Enhancing clinical microbiology for genomic surveillance of antimicrobial resistance implementation in Africa

Kajumbula, Henry M and Amoako, Daniel Gyamfi and Tessema, Sofonias K and Aworh, Mabel Kamweli and Chikuse, Francis and Okeke, Iruka N and Okomo, Uduak and Jallow, Sabelle and Egyir, Beverly and Kanzi, Aquillah M and Sesay, Abdul Karim and Alimi, Yewande Habibat and Duedu, Kwabena and Perovic, Olga (2024) Enhancing clinical microbiology for genomic surveillance of antimicrobial resistance implementation in Africa. Antimicrobial Resistance & Infection Control, 13 (1). ISSN 2047-2994

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Abstract

Surveillance is essential in the fight against antimicrobial resistance (AMR), to monitor the extent of resistance, inform prevention, control measures, and evaluate intervention progress. Traditional surveillance methods based on phenotypic antimicrobial susceptibility data offer important but limited insights into resistance mechanisms, transmission networks, and spread patterns of resistant bacterial strains. Fortunately, genomic technologies are increasingly accessible and can overcome these limitations. Genomics has the potential to advance traditional bacteriology in routine diagnosis and surveillance, it often relies on the initial isolation of bacterial strains from clinical specimens using conventional culture methods. Culture-based phenotypic characteristics are essential for making inferences about newly recognized genomic patterns. The Africa CDC Pathogen Genomics Initiative (Africa PGI) aims to enhance disease surveillance and public health partnerships through integrated, cross-continent laboratory networks equipped with the tools, human resource capacity and data infrastructure to fully leverage critical genomic sequencing technologies. For genomic surveillance of AMR, it is essential to optimize routine clinical microbiology laboratory services that are weak in many African countries. In this review, we outline shortcomings in clinical microbiology laboratories across Africa that compromise pathogen genomic epidemiology. We emphasize the necessity of investing in bacteriology and enhancing leadership capacity to fully capitalize on the advantages offered by genomic antimicrobial resistance (AMR) surveillance.

Item Type:	Article
Identification Number:	10.1186/s13756-024-01472-8
Dates:	Date Event 24 September 2024 Accepted 13 November 2024 Published Online
Uncontrolled Keywords:	Microbiology laboratory capacity, AMR surveillance, Whole genome sequencing, Laboratory quality, Workforce
Subjects:	CAH03 - biological and sport sciences > CAH03-01 - biosciences > CAH03-01-02 - biology (non-specific)
Divisions:	Faculty of Health, Education and Life Sciences > College of Life Sciences
Depositing User:	Gemma Tonks
Date Deposited:	18 Nov 2024 15:05
Last Modified:	18 Nov 2024 15:05
URI:	https://www.open-access.bcu.ac.uk/id/eprint/15972

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