Over the last few decades, antibiotic-resistant bacteria and their resistance genes have become important environmental contaminants. These genes can accumulate in water or soil and hence enter the human food chain, for example through raw ingested vegetables.
To evaluate possible contamination of soils, which may result from practices such as irrigation with contaminated water or application of organic fertilizers, methods of microbiology that directly analyze the genetic material of bacteria, in particular quantitative PCR (qPCR), are frequently used. Although such methods are considered the best choice for testing soil contamination with antibiotic-resistant bacteria, it is suspected that they may be insufficient to assess possible risks to human health. Thus, a simplistic reading of analysis of antibiotic-resistant bacteria in soils may lead to the (incorrect) conclusion that there is no risk of transmission to humans. The aim of this study was to alert the scientific community to this problem.
Thus, using experimental evidence, it has been demonstrated that the amount of antibiotic resistance genes that can be determined in soils, based on commonly used DNA extraction procedures and qPCR analyzes, clearly exceeds what can be considered negligible. The quantification limits (LOQ) of the tested antibiotic resistance genes (vanA, qnrS, blaTEM, blaOXA, blaIMP, blaVIM) were found to be approximately 10 000 gene copies per gram of dry soil, regardless the soil type tested, which value was only about 10 times higher than detection levels. These values, considered too high to ensure that there are no risks of propagation and transmission, result from intrinsic aspects of extraction and DNA analysis techniques and not from operational failures. The implication of this technical limitation, if ignored, will be to allow a successive accumulation of antibiotic resistance genes in soils, which will only be noticeable when very high doses are reached and already pose high risks to human health.
The publication, supervised by Prof. Célia Manaia, can be consulted in full at this link.