Global AMR Surveillance Projects

About AMR surveillance projects

AMR surveillance projects is a database of current and past surveillance, and epidemiology of drug-resistant infections projects carried out by SEDRIC members. These projects cover a wide variety of topics, including, but not limited to surveillance, epidemiology, microbiology, mathematical modelling, diagnosis, data science, data governance, health systems, health policy, health economics, veterinary medicine, social science, policy development and public engagement.

How to submit an AMR surveillance project

Submit a project by completing the project submission form.

Showing 5 out of 5 current projects
Molecular epidemiology of carbapenemase-producing Enterobacteriaceae (CPE) circulating in the public healthcare sector in KwaZulu-Natal, South Africa (2016-2026)
01 September 2020 – 01 September 2026
South Africa

Topic(s) Epidemiology and surveillance, Microbiology, “One Health”

Author(s) Principal Investigator Dr Yogandree Ramsamy Co Investigators: Dr S Maphumulo, Dr R Singh, Dr A Niehaus, Dr NR Mvelase, Dr K Lutchminarain, Dr P Bhola, Dr P Ramjathan, Dr Y Mahabeer, Dr P Mahabeer, Dr S Haffejee, Dr L Sookan, Dr Khine Swe Swe Han (Senior author, HoD)

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Project description
Multi-drug resistant (MDR) organisms are a global phenomenon that threatens the future management of serious infections. Infections caused by CPE, have emerged as one of the world’s greatest health threats. A few published studies report the existence of CPE in Africa but in general, there is no complete surveillance dataset that describes the molecular epidemiology of CPE and its burden on the African health care system. Surveillance cultures are recommended for detecting CPE as the prompt identification of CPE carriers forms an integral part of the interventional strategies and infection control measures required to curb the global threat of hospital infections due to CPE.

1. To determine the molecular epidemiology of CPE in KwaZulu-Natal over a 10 year period (January 2016- December 2026).
2. To establish the prevalence of CPE within a specific geographical location in Africa.
3. To determine the most prevalent CPE in KwaZulu-Natal, South Africa.

Study implications
1. To provide scientific evidence to determine the molecular epidemiology and geographical distribution of CPE in KwaZulu-Natal, South Africa.
2. The evidence generated will assist in informing future empiric antibiotic prescribing for suspected CPE infections. Newer antibiotic agents are active against certain CPE molecular types.

Funding and affiliations
1. Institute Mérieux-ICAN Young Investigator Award in Antimicrobial resistance (AMR).
2. Department of Medical Microbiology, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
National Health Laboratory Service, Durban, South Africa

Molecular Epidemiology and Antimicrobial Resistance Determinants of Neisseria gonorrhoeae in Kampala, Uganda
11 December 2019 – 30 June 2022

Topic(s) Genomics, Epidemiology and surveillance

Project description
The project aim is to elucidate the genomic epidemiology and antimicrobial resistance determinants associated with NG among the strains circulating in Kampala Uganda. The specific aims are as follows;
• To describe the NG AMR Surveillance Programme in Kampala, Uganda and the emerging phenotypic antimicrobial susceptibility data generated using E-test
• To determine the genomic epidemiology of NG strains circulating in Kampala, Uganda using WGS and compare findings with behavioural, demographic and clinical data
• To identify the molecular AMR determinants associated with decreased susceptibility and/or resistance to NG using WGS and correlate with phenotypic data
Whole-genome sequencing of presumably the largest biorepository of NG isolates (n=1356) on the African continent will give an unprecedented snapshot into the genomic diversity of the organism in our settings and possibly unveil unknown AMR mechanisms.

Funding and affiliations
Infectious Diseases Institute, Makerere University Kampala Uganda
WHO Collaborating Centre for Gonorrhoea and other STIs, Orebro, Sweden

Antimicrobial Resistance in Communities and Hospitals in Kenya
01 October 2018 – 30 September 2021

Topic(s) Epidemiology and surveillance

Author(s) Douglas R. Call, Sylvia Omulo, Ulzii-Orshikh Luvsansharav, Guy H. Palmer, Surie Diya, Rachel M. Smith

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Project description
The Antimicrobial Resistance in Communities and Hospitals (ARCH) study employs a cross-sectional design to investigate the prevalence and risk factors for colonization with multi-drug resistant organisms (MDRO) in the community and among hospitalized patients in urban and rural sites in Kenya. At these sites, 768 adults and 768 children are enrolled in the community, and 509 patients (total) are enrolled at hospital sites over a 12-month period. During enrollment, household and/or participant interviews are conducted and samples (stool/rectal swabs and nasal swabs) collected from consenting participants. Samples are tested for three MDROs i.e. extended-spectrum cephalosporin-resistant Enterobacteriaceae (ESCrE) and carbapenem-resistant Enterobacteriaceae (CRE) from stool samples, and methicillin-resistant Staphylococcus aureus (MRSA) from nasal swabs. Study data will be analyzed to estimate the prevalence and risk factors for colonization with ESCrE, CRE and MRSA in these settings, and to determine the degree of genetic relatedness between MDROs in community and hospital sites.

