (753nt, G233A, p.Thr78Met) | di-trans,poly-cis-decaprenylcistransferase | ||
| R1 | dcaP (1332nt, G395T, p.Pro132Glu) | DcaP-like protein | ||
| R1 | Udp (720nt, T35C, p.Leu 12 Ser) | UDP-2,3-diacylglucosamine diphosphatase | ||
| R2 | abcT (A1844T, p.Glu615Val) | ABC transporter | abcT | |
| R2 | actP (A1144G, p.Thr382Ala) | acetate permease | actP | |
| R2 | gtrOC3 (535th A loss, p.Asn179Ile fs Ter7) | LPS/ LOS biosynthesis | gtrOC3 | |
| R2 | phoH (1011nt, 103th A loss) | phosphohydrolase | phoH | |
| R2 | decT (753nt, G233A, p.Thr78Met) | di-trans,poly-cis-decaprenylcistransferase | ||
| R2 | dcaP (1332nt, G395T, p.Pro132Glu) | DcaP-like protein | ||
| R2 | Udp (720nt, T35C, p.Leu 12 Ser) | UDP-2,3-diacylglucosamine diphosphatase | ||
| R5 | gtr9 (IS4 insertion) | Capsule biosynthesis | gtr9 | |
| R5 | abcT (A1844T, p.Glu615Val) | ABC transporter | abcT | |
| R5 | actP (A1144G, p.Thr382Ala) | acetate permease | actP | |
| R5 | gtr0C3 (535th A loss, p.Asn179Ile fs Ter7) | LPS/ LOS biosynthesis | gtr0C3 | |
| R5 | phoH (1011nt, 103th A loss) | phosphohydrolase | phoH | |
| R5 | decT (753nt, G233A, p.Thr78Met) | di-trans,poly-cis-decaprenylcistransferase | ||
| R5 | dcaP (1332nt, G395T, p.Pro132Glu) | DcaP-like protein | ||
| R5 | Udp (720nt, T35C, p.Leu 12 Ser) | UDP-2,3-diacylglucosamine diphosphatase | ||
| R6 | abcT (A1844T, p.Glu615Val) | ABC transporter | abcT | |
| R6 | actP (A1144G, p.Thr382Ala) | an acetate permease | actP | |
| R6 | phoH (1011nt, 103th A loss) | phosphohydrolase | phoH | |
| R6 | decT (753nt, G233A, p.Thr78Met) | di-trans,poly-cis-decaprenylcistransferase | ||
| R6 | dcaP (1332nt, G395T, p.Pro132Glu) | DcaP-like protein | ||
| R6 | Udp (720nt, T35C, p.Leu 12 Ser) | UDP-2,3-diacylglucosamine diphosphatase | ||
| R7 | gtr9 (IS5 insertion) | Capsule biosynthesis | gtr9 | |
| R7 | abcT (A1844T, p.Glu615Val) | ABC transporter | abcT | |
| R7 | actP (A1144G, p.Thr382Ala) | an acetate permease | actP | |
| R7 | phoH (1011nt, 103th A loss) | phosphohydrolase | phoH | |
| R7 | decT (753nt, G233A, p.Thr78Met) | di-trans,poly-cis-decaprenylcistransferase | ||
| R7 | dcaP (1332nt, G395T, p.Pro132Glu) | DcaP-like protein | ||
| R7 | Udp (720nt, T35C, p.Leu 12 Ser) | UDP-2,3-diacylglucosamine | ||
| R8 | abcT (A1844T, p.Glu615Val) | ABC transporter | abcT | |
| R8 | actP (A1144G, p.Thr382Ala) | an acetate permease | actP | |
| R8 | gtrOC3 (535th A loss, p.Asn179Ile fs Ter7) | LPS/ LOS biosynthesis | gtrOC3 | |
| R8 | phoH (1011nt, 103th A loss) | phosphohydrolase | phoH | |
| R8 | decT (753nt, G233A, p.Thr78Met) | di-trans,poly-cis-decaprenylcistransferase | ||
| R8 | dcaP (1332nt, G395T, p.Pro132Glu) | DcaP-like protein | ||
| R8 | Udp (720nt, T35C, p.Leu 12 Ser) | UDP-2,3-diacylglucosamine diphosphatase | ||
| R10 | gtr9 (559th T loss, p. Leu187Tyr fs Ter3) | Capsule biosynthesis | gtr9 | |
| R10 | abcT (A1844T, p.Glu615Val) | ABC transporter | abcT | |
| R10 | actP (A1144G, p.Thr382Ala) | an acetate permease | actP | |
| R10 | phoH (1011nt, 103th A loss) | phosphohydrolase | ||
| R10 | decT (753nt, G233A, p.Thr78Met) | di-trans,poly-cis-decaprenylcistransferase | ||
| R10 | dcaP (1332nt, G395T, p.Pro132Glu) | DcaP-like protein | ||
| R10 | Udp (720nt, T35C, p.Leu 12 Ser) | UDP-2,3-diacylglucosamine diphosphatase | ||
| R10 | isoS (1698nt, 655th T loss, p.Ser 219 Pro fs Ter23) | 2-isopropylmalate synthase | ||
| R10 | LptD (2439nt, 2395th G to T, p.Val 799 Phe) | LPS- assembly protein | ||
| R10 | long-chain fatty acid--CoA ligase (1680nt,1240th T to A, p.Phe 414 Ile) | long-chain fatty acid--CoA ligase | ||
| R12 | abcT (1A1844T, p.Glu615Val) | ABC transporter | abcT | |
| R12 | actP (A1144G, p.Thr382Ala) | an acetate permease | actP | |
