Background
Methods
Bacterial isolates
Antimicrobial susceptibility testing, serotyping and phage typing
Bacterial DNA extraction
Detection and characterization of beta-lactamase enzymes
Gene/target | Primer | Sequence 5’-3’ | Amplicon size | AT °C | Ref | Remark |
---|---|---|---|---|---|---|
BLATem Gene | TEM-F1 | ATGAGTATTCAACATTTCCG | 862-bp | 55 | [34] | |
TEM-R1 | GACAGTTACCAATGCTTAATCA | |||||
blaTEM-F2 | TAA CCA TGAGTGATAACACT | [34] | sequencing | |||
blaTEM-R2 | CCGATCGTT GTCAGAAGTAA | |||||
BLA SHV gene | Bla SHV-F1 | CTTTACTCGCCTTTATCG | 827-bp | 56 | [34] | |
Bla SHV-R1 | TCCCGC AGATAAATCACCA | |||||
blaSHV-F2 | ACTGCCTTTTTG CGCCAGAT | [34] | sequencing | |||
blaSHV-R2 | CAGTTCCGTTTCCCAGCGGT | |||||
Bla OXA-1 | OXA-1-F | ATGAAAAACACAATACATATCAAC | 755-bp | 48 | [13] | |
OXA-1-R | TTTCCTGTAAGTGCGGACAC | |||||
Bla OXA −4 | OXA-4-F | TCAACAGATATCTCTACTGGT | 216 bp | 54 | [13] | |
OXA-4-R | TTTATCCCATTTGAATATG | |||||
Bla OXA-10 | OXa 10-F | TCAACAAATCGCCAGAGAAG | 277 bp | 57 | [13] | |
Oxa-10-R | TCCCACACCAGAAAAACCA | |||||
bla PER | Per1-F | AATTTGGGCTTAGGGCAGAA | 925 bp | 55 | [50] | |
Per1-R | ATGAATGTCATTATAAAAGC | |||||
blaPSE | blaPSE-F | TGCTTCGCAACTATGACTAC | [42] | |||
blaPSE-R | AGCCTGTGTTTGAGCTAGAT | |||||
blaCYM | blaCMY2-F | TGGCCGTTGCCGTTATCTAC | 868 | 57 | [9] | |
blaCMY2-R | CCCGTTTATGCACCCATGA | |||||
CTX-M group I | CTXM1-F3 | GACGATGTCACTGGCTGAGC | 499 | 55 | [38] | |
CTXM1-R2 | AGCCGCCGACGCTAATACA | |||||
CTX-M group II | TOHO1-2 F | GCGACCTGGTTAACTACAATCC | 351 | 55 | [38] | |
TOHO1-1R | CGGTAGTATTGCCCTTAAGCC | |||||
CTX-M group III | CTXM825F | CGCTTT GCCATGTGCAGCACC | 307 | 55 | [38] | |
CTXM825R | GCT CAGTACGATCGAGCC | |||||
CTX-M group IV | CTXM914F | GCTGGAGAAAAGCAGCGGAG | 474 | 62 | [38] | |
CTXM914R | GTAAGCTGACGCAACGTCTG |
Investigation of quinolone resistance mechanism
Gene | Primer name | Primer sequence (5′ to 3′) | Product size | AT in °C | References |
---|---|---|---|---|---|
gyrA | GyrAFP | AAATCTGCCCGTGTCGTTGGT | 344 bp | 58 | [16] |
GyrARP | GCCATACCTACTGCGATACC | ||||
gyrB | GyrB FP | GAATACCTGCTGGAAAACCCAT | 446 bp | 57 | [16] |
GyrB RP | CGGATGTGCGAGCCGTCGACGTCCGC | ||||
parC | ParC FP | AAGCCGGTACAGCGCCGCATC | 395 bp | 57 | [16] |
ParC RP | GTGGTGCCGTTCAGCAGG | ||||
ParE | ParE FP | TCTCTTCCGATGAAGTGCTG | 240 bp | 55 | [12] |
ParE RP | ATACGGTATAGCGGCGGTAG | ||||
qnrA | qnrA FP | ATTTCTCACGCCAGGATTTG | 516 bp | 53 | [43] |
qnrA RP | GATCGGCAAAGGTTAGGTCA | ||||
qnrB | qnrB FP | GATCGTGAAAGCCAGAAAGG | 469 bp | 53 | [43] |
qnrB RP | ACGATGCCTGGTAGTTGTCC | ||||
aac(6’)-Ib | aac(6’)-Ib FP | TTGCGATGCTCTATGAGTGGCTA | 482-bp | 55 | [36] |
