Background
Materials and methods
Bacterial strains
Study design and participants
Phenotypic characterisation
Biofilm formation assay
Genomic characterisation
Epidemiological investigation and data analysis
Results
Epidemiological investigation and risk factors associated with colonisation
Variable | Subjects with ARB-positive, n = 37 | Subjects with ARB-negative, n = 61 | Univariate analysis | P-value | |
---|---|---|---|---|---|
n (%) | OR | 95% CI | |||
Age ≥ 90 years, n (%) | 12 (32.4) | 13 (21.3) | 1.77 | 0.71–4.45 | 0.22 |
Male sex, n (%) | 14 (37.8) | 15 (24.6) | 1.87 | 0.77–4.52 | 0.16 |
Ward, n (%) | 0.92 | ||||
1st floor | 10 (27.0) | 17 (27.9) | 0.96 | 0.38–2.40 | 0.93 |
2nd floor | 14 (37.8) | 25 (41.0) | 0.88 | 0.38–2.03 | 0.76 |
3rd floor | 13 (35.1) | 19 (31.1) | 1.20 | 0.50–2.85 | 0.68 |
Dementia | 15 (40.5) | 31 (50.8) | 0.66 | 0.29–1.51 | 0.32 |
Strokes (cerebral infarction/ cerebral haemorrhage) | 16 (43.2) | 11 (18.0) | 3.46 | 1.38–8.70 | 0.007** |
Cardiovascular diseases | 15 (40.5) | 19 (31.1) | 1.51 | 0.64–3.53 | 0.34 |
Diabetes | 10 (27.0) | 10 (16.4) | 1.89 | 0.70–5.10 | 0.21 |
Cancers | 1 (2.7) | 5 (8.2) | 0.40a | ||
Fractures | 5 (13.5) | 11 (18.0) | 0.71 | 0.23–2.24 | 0.56 |
Arthropathy | 2 (5.4) | 2 (3.3) | 0.63a | ||
Dysarthria or dysphagia | 13 (35.1) | 12 (19.7) | 2.21 | 0.88–5.57 | 0.09 |
Inappropriate oral care | 18 (48.6) | 26 (42.6) | 1.28 | 0.56–2.90 | 0.56 |
Denture wearing | 24 (64.9) | 32 (52.5) | 1.67 | 0.72–3.88 | 0.23 |
Percutaneous endoscopic gastrotomy tubes (PEG tubes) | 6 (16.2) | 0 (0.0) | 0.002a,** |
Phenotypic and genomic characterisation
Isolate’s code | Species | Patients’ ward (floor) | POT code | MIC (μg/mL) | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ABPC | PIPC | T/P | A/S | CEZ | CAZ | CTX | CZOP | CPDX | IMP | MEPM | AMK | CPFX | FOM | ST | ||||
61E | Acinetobacter baumannii | 3 | 8–13-0 | – | 4 (S) | ≤8 (S) | ≤2 (S) | – | 1 (S) | 4 (S) | ≤0.5 (S) | – | 1 (S) | ≤0.25 (S) | ≤1 (S) | ≤0.25 (S) | > 128 (R) | ≤20 (S) |
66C | Acinetobacter baumannii | 3 | 8–13-0 | – | 16 (S) | ≤8 (S) | ≤2 (S) | – | 2 (S) | 8 (S) | ≤0.5 (S) | – | ≤0.25 (S) | ≤0.25 (S) | ≤1 (S) | ≤0.25 (S) | > 128 (R) | ≤20 (S) |
