Table 3.
Carbapenem‐resistant isolates identified and characterized in this study
| Closest species identified by BLAST using 16S rDNA genea | Isolate# | Inhibition zone (diameter in mm)b | Carba NPc | Carbape nemase gene (%identityd) | |||||
|---|---|---|---|---|---|---|---|---|---|
| MP | IM | CF | CI | GE | TE | ||||
| Aeromonas veronii | W7‐1 | 23 | 20 | 40 | 39 | 27 | 25 | – | N/A |
| Aeromonas veronii | W7‐2 | 5 | 0 | 31 | 34 | 22 | 11 | – | N/A |
| Cupriavidus gilardii | W2‐2 | 1 | 20 | 40 | 36 | 0 | 28 | – | N/A |
| Cupriavidus gilardii | W2‐5 | 2 | 20 | 40 | 36 | 0 | 29 | – | N/A |
| Enterobacter asburiae | W6‐1 | 0 | 0 | 32 | 39 | 27 | 28 | + | bla IMI‐2 (100%) |
| Enterobacter asburiae | W6‐2 | 0 | 0 | 34 | 39 | 27 | 27 | + | bla IMI‐2 (100%) |
| Enterobacter asburiae | W6‐3 | 0 | 0 | 31 | 39 | 25 | 26 | + | bla IMI‐2 (100%) |
| Enterobacter asburiae | W6‐4 | 0 | 0 | 32 | 34 | 25 | 25 | + | bla IMI‐2 (100%) |
| Enterobacter asburiae | W6‐5 | 0 | 0 | 36 | 41 | 26 | 29 | + | bla IMI‐2 (100%) |
| Enterobacter asburiae | W6‐7 | 0 | 0 | 35 | 39 | 27 | 28 | + | bla IMI‐2 (100%) |
| Enterobacter asburiae | W6‐8 | 0 | 0 | 37 | 36 | 28 | 28 | + | bla IMI‐2 (100%) |
| Pseudomonas alcaligenes | W1‐4 | 18 | 26 | 29 | 39 | 24 | 22 | – | N/A |
| Pseudomonas alcaligenes | W4‐5 | 11 | 26 | 15 | 47 | 29 | 27 | – | N/A |
| Pseudomonas alcaligenes | W5‐5 | 8 | 15 | 10 | 38 | 25 | 24 | – | N/A |
| Pseudomonas alcaligenes | W5‐7 | 17 | 24 | 9 | 34 | 25 | 21 | – | N/A |
| Pseudomonas alcaligenes | W5‐8 | 14 | 25 | 12 | 40 | 26 | 20 | – | N/A |
| Pseudomonas cedrina | W9‐8 | 11 | 13 | 16 | 27 | 33 | 33 | – | N/A |
| Pseudomonas geniculata | W8‐10 | 0 | 21 | 43 | 37 | 0 | 31 | – | N/A |
| Pseudomonas otitidis | W3‐5 | 11 | 20 | 26 | 33 | 26 | 25 | – | N/A |
| Pseudomonas otitidis | W4‐1 | 15 | 22 | 27 | 41 | 29 | 23 | – | N/A |
| Pseudomonas otitidis | W4‐2 | 14 | 24 | 29 | 39 | 32 | 21 | – | N/A |
| Pseudomonas otitidis | W4‐3 | 1 | 21 | 27 | 41 | 31 | 25 | – | N/A |
| Pseudomonas otitidis | W4‐6 | 10 | 18 | 24 | 39 | 28 | 22 | – | N/A |
| Pseudomonas otitidis | W4‐7 | 10 | 21 | 27 | 39 | 30 | 23 | – | N/A |
| Pseudomonas otitidis | W4‐8 | 10 | 21 | 25 | 37 | 29 | 21 | – | N/A |
| Pseudomonas otitidis | W5‐3 | 14 | 22 | 25 | 30 | 24 | 20 | – | N/A |
| Pseudomonas otitidis | W5‐4 | 0 | 18 | 21 | 30 | 22 | 15 | – | N/A |
| Pseudomonas stutzeri | W3‐4 | 11 | 19 | 22 | 14 | 23 | 25 | – | N/A |
| Stenotrophomonas maltophilia | W1‐2 | 0 | 0 | 0 | 19 | 0 | 8 | + | bla L1 (99%) |
| Stenotrophomonas maltophilia | W1‐3 | 0 | 0 | 8 | 26 | 21 | 20 | + | bla L1 (84%) |
