5.4 Samples versus isolates

So far, we have been talking about sampling and sample size calculations without specifying whether we mean animal specimen samples (such as faecal or caecal samples) or a bacterial isolate. In general, sample size calculations in AMR studies are based on the number of bacterial isolates.

The type of bacteria you are sampling affects the proportion of samples in which isolates can be expected to be identified, and therefore the final sample size calculation for ‘animal samples’ from which isolates are obtained.

When sampling for AMR in commensal bacteria, there is a very high chance that the target bacterial species will be isolated from all collected samples. For example, caecal samples will almost certainly contain intestinal bacteria such as E. coli and E. faecium. Therefore, one sample is assumed to represent one or more isolates.

In contrast, when sampling for zoonotic bacteria, not all animal samples will contain disease-causing bacteria. For example, Salmonella spp. might be isolated from 40% of poultry samples, whereas Campylobacter spp. might only be isolated from 10% of poultry samples. Therefore, we need to increase the sample size proportional to the expected prevalence. Activity 8 invites you to consider this.