I went on a ward round in Juba a couple of years ago. The temperature was about 45°C and we had over 40 patients to see. We came across a man with a very high fever. The automatic diagnosis was malaria, but the consultant in charge of the ward round thought he might have typhoid. There were no facilities for a microbiological workup, so he simply ordered a combination of quinine and a broad spectrum antibiotic. However, with the modern generation of high-speed gene sequencing techniques it would be impossible to test him for any serious bacterial infection. A facility for rapid bedside diagnosis would have many advantages in low-income settings. Firstly, it would assist in normal patient care by targeting therapy more accurately. Secondly, it would save on resources. Thirdly, it is likely to reduce overall antibiotic use and hence the incidence of antibiotic resistance. Lastly, it will enable targeted contact tracing. For example, if three patients were admitted with the same bacterium, then their addresses could be compared and if their homes were in close proximity, further enquiries and public health initiatives could be undertaken.
The cost of rapid gene sequencing is following Moore’s Law and will soon be under £100 per sample. The point will soon be reached when rapid gene sequencing is less expensive than conventional microbiological culture. In a country like South Sudan, it may be possible to bypass normal culture technology and move straight to sequencing techniques. After all many developing countries have bypassed landline telephone technology and moved straight onto mobile phones. It would be interesting to carry out a health economic analysis to determine the point where sequencing techniques would become the most cost-effective option in a low-income country context. Such an analysis would need to take into account all of the advantages above, including that of contact tracing. If sequencing techniques could be extended to parasites, then the method will become more cost-effective still.