Antibiotic resistance in bacteria isolated from the deep terrestrial subsurface

Area of Science:

• Microbiology
• Environmental Science
• Genetics

Background:

• Antibiotic resistance is a growing global concern.
• The terrestrial deep subsurface is an understudied environment regarding microbial antibiotic resistance.
• Understanding resistance in isolated environments can reveal novel resistance mechanisms.

Purpose of the Study:

• To investigate antibiotic resistance in bacteria from two distinct deep subsurface environments.
• To determine the prevalence of antibiotic resistance and multiple resistance among isolated strains.
• To explore potential novel antibiotic resistance genes and mechanisms in long-isolated bacteria.

Main Methods:

• Isolation of 154 bacterial strains from sediments at the Savannah River Site (SRS) and Hanford Site (HS).
• Phylogenetic analysis using 16S rRNA gene sequences to assess bacterial diversity.
• Screening of all isolates for resistance to 13 different antibiotics using selective media.

Main Results:

• All isolated bacterial strains were phylogenetically diverse, belonging to several genera across multiple phyla.
• 90% of the strains showed resistance to at least one antibiotic.
• High frequencies of resistance were observed, with 86% of SRS strains and 62% of HS strains resistant to multiple antibiotics. Nalidixic acid, mupirocin, and ampicillin resistance were most common.

Conclusions:

• Antibiotic resistance is prevalent in terrestrial deep subsurface bacteria.
• Higher resistance at SRS may be linked to surface influences like agricultural antibiotic use.
• The significant resistance in HS strains, despite no anthropogenic antibiotic exposure, suggests the potential presence of novel resistance genes or mechanisms due to long isolation.