TABLE 3.
Existence of plasmid-mediated quinolone resistance genes, tet genes, mutations in the target [gyrA, tet(A)] and regulatory (RamR-A) genes, and expression of efflux pump genes (ramA and acrB) in XDR Salmonella enterica serovars showing ciprofloxacin and/or tigecycline resistance.
| Isolate no. | Serovar | PMQR pattern | tet genes |
Target gene mutationa
|
RamR-A regulatory gene mutationa
|
Expression level
|
Accession numberb | ||||
| gyrA | tet(A) | ramR/ramR | ramR binding site | ramA | acrB | oqxB | |||||
| 1 | Typhimurium | qnrA; qepA | tet(A) | S83A; D87V | – | F146L; Del G69–A72; Ins (3 nt) C235 | T-97C; Del T–288/A–285 | 10.04 | 7.61 | ND | MT725561; MT725590; MT743008 |
| 2 | Typhimurium | qnrA; qnrS; qepA | tet(A); tet(B) | S83Y; D87R | L121P | F146L; Ins (3 nt) G484; Ins (3 nt) C235; Del A67–G69 | T-97C; Del T–288/A–285 | 10.10 | 8.09 | ND | MT725562; MT725591; MT743009 |
| 3 | Untypable | qnrA; qnrB; qnrS; qepA | tet(A); tet(B) | S83T; D87R | L121T | G186R; F149L; D104G; N87S; H82R; Ins (7 nt) G321; Ins (5 nt) C252; Del T65–G69 | T-97C; V28M; Del T–288/A–285 | 16.33 | 10.84 | ND | MT725563; MT725592; MT743010 |
| 4 | Magherafelt | qnrS; qepA | tet(A) | S83L | – | F148L; Ins (7 nt) G319; Ins (3 nt) C235; Del G69–A72 | T-97C; Del T–288/A–285 | 10.55 | 9.92 | ND | MT725564; MT725593; MT743011 |
| 5 | Typhimurium | qnrA; qepA; oqxA; oqxB | tet(A) | S83F | L121P | F148L; Ins (6 nt) T319; Ins (3 nt) C235; Del G69–A72 | T-97C | 5.10 | 2.83 | 1.4 | MT725565; MT725594; MT743012 |
| 6 | Takoradi | qnrS; qepA; oqxA; oqxB | tet(A); tet(B) | S83F; D87Y | F120S; L121A | G186R; F149L; D104G; N87S; H82R; Ins (7 nt) G321; Ins (5 nt) C252; Del T65–G68 | V28M; Del T–288/C–285 | 12.21 | 11.12 | 4.3 | MT725566; MT725595; MT743013 |
| 7 | Labadi | qnrA; qnrS; qepA | tet(A); tet(B) | S83V; D87S | L121P | F149L; A102V; N87S; H82R; Ins (7 nt) G324; Ins (5 nt) C252; Del T65–G69 | I40L; V28M; Del T–288/A–285; Del G–52/A–49 | 22.68 | 20.90 | ND | MT725567; MT725596; MT743014 |
| 8 | Typhimurium | qnrS; qepA | tet(A); tet(B) | S83Y | – | G182R; F145L; G109S; L72F; Del G307–C309; Del G251–C254; Del G64–G69 | T-97C; I40L | 8.11 | 6.62 | ND | MT725568; MT725597; MT743015 |
| 9 | Jedburgh | qnrA; qepA | tet(A) | S83L; D87N | – | F145L; S84G; G182R; Del C307–G309; Del C254–A257; Del T65–G69 | T-97C; Del T–288/A–285; Del T–89/T–87 | 11.35 | 8.12 | ND | MT725569; MT725598; MT743016 |
| 10 | Alfort | qnrA; qnrB; qnrS; qepA; oqxA; oqxB | tet(A); tet(B) | D87F | G181D | G186R; F149L; D104G; N87S; H82R; Ins (7 nt) G321; Ins (5 nt) C252; Del T65–G69 | V28M; Del T–288/A–285 | 15.86 | 13.66 | 10.1 | MT725570; MT725599; MT743017 |
| 11 | Typhimurium | qnrA; qnrB; qnrS; qepA; oqxA; oqxB | tet(A) | S83F; D87A | G181D | G186R; F149L; D104G; N87S; H82R; Ins (7 nt) G321; Ins (5 nt) C252; Del T65–G69 | T-97C; V28M; Del T–288/A–285 | 12.80 | 8.24 | 5.4 | MT725571; MT725600; MT743018 |
| 12 | Typhimurium | qnrS; qepA | tet(A); tet(B) | S83E | – | G182R; F145L; G109S; L72F; Del G251–C254; Del T65–G69; Del G307–C309 | I40L; Del T–288/A–285; Del T–89/T–87 | 14.83 | 9.51 | ND | MT725572; MT740093; MT743019 |
| 13 | Untypable | – | tet(A); tet(B) | S83F | – | F148L; Ins (7 nt) G319; Ins (3 nt) C235; Del G69–A72 | T-97C; Del T–288/A–285 | 10.91 | 7.44 | ND | MT725573; MT725601; MT743020 |
| 14 | Blegdam | qnrA; qepA | tet(A); tet(B) | S83F | – | F149L; Ins (7 nt) G321; Ins (5 nt) C252; Del T65–G69 | T-97C | 7.11 | 4.38 | ND | MT725574; MT725602; MT743021 |
