Background
Methods
Bacterial isolates
VAG PCR
ExPEC VAGs, cnf1, cnf2, cnf3, ehaA and ehaG PCR
Phylogenetic group PCR
MLVA
Stx subtyping
Oxford Nanopore MinION sequencing
Illumina MiSeq sequencing
Sequence analysis
Results
PCR
Pathotype | ExPECa | All IPECb | Otherc | IPEC VF onlyd | IPEC/EXPECe |
---|---|---|---|---|---|
Number | 50 | 115 | 3 | 7 | 108 |
Percent | 29.7% | 68.5% | 1.8% | 4.2% | 64.3% |
Phylogroup | A | B1 | B2 | D | |||
---|---|---|---|---|---|---|---|
Subgroup | A0 | A1 | B1 | B2_2 | B2_3 | D1 | D2 |
aEPEC | 5 | 7 | 17 | 7 | 8 | 4 | 1 |
tEPEC | 0 | 0 | 0 | 0 | 1 | 0 | 0 |
STEC | 0 | 1 | 24 | 0 | 0 | 6 | 0 |
ETEC | 0 | 8 | 11 | 0 | 0 | 1 | 1 |
EAEC | 0 | 0 | 1 | 0 | 0 | 1 | 0 |
EIEC | 2 | 0 | 1 | 0 | 0 | 0 | 0 |
STEC/ETEC | 0 | 0 | 0 | 0 | 0 | 0 | 1 |
NTEC | 0 | 1 | 0 | 0 | 6 | 0 | 0 |
NON-IPEC | 8 | 18 | 10 | 0 | 6 | 8 | 3 |
Σ Subgroups | 15 | 35 | 64 | 7 | 21 | 20 | 6 |
Σ Phylogroups | 50 (29.8%) | 64 (30.1%) | 28 (16.7%) | 26 (15.5%) |
ExPEC associated VAG | Comment | Frequency |
---|---|---|
iss
| Increased serum survival gene | 48.8% |
traT
| Gene encoding complement resistance protein | 45.2% |
fyuA
| Ferric yersiniabactin uptake receptor gene | 42.3% |
iucD
| Aerobactin biosynthesis gene | 24.4% |
iutA
| Ferric aerobactin receptor gene | 23.8% |
sitA
| Iron/manganese transport system periplasmic binding protein gene | 23.2% |
kpsS
| Capsule polysaccharide export protein gene | 18.5% |
tsh
| Temperature-sensitive hemagglutinin autotransporter gene | 15.5% |
iroC
| Salmochelin siderophore system gene | 12.5% |
vat
| Vacuolating autotransporter toxin gene | 11.3% |
fbpB
| Gene associated with urinary tract infections | 10.1% |
sat
| Secreted autotransporter toxin gene | 9.5% |
ibeA
| Invasion protein gene | 8.3% |
etsA
| Macrolide-specific efflux protein gene | 4.2% |
cnf1
| Gene encoding the cytotoxic necrotizing factor 1 | 3.6% |
sfaS
| S-fimbrial adhesin gene | 1.8% |
papC
| P-fimbriae outer membrane usher protein gene | 1.8% |
tosA
| Repeat-in-toxin gene | 1.8% |
cnf2
| Gene encoding the cytotoxic necrotizing factor 2 | 0.6% |
cnf3
| Gene encoding the cytotoxic necrotizing factor 3 | NDa |
Sequencing
Gene name (FHI-NMBU-03 chromosome) | Comment | Associated pathovar | % identity | Cover. | BLAST sequence |
---|---|---|---|---|---|
aatB
| Autotransporter adhesin and virulence factor of avian pathogenic Escherichia coli. | APEC | 98.43 | 1017 / 1017 | JX402062 |
herA
| Archaeal bi-polar DNA helicase | Unknown | 99.47 | 1686 / 1686 | NZ_NLRN01000019 |
aslA
| Arylsulfatase gene | ExPEC (Invasive K1 strains) | 98.55 | 1656 / 1656 | CU928163 |
aufC
| Fimbrial usher protein gene | UPEC | 99.50 | 2595 / 2595 | KE702411 |
cesAB
| Enteropathogenic Escherichia coli chaperone for the type-III translocator proteins | EPEC/STEC | 100.00 | 324 / 324 | FM986651 |
cesD2
| A second chaperone for the type III secretion translocator protein EspD | EPEC/STEC | 98.28 | 407 / 408 | NC013364 |
cesT
| A bivalent enteropathogenic Escherichia coli chaperone required for translocation of both Tir and Map | EPEC/STEC | 100.00 | 471 / 471 | LT903847 |
chuA
| E.coli hemeutilization protein A gene | ExPEC | 99.65 | 1983 / 1983 | LT827011 |