aac(6’)-Ib-RP
| CTCGAATGCCTGGCGTGTTT | ||||
aac(6’)-Ib-cr-seq
| CGTCACTCCATACATTGCAA (for sequencing of aac(6’)-Ib-cr | ||||
qepA | QepA FP | CGTGTTGCTGGAGTTCTTC | 403 bp | 59 | [7] |
QepA RP | CTGCAGGTACTGCGTCATG | ||||
QnrD | QnrD FP | CGAGATCAATTTACGGGGAATA | 565 bp | 53 | [8] |
QnrD RP | AACAAGCTGAAGCGCCTG | ||||
QnrS | QnrS FP | ACGACATTCGTCAACTGCAA | 417 bp | 53 | [43] |
QnrS RP | TAAATTGGCACCCTGTAGGC |
Results
Resistance to beta-lactam antimicrobials and beta-lactamase genes in Salmonella isolates from animals and humans
Source | Total no. of isolates |
aResistant to ≥ one of beta-lactams (%) |
bla genes detectedb
| Not detected | No.(%) positive for bla genes | ||
---|---|---|---|---|---|---|---|
blaTEM
|
blaOXA10
|
blaCTX-M
| |||||
Cattle | 50 | 16(32) | 12 | - | - | 4 | 8(75) |
Poultry | 26 | 13(50) | 12 | - | 1 | 12(92.3) | |
Swine | 8 | 2(25) | 1 | - | - | 1 | 1(50) |
Human | 68 | 12(17.7) | 9 | 1 | 1 | 2 |
c10(83.3) |
Total | 152 | 43(28.3) | 34 | 1 | 1 | 8 | 34(79.1) |
Serotype | Total | Host (No.) | No. resistant to Beta-lactam(%) | Beta-lactam R-profile |
bla positive(%) |
bla type | |
---|---|---|---|---|---|---|---|
Intermediate | Resistant | ||||||
Aberdeen | 1 | C | - | - | - | - | - |
Agona | 1 | C | - | - | - | - | - |
Braenderup | 3 | C(2), H(1) | - | - | - | - | - |
Concord | 1 | H | 1(100) | Fox | AmpAmcCroCf | 1(100) | OXA-10 and blaCTX-M-15 |
Dublin | 3 | C | 2(66.7) | Cf | - | - | - |
Enteritidis | 2 | H | - | - | - | - | - |
Haifa | 4 | C(3), P(1) | 1P(25) | Amp | - | - | - |
Heidelberg | 1 | S | 1(100) | Amc | AmpCf | 1(100) | TEM-1 |
I:6;7,14:-:I,w | 1 | C | 1(100) | - | AmpAmcCf | 1(100) | TEM-1 |
I: Rough-O:I:1,2 | 1 | S | - | - | - | - | - |
Kentucky | 10 | C(6), | 6(100) | - | AmpAmcCf | 6(100) | TEM-1 |
P(2) | 2(100) | - | AmpAmcCf | 2(100) | TEM-1 | ||
H(2) | 2(100) | Fox | AmpAmcCf | 2(100) | TEM-1 | ||
Amc | AmpCf | ||||||
Kottbus | 8 | C(1), H(7) | - | - | - | - | - |
Livingstone var.14+ | 2 | C(1), S(1) | - | - | - | - | - |
Miami | 5 | H(3), S(2) | - | - | - | - | - |
Mikawasima | 2 | C(2) | - | - | - | - | |
Newport | 2 | H(2) | - | - | - | - | - |
Saintpaul | 33 | P(20) | 10(50) | AmcCf | Amp | 4(100) | TEM-57 |
- | AmpAmcCf | 4(100) | TEM-57 | ||||
Amc | AmpCf | 2(100) | TEM-57 | ||||
C(10) | 2(20) | Amc | AmpCf | 2(100) | TEM-1 | ||
S(2) | - | - | - | - | - | ||
H(1) | 1(100) | Amc | AmpCf | 1 | TEM-1 | ||
Typhimurium | 42 | C(12) | 2(16.7) | - | AmpAmcCf | 2(100) | TEM-1 |
P(3) | - | - | - | - | - | ||
S(1) | 1(100) | ||||||
H(26) | 6(64.5) | 5(83.3) | TEM-1 | ||||
Cf | - | - | - | ||||
