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arpcard / amr_curation

A public repository for collective curation of antimicrobial resistance (AMR) genes and mutations. Submit, discuss, and resolve AMR curation issues.
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Species discrepancy for OXA-258-like class D beta-lactamase OXA-1251 #106

Open iorga opened 1 month ago

iorga commented 1 month ago

Dear all,

Historically, all OXA-258-like beta-lactamases were found in Achromobacter spp., one paper considering OXA-258 as a species-specific marker for Achromobacter ruhlandii.

OXA-1251 has 99.3% sequence identity with OXA-258, and was reported to be isolated from a clinical Pseudomonas aeruginosa strain. This is very unusual compared with all other OXA-258-like beta-lactamases. The corresponding genome was not deposited to the NCBI, so no further information can be obtained.

@danielhhaft or @feldgard , could you please double check the species of this isolate with the depositing authors, and ideally ask them to deposit the whole genome ? Thank you in advance.

Bogdan

danielhhaft commented 1 month ago

Thank you Bogdan for the shrewd analysis. I'm sure you're right about the species.

I emailed the submitter, and asked that the species identification be checked. But it's August, a slow time for hearing back from people, and I don't have a reply yet. I'll check the status in another two weeks or so.

Best regards,

Daniel Haft NCBI