TABLE 2.
Field isolates and other test strains used in this study
| Isolate no.a | Species | Geneb | Intensityc | Thresholdd |
|---|---|---|---|---|
| 1 | Acinetobacter sp. | None | 11,130 | |
| 2 | Acinetobacter sp. | None | 1,113 | |
| 3 | Acinetobacter woffii | None | 259 | |
| 4 | Escherichia coli | None | 4,549 | |
| 5 | Escherichia coli | None | 15,589 | |
| 6 | Pantoea sp. | None | 17,606 | |
| 7 | Providencia rettgeri | None | 12,467 | |
| 9 | Pseudomonas putida | None | 23,694 | |
| 10 | Ralstonia pickettii | None | 15,160 | |
| 11 | Aeromonas hydrophila | tet(A) | 4,895 | 4,035 |
| 12 | Aeromonas hydrophila | tet(A) | 33,819 | 26,808 |
| 13 | Citrobacter freundii | tet(A) | 65,535 | 51,741 |
| 14 | Citrobacter freundii | tet(A) | 62,044 | 48,931 |
| EC3e | Escherichia coli | tet(A),(B) | 65,535 | 73,099 |
| EC4 | Escherichia coli | tet(A) | 26,433 | 21,129 |
| EC5 | Escherichia coli | tet(A) | 65,535 | 52,592 |
| EC6 | Escherichia coli | tet(A) | 26,002 | 20,713 |
| EC8 | Escherichia coli | tet(A) | 49,000 | 38,695 |
| EC9 | Escherichia coli | tet(A) | 14,199 | 11,304 |
| 15 | Escherichia coli | tet(A) | 61,251 | 55,416 |
| SSuTA1 | Escherichia coli | tet(A) | 48,778 | 38,454 |
| SSuTA2 | Escherichia coli | tet(A) | 38,426 | 30,303 |
| SSuTCH1 | Escherichia coli | tet(A) | 33,717 | 26,769 |
| SSuTCH2 | Escherichia coli | tet(A) | 36,390 | 28,889 |
| SSuTCH3 | Escherichia coli | tet(A) | 9,964 | 8,073 |
| 17 | Pseudomonas fluorescens | tet(A) | 48,640 | 39,580 |
| 18 | Pseudomonas fluorescens | tet(A) | 61,988 | 51,568 |
| 19 | Pseudomonas fluorescens | tet(A) | 29,881 | 24,043 |
| 20 | Pseudomonas fluorescens | tet(A) | 51,838 | 41,179 |
| 22 | Pseudomonas sp. | tet(A) | 59,082 | 46,700 |
| 24 | Brevundimonas vesicularis | tet(B) | 60,669 | 51,384 |
| 25 | Enterobacter sakazakii | tet(B) | 59,673 | 50,585 |
| SSuT1 | Escherichia coli | tet(B) | 24,672 | 20,814 |
| SSuT2 | Escherichia coli | tet(B) | 34,982 | 29,552 |
| SSuT3 | Escherichia coli | tet(B) | 52,593 | 44,385 |
| SSuTA3 | Escherichia coli | tet(B) | 61,319 | 48,373 |
| 26 | Serratia liquifaciens | tet(B) | 64,873 | 57,964 |
| 27 | Citrobacter freundii | tet(D) | 12,974 | 10,353 |
| 28 | Citrobacter freundii | tet(D) | 8,499 | 6,872 |
| 29 | Aeromonas hydrophila | tet(E) | 65,535 | 60,134 |
| 30 | Aeromonas hydrophila | tet(E) | 23,357 | 18,635 |
| 31 | Aeromonas hydrophila | tet(E) | 63,840 | 50,459 |
| 32 | Aeromonas hydrophila | tet(E) | 39,391 | 31,303 |
| 33f | Escherichia coli | tet(G) | 32,777 | 25,887 |
| 34 | Acinetobacter radioresistens | tet(H) | 42,763 | 37,004 |
| EC2 | Escherichia coli | tet(H) | 65,535 | 51,935 |
| 35 | Moraxella sp. | tet(H) | 60,039 | 53,763 |
| EC1 | Escherichia coli | tet(Z) | 65,535 | 52,207 |
a
Isolate reference number. Both EC2 and EC3 harbored cloned genes and do not represent field isolates.
b
Gene detected by the DNA microarray. Gene identity was confirmed by previous work (14) or by PCR with gene-specific primers (strains designated with an SSuT prefix).
c
Median pixel intensity of the microarray probe.
d
Detection threshold based on the average median pixel intensity for tet probes plus 3 × SD.
e
EC3 was clearly positive for both tet(A) and tet(B).
f
Isolate 33 harbored plasmid R714a from a strain of Providencia (13).