| 15 | Infantis | qnrA; qepA | tet(A) | – | L121P | F145L; Del G69–A72; Del G251–C254; Del G307–C309 | T-97C | 7.31 | 4.68 | ND | MT725575; MT725603; MT743022 |
| 16 | Enteritidis | qnrA; qepA | tet(A); tet(B) | – | – | F145L; Del G69–A72; Del G251–C254; Del G307–C309 | T-97C | 7.61 | 5.20 | ND | MT725576; MT725604; MT743023 |
| 17 | Typhimurium | qnrA; qnrS; qepA | tet(A); tet(B) | S83F | – | Ins (6 nt) C411; Ins (3 nt) G377; Del G307–G309; Del G251–C254; Del G69–A72 | Del T–288/A–285 | 12.19 | 10.73 | ND | MT725577; MT725605; MT743024 |
| 18 | Paratyphi C | qnrS; qepA | tet(A); tet(X4) | D87Y | – | F148L; Ins (7 nt) G319; Ins (3 nt) C235; Del G69–A72 | – | 6.21 | 2.50 | ND | MT725578; MT725606; MT743025 |
| 19 | Typhimurium | qnrA; qnrB; qnrS; qepA; oqxA; oqxB | tet(A) | S83V | – | F145L; Del G307–C309; Del C254–A257; Del G69–A72 | T-97C | 4.60 | 3.97 | 1.1 | MT725579; MT725607; MT743026 |
| 20 | Typhimurium | qnrB; qnrS; qepA | tet(A); tet(B) | – | – | F150L; N88S; H83R; Ins (7 nt) G326; Ins (5 nt) C257; Ins (5 nt) G64 | – | 8.32 | 3.84 | ND | MT725580; MT725608; MT743027 |
| 21 | Bardo | qnrA; qnrB; qnrS; qepA; oqxA; oqxB | tet(A) | D87Y | – | F147L; Ins (4 nt) A319; Ins (3 nt) C235; Del G69–A72 | T-97C; Del T–288/A–285; Del G–52/A–49 | 24.20 | 19.23 | 10.9 | MT725581; MT740094; MT743028 |
| 22 | Sandiego | qnrA; qnrB; qnrS; qepA | tet(A); tet(B) | D87A | L121P | G186R; F148L; G112S; Ins (3 nt) T520; Ins (7 nt) G319; Ins (3 nt) C235; Del G69–A72 | T-97C; Del T–288/A–285; Del A–89/T–87 | 16.85 | 11.77 | ND | MT725582; MT725609; MT743029 |
| 23 | Typhimurium | oqxA | tet(A); tet(B) | S83I | – | F148L; Ins (7 nt) G319; Ins (3 nt) C235; Del G69–A72 | – | 1.6 | 1.1 | ND | MT725583; MT725610; MT743030 |
| 24 | Magherafelt | qnrS; qepA | tet(A); tet(B) | S83A; D87Y | – | F149L; N87S; H82R; Ins (3 nt) G493; Ins (7 nt) G321; Ins (5 nt) C252; Del T65–G69 | T-97C; V28M; Del T–288/A–285 | 19.25 | 13.22 | ND | MT725584; MT725611; MT743031 |
| 25 | Jedburgh | qnrS; qepA | tet(A); tet(B) | D87A | L121p | G182R; F145L; G109S; L72F; Del G307–C309; Del G251–C254; Del T65–G69 | T-97C; I40L; Del T–288/A–285 | 14.18 | 10.74 | ND | MT725585; MT725612; MT743032 |
| 26 | Wingrove | qnrS; qepA | tet(A) | D87S | G181D | F147L; Ins (6 nt) C408; Del G307–C309; Del G251–C254; Del T65–G69 | T-97C | 6.66 | 4.09 | ND | MT725586; MT740095; MT743033 |
| 27 | Untypable | – | tet(A); tet(B) | D87G | L121p | F149L; A102V; N87S; H82R; Ins (7 nt) G321; Ins (5 nt) C252; Del T65–G69 | T-97C; C-109T | 9.44 | 6.42 | ND | MT725587; MT725613; MT743034 |
| 28 | Typhimurium | qnrS; qepA, oqxB | tet(A) | D87Y | – | F149L; N87S; H82R; Ins (7 nt) G321; Ins (5 nt) C252; Del T65–G68 | T-97C | 5.41 | 3.82 | ND | MT725588; MT740096; MT743035 |
| 29 | Typhimurium | qnrA; qnrB; qnrS; qepA | tet(A); tet(B) | S83L; D87G | – | F148L; Ins (7 nt) G319; Ins (3 nt) C235; Del G69–A72 | T-97C; Del T–288/A–285 | 11.33 | 8.74 | ND | MT725589; MT725614; MT743036 |
PMQR, plasmid-mediated quinolone resistance; Ins, insertion; Del, deletion; nt, nucleotide; ND, not detected. Isolate numbers in bold were sensitive to tigecycline and resistant to ciprofloxacin. Other isolates exhibited co-resistance to ciprofloxacin and tigecycline. All isolates were nalidixic acid resistant.
aMutations were detected after comparison with the respective gene in the complete genome of S. enterica serovar Typhimurium LT2 (GenBank accession number NC_003197).
bGenBank accession numbers were assigned for gyrA, tet(A), and ramR-A genes, respectively.