Background
Methods
A. baumannii strains
PCR confirmation of the A. baumannii isolates
Antibiotic susceptibility testing
Detection of antibiotic resistance genes and virulence factors
Target gene | Primer Sequence (5′-3′) | Size of product (bp) | PCR conditions | Volume (50 μl) |
---|---|---|---|---|
draBC
| GCTGGGCAGCAAACTGATAACTCTC CATCAAGCTGTTTGTTCGTCCGCCG | 750 | 1 cycle: 95 0C ------------ 4 min. 30 cycle: 95 0C ------------ 50 s 58 0C ------------ 60 s 72 0C ------------ 45 s 1 cycle: 72 0C ------------ 8 min | 5 μL PCR buffer 10X 1.5 mM Mgcl2 200 μM dNTP (Fermentas) 0.5 μM of each primers F & R 1.25 U Taq DNA polymerase (Fermentas) 2.5 μL DNA template |
cnf1
| AAGATGGAGTTTCCTATGCAGGAG CATTCAGAGTCCTGCCCTCATTATT | 498 | ||
csgA
| ACTCTGACTTGACTATTACC AGATGCAGTCTGGTCAAC | 200 | ||
cvaC
| CACACACAAACGGGAGCTGTT CTTCCCGCAGCATAGTTCCAT | 680 | ||
iutA
| GGCTGGACATCATGGGAACTGG CGTCGGGAACGGGTAGAATCG | 300 | ||
fyuA
| TGATTAACCCCGCGACGGGAA CGCAGTAGGCACGATGTTGTA | 880 | ||
cnf2
| AATCTAATTAAAGAGAAC CATGCTTTGTATATCTA | 543 | 1 cycle: 94 0C ------------ 6 min. 34 cycle: 95 0C ------------ 50 s 58 0C ------------ 70 s 72 0C ------------ 55 s 1 cycle: 72 0C ------------ 10 min | 5 μL PCR buffer 10X 2 mM Mgcl2 150 μM dNTP (Fermentas) 0.75 μM of each primers F & R 1.5 U Taq DNA polymerase (Fermentas) 3 μL DNA template |
kpsMT II | GCGCATTTGCTGATACTGTTG CATCCAGACGATAAGCATGAGCA | 272 | ||
PAI
| GGACATCCTGTTACAGCGCGCA TCGCCACCAATCACAGCCGAAC | 930 | ||
papC
| GACGGCTGTACTGCAGGGTGTGGCG ATATCCTTTCTGCAGGGATGCAATA | 328 | ||
fimH
| TGCAGAACGGATAAGCCGTGG GCAGTCACCTGCCCTCCGGTA | 508 | 1 cycle: 95 0C ------------ 4 min. 34 cycle: 94 0C ------------ 60 s 56 0C ------------ 45 s 72 0C ------------ 60 s 1 cycle: 72 0C ------------ 10 min | 5 μL PCR buffer 10X 2 mM Mgcl2 200 μM dNTP (Fermentas) 0.5 μM of each primers F & R 1.5 U Taq DNA polymerase (Fermentas) 5 μL DNA template |
ibeA
| AGGCAGGTGTGCGCCGCGTAC TGGTGCTCCGGCAAACCATGC | 170 | ||
PapG II-III | CTGTAATTACGGAAGTGATTTCTG ACTATCCGGCTCCGGATAAACCAT | 1070 | ||
sfa/focDE | CTCCGGAGAACTGGGTGCATCTTAC CGGAGGAGTAATTACAAACCTGGCA | 410 | ||
traT
| GGTGTGGTGCGATGAGCACAG CACGGTTCAGCCATCCCTGAG | 290 | ||
aadA1
