Advancing genomics to track pathogen spread


By Dr. Tim Sandle
July 9, 2024

Patients receive treatment for dengue fever in Dhaka's Shaheed Suhrawardy Medical College Hospital. More than 1,000 people have died this year in Bangladesh's worst outbreak of the mosquito-borne disease - Copyright AFP Munir UZ ZAMAN

A new method to map the spread and evolution of pathogens, together with their responses to vaccines and antibiotics, provides key insights to help predict and prevent future outbreaks.

This is an approach that combines a pathogen’s genomic data with human travel patterns, taken from anonymised mobile phone data. The collected data is subject to analysis using an algorithm.

The development comes from researchers from the Wellcome Sanger Institute, University of the Witwatersrand and National Institute for Communicable Diseases in South Africa, the University of Cambridge, and partners across the Global Pneumococcal Sequencing project.

The scientists integrated genomic data from nearly 7,000 Streptococcus pneumoniae (pneumococcus) samples collected in South Africa with detailed human mobility data. Pneumococcus is a bacterium that is a leading cause of pneumonia, meningitis, and sepsis worldwide

This collection of data enabled the scientists to see how these bacteria, which cause pneumonia and meningitis, move between regions and evolve over time.

The findings suggest initial reductions in antibiotic resistance linked to the 2009 pneumococcal vaccine may be only temporary, as non-targeted strains resistant to antibiotics such as penicillin gained a 68 percent competitive advantage.

This innovation is the first-time researchers have been able to precisely quantify the fitness – their ability to survive and reproduce – of different pneumococcal strains. The insight could inform vaccine development to target the most harmful strains and may be applicable to other pathogens.

This overcomes one of the challenges posed by many infectious diseases such as tuberculosis, HIV, and COVID-19 exist in multiple strains or variants circulating simultaneously, making them difficult to study. An example is with Pneumococcus, where there are over 100 types and 900 genetic strains globally.

Pneumonia alone kills around 740,000 children under the age of five each year, making it the single largest infectious cause of death in children and pneumococcal diversity hampers control efforts, as vaccines targeting major strains leave room for others to fill the vacant niches.

How these bacteria spread, how vaccines affect their survival, and their resistance to antibiotics remains also poorly understood. Until now.

The researchers analysed genome sequences from 6,910 pneumococcus samples collected in South Africa between 2000 and 2014 to track the distribution of different strains over time. They combined these data with anonymised records of human travel patterns collected by Meta. From this, the researchers developed computational models which revealed pneumococcal strains take around 50 years to fully mix throughout South Africa’s population, largely due to localised human movement patterns.

Next the scientists discovered that while introduction of a pneumococcal vaccine against certain types of these bacteria in 2009 reduced the number of cases caused by those types, it also made other non-targeted strains of these bacteria gain a 68 per cent competitive advantage, with an increasing proportion of them becoming resistant to antibiotics such as penicillin. This suggests that the vaccine-linked protection against antibiotic resistance is short-lived.

The research has been published in the science journal Nature, titled “Geographic Migration and Fitness Dynamics of Streptococcus pneumonia.”