Labs for genomic sequencing of micro-organisms strengthened

Rumbidzayi Zinyuke-Senior Health Reporter

The capacity of laboratories to perform genomic sequencing for anti-microbial resistance in bacteria and viruses that could be of public health concern will be strengthened by Government, building on the progress made during the Covid-19 pandemic.

Genomic sequencing involves recording a virus’s genetic code, and comparing the sequence to previous samples. This technique allows researchers to track the spread of viruses, how the viruses are changing and also how to develop vaccines, therapeutics, diagnostic assays as well as decisions on public health and social measures.

Now, in a study published in The Lancet Microbe journal, genome sequencing has been used to study another deadly disease, typhoid fever, and how it is starting to overcome defences against it.

Genomic sequencing was one of the valuable tools in the global, regional, and national response to the Covid-19 pandemic.

Speaking at a World Antimicrobial Resistance Awareness week conference, Ministry of Health and Child Care director for epidemiology and disease control Dr Rudo Chikodzore said Zimbabwe could leverage on the progress made in the Covid 19 genomic sequencing to track other viruses.

“Essentially we are on a drive to improve our laboratory capacities. You will note that during the Covid period, we managed to get genomic sequencing occurring within the country and we are trying to expand it beyond Covid 19 but also to look at issues of AMR and other issues where we can benefit from the genomic sequencing capacities that we have already from the Covid 19 period,” she said.

AMR occurs when bacteria, viruses, fungi and parasites change over time and no longer respond to medicines, making infections harder to treat and increasing the risk of disease spread, severe illness and death. As a result of drug resistance, antibiotics and other antimicrobial medicines become ineffective and infections become increasingly difficult or impossible to treat.

For many developed countries, whole genome sequencing is a technology that has transformed the understanding of antimicrobial resistance as it lets scientists rapidly predict whether bacteria are resistant to antibiotics based on genetic information.

Antimicrobial resistance prediction from whole genomic sequencing data is an emerging application of machine learning, which could improve antimicrobial resistance surveillance and outbreak monitoring.

Zimbabwe has already made headway towards this.

The results of a genomic survey of typhoid fever in Zimbabwe published last year showed how the bacteria behind recent outbreaks had evolved extra levels of antimicrobial resistance. Researchers from the National Microbiology Reference Laboratory, Quadram Institute and University of East Anglia were part of the locally-led effort to trace the spread of resistance genes, which is now supporting management of the disease.

The genomic analysis contributed to the decision to initiate a mass typhoid vaccination campaign in Harare. Ongoing genomic surveillance could also identify any “escape mutants” allowing healthcare authorities in the country to react swiftly and help control typhoid fever and its devastating effects.

“We are also pushing to have microscopic culture and sensitivity at the lowest level possible in the health facilities so that we are aware of the sensitivities of some of the bacteria, the fungi that we are dealing with closer to the community. These are some of the drives we are undertaking as a Ministry,” said Dr Chikodzore.