| Stenotrophomonas maltophilia | W1‐5 | 0 | 0 | 10 | 26 | 24 | 22 | + | bla L1 (83%) |
| Stenotrophomonas maltophilia | W1‐6 | 0 | 0 | 0 | 26 | 22 | 21 | + | bla L1 (90%) |
| Stenotrophomonas maltophilia | W2‐1 | 0 | 0 | 13 | 27 | 12 | 14 | + | bla L1 (92%) |
| Stenotrophomonas maltophilia | W2‐3 | 0 | 0 | 24 | 26 | 19 | 19 | + | bla L1 (84%) |
| Stenotrophomonas maltophilia | W2‐4 | 0 | 0 | 11 | 25 | 11 | 15 | + | bla L1 (89%) |
| Stenotrophomonas maltophilia | W2‐6 | 2 | 0 | 12 | 29 | 11 | 13 | + | bla L1 (89%) |
| Stenotrophomonas maltophilia | W2‐7 | 0 | 0 | 12 | 25 | 11 | 12 | + | bla L1 (89%) |
| Stenotrophomonas maltophilia | W2‐8 | 0 | 0 | 13 | 37 | 12 | 13 | + | bla L1 (89%) |
| Stenotrophomonas maltophilia | W3‐1 | 0 | 0 | 11 | 25 | 11 | 11 | + | bla L1 (89%) |
| Stenotrophomonas maltophilia | W3‐2 | 0 | 0 | 11 | 22 | 5 | 11 | + | bla L1 (92%) |
| Stenotrophomonas maltophilia | W3‐6 | 0 | 0 | 0 | 22 | 12 | 12 | + | bla L1 (99%) |
| Stenotrophomonas maltophilia | W3‐7 | 0 | 0 | 12 | 26 | 11 | 15 | + | bla L1 (89%) |
| Stenotrophomonas maltophilia | W3‐8 | 0 | 0 | 12 | 28 | 14 | 14 | + | bla L1 (89%) |
| Stenotrophomonas maltophilia | W4‐4 | 0 | 0 | 0 | 24 | 16 | 13 | + | bla L1 (93%) |
| Stenotrophomonas maltophilia | W8‐1 | 0 | 0 | 12 | 37 | 21 | 20 | + | bla L1 (89%) |
| Stenotrophomonas maltophilia | W8‐2 | 0 | 0 | 0 | 26 | 7 | 14 | + | bla L1 (94%) |
| Stenotrophomonas maltophilia | W8‐3 | 0 | 0 | 9 | 31 | 23 | 22 | + | bla L1 (84%) |
| Stenotrophomonas maltophilia | W8‐4 | 0 | 0 | 0 | 24 | 19 | 11 | + | bla L1 (94%) |
| Stenotrophomonas maltophilia | W8‐5 | 0 | 0 | 0 | 24 | 17 | 11 | + | bla L1 (94%) |
| Stenotrophomonas maltophilia | W8‐7 | 0 | 0 | 0 | 37 | 15 | 20 | + | bla L1 (94%) |
| Stenotrophomonas maltophilia | W8‐8 | 0 | 0 | 0 | 37 | 18 | 20 | + | bla L1 (92%) |
| Stenotrophomonas maltophilia | W8‐9 | 0 | 0 | 13 | 37 | 25 | 20 | + | bla L1 (88%) |
| Stenotrophomonas maltophilia | W8‐11 | 0 | 0 | 13 | 37 | 20 | 19 | + | bla L1 (89%) |
| Stenotrophomonas maltophilia | W8‐12 | 0 | 0 | 13 | 37 | 27 | 21 | + | bla L1 (89%) |
| Stenotrophomonas maltophilia | W9‐1 | 0 | 0 | 11 | 32 | 11 | 20 | + | bla L1 (84%) |
| Stenotrophomonas maltophilia | W9‐2 | 13 | 0 | 11 | 29 | 12 | 18 | + | bla L1 (83%) |
| Stenotrophomonas maltophilia | W9‐3 | 0 | 0 | 9 | 37 | 25 | 23 | + | bla L1 (89%) |
| Stenotrophomonas maltophilia | W9‐4 | 0 | 0 | 9 | 30 | 0 | 16 | + | bla L1 (88%) |
| Stenotrophomonas maltophilia | W9‐5 | 0 | 0 | 11 | 32 | 27 | 21 | + | bla L1 (84%) |
| Stenotrophomonas maltophilia | W9‐6 | 0 | 0 | 0 | 28 | 11 | 13 | + | bla L1 (94%) |
| Stenotrophomonas maltophilia | W9‐7 | 0 | 0 | 16 | 29 | 11 | 15 | + | bla L1 (92%) |