25E | Acinetobacter baumannii | 2 | 32–20-41 | – | 16 (S) | ≤8 (S) | > 16 (R) | – | 4 (S) | 16 (I) | > 16 (R) | – | > 8 (R) | 4 (I) | 2 (S) | 2 (I) | <=32 (S) | ≤20 (S) |
13C | Acinetobacter baumannii | 3 | 104–12-10 | – | 8 (S) | ≤8 (S) | ≤2 (S) | – | 4 (S) | 8 (S) | ≤0.5 (S) | – | ≤0.25 (S) | ≤0.25 (S) | ≤1 (S) | 0.25 (S) | > 128 (R) | ≤20 (S) |
41C | Acinetobacter baumannii | 2 | 104–12-10 | – | 32 (I) | 16 (S) | 4 (S) | – | 8 (S) | 8 (S) | 1 (S) | – | ≤0.25 (S) | 0.5 (S) | ≤1 (S) | ≤0.25 (S) | > 128 (R) | ≤20 (S) |
45C | Acinetobacter baumannii | 2 | 104–12-10 | – | 32 (I) | 32 (I) | 4 (S) | – | 8 (S) | 16 (I) | 2 (S) | – | ≤0.25 (S) | 1 (S) | ≤1 (S) | ≤0.25 (S) | 128 (I) | ≤20 (S) |
50E-B | Acinetobacter baumannii | 2 | 104–12-10 | – | 8 (S) | ≤8 (S) | ≤2 (S) | – | 2 (S) | 4 (S) | ≤0.5 (S) | – | ≤0.25 (S) | ≤0.25 (S) | ≤1 (S) | ≤0.25 (S) | 128 (I) | ≤20 (S) |
51E | Acinetobacter baumannii | 2 | 104–12-10 | – | 4 (S) | ≤8 (S) | ≤2 (S) | – | 2 (S) | 4 (S) | ≤0.5 (S) | – | ≤0.25 (S) | ≤0.25 (S) | ≤1 (S) | ≤0.25 (S) | 128 (I) | ≤20 (S) |
52E | Acinetobacter baumannii | 2 | 104–12-10 | – | 8 (S) | ≤8 (S) | ≤2 (S) | – | 4 (S) | 8 (S) | ≤0.5 (S) | – | ≤0.25 (S) | ≤0.25 (S) | ≤1 (S) | ≤0.25 (S) | 128 (I) | ≤20 (S) |
12C-C | Acinetobacter baumannii | 3 | 104–13-8 | – | 8 (S) | ≤8 (S) | ≤2 (S) | – | 2 (S) | 8 (S) | ≤0.5 (S) | – | ≤0.25 (S) | ≤0.25 (S) | 2 (S) | ≤0.25 (S) | 128 (I) | ≤20 (S) |
70C | Acinetobacter nosocomialis | 2 | 2090-44-10 | – | > 64 (R) | > 64 (R) | 16 (I) | – | > 16 (R) | > 32 (R) | > 16 (R) | – | ≤0.25 (S) | 1 (S) | ≤1 (S) | 0.5 (S) | 128 (I) | ≤20 (S) |
67C-B | Acinetobacter sp. close to 13TU | 3 | 3045-12-10 | – | 64 (I) | 32 (I) | ≤2 (S) | – | > 16 (R) | > 32 (R) | 2 (S) | – | ≤0.25 (S) | 0.5 (S) | 2 (S) | 1 (S) | 128 (I) | ≤20 (S) |
59C-B | Acinetobacter sp. close to 13TU | 3 | 3109-12-10 | – | 64 (I) | 16 (S) | ≤2 (S) | – | 4 (S) | 8 (S) | 4 (S) | – | ≤0.25 (S) | 0.5 (S) | 2 (S) | ≤0.25 (S) | 128 (I) | ≤20 (S) |
56C | Acinetobacter ursingii | 2 | 4000-50-16 | – | > 64 (R) | > 16 (R) | > 16 (R) | – | > 16 (R) | > 32 (R) | > 16 (R) | – | ≤0.25 (S) | 0.5 (S) | ≤1 (S) | 1 (S) | 64 (S) | > 40 (R) |
