TABLE 3.
Putative virulence-associated functions encoded on the large resistance plasmid pSMS35_130 and in genomic islands of the SMS-3-5 chromosome
| Namea | CDS | Location | Function | Gene(s) | Distributionb | Best hitc |
|---|---|---|---|---|---|---|
| hlyF | EcSMS35_A0098 | pSMS | Hemolysin gene from avian E. coli isolate (56) | hlyF | APEC O1 (pAPEC-O1-ColBM) | P1658/97 (plasmid) |
| ompT | EcSMS35_A0099 | pSMS | Outer membrane protease gene (72) | ompT | APEC O1 (pAPEC-O1-ColBM) | pAPEC-O2-ColV (plasmid) |
| colB′ | EcSMS35_A0106-A0107 | pSMS | Colicin-B biosynthesis and immunity proteins (75, 76) | cba′, cbi′d | APEC O1 (pAPEC-O1-ColBM) | pAPEC-O1-ColBM (plasmid) |
| colM | EcSMS35_A0111-A0112 | pSMS | Colicin-M biosynthesis and immunity proteins (44, 62) | cma, cmi | APEC O1 (pAPEC-O1-ColBM) | pAPEC-O1-ColBM (plasmid) |
| Col | EcSMS35_0116-0121 | Chre | Uropathogen-specific colicin biosynthesis and immunity proteins | UPEC, APEC O1 | UTI89 | |
| Flag-2 | EcSMS35_0241-0284 | Chr | Lateral flagellar operon (69) | lafABCDEFKSTUVWZ, lfgABCDEFGHIJKLMN, lfhAB, lfiEFGHIJMNPQR | E. coli O42 | |
| sit-sitABCD | EcSMS35_3170-3173 (chromosome) | pSMS/Chr | Iron/manganese transport system | sitABCD | APEC O1 (pAPEC-O1-ColBM) | pAPEC-O2-ColV (plasmid) |
| EcSMS35_A0081-A0084 (pSMS35) | gene clusters (73) | |||||
| iut/iuc | EcSMS35_3178-3182 | Chr | Aerobactin biosynthesis and transport system gene cluster (22) | iucABCD, iutA | APEC O1 (pAPEC-O1-ColBM) | pAPEC-O1-ColBM (plasmid) |
| kps | EcSMS35_3219-3235 | Chr | Polysialic acid capsule biosynthesis operon (3) | kpsCDEFMTUS, neuABCDES | APEC O1, UPEC | UTI89 |
| gsp | EcSMS35_3238-3248 | Chr | General secretion pathway operon | gspCDEFGHIJKLM | APEC O1, UTI89, 536 | UTI89 |
| TTS | EcSMS35_4018-4024 | Chr | Putative type III secretion system, chaperone and effector components | Shigella dysenteriae Sd197 (20%)f | ||
| HRA-1 | EcSMS35_4755 | Chr | Heat-resistant agglutinin 1 (51) | UTI89, CFT073 | E. coli O9:H10:K99 | |
| GimA | EcSMS35_4856-4869 | Chr | Cell invasion and carbon metabolism (35) | ibeRAT, cglDECT, gcxCIKR, ptnCKE | APEC O1, UTI89 | E. coli A0 34/86 |
| Fim1 | EcSMS35_0146-52 | Chr | Putative fimbrial biosynthesis operons | (K12, APEC, UPEC)g | ||
| Fim2 | EcSMS35_0575--80 | K12, EHEC | Sakai | |||
| Fim3 | EcSMS35_2175-85 | K12, O157:H7 | Sakai | |||
| Fim4 | EcSMS35_2491-97 | Shigella sonnei Ss046 (50%) | ||||
| Fim5 | EcSMS35_2509-13 | CFT073 | CFT073 | |||
| Fim6 | EcSMS35_3921-29 | |||||
| Fim7 | EcSMS35_4093-96 | Shigella flexneri 5b 8401 | ||||
| LPS1 | EcSMS35_1020-28 | |||||
| LPS2 | EcSMS35_2255-68 | Chr | Putative lipopolysaccharide biosynthesis operons | |||
| LPS3 | EcSMS35_3959-67 | UPEC, APEC O1 | 536 |
b
Among completed E. coli strains (K-12, EDL933, Sakai, APEC O1, UTI89, CFT073, and 536) or pathotypes (UPEC, UTI89, CFT073, and 536; EHEC, EDL933 and Sakai).
c
According to nucleotide sequence BLAST comparison with NCBI nr database.
d
Truncated genes.
e
Chr, chromosome.
f
Percentage of query region covered by best hit.
g
Gene cluster with weak similarity present in non-EHEC strains.