Disparate Antibiotic Resistance Gene Quantities Revealed across 4 Major Cities in California: A Survey in Drinking Water, Air, and Soil at 24 Public Parks

Abstract

Widespread prevalence of multidrug and pandrug-resistant bacteria has prompted substantial concern over the global dissemination of antibiotic resistance genes (ARGs). Environmental compartments can behave as genetic reservoirs and hotspots, wherein resistance genes can accumulate and be laterally transferred to clinically relevant pathogens. In this work, we explore the ARG copy quantities in three environmental media distributed across four cities in California and demonstrate that there exist city-to-city disparities in soil and drinking water ARGs. Statistically significant differences in ARGs were identified in soil, where differences in blaSHV gene copies were the most striking; the highest copy numbers were observed in Bakersfield (6.0 × 10–2 copies/16S-rRNA gene copies and 2.6 × 106 copies/g of soil), followed by San Diego (1.8 × 10–3 copies/16S-rRNA gene copies and 3.0 × 104 copies/g of soil), Fresno (1.8 × 10–5 copies/16S-rRNA gene copies and 8.5 × 102 copies/g of soil), and Los Angeles (5.8 × 10–6 copies/16S-rRNA gene copies and 5.6 × 102 copies/g of soil). In addition, ARG copy numbers in the air, water, and soil of each city are contextualized in relation to globally reported quantities and illustrate that individual genes are not necessarily predictors for the environmental resistome as a whole.

Commercially available garden products as important sources of antibiotic resistance genes—a survey

“…Findings here are also in accord with relative gene abundances in poultry manure (Cheng et al 2013), and in soils amended with dairy manure (Dungan et al 2019;McKinney et al 2018;Munir and Xagoraraki 2011) and composted dairy manure (Tien et al 2017;Jacobs et al 2019). Additionally, relative gene quantities in soils from 6 Los Angeles parks (Echeverria-Palencia et al 2017) are more comparable to the recently landscaped soils than the native soils.…”

Influence of soil characteristics and metal(loid)s on antibiotic resistance genes in green stormwater infrastructure in Southern California

“…Each qPCR reaction was conducted in 96-well reaction plates using StepOne Plus qPCR system (Applied Biosystems, Foster City, CA, USA) with a final reaction volume of 25 μL, containing 1.25 μL of each primer, 12.5 μL of PowerUp SYBR Green Master Mix (Applied Biosystems, Foster City, CA, USA), 2 μL of soil DNA extracts (approximately 5-100 ng DNA), and 10 μL of molecular-grade water (Thermo Fisher Scientific, Waltham, MA, USA). Primer concentrations (Table S1) and thermocycling conditions (Table S2) were optimized as described previously (Echeverria--Palencia et al, 2017). DNA standards were designed using sequences from the National Center for Biotechnology Information (NCBI) database and obtained through Integrated DNA Technologies (IDT) (Coralville, IA, USA).…”

Detection of antimicrobial resistance genes in urban air

“…Culture‐independent approaches, like 16S rRNA gene sequencing, provide taxonomic identification usually only on the genus level. Quantitative real‐time polymerase chain reaction (PCR) analysis of ARGs only targets a limited number of genes (Echeverria‐Palencia et al, 2017 ; Fluit et al, 2001 ). Whole‐genome shotgun sequencing provides suitable data for metagenomic analysis.…”

“…Quantitative real-time polymerase chain reaction (PCR) analysis of ARGs only targets a limited number of genes (Echeverria-Palencia et al, 2017;Fluit et al, 2001). Whole-genome shotgun sequencing provides suitable data for metagenomic analysis.…”