External quality assessment of bacterial identification and antimicrobial susceptibility testing in African national public health laboratories, 2011–2016

Abstract

27Background: In 2002, the World Health Organization (WHO) launched a regional microbiology external 28 quality assessment (EQA) programme for national public health laboratories in the African region, initially 29 targeting priority epidemic-prone bacterial diseases, and later including other common bacterial pathogens. 30Objectives: The aim of this study was to analyse the efficacy of an EQA programme as a laboratory quality 31 system evaluation tool. 32 Methods:We analysed the proficiency of laboratories' performance of bacterial identification and AST for the 33 period 2011-2016. Overall, 81 laboratories from 45 countries participated. 34The National Institute for Communicable Diseases of South Africa provided technical coordination following 35 an agreement with WHO, and supplied EQA samples of selected bacterial organisms for microscopy (Gram 36 stain), identification, and antimicrobial susceptibility testing (AST). National public health laboratories, as well 37 as laboratories involved in the Invasive Bacterial Diseases Surveillance Network, were enrolled by the WHO 38 Regional Office for Africa to participate in the EQA programme. 39 Results: We analysed participants' results of 41 surveys, which included the following organisms sent as 40 challenges: Streptococcus pneumonia, Haemophilus influenza, Neisseria meningitidis, Salmonella Typhi, 41 Salmonella Enteritidis, Shigella flexneri, Staphylococcus aureus, Streptococcus agalactiae, Streptococcus 42 anginosus, Enterococcus faecium, Serratia marcescens, Acinetobacter baumannii, and Enterobacter cloacae. 43Overall, 76% of participants obtained acceptable scores for identification, but a substantial proportion of AST 44 scores were not in the acceptable range. 45 Conclusion:In the African Region, implementation of diagnostic stewardship in clinical bacteriology is 46 generally suboptimal. This report illustrates that AST is poorly done compared to microscopy and identification. 47It is critically important to make the case for implementation of quality assurance in AST, as it is the 48 cornerstone for antimicrobial resistance surveillance reporting and implementation of the Global Antimicrobial 49 Resistance Surveillance System. 50 100 laboratories for continuous capacity assessment, for example to obtain information on their facilities, capacity, 101 and staff competence. Preparation of the samples included quality control and validation of survey material 102 before dispatch. The programme followed the ISO/IEC 17043 guidelines and all samples were packaged and 103 shipped according to International Air Transport Association Packing Instructions P650. 4 104Concurrently, five referee laboratories tested the isolates and their results determined whether the specimen 105 panels were suitable for distribution to participants. For this analysis, participating laboratories' bacterial 106 identification and AST results for the period 2011-2016 were identified from the programme database.

Antimicrobial Resistance Surveillance in Low- and Middle-Income Countries: Progress and Challenges in Eight South Asian and Southeast Asian Countries

“…One component of IDSR implementation involved establishing and strengthening laboratory capacity and accordingly several countries in the Africa region established national reference and regional public health laboratories. These laboratories are involved in surveillance of epidemic prone and other bacterial pathogens causing meningitis, sepsis and diarrhea (181). This existing laboratory network could be utilized for AMR surveillance activities in individual countries.…”

“…This existing laboratory network could be utilized for AMR surveillance activities in individual countries. However, proficiency testing between 2011 and 2016 for identification and AST of 13 bacterial pathogens in 81 laboratories across 45 African countries showed acceptable scores for microbial identification but poor scores for AST (181). Although there is a huge opportunity to take advantage of existing public health laboratory networks for AMR surveillance, there is a need for capacity building of these existing laboratories.…”

The Role of Molecular Testing in Pediatric Meningitis Surveillance in Southern and East African Countries, 2008–2017

“…Diagnosis historically depends on cerebrospinal fluid (CSF) examination and bacterial culture; the latter remains the reference standard for pathogen detection because of its specificity. Many African microbiology laboratories lack resources and capacity to reliably confirm etiology or perform characterization of pathogens [ 8 ]. Polymerase chain reaction (PCR) has the advantage of faster turnaround time and improved sensitivity, particularly when Gram stain or culture results are negative [ 9 , 10 ].…”

COVID-19 pandemic and antimicrobial resistance: Another call to strengthen laboratory diagnostic capacity in Africa

“…17 An external quality assessment report indicated poor performance of AST in several African countries. 18 Quality assurance in AST is key for reporting and implementation of the Global Antimicrobial Resistance Surveillance System 19 ; laboratories in Africa have to be supported with the needed investments for better performance.…”