68E | Acinetobacter baylyi | 2 | – | 4 (S) | 8 (S) | ≤2 (S) | – | 4 (S) | 8 (S) | ≤0.5 (S) | – | ≤0.25 (S) | ≤0.25 (S) | ≤1 (S) | ≤0.25 (S) | ≤32 (S) | ≤20 (S) | |
25C | Acinetobacter sp. | 2 | 4000-2-16 | – | > 64 (R) | 16 (S) | 4 (S) | – | 8 (S) | 8 (S) | ≤0.5 (S) | – | ≤0.25 (S) | ≤0.25 (S) | ≤1 (S) | ≤0.25 (S) | > 128 (R) | ≤20 (S) |
32E | Acinetobacter sp. | 2 | 4000-2-16 | – | 16 (S) | ≤8 (S) | ≤2 (S) | – | 16 (I) | 8 (S) | ≤0.5 (S) | – | ≤0.25 (S) | ≤0.25 (S) | ≤1 (S) | ≤0.25 (S) | 128 (I) | ≤20 (S) |
65C | Acinetobacter sp. | 3 | 4000-2-16 | – | 16 (S) | ≤8 (S) | ≤2 (S) | – | > 16 (R) | 16 (I) | 1 (S) | – | ≤0.25 (S) | 0.5 (S) | 2 (S) | 0.5 (S) | 128 (I) | ≤20 (S) |
71C | Acinetobacter sp. | 1 | 4064-4-1 | – | 8 (S) | ≤8 (S) | ≤2 (S) | – | 8 (S) | 8 (S) | 1 (S) | – | ≤0.25 (S) | ≤0.25 (S) | 2 (S) | ≤0.25 (S) | ≤32 (S) | ≤20 (S) |
73E | Escherichia coli | 1 | 49–56-83 | > 16 (R) | > 64 (R) | ≤8 (S) | 16 (I) | > 16 (R) | > 16 (R) | > 32 (R) | > 16 (R) | > 4 (R) | ≤0.25 (S) | ≤0.25 (S) | 2 (S) | > 2 (R) | – | ≤20 (S) |
43E | Escherichia coli | 2 | 49–58-19 | > 16 (R) | > 64 (R) | ≤8 (S) | 4 (S) | > 16 (R) | 8 (R) | 16 (R) | 16 (R) | > 4 (R) | ≤0.25 (S) | ≤0.25 (S) | 4 (S) | > 2 (R) | – | ≤20 (S) |
95E | Escherichia coli | 1 | 49–62-235 | > 16 (R) | > 64 (R) | ≤8 (S) | > 16 (R) | > 16 (R) | 4 (S) | > 32 (R) | > 16 (R) | > 4 (R) | ≤0.25 (S) | ≤0.25 (S) | 32 (I) | > 2 (R) | – | > 40 (R) |
77E | Escherichia coli | 1 | 49–122-83 | > 16 (R) | > 64 (R) | ≤8 (S) | 8 (S) | > 16 (R) | 4 (S) | 32 (R) | > 16 (R) | > 4 (R) | ≤0.25 (S) | ≤0.25 (S) | 4 (S) | > 2 (R) | – | ≤20 (S) |
7C | Klebsiella pneumoniae | 3 | – | > 16 (R) | 16 (S) | ≤8 (S) | 4 (S) | 1 (S) | ≤0.5 (S) | ≤1 (S) | ≤0.5 (S) | ≤2 (S) | 0.5 (S) | ≤0.25 (S) | ≤1 (S) | ≤0.25 (S) | > 128 (R) | ≤20 (S) |
87C | Klebsiella pneumoniae | 2 | – | > 16 (R) | 4 (S) | ≤8 (S) | 4 (S) | 1 (S) | ≤0.5 (S) | ≤1 (S) | ≤0.5 (S) | ≤2 (S) | ≤0.25 (S) | ≤0.25 (S) | 2 (S) | ≤0.25 (S) | ≤32 (S) | ≤20 (S) |
