I Okeke, University of Ibadan - Pathogenic lineages of enteric bacteria in Nigeria

Lead Research Organisation: The Wellcome Trust Sanger Institute
Department Name: Research Directorate

Abstract

Childhood diarrhoea and bacterial bloodstream infections account for a considerable proportion of illnesses and deaths among children under five years of age worldwide. The under-five mortality produced by these infections is disproportionately high in Nigeria and other parts of Africa. This study proposes to examine two causes of these infections, enteroaggregative Escherichia coli and Salmonella, and to identify bacterial lineages that account for a significant proportion of childhood diarrhoeas and invasive infections among Nigerian children. Stool specimens will be obtained from children with diarrhoea and from healthy children attending clinics in Ibadan, Nigeria. E. coli and Salmonella will be isolated from the specimens and characterized at the molecular level to identify disease-causing strains and the disease-causing genes these subtypes carry. Enteroaggregative Escherichia coli and Salmonella isolates will be subjected to further analysis, involving sequencing parts of their genomes. The resulting DNA sequences will be compared to determine inter-relationships among different genetic lineages of bacteria isolated in this study and between these isolates from Nigeria and strains other parts of the world. These analyses will reveal how disease-causing lineages change over time and are transmitted locally and globally.

This research will improve our understanding of the epidemiology and evolution of two important but under-addressed bacterial pathogens. The study will determine which subgroups of enteroaggregative Escherichia coli and Salmonella are more likely to cause disease and whether there are subtypes that are associated with life-threatening disease. This is important for the study location, Nigeria, because very little is known about locally-prevalent subtypes within the country or in neighbouring countries. Identification and characterization of predominant subgroups serve as the basis for devising diagnostics to better their detection and surveillance. The findings from this study will also inform vaccine development and vaccine use policy because the most harmful subtypes can be targetted. This research will also determine whether healthy individuals carry these organisms, and if so, to what extent. Understanding healthy carriage is key to determining how these organisms are maintained and transmitted in communities.

The study will use molecular methods to characterize the strains in a laboratory to be set up at the University of Ibadan and lead by the African Research Leader Candidate who is co-investigator on this grant. The African Research Leader will additionally build on collaborative links with other regional laboratories and extend some of the expertise built at Ibadan to those labs. The research will therefore build capacity in the area of molecular bacteriology and provide a collaborative link between West African scientists and the Wellcome Trust Sanger Institute, where the principal investigator is located.

Technical Summary

Enteric pathogens such as diarrhoeagenic Escherichia coli and Salmonella enterica are important causes of childhood illness and death in African countries. Very little is known about the epidemiology of these bacteria in Nigeria, including which lineages account for the burden of disease. In this proposal, we plan to determine the contributions of two enteric pathotypes, enteroaggregative E. coli (EAEC) and Salmonella, using a case-control study design. We will use sequence-based methods to identify predominant diarrheagenic lineages of both pathotypes in Nigeria and elucidate their recent evolutionary history. We will additionally use sequence-based methods to subtype invasive isolates recovered during the period of the case-control study and determine whether Salmonella lineages recovered from invasive infections are associated with diarrhoea and/or carried asymptomatically by healthy individuals. The study will yield information on the evolution and phylogeography typhoidal and non-typhoidal Salmonella and their role in invasive infections, which is relatively sparse for West Africa. It will additionally identify and characterize hypervirulent EAEC lineages, about which there is little information worldwide. Following characterization of key virulent lineages, we will devise DNA-based tests to facilitate their detection for epidemiological research and surveillance. Identification of such lineages will also inform vaccine development and public health policy.

The research will be performed in the laboratory of an African Research Leader Candidate based at the University of Ibadan, the Co-I on this proposal, in collaboration with PI based at the Wellcome Trust Sanger Institute in Cambridge. The study will bring molecular bacteriology expertise to an important research centre in West Africa, facilitate training and capacity building and provide an important collaborative link for the Wellcome Trust Sanger Institute in West Africa.

Planned Impact

Beneficiaries of the research
1. Scientists and students at the University of Ibadan, Nigeria: The Co-I will establish a molecular microbiology research laboratory in the school of Pharmacy. Her presence and research will strengthen molecular expertise at the Faculty of Pharmacy, in UI's three other microbiology departments (in Medicine, Science and Veterinary Medicine) as well as more broadly at the institution. Multiple undergraduate and post-graduate students will receive intensive training in molecular microbiology and the molecular biology content of undergraduate and postgraduate curricular will be strengthened. The University of Ibadan will also benefit from having a senior scientist with pharmaceutical credentials in its Pharmaceutical Microbiology Department.

