SA’s health data could have halted listeriosis
HEALTH data played a significant role in identifying the root cause of the listeriosis disease in South Africa. Addressing the South African Parliament, Dr Aaron Motsoaledi outlined how the data gathering process unfolded.
He said: “In July 2017, doctors from neonatal units at Chris Hani-Baragwanath and Steve Biko Academic Hospitals alerted the National Institute of Communicable Diseases (NICD) about unusually high numbers of babies with listeriosis, which they were not used to seeing.”
Because there was no notifiable data to make a conclusion, NICD started gathering data.
They contacted all laboratories in the laboratory network of about 265 public laboratories under the National Health Laboratory Service (NHLS).
He said this was easy, because the NICD was part of the NHLS and had access to all the data of the NHLS.
NICD started gathering this data tracing backwards from January 1, 2017, and used the data to construct graphs to see the trends. For comparison they had to do each year from 2013 in order to do a year-to-year comparison to see if 2017 deviated substantially from all the other years.
The problem was encountered with private laboratories, because they were not part of the NHLS and NICD had no direct access to their data.
Motsoaledi said: “Their information started trickling in only by September 2017, especially data from 2013, which they did not necessarily keep at hand, because they were not obliged to notify.
“By November 2017, the NICD had collated data that showed 557 laboratory-confirmed listeriosis cases, which have been reported from all provinces.”
Based on the statements by the health minister there’s no doubt that health data was instrumental in nailing down the listeriosis disease.
What is noteworthy, however, is the fact that:
There was no data about listeriosis before this outbreak (according to the minister there was no requirement to collect such data).
The public sector and private sector health data is separated, and this was one of the obstacles faced by the Health Ministry in identifying this disease quicker.
On the basis of this information it can be concluded that had the Health Ministry gathered and analysed national data irrespective of whether it was required or not, it would have picked up this challenge earlier.
It is also clear that for a better national health decision making process there’s a need for private and public health data to be integrated.
This catastrophe, which was partly inspired by lack of data, should serve as a lesson for the National Health Ministry to place high value on health data (gathering, analysis and sharing).
The US Health Department realised the value of sharing and enabling access to health data and information as a result in addressing the challenge with cancer they championed the establishment of the Genomic Data Commons (GDC), which is currently one of the largest data repositories of its kind on the planet (genomic cancer data).
The GDC is a digital warehouse, one currently storing five petabytes (or five million gigabytes) of molecular-level information on cancerous tumours, accompanied by heavily detailed (but anonymised) data on the patients and the treatments they underwent, all collected from US National Cancer Institute (NCI).
The GDC centralises, standardises and makes accessible data from large-scale NCI programmes such as The Cancer Genome Atlas (TCGA) and its paediatric equivalent, Therapeutically Applicable Research to Generate Effective Treatments (Target).
Together, TCGA and Target represent some of the largest and most comprehensive cancer genomics datasets in the world, comprising more than two petabytes of data (one petabyte is equivalent to 223 000 DVDs filled to capacity with data).
In addition, the GDC accepts submissions of cancer genomic and clinical data from researchers around the world who wish to share their data broadly.
In so doing, researchers are able to use the state-of-the-art analytic methods of the GDC, allowing them to compare their findings with other data in the GDC.
Data in the GDC, representing thousands of cancer patients and tumours, is harmonised using standardised software algorithms so that it can be accessible and be broadly useful to any cancer researcher.
As a growing knowledge system for cancer, the GDC also enables researchers to submit data, and harmonises these data for import into the GDC.
As more researchers add clinical and genomic data to the GDC, it will become an even more powerful tool for making discoveries about the molecular basis of cancer that may lead to better care for patients.
The GDC example illustrates what can be done to address health challenges through placing high value on data and sharing it.
Time bomb
One major lesson that should be taken into account is the shareability of data. The silo approach to health data in South Africa and the African continent broadly is a ticking time bomb.
Recently, a number of countries in the SADC have stopped importing products affected by the listeriosis outbreak from South Africa.
At the same time, not even a single one of those countries has reported a case of listeriosis.
Is it possible that they were eating the cold meat from Enterprise and yet not suffering similar health challenges experienced in South Africa?
Or is it a case of poor health data in those countries that there’s nothing yet to report about health challenges resulting from eating cold meat from Enterprise in South Africa?
Whatever the case here, the lesson for the African continent is that there’s a need for countries to make their health data available and shareable.
This approach will improve how the continent responds to health challenges and more importantly be better prepared to address health challenges.
The listeriosis outbreak in South Africa should serve as the motivator for action to be taken about health data across diseases irrespective of whether they are posing a challenge or not.
The country and the continent need a health information dashboard to keep decision makers and society at large informed about health provisions and challenges on time.
In his concluding remarks Minister Motsoaledi had this to say about health data:
“We are prepared to help the families in whatever way, including giving them information and data, and advise if they so wish to litigate”.
May the Ministry of Health act on making health data and information available for all to make informed decisions about health.
Wesley Diphoko is the founder of Kaya Labs. He also serves as the current chairperson of the IEEE – Industry Connections on Open Data Initiative.