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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
Whole genome sequencing precision medicine strategy to shorten treatment for rifampicin-resistant tuberculosis (SMARTT): a pragmatic, randomised, single-blind phase 4 trial

Van Rie A, Conceição E, Ndebele F, Wells F, Paulse A, Mekonnen…

The Lancet Respiratory Medicine 14:521-532

View DOI
2026
Draft genome sequence of Legionella pneumophila strains isolated from engineered water systems in Brazil

de Melo Ferrari D, Machado E, Conceição E, Sharma A, Lima S,…

Microbiology Resource Announcements 15:e0133225

View DOI PDF
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