cif
| Type III secreted effector | EPEC/STEC | 100.00 | 849 / 849 | AF497476 |
csgA
| Major curlin subunit | Several | 99.56 | 459 / 459 | CP023388 |
csgB
| Minor curlin subunit | Several | 99.56 | 456 / 456 | CP027060 |
csgE
| Curli production assembly/transport component | Several | 98.70 | 386 / 390 | NC_011750 |
csgF
| Curli production assembly/transport component | Several | 98.08 | 417 / 417 | NC_011750 |
csgG
| Curli production assembly/transport component | Several | 97.72 | 834 / 834 | CP003034 |
cvaA
| Colicin V secretion protein gene | Several | 100.00 | 1242 / 1242 | GG773553 |
Death on curing RelE/ParE family toxin gene | Component of Toxin-antitoxin (TA) system | Several | 100.00 | 272 / 276 | CP023388 |
eae (subtype Beta2) | Intimin - Necessary for the production of attaching and effacing lesions on tissue culture cells | EPEC/STEC | 100.00 | 2820 / 2820 | AB647493 |
ecpA
| Common pilus major fimbrillin subunit | Several | 98.47 | 588 / 588 | BA000007 |
ecpD
| Fimbria adhesin of the E.coli common pilus | Several | 99.64 | 1644 / 1644 | CP019777 |
elfC
| Putative fimbrial usher protein | Several | 99.73 | 2595 / 2595 | CP021288 |
entA
| Enterobactin biosynthesis gene | Several | 96.12 | 747 / 747 | CP027060 |
entE
| Enterobactin biosynthesis gene | Several | 95.65 | 1611 / 1611 | CP027060 |
entH
| Enterobactin biosynthesis gene | Several | 94.93 | 414 / 414 | CP027060 |
escC
| Outer membrane secretin | EPEC/STEC | 91.68 | 1539 / 1539 | AP010958 |
escD
| Type III secretion system inner membrane ring protein | EPEC/STEC | 99.10 | 1221 / 1221 | BA000007 |
escF
| Type III secretion system needle major subunit | EPEC/STEC | 100.00 | 222 / 222 | NC_002695 |
escJ
| Required for the formation of the type III Secretion Apparatus | EPEC/STEC | 91.62 | 573 / 573 | AP010958 |
escN
| Type III secretion ATPase | EPEC/STEC | 100.00 | 1341 / 1341 | BA000007 |
escR
| Type III secretion system export apparatus protein gene | EPEC/STEC | 99.69 | 654 / 654 | BA000007 |
escS
| Type III secretion system export apparatus protein gene | EPEC/STEC | 100.00 | 270 / 270 | BA000007 |
escT
| Type III secretion system export apparatus protein gene | EPEC/STEC | 99.61 | 777 / 777 | BA000007 |
escU
| Type III secretion system LEE export apparatus switch protein gene | EPEC/STEC | 96.15 | 1038 / 1038 | AP010958 |
escV
| Translocase of the type III secretion system | EPEC/STEC | 99.70 | 2028 / 2028 | BA000007 |
espA
| Type III secretions system gene | EPEC/STEC | 100.00 | 573 / 573 | AJ225016 |
espG
| Type III secretion system effector, which localize to the Golgi apparatus and disrupt its architecture | EPEC/STEC | 98.41 | 1197 / 1197 | BA000007 |
etgA
| Lytic transglycosylase | EPEC/STEC | 100.00 | 459 / 459 | FM986650 |
fdeC
| Mediates E. coli adhesion to mammalian cells and extracellular matrix | ExPEC/STEC | 97.86 | 4251 / 4251 | CP019777 |
sfaH
| S-fimbrial protein subunit gene | ExPEC | 98.56 | 903 / 903 | KT444704 |
flgD
| Flagellar basal body rod modification protein gene | Several | 96.55 | 696 / 696 | CP027060 |
flgM
| Negative regulator of flagellin synthesis | Several | 98.97 | 290 / 294 | CP028192 |
fmlA
