Overview of R (A – G) and Y (T – C) base ambiguity for 264 isolates from 32 species, sequenced with Oxford Nanopore Technologies using Kit 14
| Species | Total samples | Samples with >50 ambig. P | Mean R (A – G) ambiguity per sample (min/max) | Mean Y (T – C) ambiguity per sample (min/max) | Motif type | Reference |
|---|---|---|---|---|---|---|
| Achromobacter xylosoxidans | 1 | 0 (0%) | 6 | 4 | NA | a |
| Acinetobacter baumannii | 15 | 5 (33.33%) | 22.53 (0/109) | 19.87 (0/83) | NA | a |
| Acinetobacter junii | 1 | 1 (100%) | 279 | 223 | CARATG CATYTG | a |
| Acinetobacter mesopotamicus | 1 | 1 (100%) | 53 | 28 | NA | a |
| Acinetobacter radioresistens | 1 | 1 (100%) | 175 | 150 | RA TY | a |
| Acinetobacter soli | 1 | 0 (0%) | 12 | 11 | NA | a |
| Bordetella pertussisd | 40 | 0 (0%) | 0.1 (0/1) | 0.2 (0/1) | NA | (Wagner et al. 2023) |
| Chryseobacterium arthrosphaerae | 1 | 0 (0%) | 13 | 7 | NA | a |
| Chryseobacterium gleum | 1 | 1 (100%) | 218 | 217 | RACGC GCGTY | a |
| Citrobacter freundii | 3 | 3 (100%) | 145.67 (49/329) | 137.67 (39/319) | CRATGTCGACATYG | a |
| Citrobacter portucalensis | 2 | 2 (100%) | 29 (26/32) | 29 (28/30) | RA TY | a |
| Enterobacter cloacae | 1 | 1 (100%) | 153 | 162 | NA | a |
| Enterobacter hormaechei | 5 | 1 (20%) | 15.60 (4/45) | 15.60 (6/42) | NA | a |
| Enterococcus faecalis | 10 | 10 (100%) | 250.40 (223/275) | 249.00 (210/270) | TRAG CTYA | c |
| Enterococcus faecium | 19 | 2 (10.53%) | 15.74 (0/27) | 14.63 (0/28) | RACC GGTY | (Dabernig-Heinz et al. 2024)b |
| Escherichia coli | 8 | 3 (37.50%) | 31.38 (2/118) | 29.31 (4/111) | NA | a |
| Escherichia flexneri | 10 | 9 (90%) | 49.10 (19/88) | 44.70 (18/88) | RAT ATY | a |
| Klebsiella aerogenes | 1 | 0 (0%) | 22 | 17 | NA | a |
| Klebsiella michiganensis | 1 | 1 (100%) | 56 | 42 | NA | a |
| Klebsiella pneumoniae | 70 | 38 (54.29%) | 97.04 (3/835) | 92.47 (3/847) | RACG CGTY | (Viehweger et al. 2021)a,b |
| Klebsiella oxytoca | 1 | 0 (0%) | 5 | 9 | NA | a |
| Listeria monocytogenes | 17 | 3 (17.65%) | 37.94 (0/514) | 40.82 (0/557) | NA | b |
| Micrococcus luteus | 1 | 1 (100%) | 172 | 220 | CRAC GTYG | a |
| Proteus mirabilis | 1 | 1 (100%) | 45 | 43 | CRAC GTYG | a |
| Pseudomonas aeruginosa | 19 | 6 (33.33%) | 389.17 (0/2251) | 387.56 (0/2290) | AARACC GGTYTT | a |
| Pseudomonas asiatica | 2 | 1 (50%) | 145 (0/290) | 144.50 (0/289) | CCRA TYGG | a |
| Pseudomonas stutzeri | 1 | 0 (0%) | 14 | 16 | NA | a |
| Salmonella enterica | 2 | 1 (50%) | 41.5 (7/76) | 42.5 (7/78) | NA | a |
| Stenotrophomonas maltophilia | 1 | 1 (100%) | 229 | 171 | TACRAC GTYGTA | a |
| Serratia marcescens | 4 | 4 (100%) | 107.75 (68/178) | 99.5 (67/171) | CCRA TYGG | a |
| Shewanella algae | 2 | 2 (100%) | 71.5 (37/106) | 50 (32/68) | NA | a |
| Staphylococcus aureus | 20 | 8 (40%) | 23.35 (0/99) | 23.35 (0/97) | RACC GGTY | b |
[i] Only chromosomal contigs were analyzed, and only “superaccurate” basecalling models were used. Chromosomes were coverage-masked by N if below a read depth of 10×. N positions were not considered for the table to avoid overestimating one base ambiguity.
[ii] aSequenced strains received from Leibniz-Institute of Photonic Technology, Optisch-Molekulare Diagnostik und Systemtechnologie.
[iii] bSequenced strains received from Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz.
[iv] cOwn samples from the Jena University Hospital.
[v] dSequenced with Kit 12; resequencing via Kit 14 showed no differences.