Resistance
-m resistance
The resistance module detects acquired antimicrobial resistance genes and chromosomal point mutations associated with reduced antimicrobial susceptibility in Staphylococcus aureus.
It screens for resistance determinants across multiple antibiotic classes, including:
- Aminoglycosides
- Beta-lactams
- Fluoroquinolones
- Oxazolinidones
- MLSB
- Rifampicin
- Tetracyclines
- Glycopeptides
A curated set of FASTA files containing representative resistance gene sequences are bundled with the module and stored in the /data directory.
All detected genes are annotated as follows:
- No annotation**: exact nucleotide match
^: inexact nucleotide match but perfect amino acid match*: inexact nucleotide and inexact amino acid match?: incomplete match-X%: truncated amino acid sequence
The module screens specific chromosomal loci for point mutations known to confer resistance.
| Locus | Mutation targets | Associated phenotype |
|---|---|---|
gyrA |
S84L, E88K, E88G |
Fluoroquinolones-R |
gyrB |
T451S |
Fluoroquinolones-R |
parC |
S80F, S80Y, E84K, E84G, E84V |
Fluoroquinolones-R |
rpoB |
H481Y, H481N, L466N, A473T, A477T |
Rifampicin-R |
23S rRNA |
G2576T, G2447T, T2500A |
Linezolid-R |
Parameters
Hits are filtered using minimum alignment identity and coverage thresholds:
-
--min_id_res
Minimum alignment percentage identity (default: 90) -
--min_cov_res
Minimum alignment percentage coverage (default: 80)
All hits with 80–90% identity or 40–80% coverage are reported as spurious hits.
Resistance Score
A resistance score is calculated to categorize isolates based on a hierarchy of clinical resistance.
Scoring criteria:
- 3:
vanAorvanBdetected (Vancomycin resistance) - 2:
mecAormecCdetected (Methicillin resistance – MRSA) - 1:
blaZdetected (Penicillin/Beta-lactamase resistance) - 0: No key resistance drivers detected
Output
Results are grouped by antibiotic class and reported individually.
| Field | Description |
|---|---|
res_score |
Resistance score (0–3) |
res_gene_count |
Number of genes conferring resistance |
res_class_count |
Number of classes with at least one resistance determinants |
Amino_res |
Detected aminoglycoside resistance genes |
Bla_res |
Detected beta-lactamase genes |
Flq_res |
Genes/mutations conferring fluoroquinolone resistance |
Gly_res |
Detected glycopeptide resistance genes |
Mec_res |
Detected methicillin resistance genes |
MLSB_res |
Detected macrolide/streptogramin B/lincosamide resistance genes |
Oxa_res |
Genes/mutations conferring oxazolinidones resistance |
Rif_res |
Genes/mutations conferring rifampicin resistance |
Tet_res |
Detected tetracycline resistance genes (tet family) |
spurious_resistance_hits |
Genes with weak hits |
truncated_resistance_hits |
Genes with truncations |
For res_gene_count and res_class_count the following criteria is used:
-
The presence of resistance mutations do not contribute to the resistance gene count
-
Mutations do contribute to the drug class count
-
Genes reported in the truncated_resistance_hits and spurious_resistance_hits columns do not contribute to the counts
List of genes
| Gene | Drug Class | Variants^ | Reference number^^ | Citation |
|---|---|---|---|---|
| AAC(6')-Ie-APH(2'')-Ia | aminoglycoside antibiotic | 1 | 3002597 | Daigle DM, et al. 1999 |
| ANT(4')-Ia | aminoglycoside antibiotic | 1 | 3002623 | Santanam P and Kayser FH. 1978 |
| ANT(4')-Ib | aminoglycoside antibiotic | 1 | 3003905 | McDougal LK, et al. 2010 |
| APH(3')-IIIa | aminoglycoside antibiotic | 1 | 3002647 | Trieu-Cuot P and Courvalin P. 1983 |
| ANT(6)-Ia | aminoglycoside antibiotic | 1 | 3002626 | Gill SR, et al. 200 |
| ANT(9)-Ia | aminoglycoside antibiotic | 1 | 3002630 | Murphy et al. 1985 |
| mecA | penicillin beta-lactam | 291 | 3000617 | Ubukata K, et al. 1989 |
| mecC | penicillin beta-lactam | 6 | 3001209 | Garcia-Alvarez L, et al. 2011 |
| blaZ | penicillin beta-lactam | 473 | 3000621 | McLaughlin JR, et al. 1981 |
| blaZ mecC-type | penicillin beta-lactam | 5 | 3005097 | Shore AC, et al. 2011 |
| cfrA | phenicol antibiotic | 1 | 3003441 | Schwarz S, et al. 2000 |
| poxtA | oxazolinidone antibiotic | 1 | 3004470 | Antonelli A, et al. 2018 |
| ermA | streptogramin antibiotic, streptogramin B antibiotic, streptogramin A antibiotic, lincosamide antibiotic, macrolide antibiotic | 1 | 3000347 | Malhotra-Kumar S, et al. 2008 |
| ermB | streptogramin antibiotic, streptogramin B antibiotic, streptogramin A antibiotic, lincosamide antibiotic, macrolide antibiotic | 1 | 3000375 | Yu L, et al. 1997 |
| ermC | streptogramin antibiotic, streptogramin B antibiotic, streptogramin A antibiotic, lincosamide antibiotic, macrolide antibiotic | 1 | 3000250 | Shivakumar AG and Dubnau D. 1981 |
| ermT | streptogramin antibiotic, streptogramin B antibiotic, streptogramin A antibiotic, lincosamide antibiotic, macrolide antibiotic | 1 | 3000595 | Tannock GW, et al. 1994 |
| msrA | streptogramin antibiotic, streptogramin B antibiotic, macrolide antibiotic | 1 | 3000251 | Poole K. 2005 |
| tetM | tetracycline antibiotic | 3 | 3000186; SAV0398; M21136.1 | Akhtar M, et al. 2009 |
| tetK | tetracycline antibiotic | 1 | 3000178 | Roberts MC. 2005 |
| vanA | glycopeptide antibiotic | 1 | 3000010 | Marshall CG, et al. 1997 |
| vanB | glycopeptide antibiotic | 1 | 3000013 | Marshall CG, et al. 1997 |
Note:
^ : Number of variants in the database;
^^: Reference sequence of each variant. If multiple variants are present, but only one reference is reported, it means that all variants have the same reference from the same database.