NGSocomial Infections: High-Resolution Views of Hospital-Acquired Infections Through Genomic Epidemiology.

Hospital outbreak investigations are high-stakes epidemiology. Contacts between staff and patients are numerous; environmental and community exposures are plentiful; and patients are highly vulnerable. Having the best data is paramount to understanding an outbreak in order to stop ongoing transmission and prevent future outbreaks. In the past 5 years, the high-resolution view of transmission offered by analyzing pathogen whole-genome sequencing (WGS) is increasingly part of hospital outbreak investigations. Concerns over speed and actionability, assay validation, liability, cost, and payment models lead to further opportunities for work in this area. Now accelerated by funding for COVID-19, the use of genomics in hospital outbreak investigations has firmly moved from the academic literature to more quotidian operations, with associated concerns involving regulatory affairs, data integration, and clinical interpretation. This review details past uses of WGS data in hospital-acquired infection outbreaks as well as future opportunities to increase its utility and growth in hospital infection prevention.

Transparency, trust, and community welfare: towards a precision public health ethics framework for the genomics era.

Infectious disease control is experiencing a paradigm shift, as pathogen sequencing technologies and digital applications are increasingly implemented for control of diseases such as tuberculosis, Ebola, and COVID-19. A new ethical framework should be a critical part of this emerging paradigm to ensure that the benefit of precision public health interventions based on advances in genomics research is not outweighed by the risks they pose to individuals, families, and vulnerable segments of the population. We suggest that the ethical framework guiding practice in this domain combines standard precepts from public health ethics with emerging ethics principles from precision medicine.