Transforming AMR surveillance in Nepal through data automation

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Antimicrobial resistance (AMR) data is vital for informing local interventions, enabling hospitals to improve infection control and treatment strategies. With Fleming Fund Country Grant investment, the Robotic Process Automation technology was introduced − now operational in 23 out of 26 hospitals − to support Nepal’s AMR national surveillance network.

Before, hospitals in Nepal used the Laboratory Information Management Systems (LIMS) software for data recording. This process of managing and extracting data for sharing with the National Public Health Laboratory (NPHL) remained time-consuming and labour-intensive, resulting in delays and pressure on staff.

The ‘bot’ innovation automates repetitive data tasks for national and international reporting, streamlining data management and drastically reducing the time taken at AMR surveillance sites for reporting and generating critical insights.

(Above): Jyoti Acharya (right), Chief Medical Laboratory Technologist at Bir Hospital, Nepal’s oldest tertiary-level government hospital, mentor's microbiologist Sanju Maharjan (left) in bacterial culture techniques using an agar plate. Credit: Angad Dhakal, FHI360.

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Nepal’s AMR surveillance efforts faced obstacles due to disjointed data collection and reporting, making accurate assessments of the AMR burden and policy decisions difficult. Progress was made by implementing a structured national AMR surveillance system, supported by the Fleming Fund and implemented by FHI360.

The Fleming Fund supported the NPHL as the central hub for AMR, with data collected from 26 surveillance sites. This has been crucial in shaping policy reforms, laboratory guidelines, infection prevention and control policies, and initiating hospital Antimicrobial Stewardship programmes. Nepal also contributes AMR and antimicrobial use data to the Global Antimicrobial Resistance and Use Surveillance System (GLASS) to facilitate evidence-based decision-making at local, national, and global levels.

Challenges in AMR reporting

Kanti Children’s Hospital and Bir Hospital are high-level facilities among the busiest in the country’s AMR surveillance network. Bir hospital, the oldest hospital in Nepal, and Kanti provides specialised care, advanced diagnostics, and are referral centres for primary and secondary care facilities. Both had LIMS to digitise laboratory data from paper records, with teams extracting and managing data according to national reporting requirements.

At Kanti Children’s Hospital, medical laboratory technologist Gyani Singh and her team handle around 200 patient samples daily, performing analyses that generate individual patient test results. They also submit AMR data to NPHL, ensuring that critical information from each sample is accurately recorded.

The Bir Hospital team, led by Chief Medical Laboratory Technologist Jyoti Acharya, processes over 300 patient samples daily with a similar system in place. LIMS enabled the hospitals to record comprehensive patient and test information, pathogen presence, and Antimicrobial Susceptibility Testing (AST) data.

While the software streamlined report generation, it was unable to adequately compile data for national reporting. To submit the required data for AMR surveillance to NPHL, the arduous process often took two to three days each month.

“The heavy workload resulted in no data being submitted, leaving key information unreported. Collecting AMR data in pediatric hospitals is crucial for understanding AMR patterns in children, who are a particularly vulnerable population,” said Gyani.

Transformation with Bot integration

The system retrieves data directly from the hospitals’ LIMS and categorises and analyses AMR samples. This automation has significantly reduced manual data entry, enabling timely submissions to NPHL and allowing Gyani’s team to concentrate on critical laboratory functions.

“The process was extremely stressful and took valuable time away from our main laboratory work. What previously took over a week is now completed in minutes,” said Singh. “The bot has been a tremendous relief; it facilitates timely data submission and garners recognition for our efforts. With regular and prompt data sharing, we receive immediate feedback on data quality from NPHL, helping us maintain accuracy and improve reporting.”

At Bir Hospital, Acharya's team has experienced remarkable improvements. The bot now processes daily data in minutes for reporting as needed. “Before the bot, it took us days to prepare data for reporting. This automation has empowered the team to multitask effectively, allowing them to focus on vital microbiology work while ensuring accurate data,” said Acharya.

AMR surveillance and evidence

By significantly reducing the burden of data extraction and categorisation, the bot has enabled laboratory teams to focus on quality assurance and error reduction in sample testing - improving reporting nationally and for GLASS submissions.

At Bir Hospital, the bot’s ability to systematically manage raw data has elevated the hospital’s role in data generation. AST data from Bir and other sites have informed the national antimicrobial treatment guidelines, drug policies, guided antimicrobial stewardship programmes, and infection prevention and control efforts.

The data allows hospital management to implement infection prevention and hospital cleanliness strategies when healthcare associated infections rise or to advise government bodies when community acquired infections surge. For example, “providing evidence that helps the government develop strategies for infection control, working with Water, Sanitation and Hygiene projects to take a holistic approach,” said Acharya.

Adaptation and sustainability

The bot’s user-friendly design required minimal training. Safeguards were implemented to protect data confidentiality, which helped build trust in the system and facilitated its smooth adoption across sites.

The underlying challenge lies in sustaining the bot beyond the Fleming Fund Country Grant in Nepal (FFCGN)'s project support. The hospitals’ capacity to maintain and support this technology will prove essential to AMR surveillance – system updates may require some modifications to the bot to ensure compatibility.

Project Director at FHI 360, Dr Ritu Amatya, said: “The bot's success highlights the importance of developing sustainability plans and preparing for technological adaptations and how such partnerships can improve AMR surveillance in Nepal, and strategies to ensure the longevity of these advancements.

“Most importantly, we need to create systems that turn standardised data into meaningful insights, guiding decisions and actions to further strengthen AMR surveillance in Nepal and significantly improve our healthcare systems.”