infexn: Mapping pathogens and ARGs using direct-from-sample NGS test.

We propose to make genomics applicable and accurate with our standardized workflow combined with a validated and automated bioinformatics pipeline at a cost affordable to be implemented on-site at healthcare centers. By implementing our test at multiple sites, we enable continuously collection and reporting of data on real-time dashboard.

Dr. Anirvan Chatterjee, C.E.O, HaystackAnalytics Pvt. Ltd.

In India, 33% of the total ailing population suffer from infectious disease.  Despite policy initiatives to control and eradicate infectious diseases, none could bring any landmark changes. Geographical overlap of infectious diseases with similar clinical presentations, re-emergence of past endemic and rare infectious diseases, high prevalence of antimicrobial resistant pathogens adds on further complexity. One of the major challenges faced by healthcare centers in India, when dealing with infectious diseases, is the  lack of timely identification. We provide a direct-from-sample, on-site sequencing to simultaneously identify bacteria, fungi and antibiotic resistance genes from clinical samples coupled with a real-time epidemiological dashboard as a comprehensive solution. Robust and easy-to-interpret real-time epidemiological data depicting geographical distribution of pathogen burden, can be used to promptly manage patient therapy, resource utilization and disseminate preventive measures to the general public to contain the spread of the infection.Empowering healthcare centers on prevalent infections in distinct geographical spaces can ensure sufficient supply of medical resources in tandem with the prevalent infection and implementation of preventive measures to combat the spread of infection.  To implement these short-term and long-term action points, we need evidence-driven data on the causative pathogens, associated antimicrobial resistant genes, transmission trends, geographical distribution of the pathogens. 

Physicians and medical personnel will directly benefit from the dashboard as it provides an on-ground solution to manage infectious diseases. NGS-based data used in the dashboard assures the accuracy and validity of the data. Real-time reporting ensures that the physicians have immediate access to the prevalence and incidence of infectious diseases present in distinct geography. The dashboard would be extremely beneficial, if an area is prone to multiple infectious agents with overlapping clinical presentations. Such data enables streamlining of therapy, increases awareness of the disease in the masses and formulates evidence-based AMSP and hospital infection control. 

Patients have a huge benefit as they are provided with appropriate antimicrobial therapy, preventing unnecessary health burden from the usage of empirical antibiotic therapy, negating extended hospital stays and will have improved health outcomes.

With a predictive value to the analysis, the data will inform decision-makers on geographical location for interventions, identify high risk groups, allocate resources based on need, formulate action points to be implemented at specific healthcare centers at distinct geographical locations. An informative and verified database with quick data analytics and graphic representation accessible to the public,  can lead to transparent, effective and actionable infection control measures. 

 Our solution will aid in early detection of causative pathogens and associated ARGs, aiding clinical decision making and improving patient outcomes. 

Pathogens and associated ARGS identified from patient samples will aid in better adherence to AMSP and hospital infection control.

Data obtained from the genome sequencing center will be uploaded to a free-to-use dashboard that can be used by policy makers to implement better intervention schemes, preventive and control measures.

Significant findings will be integrated into peer-review publication.

The solution is expected to have a tangible impact on the infectious disease diagnostics.Through our genome sequencing centers(GSC), we  aim to enable tertiary care centers to perform NGS-based tests as part of routine clinical workflow. This would provide clinicians with a versatile tool for infectious disease diagnosis and aid in clinical decision making. This will lead to reduced economic and health burden of patients with infectious disease as appropriate therapy is initiated promptly and unnecessary antibiotic administration is discontinued. The data from the GSCs will be fed to the dashboard, providing real time information on prevalent disease and ARGs present for the particular geography. This would further inform on prevalence, incidence, transmission dynamics of both the pathogen and associated ARGs, leading to efficient and effective policymaking.

Impact over next year would be assessed by successful implementation of genome sequencing centers  in alteast  5 tertiary health care centers with at atleast 3-5 infexn test being done per day. Impact of infexn test within these tertiary centre will be assessed by the clinical findings such as concordance with culture and other serological tests, adjudication with clinical symptoms and impact on  treatment regimens and duration of hospital stays. 

The test results of the infexn test will be used for data analysis and real time dashboard. 

A pilot implementation of realtime dashboard across these five centers. 

These findings will be disseminated through peer reviewed journals. 

Next three years

Successful implementation of genome sequencing centers and infexn testing in primary and secondary healthcare center within India.

Upgrade and streamline real time dashboard with insights obtained from the pilot studies. 

Expand the solution to atleast 1 other LMIC. 

These findings will be disseminated through peer reviewed journals. 

a. To evaluate the operationability of performing infexn by integrating infexn into clinical setting and workflow.

Measurable outcome: 

1. Implementation of genome sequencing center at tertiary healthcare center.

2. Perform at least 3-5 samples per day in each center. Expand the sample type to include more sterile body fluids, joint fluids, tissue biopsy etc

b. Evaluate the clinical utility of implementing infexn tests at tertiary healthcare centers.

Measurable outcomes: 

1. Evaluate the accuracy of infexn test results by comparing with culture and serological tests routinely performed at the hospital and also by correlating to clinical symptoms. 

2. Impact of infexn in changing treatment regimens and reducing the duration of hospital stay. 

3. Realtime Dashboard: Implement a realtime dashboard by incorporating data obtained from the tertiary healthcare center.

Major barriers involved in implementation of infexn at tertiary care hospitals is lack of awareness on NGS based testing and its clinical utility and importance among physicians. This barrier is being overcome by conducting webinars and scientific binders discussing the utility of NGS in Clinics. 

Our test can be expanded to include various sample types such as joint fluid, population group such as neonates and pathogen group such as viruses as well increase the coverage of ARGs. We require funding for R&D activities to upgrade our solution. Further funding will be required for equipment and reagent procurement and operational activities. We are pursuing grants and investment for the same.

The trinity  AMR Challenge is well aligned with our goal of combating the global threat of AMR through big data analytics especially in India. With the funding we will be able to expand our solution to include more geographical localities including rural regions within India and outside India.

The solution uses a strategy of on-site testing and evaluation in order to minimise turn around time.Challenges around ease of workflow implementation and impact on routine use need to be addressed which can vary across different geographies. The epidemiology and trends of infectious disease can vary and need to be addressed accordingly. This can be addressed through pilots in varied settings and geographies.With enhanced funding we would be able to scale up our implementation sites. 

Challenge funding will be used to further used strengthen our infrastructure, logistics, operations and data management and analytic platforms.

With trinity challenge, we look forward to establishing meaningful and fruitful collaborations that can strengthen our workflow and modalities. We hope to get mentoring and guidance on advanced scientific and technical aspects and reachout to international experts and markets. 

We envision to  effectively contribute to tackle AMR which requires sound scientific expertise. Collaborators with academic institutes such as   Imperial College, and University of Oxford with profound expertise in infectious disease and NGS and can help provide mentorship and scientific advisory to fine-tune our solution to be an efficient and effective solution across the globe. This would also enhance knowledge sharing and facilitate international collaboration.

Collaboration with aws, Google and Microsoft will gretly enhance in upgrading and strengthening our analytic platform ensuring tight security towards data privacy and enhancing data storage, management and analysis.

We would like to further collaborate with Indian Council of Medical Research(ICMR). As a well-established organization involved in constant generation of public health data and engaged in directly in formulating public policies and guidelines, association with ICMR will aid in rapid dissemination of our solution and its results to a wider audience.