9.2 AMR indicators

AMR indicators are metrics used to track and assess the prevalence and/or control of AMR. The choice of AMR indicator depends very much on the objectives and purpose of the surveillance.

For example, when monitoring trends in humans using untreated sewage, the focus may be on detecting resistant pathogens that are of low prevalence in humans but of high public health relevance. In contrast, when evaluating the effectiveness of an intervention, indicators must be measurable at all times – even if the immediate public health relevance is of less importance. Of course, the indicator of choice is also dependent on the laboratory capacity present in the region, or whether qPCR or sequencing facilities are available or not.

Some studies on AMR in the environment measure genes using qPCR and metagenomics (such as WGS) rather than using culture techniques and quantifying live bacteria. Compared to human and animal surveillance, environmental research more often addresses specific ARGs or metagenomic analyses; however, if the surveillance activity is to support human or animal health, or if the aim is to integrate analyses from different surveillances, choosing an indicator that is meaningful for the human or animal health sectors often means considering culturing and counting bacteria as well.

A common indicator

E. coli is a common indicator of (animal or human) faecal contamination in water and soil (Anjum et al., 2021), and can also harbour ARGs.

The presence of resistant E. coli can be used as a proxy and indicates the presence of (faecal) resistant organisms from human or animal sources. It is also a good candidate for measuring the same microbe across the human, animal and environment sectors, as it is already an established AMR indicator in human and animal health. Because of this, methods for its isolation are often familiar and many protocols exist (Figure 11). On the other hand, focusing on just a single bacterium has the disadvantage that ARGs present in other species are overlooked. This means that analyses of E. coli are not representative of the whole bacterial community.

Figure 11 E. coli growing on MacConkey agar (a culture medium used to isolate Gram-negative rod bacteria such as E. coli).

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A series of images is shown that represent the wide variety of bacterial colony type growing on specialised selective media. Images show colonies of differing size, shape and texture, growing on agar plates that range between pale yellow, red, blue and black.

Figure 11 E. coli growing on MacConkey agar (a culture medium used to isolate Gram-negative rod bacteria such as E. coli).