2. Scientists and the Wellcome Trust Sanger Institute, and their collaborators: Researchers interested in global phylogeography of bacterial lineages will have a partnership through which they can obtain representative strains from a West African site other than the MRC Gambia.

3. Students and trainees at the University of Ibadan: The University of Ibadan is working to increase and improve the molecular biology content of its bioscience curricula. Students enrolled at the University will have the opportunity to enroll in basic and applied molecular biology courses taught by the CoI who has taught molecular biosciences at a highly selective US university for over a decade.

4. African Microbiologists: As part of this project, partnerships among other West African laboratories that have been initiated will be strengthened and molecular expertise will be shared among them. Included in the already recruited nucleus are Obafemi Awolowo University, Ile-Ife, Nigeria (Microbiology in the Pharmacy, Medicine and Science Faculties), Nnamdi Azikiwe University, Awka (Pharmaceutical Microbiology) and the University of Ghana Medical School. The partnership will extend to other microbiology departments and will also forge links with other African scientists, from Kenya and Malawi, that collaborate with the Wellcome Trust Sanger Institute on an on-going basis.

5. Diaspora Nigerian microbiologists: Nigerian Post doctoral fellows currently based abroad will be invited to participate in the research and/or serve as resource personnel in workshops. Other Diaspora scientists could see the Co-I's return to Nigeria as a model for re-entry and establishment of a productive research program.

6. Scientists involved in vaccine development research and vaccine policy development will benefit from the data obtained in this research.

7. Public health researchers who wish to understand healthy carriage of EAEC and non-typhoidal Salmonella and how this might affect transmission and endemicity of these pathogens.

8. New, more sensitive and specific, diagnostic protocols for enteric pathogens will be developed and made available to clinical diagnostic laboratories in Nigeria and similar countries

9. Nigeria has seen vaccine boycotts and spurious AIDS cures, all of which undermine health care delivery and public health. Boosting in-country molecular microbiology research could help engender societal trust in infectious disease interventions in civil society.

Publications


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Okeke IN (2016) Laboratory systems as an antimicrobial resistance containment tool in Africa in African Journal of Laboratory Medicine
 
Description National Antimicrobial Resistance Working Group
Geographic Reach Africa 
Policy Influence Type Membership of a guideline committee
URL http://ncdc.gov.ng/news/65/combating-antimicrobial-resistance-in-nigeria%3A-merging-all-hands%2C-ass...
 
Description Research Networks for Health Innovations in Sub-Saharan Africa
Geographic Reach Africa 
Policy Influence Type Membership of a guideline committee
 
Description Strengthening the role of laboratories in tracking antimicrobial resistance in East Africa
Geographic Reach Africa 
Policy Influence Type Participation in a advisory committee
URL http://www.cddep.org/publications/east_africa_public_health_laboratory_networking_project#sthash.RfD...
 
Description Severe Typhoid in Africa
Amount $465,447 (USD)
Organisation International Vaccine Institute (IVI) 
Sector Charity/Non Profit
Country Korea, Republic of
Start 10/2016 
End 09/2018
 
Description TWAS visiting expert award
Amount $2,200 (USD)
Organisation The World Academy of Science 
Sector Academic/University
Country Italy, Italian Republic
Start 03/2016 
End 03/2017
 
Description Clinical collaboration for case-control study 
Organisation University of Ibadan
Department Department of Biochemistry
Country Nigeria, Federal Republic of 
Sector Academic/University 
PI Contribution We are contributing etiologic information to infantile diarrhea cases retrospectively. This information would not otherwise have been available.
Collaborator Contribution Pediatrician Dr Adedayo Adepoju contributed to study design and is supervising clinical personnel aiding with sample collection for our case-control study.
Impact No outcomes yet
Start Year 2015
 
Description Epidemiological consult for case-control study 
Organisation London School of Hygiene and Tropical Medicine (LSHTM)
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Academic/University 
PI Contribution We are performing a case-control study to which Dr Clare Flach will contribute as a collaborator.
Collaborator Contribution Dr Clare Flach provides study design and statistical expertise for our project. She ratified our case-control design and sample size calculations at the inception of our research and will contribute to data analysis later on.
Impact No outputs yet
Start Year 2014