Table 1.
Antibiotic susceptibility and antimicrobial resistance genes of Raoultella ornithinolytica obtained from a calf with sepsis.
| Antimicrobial | Antimicrobial susceptibility (disk diffusion) | Antimicrobial resistance genes | ||||
|---|---|---|---|---|---|---|
| Locus† | % Identity | % Query coverage | Contig (length) | Predicted contig origin‡ | ||
| Ampicillin | Resistant | blaORN§ | 99.89 (1 SNP) | 100 | Node 34 (60566) | Chromosome (0.947) |
| blaTEM-1B | 100 | 100 | Node 87 (17794) | Plasmid (0.983) | ||
| Amoxicillin—clavulanic acid | Susceptible | / | / | / | / | / |
| Apramycin | Susceptible | / | / | / | / | / |
| Ceftiofur | Susceptible | / | / | / | / | / |
| Cefquinome | Susceptible | / | / | / | / | / |
| Doxycycline | Resistant | tet(D) | 100 | 100 | Node 128 (3634) | Plasmid (0.954) |
| Tetracycline | Resistant | tet(D) | 100 | 100 | Node 128 (3634) | Plasmid (0.954) |
| Enrofloxacin | Intermediate | qnrS1 | 100 | 100 | Node 103 (10631) | Plasmid (0.967) |
| Florfenicol | Susceptible | / | / | / | / | / |
| Flumequine | Susceptible | qnrS1 | 100 | 100 | Node 103 (10631) | Plasmid (0.967) |
| Gentamicin | Resistant | aac(3)-IIa | 100 | 100 | Node 87 (17794) | Plasmid (0.983) |
| Streptomycin | Resistant | aph(3")-Ib | 99.88 (1 SNP) | 100 | Node 103 (10631) | Plasmid (0.967) |
| Spectinomycin | Susceptible | / | / | / | / | / |
| Sulfa-trimethoprim | Resistant | sul2 | 100 | 100 | Node 103 (10631) | Plasmid (0.967) |
| dfrA14 | 100 | 100 | Node 38 (55589) | Plasmid (0.724) | ||
| Fosfomycin | Not tested | fosA | 99.52 (2 SNPs) | 100 | Node 41 (50833) | Chromosome (0.994) |
Detected by both making an assembly with SPAdes and BLASTing, and direct read mapping with SRST2, against the ResFinder database containing a curated catalog of AMR genes.
Determined using mlplasmids. Between brackets the range of posterior probability is given. Klebsiella pneumoniae was used as species model, given it's close genetic relationship with Raoultella sp.
Gene is present as blaPLA (NCBI accession NG_049969.1) in the ResFinder database derived from R. planticola, but inspection demonstrated the isolate gene to correspond to blaORN (NCBI accession NG_049386.1—for which % identity and % query coverage values are presented) derived from R. ornithinolytica (see Supplementary Material).