| Stenotrophomonas maltophilia | W9‐12 | 0 | 0 | 10 | 34 | 26 | 24 | + | bla L1 (83%) |
| Stenotrophomonas maltophilia | W10‐1 | 0 | 0 | 0 | 28 | 10 | 17 | + | bla L1 (88%) |
| Stenotrophomonas maltophilia | W10‐2 | 0 | 0 | 0 | 27 | 8 | 16 | + | bla L1 (89%) |
| Stenotrophomonas maltophilia | W10‐3 | 0 | 0 | 0 | 28 | 11 | 15 | + | bla L1 (89%) |
| Stenotrophomonas maltophilia | W10‐5 | 0 | 0 | 0 | 29 | 6 | 14 | + | bla L1 (89%) |
| Stenotrophomonas maltophilia | W10‐6 | 0 | 0 | 0 | 27 | 10 | 15 | + | bla L1 (89%) |
| Stenotrophomonas maltophilia | W10‐7 | 0 | 0 | 0 | 27 | 9 | 15 | + | bla L1 (89%) |
| Stenotrophomonas maltophilia | W10‐8 | 0 | 0 | 0 | 27 | 16 | 14 | + | bla L1 (88%) |
| Stenotrophomonas maltophilia | W10‐9 | 0 | 0 | 0 | 28 | 4 | 14 | + | bla L1 (89%) |
| Stenotrophomonas maltophilia | W10‐10 | 0 | 0 | 0 | 27 | 15 | 11 | + | bla L1 (85%) |
| Stenotrophomonas maltophilia | W10‐11 | 0 | 0 | 10 | 28 | 0 | 15 | + | bla L1 (84%) |
| Stenotrophomonas maltophilia | W10‐12 | 0 | 0 | 13 | 28 | 0 | 14 | + | bla L1 (92%) |
| Stenotrophomonas pavanii | W5‐1 | 0 | 0 | 12 | 32 | 13 | 18 | – | N/A |
| Stenotrophomonas pavanii | W5‐2 | 0 | 0 | 11 | 27 | 9 | 17 | – | N/A |
| Stenotrophomonas pavanii | W5‐6 | 0 | 0 | 10 | 28 | 0 | 17 | – | N/A |
Note.For each isolate, we obtained their 16S rDNA sequence and used BLAST (Altschul et al., 1997) to determine the closest known strain. In all cases, the DNA identity between our isolate and the top BLAST known strain hit was ≥98% (≥99% for most isolates).
MP: meropenem; IM: imipenem; CF: cefotaxime; CI: ciprofloxacin; GE: gentamicin; TE: tetracycline. To determine whether our isolates were Resistant (highlighted in red), Intermediate (highlighted in yellow) or Sensitive (no highlight) to the antibiotics tested, we used the CLSI zone diameter clinical breakpoint values (Clinical and Laboratory Standards Institute, 2017). For taxa in which the CLSI zone diameter breakpoint values were not available, we used the Enterobacteriaceae values.
All CarbaNP‐positive isolates (carbapenemase‐producing isolates) were positive when the test was performed measuring the hydrolysis of both meropenem and imipenem.
Only carbapenemase‐producing isolates (CarbaNP‐positive isolates) were tested by PCR to identify their potential carbapenemases. The rest of isolates were not tested because they were CarbaNP‐negative and are shown as N/A. “%identity” indicates % DNA identity (shown in parenthesis) between the reference bla IMI‐2 or bla L1 gene and the isolate bla IMI‐2 or bla L1 sequence obtained for that isolate.