| R12 | gtrOC3 (535th A loss, p.Asn179Ile fs Ter7) | LPS/ LOS biosynthesis | gtrOC3 | |
| R12 | phoH (1011nt, 103th A loss) | phosphohydrolase | phoH | |
| R12 | decT (753nt, G233A, p.Thr78Met) | di-trans,poly-cis-decaprenylcistransferase | ||
| R12 | dcaP (1332nt, G395T, p.Pro132Glu) | DcaP-like protein | ||
| R12 | Udp (720nt, T35C, p.Leu 12 Ser) | UDP-2,3-diacylglucosamine diphosphatase | ||
| R13 | No PCR product of gtr9 | Capsule biosynthesis | gtr9 | |
| R13 | abcT (A1844T, p.Glu615Val) | ABC transporter | abcT | |
| R13 | actP (A1144G, p.Thr382Ala) | an acetate permease | actP | |
| R13 | phoH (1011nt, 103th A loss) | phosphohydrolase | phoH | |
| R13 | decT (753nt, G233A, p.Thr78Met) | di-trans,poly-cis-decaprenylcistransferase | ||
| R13 | dcaP (1332nt, G395T, p.Pro132Glu) | DcaP-like protein | ||
| R13 | Udp (720nt, T35C, p.Leu 12 Ser) | UDP-2,3-diacylglucosamine diphosphatase | ||
| R28 | gtr9 (transposase insertion) | Capsule biosynthesis | gtr9 | |
| R33 | gtr9 (IS5 insertion) | Capsule biosynthesis | gtr9 | |
| R35 | gtrOC3 (535th A loss, p.Asn179Ile fs Ter7) | LPS/ LOS biosynthesis | gtrOC3 | |
| R39 | gtrOC3 (535th A loss, p.Asn179Ile fs Ter7) | LPS/ LOS biosynthesis | gtrOC3 | |
| R54 | gtr9 (transposase insertion) | Capsule biosynthesis | gtr9 | |
| R78 | gtrOC3 (IS5 family insertion) | LPS/ LOS biosynthesis | gtrOC3 | |
| gtr9 KO | Markerless knock out the entire gtr9 on the background of ATCC17978 | Capsule biosynthesis | gtr9 | |
| gtrOC3-delta A | Subsititute for the wild type gtr0C3 on the background of ATCC17978 | LPS/ LOS biosynthesis | gtrOC3 | |
| R81 | gtr9 (transposase insertion) | Capsule biosynthesis | gtr9 | |
| R83 | No PCR product of gtr9 | Capsule biosynthesis | gtr9 | |
| R86 | gtr9 (transposase insertion) | Capsule biosynthesis | gtr9 | |
| R115 | gtr9 (transposase insertion) | Capsule biosynthesis | gtr9 | |
| R125 | gtr1 (448th A loss, p. Met 150 Cys fs Ter22) | Glycosyltransferase | gtr1 | |
| R130 | gtr9 (transposase insertion) | Capsule biosynthesis | gtr9 | |
| R132 | gtr9 (transposase insertion) | Capsule biosynthesis | gtr9 | |
| R132 | gtr1 (448th A loss, p. Met 150 Cys fs Ter22) | Glycosyltransferase | gtr1 | |
| R134 | gtr9 (transposase insertion) | Capsule biosynthesis | gtr9 | |
| XH198 gtr9 KO | Markerless knock out the entire gtr9 on the background of XH198 | Capsule biosynthesis | gtr9 | |
| XH198 gtrOC3-KO | Markerless knock out the entire gtrOC3 on the background of XH198 | LPS/ LOS biosynthesis | gtrOC3 | |
| R518 | gtrOC3 (535th A loss, p.Asn179Ile fs Ter7) | LPS/ LOS biosynthesis | gtrOC3 | |
| R587 | gtrOC3 (535th A loss, p.Asn179Ile fs Ter7) | LPS/ LOS biosynthesis | gtrOC3 | |
Yes: After the transformation of the corresponding plasmid which contains the WT gene, the R variant can get infected by Phab24.
No: After the transformation of the corresponding plasmid which contains the WT gene, the R variant cannot get infected by Phab24.
R1-R80 are Phab24 escape mutants from ATCC17978.
R81-R587 are Phab24 escape variants from XH198.
Based on the NCBI accession number CP018664.1, ATCC17978:
AUO97_06900, gtr9, 828nt
AUO97_07355, abcT, 1932nt
AUO97_05550, actP, 1716nt
AUO97_03485, gtrOC3, 768nt
AUO97_03925, phoH, 1011nt
AUO97_06920, gtr1, 1164nt
AUO97_09800, 2-isopropylmalate synthase, isoS, 1698nt
AUO97_15295, LPS assembly protein LptD, 2439nt
AUO97_06215, long-chain fatty acid--CoA ligase, 1680nt
AUO97_17750, di-trans, poly-cis-decaprenylcistransferase, decT, 753nt
AUO97_18665, UDP-2,3-diacylglucosamine, Udp, 720nt
Interestingly, the phoH of the WT or ATCC17978 used for Sanger sequencing has 1012nt, while the phoH of CP018664.1 has 1011nt, the same as the mutated R variants. Maybe that is the reason why the phoH is annotated as the pseudogene.