| TATCCAGCTAAGCGCGAACT ATTTGCCGACTACCTTGGTC | 447 | 1 cycle: 94 0C ------------ 6 min. 33 cycle: 95 0C ------------ 70 s 55 0C ------------ 65 s 72 0C ------------ 90 s 1 cycle: 72 0C ------------ 8 min | 5 μL PCR buffer 10X 2 mM Mgcl2 150 μM dNTP (Fermentas) 0. 5 μM of each primers F & R 1.5 U Taq DNA polymerase (Fermentas) 2 μL DNA template |
aac(3)-IV
| CTTCAGGATGGCAAGTTGGT TCATCTCGTTCTCCGCTCAT | 286 | ||
sul1
| TTCGGCATTCTGAATCTCAC ATGATCTAACCCTCGGTCTC | 822 | ||
blaSHV
| TCGCCTGTGTATTATCTCCC CGCAGATAAATCACCACAATG | 768 | ||
CITM
| TGGCCAGAACTGACAGGCAAA TTTCTCCTGAACGTGGCTGGC | 462 | ||
cat1
| AGTTGCTCAATGTACCTATAACC TTGTAATTCATTAAGCATTCTGCC | 547 | ||
cmlA
| CCGCCACGGTGTTGTTGTTATC CACCTTGCCTGCCCATCATTAG | 698 | ||
tet(A)
| GGTTCACTCGAACGACGTCA CTGTCCGACAAGTTGCATGA | 577 | ||
tet(B)
| CCTCAGCTTCTCAACGCGTG GCACCTTGCTGATGACTCTT | 634 | ||
dfrA1
| GGAGTGCCAAAGGTGAACAGC GAGGCGAAGTCTTGGGTAAAAAC | 367 | ||
qnr
| GGGTATGGATATTATTGATAAAG CTAATCCGGCAGCACTATTTA | 670 | ||
imp
| GAATAGAATGGTTAACTCTC CCAAACCACTAGGTTATC | 188 | 1 cycle: 95 0C ------------ 4 min. 30 cycle: 95 0C ------------ 45 s 58 0C ------------ 60s 72 0C ------------ 40 s 1 cycle: 72 0C ------------ 5 min | 5 μL PCR buffer 10X 1.5 mM Mgcl2 100 μM dNTP (Fermentas) 1 μM of each primers F & R 1 U Taq DNA polymerase (Fermentas) 2.5 μL DNA template |
vim
| GTTTGGTCGCATATCGCAAC AATGCGCAGCACCAGGATAG | 382 | ||
sim
| GTACAAGGGATTCGGCATCG GTACAAGGGATTCGGCATCG | 569 | ||
Oxa-23-like | GATCGGATTGGAGAACCAGA ATTTCTGACCGCATTTCCAT | 501 | 1 cycle: 94 0C ------------ 5 min. 32 cycle: 95 0C ------------ 50 s 60 0C ------------ 60 s 72 0C ------------ 70 s 1 cycle: 72 0C ------------ 10 min | 5 μL PCR buffer 10X 2.5 mM Mgcl2 200 μM dNTP (Fermentas) 0.5 μM of each primers F & R 1.5 U Taq DNA polymerase (Fermentas) 2 μL DNA template |
Oxa-24-like | GGTTAGTTGGCCCCCTTAAA AGTTGAGCGAAAAGGGGATT | 246 | ||
Oxa-51-like
| TAATGCTTTGATCGGCCTTG TGGATTGCACTTCATCTTGG | 353 | ||
Oxa-58-like
| AAGTATTGGGGCTTGTGCTG CCCCTCTGCGCTCTACATAC | 599 |
Molecular typing of A. baumannii isolates using the ERIC-PCR
Data analysis
Statistical analysis
Results
ERIC typesa | Numbers and source of strains | Antibiotic resistance phenotypes | Antibiotic resistance genes | ® |
---|---|---|---|---|
I | 19,22 (Chicken meat) | SXT25, TE30, F300 |
aadA1, sul1, tetB, sim, oxa-58-like
|
cnf1, csgA, fimH
|
II | 20 (Chicken meat) | GM10, TE30, TMP5, CIP5, C30, F300 |
sul1, tetA, tetB, dfrA1, qnr, cat1, vim
|
ibeA, sfa/focDE, afa/draBC
