Once the surveillance areas (health facilities, catchment areas, and nearby laboratories), target bacteria, and antimicrobial agents have been identified, the next step is to design a sampling plan. The sampling plan should centre on diagnosing UTI cases at participating health facilities, fulfilling the definition of community-acquired UTI. The sampling plan should include the number of samples collected nationally and within each surveillance area. Additionally, the sampling plan should describe the justification for the number of samples to be collected, the types of samples, methods of sample collection, and a sampling timetable. Also, the plan should show the steps for sample collection, storage, transportation, and the number of hours allowable at each stage, given different conditions. Since the protocol proposes surveillance of routine patient care, the total number of samples to be collected depends on the duration of surveillance and the type of health facilities involved.
The sampling timetable should consider that specimens should reach the laboratory during working hours. Ideally, if the patient attends an outpatient clinic, they should provide the sample before leaving. Depending on the type of facility, the sampling will be as patients visit the hospital during clinic days. The number of samples will depend on the volume of patients presenting with signs and symptoms of UTI in selected health facilities.
2. Urine Sample Collection and Handling
At least 10 mL of clean-catch mid-stream urine (MSU) must be collected into 20 mL calibrated sterile screw-capped universal bottles lined with 0.2 mg boric acid. Boric acid reduces the rate of bacterial multiplication, which could affect the colony-forming unit (CFU) determination. The collection time should consider staff availability and the distance to the testing laboratory. In all facilities, samples should be collected between 0900 and 1200 hours. A health worker should instruct adult participants on aseptic techniques during collection and ensure the appropriate container is given to the patient. A health worker should assist parents in collecting urine specimens from children. Children above two years can be instructed and assisted by parents/guardians to collect MSU. Catheter and supra-pubic urine can be collected, processed, and interpreted per the approved standard operating procedure (SOP) in the respective laboratory. However, the urine collection and transportation SOP needs to be developed per national guidelines.
A health worker should label each specimen container with the unique identifier, location, time, and date of specimen collection. Ensure that the identification number on the form matches the ID number on the urine container.
All preserved specimens must be transported to the participating laboratory for analysis within eight hours. In case of delay, the specimen should be refrigerated 2-8oC and processed within 24hrs. Upon arrival at the laboratory, samples should be inspected and recorded to ensure compliance with a properly packed and transported sample, including ruling out sample leakages and contamination. Existing standard precaution and infection prevention and control (IPC) practices in hospitals, health clinics, and laboratories should be followed while collecting and handling specimens. At the testing laboratory, specimen volume, colour, and appearance should be documented (e.g., yellow and cloudy, dark yellow and hazy, pale yellow and clear).
4. Sample Collection Forms
Complete a sample collection form for each sample to capture descriptive information to help correctly establish drivers of community-acquired UTI caused by AMR pathogens. An example of the sample collection is attached (Annex 1). Implementing a unique sample identification numbering system between all surveillance laboratories is important so that every sample, regardless of origin, has a unique sample identification.
5. SOPs, Training, and Trialing Sample Collection
Once the sampling plan is in place, preparing a detailed standard operating procedure (SOP) will ensure that sampling and laboratory practices are standardized across sites. Necessary SOPs to implement this protocol include but are not limited to IPC practices, Selection of UTI cases at health facilities, Collection of samples, sample management (handling, storage, and preparation for transport), Sample transportation and tracking, and Laboratory procedures.
Once SOPs have been prepared, staff at health facilities should be trained on those that pertain to their roles. Training should include active participation and practice, sampling, and form completion. Following this training, staff in each surveillance area should receive supportive supervision during an initial trial period to ensure that SOPs are followed correctly and receive additional on-site guidance about procedures.
6. Review the Sampling Plan
Although the sampling plan has been developed with the best information available, it is key to revisit the plan after implementation to ensure it achieves the aims of the surveillance activities and that involved stakeholders, health facilities, and laboratories find the approach and methodology acceptable and feasible. Some points to consider during the review include: 1) Can the involved health facilities manage the number and frequency of samples being collected? 2) Is there clarity about who is responsible for collection, storage, and transport? 3) Can the involved laboratories manage the number and frequency of samples collected? 4) Is the quality of samples suitable for diagnostic testing? 5) Does the pattern of uropathogens reflect what was expected epidemiologically? If the pattern of uropathogens does not reflect what was expected, determine if the deviation could be due to sample quality, reagent quality, sample processing quality, culture or identification methods, cross-contamination between samples during collection or processing, or recording errors.