Findings from Whole Genome Sequencing in Ghana

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In Africa, AMR surveillance relies mainly on phenotypic detection of resistance via antimicrobial susceptibility testing (AST) using the disk diffusion or broth dilution methods. Although AST provides key information for surveillance and patient management, it doesn’t explain resistance mechanisms or pathogen evolution - data which is gathered through whole genome sequencing (WGS). Sequencing data also identifies emerging and re-emerging clones and can track bacterial transmission between humans, animals and the environment, information which is crucial for strengthening AMR surveillance and tackling resistance.

That’s why the Fleming Fund’s SEQAFRICA project, led by Technical University of Denmark, is supporting sequencing centres in Nigeria, Tanzania, South Africa and Ghana to improve sequencing and bioinformatics capacity for AMR surveillance across Africa.

In July 2020, Noguchi Memorial Institute for Medical Research (NMIMR) of the University of Ghana, joined the project. The institute has a next-generation sequencing core facility equipped with two Illumina MiSeqs and a bioinformatics training facility with 16 computers. Recently, NMIMR sequenced 60 isolates, including 53 extended-spectrum beta-lactamase (ESBL) positive E. coli isolates, for two Fleming Fellows, Dr. Nicholas Dayie and Mr. Solomon Asante Sefa. ESBLs are organisms resistant to a wide range of antimicrobial agents and often carry multiple resistant genes. Archived isolates from other projects have also been sequenced under SEQAFRICA, and these include:

• 5 ESBL positive K. pneumoniae
• 1 ESBL positive E. coli
• 1 carbapenem resistant A. baumannii

(Sequence data was obtained using an Illumina MiSeq System (Illumina Inc., San Diego, CA, USA) with 300-bp paired-end reads. The raw Fastq files were quality filtered to Phred score ≥ 20, filtered for minimum read length of 50bp and adaptor trimmed using BBDuk BBMap – Bushnell B. Read quality was confirmed using the FastQC tool. The resultant high-quality reads were used for de novo assembly using the SPAdes assembler v 3.13.0. The generated contig files were scanned to manually remove contigs consisting entirely of homonucleotide bases.)

The Fasta and Fastq files were made available to Fellows who had earlier received training from DTU and Fellows were referred to the CGE tools to analyse the sequences to determine resistance and virulence gene markers.

Overall, the sequence data revealed beta lactam (blaCTX-M-15, blaTEM-1, and blaOXA-1) and several other well-known non beta lactam antimicrobial resistance genes (for first line antimicrobials). blaCTX-M-15 was the predominant ESBL gene in the collection sequenced. The finding of ESBL isolates carrying multiple resistant genes suggests the need for continuous surveillance to monitor the spread of these resistant bugs. Multi-drug resistant E.coli can act as a reservoir to further spread resistant genes to other harmful pathogens.

NMIMR looks forward to working together with SEQAFRICA to expand our human resource for effective AMR surveillance in Ghana and within the African region. They have received isolates from other Fleming Fellows for processing and anticipate the throughput of sequencing will increase in the coming quarters.

Through the SEQAFRICA project, NMIMR has also sequenced 64 SARS-CoV-2 genomes which will help in monitoring the spread of COVID-19 in Ghana. Additional samples will be sequenced after we receive the required consumables/reagents we have ordered.

Bright Adu, Research Fellow at NMIMR said: “The Fleming Fund support through SEQAFRICA has been very timely and has contributed greatly to strengthening the capacity of NMIMR in using next generation sequencing technologies to track emergence of infectious pathogens. It is truly a wonderful initiative that should be sustained.” These same thoughts were shared by Kofi Bonney, a Senior Research Fellow at NMIMR.