12C-A | Klebsiella aerogenes | 3 | – | > 16 (R) | 32 (I) | 32 (I) | > 16 (R) | > 16 (R) | > 16 (R) | > 32 (R) | ≤0.5 (S) | > 4 (R) | ≤0.25 (S) | ≤0.25 (S) | ≤1 (S) | ≤0.25 (S) | 64 (S) | ≤20 (S) |
91C | Raoultella planticola | 1 | – | – | 4 (S) | ≤8 (S) | – | – | ≤0.5 (S) | ≤1 (S) | ≤0.5 (S) | – | ≤0.25 (S) | ≤0.25 (S) | ≤1 (S) | ≤0.25 (S) | 64 (S) | ≤20 (S) |
82E | Enterobacter cloacae | 1 | – | > 16 (R) | 16 (S) | 16 (S) | > 16 (R) | > 16 (R) | 16 (R) | 32 (R) | ≤0.5 (S) | > 4 (R) | ≤0.25 (S) | ≤0.25 (S) | ≤1 (S) | ≤0.25 (S) | > 128 (R) | ≤20 (S) |
102C-B | Serratia marcescens | 2 | – | 16 (I) | ≤2 (S) | ≤8 (S) | 8 (S) | > 16 (R) | ≤0.5 (S) | ≤1 (S) | ≤0.5 (S) | ≤2 (S) | 0.5 (S) | ≤0.25 (S) | ≤1 (S) | ≤0.25 (S) | ≤32 (S) | ≤20 (S) |
18C-A | Morganella morganii | 3 | – | > 16 (R) | 4 (S) | ≤8 (S) | > 16 (R) | > 16 (R) | 2 (S) | ≤1 (S) | ≤0.5 (S) | > 4 (R) | 4 (S) | ≤0.25 (S) | 8 (S) | ≤0.25 (S) | > 128 (R) | ≤20 (S) |
101E | Rahnella sp. | 1 | – | – | 4 (S) | ≤8 (S) | – | – | ≤0.5 (S) | ≤1 (S) | ≤0.5 (S) | – | 0.5 (S) | ≤0.25 (S) | ≤1 (S) | ≤0.25 (S) | ≤32 (S) | ≤20 (S) |
71E | Pseudononas aeruginosa | 1 | 207–1 | – | > 64 (I) | > 64 (I) | – | – | > 16 (R) | > 32 (R) | > 16 (R) | – | > 8 (R) | > 8 (R) | > 32 (R) | > 2 (R) | > 128 (R) | > 40 |
18C-B | Pseudononas aeruginosa | 3 | 108–2 | 4 (S) | 4 (S) | 2 (S) | ≤0.5 (S) | 0.5 (S) | 0.5 (S) | 4 (S) | ≤0.25 (S) | > 40 | ||||||
96C | Pseudononas aeruginosa | 1 | 641–0 | ≤2 (S) | ≤2 (S) | 1 (S) | 2 (S) | 1 (S) | ≤0.25 (S) | 4 (S) | 0.5 (S) | 40 | ||||||
89C | Pseudononas aeruginosa | 1 | 696–16 | 4 (S) | 4 (S) | 1 (S) | ≤0.5 (S) | 1 (S) | 0.5 (S) | 2 (S) | ≤0.25 (S) | > 40 | ||||||
59C-A | Pseudononas fluorescens/putida | 3 | – | – | 8 (S) | ≤8 (S) | – | – | 2 (S) | 16 (I) | 1 (S) | – | 1 (S) | 2 (S) | ≤1 (S) | ≤0.25 (S) | > 128 (R) | > 40 (R) |
67C-A | Pseudononas fluorescens/putida | 3 | – | – | 8 (S) | ≤8 (S) | – | – | 1 (S) | 16 (I) | ≤0.5 (S) | – | 1 (S) | 1 (S) | ≤1 (S) | ≤0.25 (S) | > 128 (R) | > 40 (R) |
82C | Pseudononas fluorescens/putida | 1 | – | – | 16 (S) | 16 (S) | – | – | 2 (S) | 32 (I) | ≤0.5 (S) | – | 0.5 (S) | 4 (I) | ≤1 (S) | ≤0.25 (S) | > 128 (R) | > 40 (R) |
