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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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Risky use of unicode characters in some entries #22

Closed tseemann closed 4 years ago

tseemann commented 5 years ago

Took me a while to hunt these down - some applications were getting "wide character" errors because they expect ASCII characters only.

This one is a non-standard prime / tick / apostrophe character, use ' instead,

>card~~~pgpB~~~AP009380.1:573192-573903 A gene that produces the protein lipid A 4’-phosphatase

Replace with beta

>card~~~OXA-424~~~KM588352:1-826 OXA-424 is a �-lactamase found in clinical isolates of Acinetobacter baumannii found in China. It is carbapenem resistant.

>card~~~OXA-425~~~KM588353:1-826 OXA-425 is a �-lactamase found in clinical isolates of Acinetobacter baumannii. It is carbapenem-resistant

>card~~~Bifidobacterium_adolescentis_rpoB_conferring_resistance_to_rifampicin~~~AP009256:1667064-1670562 Bifidobacterium are antibiotic resistant probiotics are prescribed to upkeep the population beneficial bacteria in the gut microbiome. However, horizontal gene transfer among gut microbes could create harmful antibiotic-resistant pathogenic bacteria, such as Mycobacterium tuberculosis. Lokesh et al. analyzed Bifidobacterium antitubercular drug resistance and mutations in rpo�. They found that B. animalis, B. longum and B. adolescentis showed considerable resistance to pyrazinamide, isoniazid, and streptomycin, while B. adolescentis had mutations both in the rifampicin (RIF) pocket and in regions outside the pockets, and also showed considerable resistance to RIF.

>card~~~HMB-1_beta-lactamase~~~KU961660:2032-2758 Shotgun cloning of beta-lactam resistant P. aeruginosa NRZ-03096 yielded a clone producing a novel subclass B1 enzyme with only 74.3% identity to the next nearest relative, KHM-1. The novel MBL was named HMB-1 (for Hamburg MBL). HMB-1 gene was chromosomally located as part of a Tn 3 family transposon that was named Tn 6345, where expression of bla HMB-1 in E. coli TOP10 led to increased resistance to �-lactams.

>card~~~Klebsiella_pneumoniae_OmpK37~~~AJ011502.1:301-1426 Klebsiella pneumoniae outer membrane porin protein. Is preferentially detected in porin-deficient strains. Functional characterization of this new porin revealed a narrower pore than those of porins OmpK35 and OmpK36, which did not allow penetration by certain β-lactams. Also, when a resistant strain expresses porin OmpK37 is less susceptible to cefotaxime and cefoxitin than when it is expressing either OmpK36 or OmpK35.
arpcard commented 4 years ago

thanks Torsten, I've fixed these for the next release