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PARTNERSHIPS FOR ENHANCED ENGAGEMENT IN RESEARCH (PEER)
Cycle 5 (2015 Deadline)


Characterizing and tracking of antimicrobial resistance in the water-plant-food public health interface: an emerging water, sanitation and hygiene issue


PI: Liza Korsten (Lise.korsten@up.ac.za), University of Pretoria
U.S. Partner: Manan Sharma, United States Department of Agriculture, Agricultural Research Service, Environmental Microbial and Food Safety Laboratory

Project Overview:

The main aim of this research project is to determine the prevalence of, characterize, and track antimicrobial resistance (AR) in the water-plant-food-public health interface. This will contribute to addressing the knowledge gap on the contribution of agro-ecosystems to the dissemination of AR resistance in the environment in South Africa. Access to safe potable water is a basic human right. The microbiological quality of water sources, especially surface water, are seriously compromised by municipal wastewater discharge, sewage from informal settlements with inadequate sanitation, and wastes from animal husbandry, industrial companies, hospitals, and the mining sector. With strategic resources being polluted, consumers face increased risks with potential negative effects on human health, the environment, and food security. Following consultation with key stakeholders, the research team will select study sites where the risk for fecal bacterial contamination is high due to anthropogenic activities. They will compare levels of antimicrobial resistance prevalence in rural versus urban settings and organic farming versus intensive commercial farming, which should contribute towards an improved understanding of the role of agricultural practices on driving AR development in the agricultural ecosystem. Hazard analysis coupled with pollution source tracking within a specific area will facilitate the assessment of the potential impact on public health.

The impact of this research should also provide water management services, government officials, and farmers with a knowledge base of “hotspots” where irrigation water quality has been severely compromised in South Africa. Knowledge generated during the course of the project should ultimately aid in the development of a Water and Health strategy in South Africa.
 
Summary of Recent Events

Dr. Korsten and her team have just finished the first year of this PEER project. A number of activities were carried out to kick off the project.

The Pi and her research coordinator, Dr Erika du Plessis, took part in an interview on Pretoria FM Radio, a local Afrikaans radio station in January 2017. The purpose of the interview was to discuss the background and goals of the PEER grant. The PI also visited Dr Manan Sharma their USG collaborator at the EMFSL laboratories, in Belttsville Maryland and gave a seminar presentation on their current project on irrigation water, a PEER-funded project on which EMFSL is a collaborator. She also discussed her previous work on produce safety and quality at the University of Pretoria.

A Food Safety Collaboration Workshop was held in April 2017 at the University of Pretoria. UP and UFH students as well as supervisors attended the workshop with a view to develop detailed Gantt charts including site selection, material, methods and timelines. In addition all prospective students gave PowerPoint presentations on their individual projects proposals.

Flyers were prepared to advertise projects and recruit students. After successfully recruiting students, the research topics of their dissertations were defined taking the PEER project milestones and timelines into consideration.

Reconnaissance visits have been carried out to the proposed study sites around the Eastern Cape Province between July and September 2017 and cut across Chris Hani, Amathole and Sarah Baartman District Municipalities in the Eastern Cape Province of South Africa. The sites include: 10 hospitals, 7 abattoirs, 3 wastewater treatment facilities, 5 fresh vegetable farms, 4 dairy farms, 7 rivers, 2 cattle farms, a chicken farm and an animal farm where different animals are kept. The honors students have completed one round of sampling and are currently working on the identification of their isolates using polymerase chain reaction (PCR) analysis. They will proceed with the antibiogram profiling of the isolates in the coming weeks Researchers at the University of Pretoria initially contacted Food Safety Officers of two major food retailer companies in SA. They provided the team with the names and contact details of their supplier farms. Reconnaissance visits (nine in total) to the potential sampling sites in the Gauteng province and North West Province were conducted from March to June 2017.

Collaboration was established at eight of the sites which included 7 commercial farms. Contact was also made with a small-scale farm supplying formal and informal retailers. The farm is managed by a very dynamic previously disadvantaged couple. They are supported by an Agricultural Extension Officer from the Department of Agriculture, Forestry and Fisheries (DAFF) in SA. Some of the farmers insisted that confidentiality agreements be drawn up and signed by both the farmer and UP which was finalized at the end of May 2017.

A benchmarking field trip was conducted on 10 April 2017 to one of the supplier farms in order to ensure sampling methods and analyses are done correctly. Three supervisors (1 male, 2 female) and five students (females) took part in the field trip. Subsequently, fifteen field trips to the farms were conducted during which irrigation water (river, dam, borehole, drip irrigation pipes, pivots), soil and fresh produce at harvest in the field were sampled for microbiological analysis. Fresh produce included leafy vegetables i.e. spinach, baby spinach and lettuce (i.e. frilly, crisp, butter lettuce). Hygiene indicator bacteria (E. coli and coliform) and Enterobacteriaceae counts have been determined for the collected samples. Extended spectrum β-lactamase producing isolates have been isolated using standard microbiological techniques and isolate identities confirmed.

The second round of sampling and microbiological analysis commenced at the end of September 2017. Future work will involve antimicrobial resistance profiling using phenotypic and genotypic methods. The Post Doc at UP, Dr German Vilamizar has been working full-time on identifying suitable AR gene targets, designing primers and optimization of AR detection using traditional PCR and digital droplet PCR. He also identified and obtained suitable positive control strains from established Culture collections for detecting AR from environmental (irrigation water and soil) and fresh produce samples.

In the next project year, the PI and her team plan to continue their research. Active sampling and microbiological analysis of water and fresh produce samples for selected fresh produce supply chains to be conducted by post graduate students from both UP and UFH.

A workshop with Dr Manan Sharma from EMFSL, Beltsville, Maryland and his colleagues involved with a $10 million USDA/NIFA grant funded project entitled CONSERVE (Coordinating Nontraditional Sustainable Water use in Variable Climates) is planned at the 3rd International Conference on Global Food Security from 3-6 December 2017 in Cape Town, South Africa. Prof Manan Sharma will be presenting at the conference subject to his funding to attend the conference in South Africa being approved.

Lastly, the PI plans to hold a workshop where students present their research progress and with Pi, Co-pi and Post Docs to discuss collaboration with relevant government agencies and the people involved with the National Antimictobial Resistance strategy frame work to discuss application of research results.



5-048 DuPlessis5-048 Korsten
Post doc student Dr. German Villamizar showing the PEER team the project labStudents and PEER team during the presentation

In the  next three months, the PI and her team will continue carrying out active sampling and microbiological analysis of water and fresh produce samples along the entire supply chain from the farm to the retailer by all students. They have also planned a workshop between University of Pretoria and the University of Fort Hare to discuss methods and sites with a view to develop a detailed Gantt chart with deliverables and timelines.


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