Funding and affiliations
Funding institution
US Centers for Disease Control and Prevention

Collaborating institutions:
1. Centers for Disease Control and Prevention, Kenya
2. Kenya Medical Research Institute, Kenya
3. Ministry of Health, Kenya
4. University of Nairobi Institute of Tropical and Infectious Diseases, Kenya
5. US Centers for Disease Control and Prevention, US
6. Washington State University, US
7. Washington State University Global Health – Kenya, Kenya

HATUA: Holistic Approach to Unravel Antibacterial Resistance in East Africa
01 May 2018 – 31 October 2021
United Kingdom

Topic(s) Epidemiology and surveillance, Policy

Author(s) Prof Matthew Holden, St Andrews Prof Stephen Mshana, CUHAS Dr Benon Asiimwe, Makerere Prof Stella Neema, Makerere Dr John Kiiru, KEMRI Dr Katherine Keenan, St Andrews Dr Wilber Sabiiti, St Andrews Dr Derek Sloan, St Andrews Prof Stephen Gillespie, St Andrews Dr Joseph Mwanga, CUHAS Dr Blandina Mmbaga, KCRI Prof Gibson Kibiki, EAHRC Prof David Aanensen, Sanger Prof John Stelling, Brigham Prof Allison Elliot, UVRI Dr Mike Kesby, St Andrews Dr V Anne Smith, St Andrews Prof Andy Lynch, St Andrews

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Project description
HATUA is an interdisciplinary study which is exploring the burden and drivers of antibacterial resistance associated with urinary tract infections (UTIs) across East Africa. Whilst the biological drivers of ABR in pathogens are well explored, the extent to which these are modulated by human behaviour in and around antibiotics is less understood. The consortium brings together clinical microbiological, pathogen genomic, social science and modelling data to create a unique combined ABR data set. The project established a surveillance network across Uganda, Kenya and Tanzania and recruited 1800 UTI positive patients from nine study areas. We also conducted quantitative interviews in the clinic, and the homestead, and recorded the treatment seeking behaviour of individuals. Whole genome sequencing will be used to characterize the pathogens we isolate from the patients, investigating their evolution and the genetic basis of resistance in UTI causing bacteria. Using the combined dataset , we will construct patient pathways that capture the treatment-seeking and antibiotic-use behaviour for our cohort. We aim to identify ways in which people can be influenced to follow more antibiotic friendly pathways, and disrupt the prevailing spread of ABR across the region.

Funding and affiliations
HATUA is a £2.8M, three-year Global Context Consortia Award, funded by the National Institute for Health Research (NIHR), Medical Research Council (MRC) and the Department of Health and Social Care (DHSC). The award is also part of the EDCTP2 programme.
St Andrews joins 10 partners in the Consortium:
Makerere University, Uganda
Catholic University of Health and Allied Sciences , Tanzania
Kenya Medical Research Institute, Kenya
Technical University of Mombasa, Kenya
National Museum of Kenya
Uganda Virus Research Institute, Uganda
Kilimanjaro Clinical Research Institute, Tanzania
East African Health Research Commission, Tanzania
Sanger Institute, UK
Brigham and Women’s Hospital, Harvard, USA

The Fleming Fund
31 October 2017 – 31 October 2021

Topic(s) Epidemiology and surveillance, Microbiology, Policy, “One Health”

Author(s) UK Department of Health & Social Care

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Project description
The Fleming Fund is a £265 million UK aid programme supporting up to 24 countries across Africa and Asia to tackle antimicrobial resistance. The Fund is managed by the Department of Health and Social Care and invests in strengthening surveillance systems through a portfolio of country and regional grants, global projects and fellowship schemes.

The UK Government established the programme in 2015 in response to the UK AMR Review and the WHO Global Action Plan on AMR, which called for funding to improve AMR surveillance, public awareness and responsible drug use. The programme focuses on low- and middle-income (LMIC) countries because they are expected to bear the heaviest consequences of the spread of AMR.

Our Aims
We build partnerships across sectors, governments and organisations
We equip countries to collect and use data on drug resistance
We encourage clinicians and farmers to use antibiotics better
We encourage governments to invest in tackling antimicrobial resistance for a sustainable future
We encourage policy makers to *make AMR a policy priority”

Funding and affiliations
The project is funded by UK aid, managed by the Department of Health and Social Care, in partnership with Mott MacDonald, the Management Agent.

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