High-Priority Pathogens in Nepal
Nepal’s current landscape of high-priority pathogens is
undergoing a significant transition toward granular, laboratory-based
surveillance and the implementation of a One Health framework. Under the Public
Health Service Act (2075 BS), the Ministry of Health and Population has formally
gazetted 52 priority infectious diseases, strengthening the national
reporting system and standardizing disease monitoring. From a
microbiological and epidemiological perspective, the current focus centers on
three major challenges: the accelerating burden of antimicrobial resistance
(AMR), the geographic expansion of vector-borne diseases, and the persistent
risk of zoonotic spillover. Together, these factors underscore the need for
coordinated surveillance, rapid diagnostics, and cross-sectoral collaboration.
Priority Bacterial Pathogens and AMR Dynamics
The National Public Health Laboratory (NPHL) currently
monitors 12 priority bacterial pathogens through a network of 26 sentinel
sites. Data indicates that the ESKAPE group, specifically Acinetobacter spp., Klebsiella
pneumoniae, and Escherichia coli represents
the highest clinical concern due to multi-drug resistance (MDR) phenotypes.
Acinetobacter
species: These isolates exhibit the highest resistance
levels in Nepal, with a 72% prevalence of MDR, frequently associated with
ventilator-associated pneumonia in intensive care settings.
Klebsiella
pneumoniae: Approximately 56% of isolates are MDR, with
an alarming increase in resistance to carbapenems, the current
"last-resort" antibiotic class.
Escherichia
coli: Predominantly responsible for urinary tract infections,
over 51% of isolates are MDR, and 45.6% are presumptive ESBL(Extended –spectrum
beta lactamase) ESBL- producers.
Emerging Resistance: We
are tracking a rise in Pan-Drug Resistance (PDR), defined as resistance to all
available antimicrobial categories, as well as fluoroquinolone-resistant Salmonella Typhi, which complicates the
management of Nepal's high typhoid burden.
Vector-Borne and Emerging Pathogens
Climatic shifts are driving Aedes and Phlebotomus
vectors into hilly and mountainous regions that were previously considered
non-endemic. As a result, Dengue has transitioned into a perennial public
health threat, with the 2022 epidemic reporting over 53,000 cases nationwide. Similarly,
Scrub Typhus caused by Orientia
tsutsugamushi has emerged as a high-frequency morbidity factor in weekly
EWARS reports, particularly in Sudurpaschim and Lumbini provinces. While Nepal
aims for Malaria elimination by 2025, the porous border facilitates the
importation of Plasmodium falciparum,
which remains a significant hurdle.
Zoonotic Priorities and One Health
Over 60% of infectious diseases affecting humans in Nepal
are estimated to be zoonotic in origin, underscoring the importance of a
coordinated One Health approach, In response, the government has
prioritized a set of key zoonoses, including Rabies, Avian Influenza and
Japanese Encephalitis. Rabies remains 100% fatal and causes approximately 100
human deaths annually, though the introduction of Integrated Bite Case
Management (IBCM) is improving post-exposure prophylaxis (PEP) delivery.
Strategic National Response to combat AMR
Nepal is currently implementing the National Action Plan on
AMR (2024–2028), which emphasizes five strategic pillars: awareness,
surveillance, infection prevention and control (IPC), rational use and research
investment.
Critical surveillance and policy milestones
include:
Real-time digital tools: The
transition to SORMAS and the expansion of EWARS to 134 sentinel sites.
Regulatory mandates: The
"red line" initiative on antibiotic packaging to prevent
over-the-counter sales and the prohibition of antibiotics in poultry feed.
Capacity Assessment: The
2022 Joint External Evaluation (JEE) assigned Nepal a score of 3/5 for AMR
capacity, highlighting the need for stronger subnational laboratory
infrastructure.
One Health Integration: The
SPEED project and the Fleming Fund support are currently enhancing genomic
sequencing and molecular surveillance for high-consequence pathogens.
The spatial distribution of these 52 priority infectious
diseases pathogens demonstrates significant provincial variation, shaped
by ecological niches, population density, and border dynamics. As researchers,
we utilize the Early Warning and Reporting System (EWARS) and the Annual Health
Report to track these granular shifts across the seven provinces.
Provincial Epidemiological Profiles
Koshi Province has
emerged as a critical site for Dengue virus transmission, reporting
8,102 cases in the most recent fiscal year. Furthermore, our surveillance
indicates a worrying trend of Kala-azar (Visceral Leishmaniasis) expansion into
hilly districts, with 51 cases recently confirmed in areas previously considered
low-risk.
Madhesh Province bears
a disproportionate burden of chronic bacterial infections. It reports the
highest prevalence of Leprosy in the nation (1.4 cases per 10,000
population) and remains a high-transmission zone for Tuberculosis. The
province’s long, porous border with India facilitates the constant
"spill-over" and importation of pathogens, complicating regional
elimination targets.
Bagmati Province,
specifically the Kathmandu Valley, serves as the nation’s primary Dengue
hotspot, accounting for 8,382 cases in the latest reporting cycle.
