Tool Detects Harmful Bacteria in Soil

Research out of China has created a single-cell functional tool to sequence active antibiotic resistant bacteria (ARB) in soil, a breakthrough they say could reduce health risks to humans from soil microorganisms.

Soil antimicrobial resistance (AMR) is posing increasing health risks to humans, either through direct contact or through the food chain, but AMR studies have relied mostly on environmental DNA that could come from dead/dominant cells and extracellular DNA. This can lead to potential overestimation of AMR and associated risk because the vast majority of soil microbes are yet uncultured. Active ARB in soils play a critical role in driving AMR dissemination but are not well understood.

The recent study, published in PNAS, describes a new single-cell functional tool incorporating single-cell Raman-isotope probing, single-cell sorting, and targeted metagenomics to screen and sequence active ARB in native soils.

“If you know yourself and your enemy, you can fight battles without defeat. It is thus an urgent need to understand the true AMR risk in soils,” says Professor Zhu Yongguan of the Institute of Urban Environment of the Chinese Academy of Sciences (CAS).

Based on the distinct activities of soil microorganisms toward heavy water under antibiotic treatments, active ARB in soils were directly detected in a culture-independent way. The percentage and activity of ARB in soils were quantified, and a clear elevation with human activity was revealed.

Considering the important role of highly metabolically active ARB in transmitting AMR, the researchers proposed using phenotypic resistance level as a novel parameter for AMR risk assessment, overcoming the long-standing problem wherein AMR risk assessment only relies on genetic information but lacks phenotypic information. “Although neither genomic data nor physiology studies of bacterial isolates can reliably predict the active ARB residing in soils, single-cell functional tools may provide a great solution to this problem,” says Professor Cui Li, also from the Institute of Urban Environment at CAS.

The most active ARB in soils were selected for downstream targeted metagenomic sequencing. Microbial identity, antibiotic resistance genes (ARGs), virulence factor genes (VFGs), and mobile genetic elements (MGEs) carried by the active ARB were all deciphered, pinpointing “who is doing what and how.”

Several uncultured bacteria harboring multiple ARGs were identified, demonstrating that they are important contributors to soil phenotypic resistance. Of note, one type of ARB found in soil was ranked high risk because it is a highly active pathogen carrying ARGs on MGEs. “Discovery of the highly active antibiotic resistant pathogen in soils raises an alarm for urgent need of control technologies,” says Yongguan.

This work advances the understanding of active ARB in the environment, a subject the authors claim has been largely overlooked. The described single-cell approach linking resistance phenomes to genomes can also be readily applied to other ecosystems, they says.