Mapping pathogen spread and evolution using genomic and human movement data

A new method for mapping the spread and evolution of pathogens, and their response to vaccines and antibiotics, is providing important insights to help predict and prevent future epidemics. The approach combines genomic data from pathogens with human movement patterns obtained from anonymized mobile phone data.

Researchers from the Wellcome Sanger Institute, University of the Witwatersrand, South Africa's National Institute for Communicable Diseases and the University of Cambridge, and partners in the Global Pneumococcal Sequencing Project, will study the pneumococcus infection in approximately 7,000 people. Streptococcus pneumoniae (Streptococcus pneumoniae) The samples collected in South Africa contain detailed human movement data, which sheds light on how these pneumonia- and meningitis-causing bacteria move between regions and how they evolve over time.

The survey results announced today (July 3rd) are: Naturesuggest that the initial reduction in antibiotic resistance associated with the 2009 pneumococcal vaccine may only be temporary, as non-target strains resistant to antibiotics such as penicillin gained a 68 percent competitive advantage.

This is the first time that researchers have been able to precisely quantify the fitness – the ability to survive and reproduce – of different pneumococcus strains, an insight that could aid in the development of vaccines that target the most harmful strains and could also be applied to other pathogens.

Many infectious diseases, such as tuberculosis, HIV, and COVID-19, are difficult to study because multiple strains and variants circulate simultaneously. Streptococcus pneumoniae, a bacterium that is the leading cause of pneumonia, meningitis, and sepsis worldwide, is a prime example, with over 100 species and over 900 genetic strains worldwide. Pneumonia alone kills approximately 740,000 children under the age of five each year, making it the leading cause of infectious disease deaths in children.

Pneumococcus diversity hampers control efforts because vaccines targeting the dominant strains leave room for other strains to fill niches. How these bacteria spread, how vaccines affect their survival, and resistance to antibiotics are still poorly understood.

In the new study, the researchers analyzed the genome sequences of 6,910 pneumococcal samples collected in South Africa between 2000 and 2014 to track the distribution of different strains over time. They combined these data with anonymized records of human movement patterns collected by Meta.

The team developed a computational model that showed that it would take around 50 years for pneumococcal strains to fully mix across South Africa, due mainly to regional human movement patterns.

The team found that the introduction of a pneumococcal vaccine against certain types of these bacteria in 2009 reduced the number of cases caused by those types, but at the same time other non-target strains of these bacteria gained a 68 percent competitive advantage and became more resistant to antibiotics such as penicillin, suggesting that any vaccine-related protection against antibiotic resistance is short-lived.

Dr Sophie Bellman, first author of the study and former PhD student at the Wellcome Sanger Institute, now Schmidt Scientific Fellow at the Barcelona Supercomputing Centre in Spain, said: “We found that pneumococcus generally spreads slowly, but this dynamics can change quickly and significantly with the use of vaccines and antimicrobials. Our model could also be applied to other geographies and pathogens to better understand and predict pathogen spread, in terms of drug resistance and vaccine efficacy.”

“Despite vaccination efforts, pneumonia remains one of the leading causes of death among children under five in South Africa. With ongoing genomic surveillance and adaptive vaccination strategies to counter the remarkable adaptability of these pathogens, we may be able to intervene better and curb the burden of disease,” said study author Dr Anne von Gottberg from the National Institute of Communicable Diseases in Johannesburg, South Africa.

“Pneumococcus diversity has made it unclear how specific strains spread from region to region. With this integrated approach, using bacterial genomes and human movement data, we can finally unravel that complexity and discover hidden migration routes at high resolution for the first time. This will enable researchers to predict where newly emerged high-risk strains will colonize next, helping them stay one step ahead of potential outbreaks.”

Professor Stephen Bentley, lead author of the study from the Wellcome Sanger Institute