Microbiological data from the National Public Health Laboratory (NPHL) shows
that this province also manages the highest volume of HIV viral load testing
(26% of national samples), reflecting its role as a centralized hub for
specialized clinical care.
Gandaki Province is a
key area for monitoring the altitude expansion of vector-borne diseases.
While it reported 5,846 Dengue cases, it also demonstrates the highest success
in public health interventions, achieving a 116% full immunization coverage for
children, which is vital for controlling vaccine-preventable pathogens.
Lumbini Province has
become the national epicenter for Scrub Typhus (Orientia tsutsugamushi),
reporting a staggering 4,322 cases, the highest in Nepal. Our
micro-stratification data also identifies 11 "high-risk" wards for
Malaria in this province, necessitating intensive vector control and
longitudinal surveillance.
Karnali Province faces
unique challenges due to its rugged geography and limited infrastructure. It
currently reports the highest number of Kala-azar cases (58) and suffers from a
high incidence of pediatric diarrhea (250.8 cases per 1,000 children under
five), signaling a critical need for improved Water, Sanitation, and Hygiene
(WASH) interventions.
Sudurpashchim Province
mirrors the rickettsial trends seen in Lumbini, with 3,746 reported cases of
Scrub Typhus. It also contains 9 wards categorized as "high-risk" for
Malaria, with a significant proportion of cases being imported Plasmodium
falciparum.
Research-Driven Future Outlook
To combat these threats, Nepal is operationalizing the
National Action Plan on AMR (2024–2028) and the One Health Strategy. By
integrating human, animal, and environmental surveillance; including the
Tricycle Project for ESBL E. coli and
genomic sequencing through the SPEED project; we are moving toward a
precision-based public health model. The introduction of the Typhoid Conjugate
Vaccine (TCV) and the "red line" initiative on antibiotic packaging
are pivotal steps in reducing the pathogen burden and preserving our
antimicrobial arsenal.
Ultimately, the goal of the Nepalese microbiological
community is to transition from reactive outbreak management to a proactive,
evidence-based system of national health security.
Our transition from phenotypic screening to molecular and
genomic characterization marks a significant advancement in Nepal’s ability to
map the "resistome”; the collection of all resistance genes; circulating
within our borders. As researchers, we are moving beyond simply identifying
which drugs fail to work; we are now pinpointing the specific genetic
mechanisms, such as carbapenemase and ESBL genes, that drive these resistance
patterns across human, animal, and environmental sectors.
Integrated Molecular Surveillance: The Tricycle
Project
One of the most critical milestones in our molecular
mapping was the recent completion of the Tricycle Project. This World Health
Organization (WHO)-led initiative focused on the integrated surveillance of
ESBL-producing Escherichia coli
across three sectors: humans (hospital and community), food-producing animals,
and the environment (surface water).
Microbiological data from this project and subsequent
surveillance in FY 2080/81 reveal that 45.6% of E. coli isolates in Nepal are now presumptive ESBL producers. At
the molecular level, our laboratories are specifically screening for the
following "High-Priority" resistance genes:
ESBL Genes: The blaCTX-M group
remains the dominant genotype identified in clinical isolates from provinces
with high hospital density, such as Bagmati and Koshi. We also routinely
monitor for blaSHV and blaTEM variants.
Carbapenemase Genes: To
address the rising resistance to last-resort carbapenems in Klebsiella pneumoniae and Acinetobacter, we are targeting blaNDM
(New Delhi Metallo-beta-lactamase), blaOXA-48-like, and blaKPC (Klebsiella pneumoniae carbapenemases) genes.
These genes are frequently detected in isolates from intensive care units
(ICUs) in the Kathmandu Valley.
MRSA Identification: The
molecular confirmation of Methicillin-resistant Staphylococcus aureus is performed by detecting the mecA or mecC
genes, which is vital for pediatric and surgical ward safety.
Genomic Sequencing and the SPEED Project
The launch of the Strengthening Pandemic Preparedness for
Early Detection (SPEED) project in 2024 has further enhanced our molecular
capacity. Under this framework, NPHL is expanding Whole Genome Sequencing (WGS)
capabilities to track the transmission dynamics of high-consequence pathogens.
By sequencing the entire genetic code of a pathogen, we can now determine if an
outbreak of MDR Acinetobacter in a
provincial hospital is due to a single "superbug" strain spreading
between patients or multiple independent resistance events.
This genomic data is being integrated with our digital
surveillance tools, such as SORMAS and EWARS, to provide a real-time,
high-definition view of how resistance genes are migrating across provincial
borders.
Provincial Molecular Infrastructure
The distribution of molecular diagnostic capacity is
currently being decentralized to improve national health security.
Bagmati Province (NPHL): Serves as the national hub for
genomic sequencing and high-tier molecular assays, including DNA PCR for early
infant diagnosis of HIV.
Koshi and Madhesh Provinces: Are
seeing expanded environmental surveillance and molecular screening for
waterborne pathogens like Vibrio cholerae
and Salmonella Typhi.
Sudurpashchim and Gandaki:
Recently expanded their sub-national laboratory capacity for Measles-Rubella
(MR) and other vaccine-preventable diseases, utilizing molecular tools to
confirm transmission interruption.