66E | Pseudomonas sp. | 3 | – | – | 16 (S) | 16 (S) | – | – | 4 (S) | 16 (I) | ≤0.5 (S) | – | 2 (S) | 2 (S) | 2 (S) | ≤0.25 (S) | > 128 (R) | > 40 (R) |
67E-A | Pseudomonas sp. | 3 | – | – | 4 (S) | ≤8 (S) | – | – | 1 (S) | 16 (I) | ≤0.5 (S) | – | 1 (S) | 2 (S) | ≤1 (S) | ≤0.25 (S) | > 128 (R) | > 40 (R) |
102E | Pseudononas sp. | 2 | – | – | 8 (S) | 8 (S) | – | – | 8 (S) | – | 1 (S) | – | 1 (S) | 1 (S) | ≤1 (S) | ≤0.25 (S) | – | > 40 (R) |
12E-A | Stenotrophomonas maltophilia | 3 | – | – | > 64 (R) | 16 (S) | – | – | 16 (I) | > 32 (R) | > 16 (R) | – | > 8 (R) | > 8 (R) | > 32 (R) | 2 (I) | 64 (S) | 40 (S) |
18E | Stenotrophomonas maltophilia | 3 | – | – | > 64 (R) | > 64 (R) | – | – | 2 (S) | > 32 (R) | > 16 (R) | – | > 8 (R) | > 8 (R) | > 32 (R) | 1 (S) | ≤32 (S) | ≤20 (S) |
20C | Stenotrophomonas maltophilia | 3 | – | – | > 64 (R) | > 64 (R) | – | – | 4 (S) | > 32 (R) | > 16 (R) | – | > 8 (R) | > 8 (R) | > 32 (R) | 2 (I) | > 128 (R) | ≤20 (S) |
26E | Stenotrophomonas maltophilia | 2 | – | – | > 64 (R) | 32 (I) | – | – | 2 (S) | 32 (I) | > 16 (R) | – | > 8 (R) | > 8 (R) | > 32 (R) | 1 (S) | 128 (I) | ≤20 (S) |
62C | Stenotrophomonas maltophilia | 3 | – | – | > 64 (R) | > 64 (R) | – | – | > 16 (R) | > 32 (R) | > 16 (R) | – | > 8 (R) | > 8 (R) | > 32 (R) | 2 (I) | 128 (I) | 40 (S) |
101C | Stenotrophomonas maltophilia | 1 | – | – | > 64 (R) | > 64 (R) | – | – | > 16 (R) | > 32 (R) | > 16 (R) | – | > 8 (R) | > 8 (R) | > 32 (R) | 2 (I) | 64 (S) | ≤20 (S) |
59E-C | Chryseobacterium indologenes | 3 | – | – | 64 (I) | 64 (I) | – | – | > 16 (R) | > 32 (R) | > 16 (R) | – | > 8 (R) | > 8 (R) | > 32 (R) | 1 (S) | > 128 (R) | 40 (I) |
60E | Chryseobacterium indologenes | 3 | – | – | > 64 (R) | 64 (I) | – | – | > 16 (R) | > 32 (R) | > 16 (R) | – | > 8 (R) | > 8 (R) | > 32 (R) | 1 (S) | > 128 (R) | > 40 (R) |
65E-B | Chryseobacterium indologenes | 3 | – | – | 64 (I) | 16 (S) | – | – | > 16 (R) | > 32 (R) | > 16 (R) | – | > 8 (R) | > 8 (R) | > 32 (R) | 0.5 (S) | > 128 (R) | > 40 (R) |
78E | Chryseobacterium indologenes | 1 | – | – | 64 (I) | 32 (I) | – | – | > 16 (R) | > 32 (R) | > 16 (R) | – | > 8 (R) | > 8 (R) | 32 (I) | 1 (S) | > 128 (R) | ≤20 (S) |