|
III | 21 (Chicken meat) | CL30, TE30, TMP5, E15 |
tetB, dfrA1, qnr, cmlA,
oxa-23-like |
kpsMTII, PAI, ibeA, traT, afa/draBC, cnf2, csgA, fyuA, fimH
|
IV | 12,15 (Chicken meat) | S10, GM10, SXT25, TE30, TMP5 |
aadA1, aac(3)-IV, sul1, blaSHV, tetA, dfrA1
|
kpsMTII, sfa/focDE, cnf1, iutA
|
V | 18 (Turkey meat) | TOB10, CL30, CAZ30, TE30, AZM15 |
aac(3)-IV, blaSHV, ClTM, tetA, tetB
|
cvaC, fimH
|
VI | 16 (Ovine meat) | GM10, AK30, SXT25, CL30, CAZ30, TE30, TMP5, CIP5, LEV5, MEM10, C30, F300, E15 | aadA1, aac(3)-IV, sul1, blaSHV, ClTM, tetA, tetB, dfrA1, cat1, cmlA, sim, oxa-51-like, oxa-23-like |
kpsMTII, ibeA, papC, papGII, papGIII, traT, afa/draBC, cnf1, cnf2, csgA, iutA, fimH
|
VII | 17 (Bovine meat) | S10, CAZ30, TE30, TMP5, IPM10, RA5 |
aadA1, aac(3)-IV, ClTM, dfrA1, imp
|
PAI, papC, papGIII, traT, afa/draBC, cnf1, cnf2, csgA, cvaA, iutA, fyuA, fimH
|
VIII | 7 (Bovine meat) | F300, RA5 |
aadA1, ClTM, tetA, tetB, dfrA1, cat1, imp,
oxa-51-like, oxa-24-like |
kpsMTII, PAI, papC, papGIII, traT, afa/draBC, cnf1, cnf2, csgA, iutA, fyuA, fimH
|
IX | 14 (Chicken meat) 6 (Bovine meat) | GM10, AK30, TOB10, CL30, TE30, CIP5, C30 |
aac(3)-IV, sul1, blaSHV, tetA, tetB, dfrA1
|
papGII, papGIII, afa/draBC, cnf1, cnf2, cvaC, fyuA, fimH
|
X | 9 (Camel meat) | S10, AZM15 |
aadA1, tetA
|
PAI, papC, papGII, sfa/focDE, afa/draBC, csgA, cvaC
|
XI | 11 (Camel meat) | GM10, TOB10, SXT25, TE30, C30, RA5 |
aadA1, aac(3)-IV, sul1, tetA, tetB, cmlA
|
ibeA, papGII, sfa/focDE, traT, afa/draBC, cnf2, csgA, cvaC, fimH
|
XII | 8 (Chicken meat) | S10, AK30, CAZ30, TE30, LEV5, IPM10, C30 | sul1, ClTM, tetA, tetB, qnr, cat1, cmlA, vim, oxa-51-like, oxa-23-like, oxa-24-like |
PAI, ibeA, papGII, sfa/focDE, cnf2, iutA, fimH
|
XIII | 1,3 (Chicken meat) | SXT25, TE30, TMP5, CIP5, MEM10, E15 |
aac(3)-IV, sul1, ClTM, tetA, tetB, dfrA1
|
cnf2, csgA, iutA, fimH
|
XIV | 13 (Turkey meat) | TOB10, TE30, TMP5, CIP5, LEV5, E15 |
aadA1, tetA, tetB, dfrA1, oxa-51-like,
oxa-24-like |
ibeA, papC, sfa/focDE, fimH
|
XV | 5 (Turkey meat) 4 (Bovine meat) | GM10, TOB10, SXT25, TE30, TEP5, E15 |
aac(3)-IV, sul1, tetA, tetB
|
afa/draBC, cnf1, cnf2, csgA, cvaC, fimH
|
XVI | 2 (Camel meat) 10 (Ovine meat) | S10, GM10, TE30, TMP5 |
aac(3)-IV, tetA, dfrA1,
oxa-58-like
|
sfa/focDE, afa/draBC, cnf1, csgA, cvaC, iutA, fyuA, fimH
|