No evidence given for inducible Clindamycin resistance

[iqbal-lab]

When we call inducible R for clindamycin because an erm gene is present, we don't say so in the JSON. Eg currently we have things like this

{ "expected_depth": "140", "mean_read_length": "89", "species": { "S.aureus": "Major" }, "susceptibility" :{ "Gentamicin": "S", "Penicillin": "S", "Methicillin": "S", "Trimethoprim": "S", "Erythromycin": "R", "FusidicAcid": "S", "Ciprofloxacin": "S", "Rifampicin": "S", "Tetracycline": "S", "Vancomycin": "S", "Mupirocin": "S", "Clindamycin": "R(inducible)" }, "called_variants" :{ }, "called_genes" :{ "ermC" :{ "per_cov": "99", "median_cov": "1627", "induced_resistance": "Erythromycin" } }, "virulence_toxins" :{ "PVL": "negative" } }

Really we should also say "ermC" :{ "per_cov": "99", "median_cov": "1627", "induced_resistance": "Erythromycin, Clindamycin" }

[iqbal-lab]

Proposed fixed output

For a sample an erm gene "ermC" :{ "per_cov": "99", "median_cov": "1627", "induced_resistance": [ “Erythromycin”, “Clindamycin" ] }

Then with only one entry you still keep it as a single-entry array;

"blaZ" :{ "per_cov": "99", "median_cov": "162", "induced_resistance": [ “Penicillin” ] }

[iqbal-lab]

That proposed fix was from Simon

[Phelimb]

induced_by format has changed in latests so this should be fixed