Amc | AmpCf | 2(100) | TEM-1 | ||||
Amp | - | 1(100) | TEM-1 | ||||
- | AmpAmcCf | 2(100) | TEM-1 | ||||
Virchow | 28 | C(6) | 3(50) | Amc | AmpCf | 1(33.3) | TEM-1 |
H(22) | 1(4.6) | - | AmpAmcCf | 1(100) | TEM-1 | ||
V:ROUGH-O;-;- | 1 | H(1) | 1 | - | AmpCf | - | - |
Mechanism of resistance to quinolone antimicrobials
Serotype | Zone of inhibition mm (susceptibility category) | R-pattern betalactamsa
| Mutation in QRDR | ||||
---|---|---|---|---|---|---|---|
Na | Cip |
gyrA
|
gyrB
|
parC
| |||
Cattle | Aberdeen | 19[S] | 27[I] | - | - | - | - |
Cattle | Virchow | 20[S] | 25[I] |
-
| - | - | - |
Cattle | Typhimurium PT 3 | 21[S] | 25[I] |
AmpAmcCf
| - | - | - |
Cattle | Typhimurium PT 4 | 22[S] | 27[I] |
AmpAmcCf
| - | - | - |
Cattle | Haifa | 21[S] | 25[I] |
-
| - | - | - |
Poultry | Saintpaul | 20[S] | 31[S] |
AmcCf
| - | - | - |
Cattle | Saintpaul | 17[I] | 25[I] |
AmpAmcCCf
| - | - | - |
Cattle | Saintpaul | 21[S] | 27[I] | - | - | - | - |
Poultry | Saintpaul | 20[S] | 27[I] |
-
| - | - | - |
Human | V:ROUGH-O;-:- | 22[S] | 28[I] |
AmpCf
| - | Ser463Ala | - |
Cattle | Mikawasima | 20[S] | 25[I] | - | - | Val423Gly + Asp459His | - |
Cattle | Agona | 17[I] | 31[S] | - | - | - | Thr57Ser |
Cattle | Braenderup | 17[I] | 25[I] | - | - | Val423Gly + Asp459His | Thr57Ser |
Swine | Miami | 22[S] | 27[I] | - | - | - | Thr57Ser + Tyr83Phe |
Poultry | Haifa | 0[R] | 25[I] | - | Ser83Tyr | - | - |
Cattle | Virchow | 0[R] | 26(I) |
AmpAmcCf
| Ser83Phe | - | - |
Cattle | Livingstone var.14+ | 0[R] | 24(I) | - | Ser83Phe | - | - |
Cattle | I:6;7,14:-:I,w | 7[R] | 30(I) |
AmpAmcCf
| Ser83Phe | - | - |
Swine | Livingstone var.14+ | 0[R] | 20[I] |
-
| Ser83Phe | - | - |
Cattle | Kentucky | 0[R] | 14[R] |
AmpAmcCf
| Ser83Phe + Asp87Gly | - | Thr57Ser + Ser80Ile |
Cattle | Kentucky | 0[R] | 12[R] |
AmpCf
Amc
| Ser83Phe + Asp87Gly | - | Thr57Ser + Ser80Ile |
Cattle | Kentucky | 0[R] | 11[R] |
AmpCf
Amc
| Ser83Phe + Asp87Gly | - | Thr57Ser + Ser80Ile |
Cattle | Kentucky | 0[R] | 9[R] |
AmpAmcCf
| Ser83Phe + Asp87Gly | - | Thr57Ser + Ser80Ile |
Cattle | Kentucky | 0[R] | 12[R] |
AmpCf
Amc
| Ser83Phe + Asp87Gly | - | Thr57Ser + Ser80Ile |
Cattle | Kentucky | 0[R] | 10[R] |
AmpAmcCf
| Ser83Phe + Asp87Gly | - | Thr57Ser + Ser80Ile |
Human | Kentucky | 0[R] | 8[R] |
AmpAmcCf
Fox
| Ser83Phe + Asp87Gly | - | Thr57Ser + Ser80Ile |
Human | Kentucky | 0[R] | 10[R] |
AmpCf
Amc
| Ser83Phe + Asp87Gly | - | Thr57Ser + Ser80Ile |
Poultry | Kentucky | 0[R] | 9[R] |
AmpAmcCf
| Ser83Phe + Asp87Gly | - | Thr57Ser + Ser80Ile |
Poultry | Kentucky | 0[R] | 11[R] |
AmpAmcCf
| Ser83Phe + Asp87Gly | - | Thr57Ser + Ser80Ile |