5.2 Relating sampling units to isolates

So far, we have been talking about sampling and sample size calculations without specifying whether we mean physical specimens (such as faecal or urine samples) or a bacterial isolate.

The WHO’s Global AMR Surveillance System (GLASS) sets four priority specimen types and eight priority pathogens. The four priority specimen types are:

• blood
• urine
• stool
• genital swabs.

The eight priority pathogens are:

• E. coli
• Klebsiella pneumoniae
• Acinetobacter spp.
• S. aureus
• Streptococcus pneumoniae
• Salmonella spp.
• Shigella spp.
• Neisseria gonorrhoeae.

GLASS outlines which pathogens should be isolated from which specimens [Tip: hold Ctrl and click a link to open it in a new tab. (Hide tip)] . Each hospital, region or country might have additional priority bacterial species to test for AMR.

In general, sample size calculations in AMR studies are based on the number of bacterial isolates, not the number of specimens or number of individuals (noting that there is usually one specimen per individual). Recall in Activity 3 that only 840 positive cultures were obtained from 3380 patients.

The type of bacteria being sampled affects the proportion of samples in which isolates can be expected to be identified, and therefore the final sample size calculation for the number of specimens (i.e. number of people) from which isolates are obtained. When making use of existing data in passive surveillance systems, the target population might be defined as ‘all patients presenting with gastroenteritis in hospitals’. In this case, it is likely that E. coli spp will be isolated from 100% of specimens (and therefore 100% of sampling units), because we all have E. coli spp. in our gut. Therefore, if our study is about AMR in E. coli, one specimen represents one isolate for the purpose of sample size calculations.

In other cases, not all specimens will contain disease-causing bacteria of interest. In this case, you would need to adjust the sample size based on the proportion of individuals expected to have the target pathogen isolated from their specimen sample. We’ll review an example in Activity 8.

When you plan this kind of sampling, it is always worth asking whether a sample size calculation is needed. In passive surveillance, samples submitted to a laboratory for AST to inform clinical decision-making are utilised. In some cases, these existing datasets can be analysed without first specifying a sample size, because they represent the maximum available data from all patients in the source population.

However, a sample size calculation is usually required even if the data already exist. For example, a sample comprising patient records from a single healthcare facility might be too small for the desired power. Researchers and surveillance professionals should be aware of this before beginning analysis. Additionally, as each hospital or healthcare facility might have a separate ethical review process for accessing patient records, it is often necessary to justify how many samples and hospitals are required for a research study to meet its objectives.