Background
GeneXpert machines are the frontline of TB diagnosis in Nepal. Manufactured by Cepheid, these automated molecular diagnostic devices can detect Mycobacterium tuberculosis and rifampicin resistance (a key marker for drug-resistant TB) in under 90 minutes — far faster than traditional culture methods that can take weeks.
Nepal's national TB programme has deployed GeneXpert machines across the country, from central referral hospitals in Kathmandu to district health facilities in remote hill and mountain regions. Each machine runs multiple cartridge-based tests per day, generating results that directly inform patient treatment decisions.
The problem: there was no central system to monitor these machines.
Whether a machine was running, broken, out of cartridges, or sitting inactive in a storeroom — the National Tuberculosis Control Centre (NTCC) had no real-time visibility. Programme managers relied on phone calls and emailed spreadsheets. Cartridge stock levels were unknown until facilities called to say they had run out. Machines with high error rates — a sign of technical problems or improper use — went undetected for months.
Hello World was engaged to fix this.
What We Built
The GeneXpert Management Information System (GXMIS) is a web-based platform built on Django REST Framework, React, and PostgreSQL, deployed on the NTCC's virtualized server infrastructure in Kathmandu. It serves as the single source of truth for everything GeneXpert-related across Nepal's TB programme.
Core Features
Machine Registry
The foundation of GXMIS is a complete registry of every GeneXpert machine in the country. For each machine, the system tracks:
- Serial number and module count — GeneXpert machines have 4, 16, or 48 modules; each module can run a test simultaneously
- Location — linked to Nepal's geographic hierarchy: Province → District → Municipality → Facility
- Operational status — Active, Inactive, Under Repair, Decommissioned
- Installation date and warranty information
- Module-level history — individual module replacements and repairs are tracked separately from the machine body
This registry replaced the spreadsheets that had previously been the only record of the country's GeneXpert fleet.
Real-Time Test Result Dashboard
GeneXpert machines generate result files automatically when a test completes. GXMIS collects these result files from machines at each site and parses them into the central database. The dashboard gives NTCC programme staff real-time visibility into:
- Test volume by site — how many tests are being run per day, week, and month at each facility
- Result breakdown — MTB Detected (High/Medium/Low/Trace), MTB Not Detected, Invalid, Error, No Result
- Rifampicin resistance — proportion of MTB-positive results with RIF resistance, by site and period
- Xpert MTB/XDR results — for facilities running the newer XDR cartridges that detect additional drug resistance markers
- Cartridge type utilisation — Xpert MTB/RIF, MTB/RIF Ultra, and XDR cartridges tracked separately
Programme managers can drill from national overview down to a single facility's daily result log in a few clicks.
Machine Status Monitoring and Alerts
One of the most practically useful features of GXMIS is automated machine status monitoring. The system flags:
- Inactive machines — facilities where no test results have been received for a defined period (configurable, typically 7 days)
- High error rates — machines where more than a threshold percentage of tests are returning Error or Invalid results
- Module failures — individual modules within a machine that are consistently generating errors
When these conditions are detected, GXMIS generates alerts. GeneXpert Focal Persons — district and provincial staff responsible for maintaining machines — receive automated SMS notifications with the facility name, machine serial number, and the specific issue detected.
This alone represented a significant operational improvement. Previously, a machine could sit broken for weeks before anyone at NTCC knew. Now, programme staff are notified within 24 hours.
Cartridge Stock Tracking
Each GeneXpert test consumes one cartridge. Cartridges are expensive and have expiry dates — poor stock management leads to either stock-outs (patients turned away) or waste (expired cartridges discarded). GXMIS tracks:
- Cartridges received at each facility
- Cartridges used per period (derived from test result counts)
- Estimated stock remaining
- Error cartridge rate — cartridges that produced an Error result, which may indicate storage or handling issues
Facilities with low projected stock receive automated notifications before they run out.
Ticket Management System
When a GeneXpert machine has a technical problem, someone needs to know and act. GXMIS includes a lightweight issue ticketing system where facility staff can log machine problems — error codes, mechanical issues, network connectivity failures — and track resolution status. NTCC's technical team and GeneXpert Focal Persons can assign, update, and close tickets, creating a documented maintenance history for each machine.
