The 1^st EQAsia External Quality Assessment trial: Escherichia coli and Salmonella spp. – 2021

The EQAsia project was launched in 2020 aiming to strengthen the provision of External Quality Assessment (EQA) services across the One Health sector among National Reference Laboratories/ Centres of Excellence in South and Southeast Asia. EQAsia is supported by the Fleming Fund and strives to increase the quality of laboratory-based surveillance of WHO GLASS pathogens and FAO priority pathogens.

The EQAsia Consortium includes the National Food Institute, Technical University of Denmark (DTU Food) as the Lead Grantee, the International Vaccine Institute (IVI) in South Korea, the National Institute of Health (NIH) in Thailand and the Faculty of Veterinary Science, Chulalongkorn University (CU) in Thailand.

EQASIA provides a state of the art EQA program free of charge for the South and Southeast Asian region through existing local providers (NIH Thailand and CU Thailand). The program, referred to as a “One-Shop EQA program”, is designed to enable the laboratories to select and participate in relevant proficiency tests of both pathogen identification and antimicrobial susceptibility testing (AST), in line with the requirements of the WHO GLASS. The EQA program is supported by an informatics module where laboratories can report their results and methods applied.

Three EQA trials are taking place during Feb 2021 – Feb 2022. The EQA trials focus on the WHO GLASS pathogens and FAO priority pathogens (see Section 7. References): Salmonella spp., Escherichia coli, Klebsiella pneumoniae, Shigella spp., Acinetobacter spp., Staphylococcus aureus, Streptococcus pneumoniae, Campylobacter (C. coli and C. jejuni), Enterococci (E. faecium and E. faecalis), Pseudomonas aeruginosa and Neisseria gonorrhoeae. In addition, a Matrix EQA is offered, aligning with the scope of WHO Tricycle and suggested from FAO, aiming to assess the veterinary laboratories’ ability to detect ampC beta-lactamases (ampC), extended-spectrum beta-lactamases (ESBL) and carbapenemase producing E. coli from animal caeca samples and food matrices.

For a given organism, candidate strains are assessed and validated by DTU and the external partner (United States Food and Drug Administration, FDA). The validation includes both phenotypic minimum inhibitory concentration (MIC) determination by broth microdilution, and whole genome sequencing (WGS) to detect antimicrobial resistance (AMR) genes and chromosomal point mutations. The test strains are then selected based on the phenotypic AMR profile to include a heterogeneous panel, allowing for strain variation from almost pan-resistant to fully susceptible isolates.

Each EQA trial encompasses the testing of a total of 11 test strains of a given organism. Of these, eight of the test strains are of the organism in focus (target organism), whereas three test strains are different from the targeted species (reported as non-[organism], e.g. non-Salmonella). For each of the 11 test strains, participants are requested to report which eight strains belong to the expected target organism. For the three organisms different from the expected, no further testing is required. For the remaining eight test strains of the target organism, results in relation to AST and serotyping (if relevant) are requested.

This report contains results from the first EQA trial of the EQAsia project carried out in February-April 2021. This first EQA trial includes serotyping of Salmonella spp., as well as identification and AST of Salmonella spp. and Escherichia coli. The aim of this EQA trial is to monitor the quality of AST results produced by the participating laboratories and identify underperforming laboratories in need of assistance to improve their performance in AST.

The evaluation of the participants’ results is based on international guidelines, namely the European Committee on Antimicrobial Susceptibility Testing (EUCAST) and the Clinical and Laboratory Standards Institute (CLSI). Interpretative criteria referring to both disk diffusion and MIC determination are listed in the EQA protocol (Appendix 1) and allow for the obtained results to be interpreted into categories as resistant or susceptible depending on the method used. Results in agreement with the expected interpretation are categorised as ‘1’ (correct), while results deviating from the expected interpretation are categorised as ‘0’ (incorrect). This standardized interpretation of results is necessary to allow comparison of performance between laboratories. Laboratory performance is considered acceptable if there are < 5% deviation from expected results.

Evaluation of a result as “deviating from the expected interpretation” should be carefully analysed in a route cause analysis procedure performed by individual participants (self-evaluation) when the EQA results are disclosed. The methods applied have limitations in reproducibility, thus, on repeated testing, the same strain/antimicrobial combination can result in different MIC or Inhibition Zone Diameter values differing by one-fold dilution or ±3mm, respectively. If the expected MIC/Zone Diameter is close to the threshold for categorising the strain as susceptible or resistant, a one-fold dilution/±3mm difference may result in different interpretations. Since this report evaluates the interpretations of MIC/Zone Diameter and not the values, some participants may find their results classified as incorrect even though the actual MIC/Zone Diameter measured is only one-fold dilution/±3mm different from the expected MIC/Zone Diameter. In these cases, the participants should be confident about the good quality of their AST performance.

In this report, results from laboratories affiliated with the Human Health (HH) or the Animal Health (AH) Sectors are presented separately. The laboratories are identified by codes and each code is known only by the corresponding laboratory and the organizers. The full list of laboratory codes is confidential and known only by the EQAsia Consortium.

This report is approved in its final version by a Technical Advisory Group composed by members of the EQAsia Consortium, and by the EQAsia Advisory Board members Navin Karan (Pacific Pathology Training Centre, New Zealand), Monica Lahra (WHO Collaborating Center for STI and AMR, NSW Health Pathology Microbiology, New South Wales, Australia) and Ben Howden (The Peter Doherty Institute for Infection and Immunity, Australia).