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(meta)Genomic Pathogen Surveillance and Detection

Antibiotic Resistance

Antibiotic resistance is one of the biggest public health challenges of our time. Each year in the U.S., at least 2 million people get an antibiotic-resistant infection, and at least 23,000 people die. Next-generation sequencing technologies represent fundamental shift in how we diagnose infectious disease, curb the spread of antibiotic resistance, prevent life threatening infections. PMD members have initiated a large-scale study applying high-throughput genomic surveillance to detect potential hospital transmission clusters. Further, we are extending genomic analysis to understand the transmission of antibiotic resistance and genomic variants that correlate with clinical outcomes. These approaches may ultimately serve as useful diagnostics.

Hightlighted Publications

MDRO

Multidrug resistant organisms (MDROs) are bacteria that have become resistant to more than one antimicrobial agent. Intestinal MDROs constitute a major threat to public health because they are increasingly difficult to treat and result in increased costs, morbidity, and mortality. Clostridium difficile shares many of the same characteristics as MDROs and along with MDROs has been labeled a national priority as defined by the Infectious Diseases Society of America, Centers for Medicare and Medicaid Services, and the Centers for Disease Control and Prevention. An individual’s microbiome influences the likelihood of de novo colonization and whether the MDRO persists over time leading to spread and eventual symptomatic infection. In elders, the high prevalence of MDRO colonization indicates a need to better understand how the intestinal microbiome may be used to predict and prevent the spread of these pathogens. Approaches being developed by PMD members target elder microbiome health in a way that will translate to improved pathogen screening and risk prediction, thus reducing the burden of this healthcare menace.

Hightlighted Publications

SARS-CoV-2

The seriousness, global scale and rapid spread of the SARS-CoV-2 virus has clearly demonstrated the need for active, real-time genomic surveillance of emerging pathogens. It was due to the early public release of genomic data from the first COVID-19 cases that enabled the deployment of the new generation of messenger RNA-based vaccines. As genetic variants of the virus emerged, their regional and global dissemination is tracked through a network of genomic sequencing laboratories. PMD members work with our UMass Memorial Health Network and Departments of Public health to provide real-time, genomic surveillance of the SARS-CoV-2 epidemic; and we are working to develop the laboratory and informatic infrastructure to prepare for future events as well.