Metals and Microbes: Microbial Community Diversity and Antibiotic Resistance in the Animas River Watershed, Colorado, USA

TL;DR

This study explores how metal contamination in river sediments affects microbial diversity and antibiotic resistance in Colorado, finding lower diversity and specific resistance genes in polluted areas.

Contribution

The study identifies a unique fingerprint of antibiotic resistance genes linked to metal-contaminated sediments in a mining-impacted watershed.

Findings

Bacterial diversity was significantly lower in metal-contaminated, acidic sites.

Metagenomic sequencing identified 31 ARGs, with efflux pump genes more prevalent in metal-contaminated areas.

The study highlights the potential for environmental monitoring to inform better antibiotic use.

Abstract

Antimicrobial resistant (AMR) infections are a persistent public health issue causing excess death and economic impacts globally. Because AMR in clinical settings is often acquired from nonpathogenic bacteria that surround us, environmental surveillance must be better characterized. It has been well established that metals can co-select for bacterial AMR. Furthermore, recent studies have shown that compromised microbial community diversity may lead to community invasion by antibiotic resistance genes (ARGs). Widespread legacy mining has led to acid mine drainage and metal contamination of waterways and sediments throughout the western United States, potentially compromising microbial community diversity while simultaneously selecting for AMR bacteria. Our study objectives were to survey metal contaminated sediments from the Bonita Peak Mining District (BPMD) in southwestern Colorado, USA, compared to sites downstream in Durango, CO for bacterial and ARG diversity. Sediment bacteria were characterized using 16S rRNA Ilumina and metagenomic sequencing. We found that overall, bacterial diversity was lower in metal-contaminated, acidic sites (p = 0.04). Metagenomic sequencing revealed 31 different ARGs, with those encoding for efflux pumps (mex and spe gene families) substantially more prevalent in the BPMD sites, elucidating a specific AMR marker fingerprint from the high metal concentration sediments. Raising awareness and providing antimicrobial tracking techniques to resource limited communities could help provide information needed for better antibiotic use recommendations and environmental monitoring.

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