PNGM-1, a novel subclass B3 metallo-β-lactamase from a deep-sea sediment metagenome

Abstract

Objectives: In order to find antimicrobial resistance gene(s) pre-dating the use of antibiotics through metagenomics, functional screening of a metagenomic library from the deep-seep sediments of Edison Seamount (ca. 10000 years old) was performed.

Methods: Among 60 antimicrobial-resistant clones, a single clone with the highest minimum inhibitory concentration (MIC) for ampicillin was selected. Sequence analysis revealed a new metallo-β-lactamase (MBL) gene, designated as bla_PNGM-1. PNGM-1 retains a zinc ion-binding motif (H₁₁₆XH₁₁₈XD₁₂₀H₁₂₁, H₁₉₆ and H₂₆₃), conserved in subclass B3 MBLs. The catalytic parameters of purified PNGM-1 and the MICs of β-lactams for Escherichia coli TOP10 transformants harbouring the bla_PNGM-1 gene were assessed.

Results: Antimicrobial susceptibility testing indicated reduced susceptibility to penicillins, narrow- and extended-spectrum cephalosporins, and carbapenems in E. coli TOP10 transformants harbouring the bla_PNGM-1 gene. In addition, kinetic analyses revealed that PNGM-1 hydrolysed almost all β-lactams.

Conclusions: The PNGM-1 enzyme is the first case of a subclass B3 MBL derived from a functional metagenomic library of a deep-sea sediment that pre-dates the antibiotic era.

Keywords: Antimicrobial resistance; B3 metallo-β-lactamase; Deep-sea Edison Seamount; Metagenome.