Mobile Data Helps Scientists Track Pathogen Spread and Superbug Evolution
Combining genomic data and human travel patterns in South Africa has revealed key insights into the spread, evolution, and resistance patterns of a major bacterium behind pneumonia and meningitis globally.
The approach combines a pathogen’s genomic data over 14 years with human travel patterns taken from anonymised mobile phone data during the period January 2020 to July 2021.
Researchers inferred the fitness (ability to survive and reproduce) of different pneumococcal strains using genomic data of the strains collected from both carriage and invasive disease.
Carriage data refers to asymptomatic infection while invasive disease means symptomatic infection.
The insight could inform vaccine development to target the most harmful strains and may be applicable to other pathogens.
Researchers from the University of the Witwatersrand, Johannesburg (Wits), the National Institute for Communicable Diseases (NICD), the Wellcome Sanger Institute, the University of Cambridge, and partners across the Global Pneumococcal Sequencing project1, integrated genomic data from nearly 7,000 Streptococcus pneumoniae (pneumococcus) strains collected in South Africa with detailed human mobility data2.
This enabled researchers to see how these bacteria, which cause pneumonia and meningitis3, move between regions and evolve over time.
he findings, published in Nature on 3 July, suggest that the 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% competitive advantage.
All South African data
Co-author of the study Dr Anne von Gottberg is Associate Professor in the Division of Clinical Microbiology and Infectious Diseases, School of Pathology at Wits University, and joint staff at the NICD.
Von Gottberg said: “All the data are from South Africa. Our data for invasive disease were taken from the NICD’s national surveillance collaborating with multiple surveillance partners throughout the country. Carriage data were obtained from Wits VIDA studies during some years that overlapped the national surveillance. Our study used both the NICD and Wits VIDA datasets to explore carriage (asymptomatic infection) versus disease (symptomatic infection) isolates over time.”
Wits VIDA is the Vaccines and Infectious Diseases Analytics Research Unit. Shabir Madhi, Professor of Vaccinology and Executive Director of Wits VIDA co-authored the study, for which Wits VIDA supplied carriage data.
Cebile Lekhuleni, a PhD student in the Division of Clinical Microbiology and Infectious Diseases at Wits and a researcher at the NICD, is one of the Global Pneumococcal Sequencing project partners under the leadership of Von Gottberg.
Also a co-author of the study, Lekhuleni says, “The genomic data and metadata contributed by the NICD’s national surveillance plays an important role in leveraging the power of pathogen genomics in tracking and monitoring diseases of public health concern. Through these data, collected in a systematic manner over a long period of time, we now have insights on the transmission dynamics of the pneumococcus in South Africa and supporting evidence of the fitness of important pneumococcal strains after vaccine introduction.”
Why tracking pathogens matters
Many infectious diseases such as tuberculosis, HIV, and COVID-19 are caused by multiple strains or variants circulating simultaneously, making them difficult to study.
Pneumococcus, a bacterium that is a leading cause of pneumonia, meningitis, and sepsis worldwide4, is a prime example with over 100 types and 900 genetic strains globally. Pneumonia alone kills around 740,000 children under the age of five each year5, making it the single largest infectious cause of death in children.
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 poorly understood.
Madhi says, “The findings from this study on how the pneumococcus disseminates over time adds novel insight into the epidemiology of the pneumococcus. The recent work on pneumococcus adds to the body of knowledge on pneumococcus, of which scientists in South Africa have been at the forefront of research, dating back to the first ever studies of pneumococcal vaccines in the early 1900s. Pneumococcus remains a leading cause of death from pneumonia in children and adults, indicating the need for ongoing research on its evolution, and building on the success of current vaccines which protect against some – but not all – of the pneumococcal serotypes”.