| Major F9-fimbrial subunit | ExPEC/IPEC | 96.81 | 564 / 564 | BA000007 |
fyuA
| Ferric yersiniabactin uptake receptor | ExPEC | 99.51 | 2022 / 2022 | CP016828 |
gad (1)
| Glutamate decarboxylase gene | Several | 99.64 | 1401 / 1401 | CP001671 |
gad (2)
| Glutamate decarboxylase gene | Several | 99.79 | 1401 / 1401 | FM180568 |
grlA
| Global regulator of LEE activator | EPEC/STEC | 97.56 | 409 / 414 | AP010958 |
gtrA
| Type IV O-antigen modification gene (Shigella flexneri) | Unknown | 90.08 | 363 / 363 | AF288197 |
hbp
| Hemoglobin-binding protease hbp autotransporter gene | ExPEC | 99.95 | 4131 / 4131 | CP009072 |
hlyIII
| Gene encoding inner membrane protein, hemolysin III family | ExPEC/IPEC | 98.41 | 690 / 690 | CP003034 |
ibeA
| Invasion protein gene | NMEC/APEC/AIEC | 98.61 | 1371 / 1371 | CP001855 |
ibeB
| Invasion protein gene | Several | 98.55 | 1383 / 1383 | AF094824 |
ibeC/yijP/cptA
| Invasion protein gene | Several | 99.77 | 1734 / 1734 | CP019777 |
irp1
| HMWP1 nonribosomal peptide/polyketide synthase | ExPEC | 99.65 | 9492 / 9492 | CU928163 |
irp2
| HMWP2 Yersiniabactin biosynthetic protein | ExPEC | 98.85 | 6106 / 6108 | CP006834 |
ler
| Negative autoregulator of the LEE1 operon | EPEC/STEC | 99.49 | 390 / 390 | BA000007 |
malX
| Escherichia coli pathogenicity island-marker | ExPEC | 98.61 | 1581 / 1581 | AF003742 |
MAP
| LEE effector protein gene | EPEC/STEC | 97.06 | 612 / 612 | LC053401 |
MBL-fold metallo hydrolase gene | Putative phylogroup B2 specific marker | ExPEC | 99.52 | 1044 / 1044 | CP023388 |
mdtH
| Multidrug resistance protein gene | Several | 99.83 | 1209 / 1209 | CP019777 |
mpc
| Type III secretion system regulator gene | EPEC/STEC | 92.09 | 354 / 354 | AP010953 |
mviM
| Putative virulence factor | Several | 98.70 | 924 / 924 | CU928164 |
nleA
a
| Non-LEE encoded effector A | EPEC/STEC | 99.84 | 1239 / 1239 | AB303062 |
nleB
| Non-LEE encoded effector B | EPEC/STEC | 100.00 | 981 / 981 | AB303062 |
nleC-like gene | T3SS secreted effector NleC-like protein gene | EPEC/STEC | 100.00 | 264 / 264 | CYEL01000033 |
nleG
| Non-LEE encoded effector G | EPEC/STEC | 100.00 | 576 / 576 | AB303062 |
nleH
| Non-LEE encoded effector H | EPEC/STEC | 99.75 | 812 / 812 | AP010958 |
usp/putative colicin | Uropathogenic specific protein gene | UPEC | 97.14 | 1782 / 1782 | CU651637 |
sepL
| Secretion switching protein gene | EPEC/STEC | 94.93 | 1046 / 1056 | BA000007 |
sepQ
| T3SS structure protein | EPEC/STEC | 95.53 | 918 / 918 | CP003109 |
sinH
| Intimin-like inverse autotransporter | ExPEC | 100.00 | 2178 / 2178 | NZ_NMHI01000013 |
stcD
| Putative fimbrial-like adhesin protein gene | IPEC | 99.71 | 1035 / 1035 | NC_018658 |
stfD
| Fimbrial protein gene | Unknown | 100.00 | 753 / 753 | LOFW01000008 |
tir
| Translocated intimin receptor protein gene | EPEC/STEC | 99.88 | 1650 / 1650 | DQ206455 |
xhlA
| Xenorhabdus nematophila haemolysin | Unknown | 99.73 | 372 / 372 | LDCR01000046 |
ybtA
| Yersiniabactin transcriptional regulator | ExPEC | 99.79 | 960 / 960 | CP028714 |
ydeR
| Fimbrial-like protein gene | Several | 98.41 | 504 / 504 | CU928163 |
yfcV
| Major subunit of a putative chaperone-usher fimbria | ExPEC | 97.18 | 567 / 567 | NC_011750 |