4.5 Sample collection

GLASS advocates a tiered approach to AMR surveillance. Countries start with the highest priority clinically relevant pathogens in available sample types to establish their AMR surveillance systems. Over time, further bacterial species that are of clinical importance for surveillance are identified, either from the same or additional sample types. In time, results from laboratory testing of these additional pathogens can be included in the established routine AMR surveillance.

Local clinical practice at surveillance sites determines the type of clinical samples (blood, urine, faeces, etc.) sent to the laboratory. Ideally speaking, clinical practice should be standardised according to guidelines and recognised standards, such as those from international infectious disease organisations. For example, best practice guidelines recommend that all patients presenting to hospital with symptoms of a urinary tract infection should have a urine sample taken. This may not be routine clinical practice in countries where resources for microbiology testing are limited and/or patients might have to pay for individual laboratory tests.

When reporting data to the NCC, the following information should be included for each sample: sample type, AST results and patient information, including demographics and epidemiological features.

Table 1 provides details of specimen (sample) types and the corresponding pathogens prioritised for AMR surveillance by WHO GLASS. The specimen types represent infections in the bloodstream, gastrointestinal tract and genitourinary/reproductive tract. These infections are common all around the world, so resistance in pathogens which cause them is of high concern.

Reporting for AMR surveillance focuses on thirteen WHO priority pathogens, namely Acinetobacter spp., E. coli, K. pneumoniae, P. aeruginosa, N. gonorrhoeae, N. meningitidis, H. influenzae, Salmonella spp (non-typhoidal), Salmonella enterica serovar Typhi, Salmonella enterica serovar paratyphi A., Shigella spp., S. aureus and S. pneumoniae. Countries can also include any other pathogens of local or national importance.

Blood samples are the single highest-priority specimen type for AMR surveillance. A positive blood culture sample points to a pathogen having a severe and life-threatening impact on the patient concerned. However, the collecting of blood samples is not an easy process from clinical and laboratory perspectives. Low- and middle-income countries (LMICs) often find blood sample collection expensive and technically challenging. Urine and stool samples, often easier to collect and less expensive to process, could be considered first when starting local or national AMR surveillance activities. The limited range of pathogens from urine and stool samples may also make them attractive when commencing surveillance, especially in LMICs.

As discussed in Section 4.4, AST results provide information on the degree to which pathogens are susceptible to antimicrobials routinely used to treat them. WHO recommend that countries collect the AST data for specific pathogen-antimicrobial combinations; these are based on the most concerning resistance profiles emerging worldwide. Countries report each pathogen as Susceptible (S), susceptible, Increased exposure (I) or Resistant (R) to the antimicrobials of interest. AST results corresponding to each antimicrobial can be classified as susceptible (S), intermediate (I), resistant (R), not tested or not applicable. The course Antimicrobial susceptibility testing discusses this in detail. The most recent list of WHO GLASS pathogen-antimicrobial combinations can be found in Table 7.2 of the GLASS AMR surveillance manual (2023). You can also download a copy of this table [Tip: hold Ctrl and click a link to open it in a new tab. (Hide tip)] .