9.1 Metrics of environmental AMR surveillance

Quantifying AMR in environmental water, soil and air samples requires specific methods to assess the presence and concentration of resistant microbes or ARGs.

For human and animal surveillance, AMR outcomes are often presented as prevalences; for example, the percentage of patients or farms that are positive for a specific pathogen, or as descriptions of a panel of minimum inhibitory concentrations (MICs) determined for an isolate using antimicrobial susceptibility testing.

For environmental compartments, concentrations are often used to quantify AMR in a sample. Concentrations can generally be measured for bacteria using culture-based methods, and for ARGs by techniques such as quantitative polymerase chain reaction (qPCR). When using metagenomic techniques (such as whole genome sequencing [WGS]) that are used to analyse the genetic material from environmental samples, the data is expressed as relative concentration (in terms of gene composition) but generally not absolute concentration (in terms of gene concentration per amount of environmental sample).

In the following sections you will look at the metrics for all compartments with a special focus on water, as this is the most researched compartment. Note that if you are unfamiliar with culture-based techniques or qPCR methodologies you should refer to the courses Isolating and identifying bacteria (human health), Isolating and identifying bacteria (animal health), Testing for mechanisms of resistance and Whole genome sequencing in AMR surveillance.

Water

The metric for assessing contamination of water quantitatively is the number of bacteria or genes in a litre (1000 ml) of water. Alternatively, the percentage of ESBL-producing E. coli as a proportion of all E. coli cultured can be measured, or the relative composition of all ARGs in a metagenomic analysis.

Water samples, especially wastewater samples, often contain a high concentration of human waste, representing the output from many individuals. This means that samples are often positive for the indicator of interest: that is, at least one or a few bacteria are present in every sample. This means it is common to end up with all the samples positive (100 per cent). This is not a useful number for making comparisons between samples, following trends or determining the efficiency of any intervention. Therefore, quantitation in samples is done by determining the concentration of a specific bacterium; for example, the percentage of ESBL-producing E. coli of all E. coli present or the number of ESBL-producing E. coli in a litre of water.

Water is a commonly used environmental sample for analysis. However, laboratories that usually work on human and animal surveillance might not have experience in processing water samples; similarly, laboratories working on water samples might not have experience in AMR testing. Good communication can overcome these weaknesses.

You can read more about collecting soil and air samples and the associated metrics in the extended learning section of the course.