Identification of 76 novel B1 metallo-β-lactamases through large-scale screening of genomic and metagenomic data

[agmcarthur]

@danielhhaft we've been reviewing Identification of 76 novel B1 metallo-β-lactamases through large-scale screening of genomic and metagenomic data. The authors identify 77 putative beta-lactamases by using novel HMMs. Attached are the predicted proteins run through RGI on CARD 3.2.0

UpdatedBlast.xlsx

All the named beta-lactmases in the data are RGI Perfect or Strict, the latter simply being incorrect start codon calls by the authors.

All the remainder are RGI Loose, but the spreadsheet includes the experimental results from Table 3 in the paper:

G33, G37, G58, G70, and G71 have a positive imipenem resistance test, yet are RGI Loose and unnamed. We could add a unnamed, experimentally validated environmental beta-lactamases branch to CARD, but would you consider assigning these names?

[danielhhaft]

I would consider providing names.

Names will depend on public release of the underlying sequences, with at least a nucleotide accession in an INSDC database (GenBank, EBI, or DDBJ). I've taken the translations from the Excel spreadsheet provided.

I may try to contact authors.

Incident-tracking ticket at NCBI is PD-4195.

[agmcarthur]

Thanks @danielhhaft, we'll keep this issue open pending your results.

[danielhhaft]

I just wrote to the author erik.kristiansson@chalmers.se to ask for/about their submission of the metagenome-derived orphan sequences to GenBank.

I mentioned that coming up with useful names for active enzymes was a major goal. And for me, that a secondary goal is to help improve the HMMs that help decide what is a likely beta-lactamase and what is likely not.