102C-A | Chryseobacterium indologenes | 2 | – | – | > 64 (R) | 64 (I) | – | – | > 16 (R) | > 32 (R) | > 16 (R) | – | > 8 (R) | > 8 (R) | 32 (I) | 0.5 (S) | > 128 (R) | ≤20 (S) |
64E | Aeromonas salmonicida | 3 | – | – | ≤2 (S) | ≤8 (S) | – | – | ≤0.5 (S) | 2 (S) | ≤0.5 (S) | – | ≤0.25 (S) | ≤0.25 (S) | ≤1 (S) | ≤0.25 (S) | ≤32 (S) | ≤20 (S) |
78C | Ochrobactrum sp. | 1 | – | – | > 64 (R) | > 64 (R) | – | – | > 16 (R) | 16 (I) | 2 (S) | – | 1 (S) | 1 (S) | 8 (S) | ≤0.25 (S) | > 128 (R) | > 40 (R) |
E. coli 43E | E. coli 73E | E. coli 77E | E. coli 95E | A. baumannii 13C, 41C, 45C, 50E-B, 51E, 52E | A. ursingii 56C | P. aeruginosa 71E | |
---|---|---|---|---|---|---|---|
MLST | ST131 | ST131 | ST131 | ST131 | ST130 | ST235 | |
Serotype | O25:H4 | O25:H4 | O25:H4 | O25:H4 | |||
FimH type | fimH30 | fimH30 | fimH30 | fimH30 | |||
Beta-lactam | blaCTX-M-27 (100%) | blaCTX-M-27 (100%) | blaCTX-M-27 (100%) | blaCTX-M-14 (100%) blaTEM-1B (100%) | blaADC-166 (97.74%) blaOXA-430 (99.88%) | blaCARB-2 (100%) | blaPDC-35 (100%) blaOXA-50 (99.87%) blaIMP-1 (100%) blaTEM-1B (100%) |
Aminoglycoside | aph(3″)-Ib (100%) aph(6)-Id (100%) aadA5 (100%) | aph(3″)-Ib (100%) aph(6)-Id (100%) | aph(3″)-Ib (100%) aph(6)-Id (100%) | aph(3″)-Ib (100%) aadA5 (100%) aac(3)-IId (99.88%) aac(6′)-Ib3 (99.82%) | aac(6′)-Ib3 (99.82%) aph(3″)-Ib (99.88%) aph(3′)-Ia (100%) aph(6)-Id (100%) | aac(6′)-Iae (100%) aph(3′)-II (100%) aadA1 (100%) | |
Fluoroquinolone | aac(6′)-Ib-cr (99.49%) | aac(6′)-Ib-cr (99.42%) | |||||
Fosfomycin | fosA (100%) | ||||||
MLS (Macrolide, Lincosamide, Streptogramin B) | mdf(A) (97.81%) mph(A) (100%) | mdf(A) (97.81%) | mdf(A) (97.81%) mph(A) (100%) | mph(A) (100%) mdf(A) (97.81%) | mrs(E) (100%) mph(E) (100%) | ||
Phenicol | cmlA1 (99.92%) | floR (98.35%) | catB7 (100%) | ||||
Rifampicin | ARR-3 (100%) | ||||||
Sulfonamide | sul2 (100%) sul1 (100%) | sul2 (100%) | sul2 (100%) sul1 (100%) | sul2 (100%) sul1 (100%) | sul2 (100%) sul1 (100%) | sul1 (100%) | |
Tetracycline | tet(A) (100%) | tet(A) (100%) | tet(A) (100%) | tet(39) (99.91%) | |||
Trimethoprim | dfrA17 (100%) | dfrA19 (100%) |