Manual Result Upload
Not all GeneXpert sites have reliable internet connectivity for automatic result file transfer. For these facilities, GXMIS provides a manual upload interface where site staff can upload GeneXpert result export files on a periodic basis — weekly or monthly — when they have connectivity. The system processes these files identically to automatic uploads, ensuring all sites are represented in the national data regardless of connectivity.
Report Generation
GXMIS generates a set of standard reports aligned with NTCC and HMIS reporting requirements:
- MTB/RIF Summary Report — aggregate positive and RIF-resistant counts by site and period
- GeneXpert Site Activity Report — test volumes and machine utilisation rates
- Cartridge Usage and Error Rate Report — for supply chain and quality assurance purposes
- Module History Report — maintenance and replacement records per machine
Reports are exportable as PDF and Excel, designed to match the formats NTCC uses for national and international TB programme reporting.
Technical Architecture
Server Infrastructure
GXMIS runs on the NTCC's server infrastructure in Kathmandu, virtualised using Proxmox. The virtualisation layer allows multiple services — GXMIS, the DHIS2 instance, and the eTB server — to share physical hardware while remaining isolated from each other. Nginx serves as the reverse proxy with SSL/TLS termination, handling routing between the virtualised services.
The virtualised architecture also simplifies disaster recovery: a full snapshot of the GXMIS VM can be restored in minutes if hardware fails.
Data Flow from GeneXpert Machines
GeneXpert machines save test result files to a local Windows computer at each facility. A lightweight data agent running on that computer periodically reads new result files and transmits them to the GXMIS API over HTTPS. Result files are parsed server-side — extracting patient ID, test type, cartridge type, result, error codes, and timestamps — and stored in PostgreSQL.
For sites with poor connectivity, the agent queues unsent files and retransmits when connectivity is restored, ensuring no results are permanently lost due to transient network issues.
Patient Demographic Mapping
GXMIS links test results to patient demographic data — age group, sex, and geographic location — enabling disaggregated reporting by population group. This linkage supports the TB programme's obligation to report results broken down by sex and age in alignment with WHO TB reporting standards and Nepal's HMIS requirements.
What Changed for the Programme
Before GXMIS, getting a picture of GeneXpert utilisation across Nepal required emailing district offices, waiting for replies, and manually compiling spreadsheets. The process took days and the data was always at least a week old.
After GXMIS, the national TB programme manager can open a browser and see:
- How many TB tests were run yesterday, by district
- Which machines have been inactive this week
- Whether the new XDR cartridges deployed to provincial hospitals are being used
- Which sites have fewer than two weeks of cartridge stock remaining
This shift from retrospective to real-time monitoring changed how the programme operates. Site visits are now targeted at facilities flagged by the system, rather than scheduled by rotation. Cartridge procurement is informed by actual consumption data rather than annual estimates.
Lessons from Building a Nationwide Monitoring System
Connectivity is the hardest problem. Designing for intermittent connectivity — where a facility might be offline for days — requires careful thinking about data queuing, conflict resolution, and what "real-time" actually means in practice.
Adoption requires visible value. GeneXpert Focal Persons started using GXMIS consistently only after they received their first SMS alert about a broken machine in their district before the facility had even called them about it. The system had to prove it knew things before they did.
Machine serial numbers are messier than you expect. Machines are moved between facilities, modules are swapped, and records are incomplete. Building a reliable machine registry required field verification visits as well as data cleaning — the data you receive is not the same as the data you need.
Reports must match existing formats exactly. Early versions of GXMIS generated reports that were technically correct but formatted differently from what NTCC submitted to the WHO. We had to rebuild report templates to match the established column order, terminology, and aggregation logic that programme staff already knew how to interpret.
Where GXMIS Stands Today
GXMIS is now the operational system for GeneXpert monitoring across Nepal's national TB programme. It has gone through multiple development cycles, with each phase adding capability based on operational experience — the Xpert MTB/XDR module, the improved dashboard filters, and the Focal Person notification system were all added in response to programme team feedback after initial deployment.
The system continues to evolve alongside the TB programme itself — as new GeneXpert cartridge types are introduced, as the machine fleet expands to more facilities, and as reporting requirements change with each cycle of national and international TB programme standards.
If your national programme or research institution is looking to centralise monitoring of diagnostic equipment or laboratory systems, we are happy to talk through what a system like GXMIS would look like for your context.
Get in touch with Hello World.
Hello World IT Solutions specialises in custom health information systems, DHIS2 implementation, and laboratory data management for national health programmes across Nepal and South Asia.