Using whole genome sequencing to develop Antimicrobial Resistance Reference Facility for One Health in South Africa
Lead Research Organisation:
University of East Anglia
Department Name: UNLISTED
Abstract
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Technical Summary
Antimicrobial resistance (AMR) in human pathogens is reaching a crisis point with many pathogens becoming multidrug resistant and thereby untreatable. Although much work has been done to improve surveillance for AMR in nosocomial pathogens and sexually transmitted infections, surveillance for resistance in food and waterborne pathogens, with the exception of typhoid fever, remains problematic in the developing world. This is further complicated in that AMR may not be related purely to antimicrobial use in humans, but may also be affected by antimicrobial use in food and domestic animals and the persistence of antimicrobial in the environment.
Whole genome sequencing (WGS) is proving to be a powerful tool in the identification of microbial evolution, including monitoring for the development of antimicrobial resistance. WGS is additionally the most exacting method to compare to bacterial isolates to confirm epidemiological linkage and has been invaluable in investigating food and waterborne outbreaks globally. International experience has shown WGS may be used as an alternative to conventional methods to characterise, serotype and define AMR in enteric pathogens.
This project proposes to develop WGS techniques in South Africa to characterise enteric bacteria from South Africa human, animal and environmental sources to promote the rapid investigation of food and waterborne disease outbreaks in the country, which remain a significant public health burden. Experience gained from this work will be shared across the subcontinent and possibly the greater sub-Saharan Africa region.
This project falls within: New technology innovations to improve surveillance. How can technology be used to improve and scale surveillance?
Whole genome sequencing (WGS) is proving to be a powerful tool in the identification of microbial evolution, including monitoring for the development of antimicrobial resistance. WGS is additionally the most exacting method to compare to bacterial isolates to confirm epidemiological linkage and has been invaluable in investigating food and waterborne outbreaks globally. International experience has shown WGS may be used as an alternative to conventional methods to characterise, serotype and define AMR in enteric pathogens.
This project proposes to develop WGS techniques in South Africa to characterise enteric bacteria from South Africa human, animal and environmental sources to promote the rapid investigation of food and waterborne disease outbreaks in the country, which remain a significant public health burden. Experience gained from this work will be shared across the subcontinent and possibly the greater sub-Saharan Africa region.
This project falls within: New technology innovations to improve surveillance. How can technology be used to improve and scale surveillance?
Publications
Achtman M
(2020)
Correction: Multilocus Sequence Typing as a Replacement for Serotyping in Salmonella enterica.
in PLoS pathogens
Cuypers W
(2023)
A global genomic analysis of Salmonella Concord reveals lineages with high antimicrobial resistance in Ethiopia
in Nature Communications
Djeghout B
(2018)
Ceftriaxone-resistant Salmonella Typhi carries an IncI1-ST31 plasmid encoding CTX-M-15.
in Journal of medical microbiology
Lee WWY
(2021)
Characterization of a pESI-like plasmid and analysis of multidrug-resistant Salmonella enterica Infantis isolates in England and Wales.
in Microbial genomics
Mattock J
(2022)
Genetic characterization of Salmonella Infantis from South Africa, 2004-2016.
in Access microbiology
Tau NP
(2017)
Development and evaluation of a multiple-locus variable-number tandem-repeats analysis assay for subtyping Salmonella Typhi strains from sub-Saharan Africa.
in Journal of medical microbiology
Description | The information gained fro this study were shared with the UKHSA and helped to update S. Infantis knowledge for outbreak investigation. We have now published two articles in collaboration with UKHSA this would nor have been possible without this grant. |
First Year Of Impact | 2021 |
Sector | Healthcare |
Description | Global S. Infantis |
Organisation | UK Health Security Agency |
Country | United Kingdom |
Sector | Public |
PI Contribution | Knowledge exchange, long read sequencing technology and data analysis |
Collaborator Contribution | Development of detection methods for Salmonella Infantis |
Impact | A multi-disciplinary approach to understanding the population structure of the important broiler and human pathogen Salmonella Infantis has allowed: Publications of benefit to the Salmonella research community Development of tools to investigate the risk of importing Salmonella Infantis into the UK |
Start Year | 2018 |
Description | Investigation of antibiotic resistance in Salmonella Infantis |
Organisation | Public Health England |
Country | United Kingdom |
Sector | Public |
PI Contribution | Both partners have had several discussion meetings around the reporting of S. Infantis and risk assessment. QIB have supplied informatics support through Gemma Langridge and Microbiology through John Wain. The first paper has been submitted |
Collaborator Contribution | PHE provide public health intervention experience, several genome sequences and a route to change the reporting guidelines. |
Impact | Salmonella nomenclature in the genomic era: a time for change. MA Chattaway, GC Langridge, J Wain. Scientific reports 11 (1), 1-8 Characterization of a pESI-like plasmid and analysis of multidrug-resistant Salmonella enterica Infantis isolates in England and Wales. WWY Lee, J Mattock, DR Greig, GC Langridge, D Baker, S Bloomfield, ... Microbial genomics 7 (10) |
Start Year | 2018 |
Description | UEA - PhD studentship |
Organisation | Public Health England |
Country | United Kingdom |
Sector | Public |
PI Contribution | Jenny Mattock a a PhD student funded by the NIHR, UK. By linking Jenny to the this project we allowed her to explore the genetic diversity of Salmonella Infantis in South African . Jenny visited South Africa in October 2017 and was supported to extract DNA and collect meta-data |
Collaborator Contribution | The Health Protection Resreach Unit for gastrointestinal infection has provided the student and Public Health England has provided DNA sequnce from isolates of S. Infantis from the UK |
Impact | Poster presentations at various symposia. Multidisciplionary involvement: BioiInformatics - PHE and Quadram Institute; Microbiology - NICED and UEA PhD awarded by UEA in 2020 publication - 2021 Oct 14. doi: 10.1099/mgen.0.000658 |
Start Year | 2017 |
Description | UEA - PhD studentship |
Organisation | University of East Anglia |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Jenny Mattock a a PhD student funded by the NIHR, UK. By linking Jenny to the this project we allowed her to explore the genetic diversity of Salmonella Infantis in South African . Jenny visited South Africa in October 2017 and was supported to extract DNA and collect meta-data |
Collaborator Contribution | The Health Protection Resreach Unit for gastrointestinal infection has provided the student and Public Health England has provided DNA sequnce from isolates of S. Infantis from the UK |
Impact | Poster presentations at various symposia. Multidisciplionary involvement: BioiInformatics - PHE and Quadram Institute; Microbiology - NICED and UEA PhD awarded by UEA in 2020 publication - 2021 Oct 14. doi: 10.1099/mgen.0.000658 |
Start Year | 2017 |