Chinese scholars have made progress in the study of soil in situ active antibiotic-resistant bacteria tracing and drug resistance transmission

Single-cell Raman technology assesses soil phenotypic resistance and targets sorting and sequencing of highly active drug-resistant bacteria

With the support of the National Natural Science Foundation of China (approval number: 21922608, 22176186, 42021005), the research team of Zhu Yongguan and Cui Li of the Institute of Urban Environment of the Chinese Academy of Sciences has made new progress
in the research of soil in situ active antibiotic-resistant bacteria tracing and drug resistance transmission 。 The study, titled "Active antibiotic resistome in soils unraveled by single-cell isotope probing and targeted metagenomics," was published in the Proceedings of the National Academy of Sciences on September 26, 2022 National Academy of Sciences), paper link:

The spread of antibiotic resistance (AMR) between humans, the environment, and plants and animals has greatly increased the global burden of
"One Health".
Soils are home to some of the most abundant and diverse microorganisms on Earth, with active drug-resistant bacteria playing a key role
in driving the spread of soil resistance.
Since up to 99% of soil microorganisms are not cultivating, there are few studies on soil in situ active drug resistance, making the study of antibiotic resistance in soil a huge challenge and hindering the development of
AMR environmental behavior and control strategies.
Although molecular biology techniques have advanced our understanding of the soil microbiome and the resistance group, genetic information only reflects resistance potential rather than resistance phenotypes, and cannot distinguish between the DNA of extracellular, dead or dormant bacteria, and it is still difficult to dissect the specific role of resistant microorganisms, affecting the accurate assessment
of AMR health risks.
Therefore, it is urgent to develop appropriate technical means to comprehensively analyze the important active drug-resistant bacteria
in the soil from both phenotype and genotype levels.

The research team used single-cell Raman - heavy water isotope labeling technology, in view of the complexity of soil and the impact on the effectiveness of antibiotics, by optimizing the dose of antibiotics, incubation time, and depth of spectroscopy, established a single-cell method and discriminant criteria for accurately tracing soil active drug-resistant bacteria, and used a variety of known resistant bacteria and sensitive bacteria in the soil in situ environment to verify the universality and accuracy of antibiotics in different soils and different mechanisms.
The successful extension of this method from the simple study of clinically resistant bacteria to a complex soil environment containing a large number of uncultured bacteria reveals that human activities such as agricultural cultivation and pollution emissions significantly increase the phenotypic resistance level of soils at the single-cell level and phenotypic level
.
In view of the highly active soil resistant bacteria with potential health risks identified by Raman technology, single-cell sorting and targeted metagenome sequencing techniques were used to identify most of the highly phenotypic resistant bacteria as uncultured bacteria that were previously difficult to study, as well as a new antibiotic-resistant pathogen, which proved that soil uncultured bacteria are important hosts for
AMR.

This work links multiple antibiotic resistance phenotypes and multiple genotypes, provides a new method for the analysis of a large number of uncultured resistant bacteria in the environment, and is of great value
for promoting the risk assessment of environmental resistance and the formulation of prevention and control strategies under the framework of "One Health".