AWS Big Data Blog

ICBiome uses Amazon QuickSight to empower hospitals in dealing with harmful pathogens

In response to the COVID-19 pandemic, hospitals and healthcare organizations are increasingly employing genetic sequencing to screen, track, and contain harmful pathogens. ICBiome is a startup that has been working on this problem for several years, creating innovative data analytics products using AWS to help hospitals and researchers address both community-associated and hospital-acquired infections. Building on its early focus on methicillin-resistant Staphylococcus aureus (MRSA), the company is expanding its solution to cover COVID-19 and other types of infections.

ICBiome has now integrated Amazon QuickSight embedded analytics into its solution to provide hospital investigators and other users with easy access to powerful analytics and visualizations on any device.

Empowering hospitals and communities

Many hospitals lack access to sequencing capabilities, and hospitals that have such capabilities often lack complex data processing and advanced bioinformatics expertise. Open-source platforms are limited, complex, and scale poorly. They require hardware resources and management beyond the reach of most hospitals and lack visualization software to interactively explore results without specialized know-how.

BiomeMRSA, ICBiome’s cloud-based genomics service, overcomes these gaps by providing easy access to sequencing through its Clinical Laboratory Improvement Amendments (CLIA)-certified provider, with storage, computing, analytics, and visualization delivered from the AWS Cloud. With the addition of QuickSight embedded analytics, hospital investigators can easily monitor pathogens coming through their hospital environments.

Seeing the whole picture

The company’s innovative data processing methodology enables the comparison of full genomes, as opposed to open-source platforms that only compare portions of them. With a vast and growing database of MRSA mutations, the company enables rapid identification of existing and new strains to help hospitals combat infection.

BiomeMRSA monitors intensive care unit (ICU) settings and identifies emerging MRSA transmissions. By using BiomeMRSA to monitor their ICU settings, hospitals can proactively target local reservoirs and reduce overall incidence rates of MRSA. To support its R&D in pathogen genomics, the company has received more than $1 million in funding from NIAID and state grants. In 2019, ICBiome completed an evaluation of BiomeMRSA at a major hospital. It’s now evaluating and validating BiomeMRSA at two additional hospitals.

Improving patient care and treatment cost

This capability gives hospitals the potential to transform how they manage outbreaks. Intake and weekly screenings of patients lack the resolution to determine how the disease was acquired. This means hospitals can be financially and reputationally penalized for a disease that was acquired before admission.

BiomeMRSA allows continuous monitoring of ICUs by routinely sequencing all samples and returning those samples to hospitals within days. This allows for earlier detection, mitigation of outbreaks, and the reduction of colonization rates of ICU patients by identifying transmissions where the patient was colonized but not infected. Lowering colonization rates can reduce the risk of post-care infections and costly readmissions.

ICBiome is now expanding this work to include tracking pandemics such as COVID-19. The Virginia-based company is adding a COVID-19 application, BiomeCOVID, to address the ongoing crisis. Previously deployed for real-time operations, BiomeCOVID will use genetics to greatly increase the accuracy of contact tracing by separating isolates within different lineages and further identifying unique clusters within those lineages. The company is accelerating the development of BiomeCOVID to meet the critical healthcare need.

Visualizing genomics to combat disease

Since its first NIH grant award in 2017, ICBiome has built its solutions in the AWS Cloud. To deliver rich, in-depth analytics capabilities to its customers, the company chose QuickSight for embedded dashboards in its products. According to Dr. Srini Iyer, founder and CEO of ICBiome, QuickSight provides the agility and scalability the company needs to deliver in-depth solutions quickly. “ICBiome has developed an end-to-end cloud architecture for processing genetic sequence data from bacterial and viral pathogens,” says Dr. Iyer. “Over the last year, ICBiome looked at several data analytics tools that can serve as the visual interface for our product line. We did a formal analysis of both cloud and on-premises business intelligence solutions, and ultimately decided to choose QuickSight for the security, scalability, cost, and reliability.”

The following image shows the Analytics Dashboard for BiomeMRSA:

ICBiome’s customers are centered in large hospitals and public health agencies. Security and data privacy are critical to these decision-makers, particularly because bacterial and viral samples are taken from patients in the course of clinical care. QuickSight uses the same HIPAA-compliant security architecture used by the rest of the company’s data ingestion and processing systems built on AWS.

Cost-efficient and highly scalable

Scalability is critical because the company expects to handle exponentially growing amounts of data due to the growth in whole-genome sequencing to identify pathogen strains. “We opted for Amazon QuickSight as it streamlines operational scaling and integration not just within the application layer but across the entire AWS ecosystem,” says Dante Martinez, Chief Technology Officer of ICBiome.

As a startup providing affordable solutions for hospitals, cost is a critical concern for ICBiome. Many others in its space have opted to use open-source business intelligence (BI) solutions for this reason. However, the company’s analysis showed that this wasn’t the most cost-effective route. “Many open-source BI platforms require a high level of maintenance to ensure reliability both for routine operations and lifecycle management,” says Martinez. “Given the critical nature of our application, we did not want to compromise product integrity by choosing a difficult-to-maintain open-source platform or an entry-level BI tool. Amazon QuickSight is highly cost-effective, but it is also full-featured and mature, providing an experience on par with much more expensive competitors.”

The following diagram illustrates ICBiome’s cloud architecture.

Visualizing a healthier future

The company has big plans for the embedded analytics functionality enabled by QuickSight. “Once we complete the launches of BiomeCOVID and BiomeMRSA as commercial SaaS products, we intend to bring to market other surveillance products such as BiomeCRE and BiomeSTD to track other critical threats to public health,” says Dr. Iyer. “We will also be targeting other biomedical areas where we can develop new classes of products that provide critical data analytical capabilities that are currently not feasible.”

With the landscape of public health now transformed in the wake of the COVID-19 pandemic, ICBiome will continue to expand its SaaS portfolio with Amazon to provide hospitals innovative data analytics tools in infection prevention, epidemiology, and patient care.

About the  Author

Chirag Dhull is a Principal Product Marketing Manager for Amazon QuickSight.