Researchers in South Africa have utilized genomic data and human travel patterns spanning 14 years to gain valuable insights into the spread, evolution, and resistance behaviors of a major bacterium responsible for causing pneumonia and meningitis worldwide.
A novel approach has been developed to track the spread and evolution of pathogens, along with their reactions to vaccines and antibiotics. By merging a pathogen’s genomic information with human travel patterns extracted from anonymized mobile phone data, researchers aim to better forecast and prevent future outbreaks.
Collaborating institutions such as the Wellcome Sanger Institute, University of the Witwatersrand, National Institute for Communicable Diseases in South Africa, University of Cambridge, and partners in the Global Pneumococcal Sequencing project1 have combined nearly 7,000 samples of Streptococcus pneumoniae (pneumococcus) genomic data collected in South Africa with detailed human mobility data2. This integration has allowed them to observe the movement and evolutionary trends of these bacteria, known for causing pneumonia and meningitis3.
The research findings, published in Nature on July 3rd, indicate that the initial decline in antibiotic resistance associated with the 2009 pneumococcal vaccine might only be short-lived. Non-targeted strains, resistant to antibiotics like penicillin, gained a competitive advantage of 68 per cent.
For the first time, researchers have quantified the fitness – the ability to survive and reproduce – of various pneumococcal strains accurately. This insight could aid in developing vaccines that target the most harmful strains and could be relevant for other pathogens as well.
Many infectious diseases, including tuberculosis, HIV, and COVID-19, exist in multiple strains that circulate simultaneously, posing challenges for study. Pneumococcus, a leading cause of pneumonia, meningitis, and sepsis globally4, with over 100 types and 900 genetic strains, exemplifies this issue. Pneumonia alone claims approximately 740,000 young lives annually, making it the primary infectious cause of death in children5.
The diversity of pneumococcus obstructs control measures, as vaccines targeting major strains leave gaps for other strains to occupy. The spread patterns of these bacteria, the impact of vaccines on their survival, and their antibiotic resistance are still inadequately understood.
In this recent study, researchers analyzed genome sequences from 6,910 pneumococcus samples gathered in South Africa between 2000 and 2014 to monitor the distribution of various strains over time. These data were combined with anonymous records of human mobility patterns collected by Meta2.
The research team formulated computational models that revealed it takes approximately 50 years for pneumococcal strains to completely mix throughout South Africa’s population, mainly due to localized human movement patterns.
They discovered that while the introduction of a pneumococcal vaccine targeting specific bacterial types in 2009 decreased the number of cases caused by those types6, it simultaneously conferred a 68% competitive advantage on other non-targeted strains, leading to an increased proportion of them becoming resistant to antibiotics such as penicillin. This hints that the protection against antibiotic resistance from the vaccine is transient.
Dr. Sophie Belman, the study’s lead author, mentioned the potential impact of vaccines and antimicrobials in altering the spread dynamics of pneumococcal bacteria. The models developed could be applied to different regions and pathogens to enhance understanding and prediction of pathogen spread concerning drug resistance and vaccine efficiency.
Dr. Anne von Gottberg, co-author of the study from the National Institute for Communicable Diseases in Johannesburg, South Africa, underscored the significance of continuous genomic surveillance and adaptable vaccination strategies to tackle the adaptability of these pathogens in reducing the disease burden.
Professor Stephen Bentley, the senior author of the study at the Wellcome Sanger Institute, highlighted the complexity caused by pneumococcus’s diversity in understanding the spread of individual strains from one region to another. This innovative technique merging bacterial genome and human travel data finally enables the unravelling of hidden migratory paths in high resolution for the first time. This insight could assist in anticipating the emergence of high-risk strains, thus preempting potential outbreaks.
Background Information:
- Access the partners involved in the Global Pneumococcal Sequencing project at: https://www.pneumogen.net/gps/
- The human mobility data utilized in this study are Meta Data for Good baseline data released during the 2020 SARS-CoV-2 pandemic. These data are dependent on individual consent for location sharing, with measures in place by Data for Good to preserve individual privacy in aggregated datasets.
- To learn more about pneumococcal disease, visit: https://www.cdc.gov/pneumococcal/about/
- Read more at: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5666185/
- For additional insights, refer to: https://www.who.int/news-room/fact-sheets/detail/pneumonia
- Prior to the introduction of these vaccines, 85% of pneumococcal strains were targeted. By 2014, this percentage decreased to 33.2%. This reduction was consistent across all nine provinces in South Africa.
