Using Mobile Data to Track the Spread and Evolution of Superbugs

Key insights into the global spread, evolution, and resistance patterns of a major bacterium causing pneumonia and meningitis have been revealed through the combination of genomic data and human travel patterns over 14 years in South Africa.

Future outbreaks can be predicted and prevented with the aid of new insights derived from mapping the spread and evolution of pathogens as well as their reactions to vaccinations and antibiotics. The method combines human travel patterns derived from anonymized mobile phone data with genomic information about a pathogen.

About 7,000 Streptococcus pneumoniae (pneumococcus) samples were collected in South Africa. Researchers from the Wellcome Sanger Institute, University of the Witwatersrand, National Institute for Communicable Diseases in South Africa, the University of Cambridge, and partners across the Global Pneumococcal Sequencing project integrated genomic data from these samples with detailed human mobility data. This allowed them to observe the movement and evolution over time of these bacteria, which cause meningitis and pneumonia.

According to research published in Nature, non-targeted strains of pneumococcal bacteria that are resistant to antibiotics like penicillin have gained a 68% competitive advantage, indicating that the 2009 pneumococcal vaccine may have only temporarily reduced antibiotic resistance.

For the first time, scientists have been able to measure the fitness of various pneumococcal strains precisely, or their capacity to endure and procreate. This knowledge may help develop vaccines that specifically target the most dangerous strains of the infection and may also apply to other infections.

Numerous infectious diseases, including HIV, COVID-19, and tuberculosis, are difficult to study because they circulate in multiple strains or variations at the same time.

One such example is the bacterium pneumococcus, which has over 100 types and 900 genetic strains worldwide and is the primary cause of pneumonia, meningitis, and sepsis4. Pneumonia is the leading infectious cause of death in children under five years old, accounting for about 740,000 deaths annually.

Control attempts are hampered by pneumococcal diversity because vaccinations that target dominant strains allow others to occupy the empty spaces. It is still unclear how these bacteria proliferate, how vaccinations impact their survival, and how resistant they are to antibiotics.

Researchers tracked the distribution of various strains over time in this new study by analyzing genome sequences from 6,910 pneumococcus samples that were collected in South Africa between 2000 and 2014. They merged these data with Meta's anonymized records of people's travel habits.

The scientists created computer models that showed, in large part because of regionalized human movement patterns, that pneumococcal strains take about 50 years to fully mix throughout South Africa's population.

Researchers discovered that although the introduction of a pneumococcal vaccine in 2009 against specific strains of these bacteria decreased the number of cases caused by those types, it also gave other strains of these bacteria that were not targeted a 68% competitive advantage, leading to an increase in the percentage of these strains that developed resistance to antibiotics like penicillin. This implies that the protection against antibiotic resistance associated with vaccinations is transient.

While we found that pneumococcal bacteria generally spread slowly, the use of vaccines and antimicrobials can quickly and significantly change these dynamics. Our models could be applied to other regions and pathogens to better understand and predict pathogen spread, in the context of drug resistance and vaccine effectiveness.”

Dr. Sophie Belman, Study First Author and Former Ph.D. Student, Wellcome Sanger Institute

Dr. Sophie Belman is now a Schmidt Science Fellow at the Barcelona Supercomputing Centre, Spain

“Despite vaccination efforts, pneumonia remains one of the leading causes of death for children under five in South Africa. With continuous genomic surveillance and adaptable vaccination strategies to counter the remarkable adaptability of these pathogens, we may be able to better target interventions to limit the burden of disease,” said Dr. Anne von Gottberg, Study Author, National Institute for Communicable Diseases.

The pneumococcus’s diversity has obscured our view on how any given strain spreads from one region to the next. This integrated approach using bacterial genome and human travel data finally allows us to cut through that complexity, uncovering hidden migratory paths in high-definition for the first time. This could allow researchers to anticipate where emerging high-risk strains may take hold next, putting us a step ahead of potential outbreaks.”

Stephen Bentley, Professor and Study Senior Author, Wellcome Sanger Institute