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CERI › Research Focus Areas › AMR
01

Antimicrobial
Resistance

AMR Research

Bringing together genomics, microbiology, and epidemiology to investigate how antimicrobial resistance emerges and spreads — protecting the effectiveness of life-saving medicines across Africa and globally.

Genomic Surveillance
Resistant Pathogens
Tracking Tools
AMR Policy
One Health
AMR Surveillance Index
 

Live Tracking

 
Klebsiella pneumoniae
 
82%
 
E. coli (ESBL)
 
79%
 
S. aureus (MRSA)
 
61%
 
Acinetobacter baumannii
 
88%
 
N. gonorrhoeae
 
55%
5
Priority Pathogens
12+
Countries
80+
Publications
// Research Focus

What the Team
Investigates

FOCUS · 01
Genomic Surveillance

Sequencing resistant pathogens to track the emergence, spread, and evolution of AMR genes across health systems and communities.

WGS Metagenomics Phylogenomics
FOCUS · 02

 

Resistance Tracking Tools

Developing computational tools and dashboards to monitor AMR trends, visualise resistance patterns, and support real-time surveillance.

AMRFinder
ARIBA
Dashboards
FOCUS · 03

 

Microbiology & Phenotyping

Characterising resistant isolates through laboratory-based phenotypic testing to complement and validate genomic findings.

MIC Testing
Disk Diffusion
Culture
FOCUS · 04

 

One Health AMR

Investigating resistance at the human-animal-environment interface to understand cross-species transmission and environmental reservoirs.

Zoonotic AMR
Agriculture
Environment
FOCUS · 05
Policy & Health Systems

Generating evidence to support national AMR action plans, antibiotic stewardship programmes, and health system strengthening.

NAP Stewardship IPC
FOCUS · 06
Regional Collaboration

Partnering with African health ministries, WHO, and international networks to build continent-wide AMR surveillance capacity.

Africa CDC WHO GLASS GARDP
// Research Workflow

From Sample
to Policy

STEP · 01

 

Sample Collection

Clinical, environmental, and animal samples collected through surveillance networks and health facility partnerships.

→
STEP · 02

 

Lab & Phenotyping

Culture, susceptibility testing, and MIC profiling to characterise resistance patterns phenotypically.

→
STEP · 03

 

Genomic Sequencing

Whole genome sequencing to identify resistance genes, mobile elements, and phylogenetic relationships.

→
STEP · 04

 

Bioinformatic Analysis

AMR gene detection, plasmid typing, and phylogenomic analysis using validated computational pipelines.

→
STEP · 05

 

Evidence & Policy

Findings translated into publications, surveillance reports, and actionable policy recommendations.

// Priority Focus
 

Organisms Under
Surveillance

 
Klebsiella pneumoniae Carbapenem-resistant (CRKP)
A leading cause of hospital-acquired infections with rising carbapenem resistance, tracked through genomic surveillance networks.
Critical
 
Escherichia coli Extended-spectrum β-lactamase (ESBL)
ESBL-producing E. coli monitored across community and clinical settings for transmission dynamics and resistance gene spread.
High
 
Staphylococcus aureus Methicillin-resistant (MRSA)
MRSA surveillance across healthcare facilities with whole-genome sequencing to map outbreak clusters and clonal lineages.
High
 
Acinetobacter baumannii Multidrug-resistant (MDRAB)
Tracked in ICU settings with genomic tools to understand transmission routes and the evolution of pan-drug resistance.
Critical
 
Neisseria gonorrhoeae Multidrug-resistant (MDR-GC)
Sexually transmitted AMR pathogen with diminishing treatment options, monitored through sentinel surveillance sites.
Medium
// Working With
 

Research &
Partner Network

Bioinformatics Unit

Developing and running AMR gene detection pipelines and genomic analysis workflows.

CERI Lab

Performing culture, susceptibility testing, and sequencing of clinical and environmental isolates.

Africa CDC / WHO

Contributing data to continental AMR surveillance platforms including WHO GLASS.

Health Ministries

Partnering with national health departments to implement AMR action plans and stewardship programmes.

// The People

Meet the
Team

// Research Output
 

Latest
Publications

2026
Evaluation of DNA extraction methods from clinical Mycobacterium tuberculosis primary liquid culture for whole-genome sequencing

Conceicao E, Haffejee M, Wells F, Mann B, Heupink T, Paulse A,…

BMC Genomics

View DOI PDF
2026
Targeted and whole-genome sequencing for drug resistance and genetic relatedness inference of rifampicin-resistant Mycobacterium tuberculosis: an in-depth comparison

de Diego Fuertes M, Costa Conceição E, Wells F, Rennie V, Heupink…

ERJ Open Research 12:00630-2025

View DOI
2025
Genomic Surveillance of Climate-Amplified Cholera Outbreak, Malawi, 2022–2023

Chabuka L, Choga W, Mavian C, Moir M, Morgenstern C, Tegaly H,…

Emerging Infectious Diseases 31(6):. doi: 10.3201/eid3106.240930.

View DOI PDF
2025
Unveiling novel features and phylogenomic assessment of indigenous Priestia megaterium AB-S79 using comparative genomics

Adeniji A, Chukwuneme C, Conceição E, Ayangbenro A, Wilkinson E, Maasdorp E,…

Microbiology Spectrum doi: 10.1128/spectrum.01466-24.

View DOI PDF
2022
Tuberculosis drug resistance profiling based on machine learning: A literature review

Sharma A, Machado E, Lima K, Suffys P, Conceição E

The Brazilian Journal of Infectious Diseases 26:102332

View DOI PDF