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

10 25 50
 
Description Bill and Melinda Gates Foundation Surveillance Advisors Group
Geographic Reach Multiple continents/international 
Policy Influence Type Membership of a guideline committee
 
Description Board member, The Wellcome Trust Surveillance and Epidemiology of Drug Resistant Infections Consortium (SEDRIC)
Geographic Reach Multiple continents/international 
Policy Influence Type Membership of a guideline committee
Impact The Surveillance and Epidemiology of Drug Resistant Infections Consortium (SEDRIC) is a policy think-tank that works to identify evidence gaps, describe solutions and advocate for research and policy change in antimicrobial resistance surveillance, particularly in low- and middle-income country settings.
URL https://sedric.org.uk/
 
Description National Antimicrobial Resistance Working Group
Geographic Reach Africa 
Policy Influence Type Membership of a guideline committee
Impact The Working Group steered the process towards Nigeria's National Action Plan on Antibiotic Resistance (2017) and set up a national surveillance system for antimicrobial resistance, which now reports to the WHO GLASS and is being strenghtened and extended. The working group also promotes and oversees national events to improve antimicrobial resistance awareness and encourages antimicrobial stewardship in hospitals
URL http://ncdc.gov.ng/news/65/combating-antimicrobial-resistance-in-nigeria%3A-merging-all-hands%2C-ass...
 
Description Nigerian Antimicrobial Resistance National Action Plan
Geographic Reach Africa 
Policy Influence Type Participation in a national consultation
Impact Increased the awareness of the problem of antimicrobial resistance in Nigeria. Provided global awareness that Nigeria is invested in addressing this problem
 
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 Surveillance and Epidemiology of Drug Resistant Infections Consortium (SEDRIC)
Geographic Reach Multiple continents/international 
Policy Influence Type Membership of a guideline committee
URL https://wellcome.ac.uk/what-we-do/our-work/surveillance-and-epidemiology-drug-resistant-infections-c...
 
Description WHO Working Group on the role of vaccines against antimicrobial resistance (VAC-AMR)
Geographic Reach Multiple continents/international 
Policy Influence Type Participation in a advisory committee
 
Description World Health Organization Vaccine Advisory Committee on Antimicrobial Resistance
Geographic Reach Multiple continents/international 
Policy Influence Type Membership of a guideline committee
Impact WHO description: The board provides advice to WHO on its action on the role of vaccines against Antimicrobial Resistance (AMR). It generates global WHO guidance on priority actions aimed to strengthen the role of vaccines against AMR, and is developing a semi quantitative framework of value attribution to vaccines regarding their role against AMR. The board is engaged in a value attribution exercise to support prioritization of investment decisions on vaccine development and use. Since the committee began its work and completed the value attribution excercise, there has been better awareness of the role that vaccines play and could play in containing antimicrobial resistance.
 
Description African Journal of Laboratory Medicine: Special issue on the role in African laboratories in AMR surveillance
Amount $39,997 (USD)
Funding ID OPP1178631 
Organisation Bill and Melinda Gates Foundation 
Sector Charity/Non Profit
Country United States
Start 08/2017 
End 12/2018
 
Description Minimal genomics lab for AMR surveillance & diagnostics in provincial low-income settings_2018 GCAM
Amount $200,000 (USD)
Funding ID OPP1210746 
Organisation Bill and Melinda Gates Foundation 
Sector Charity/Non Profit
Country United States
Start 03/2018 
End 08/2020
 
Description NIHR Global Health Research Unit on Genomic Surveillance of Antimicrobial Resistance
Amount £6,863,271 (GBP)
Funding ID 16/136/111 
Organisation National Institute for Health Research 
Sector Public
Country United Kingdom
Start 10/2020 
End 09/2021
 
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
Start 03/2016 
End 03/2017
 
Description Bioinformatics collaboration for Pathogenic Lineages of Enteric Bacteria in Nigeria 
Organisation The Wellcome Trust Sanger Institute
Department Pathogen Genomics
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution Nothing to add
Collaborator Contribution We welcome Professor Nicholas Thomson to our research group. Nick is one of the foremost authorities on Escherichia coli pathogen genomics and will oversee bioinformatics associated with this project. This fills the expertise gap generated when post doc bioinformatician Dr Chinyere Okoro relocated close to the start of the project, provides a means to train Nigerian students in bioinformatics and allows Nick to serve as lead UK collaborator, which Professor Gordon Dougan has stepped back on.
Impact None yet
Start Year 2018
 
Description Clinical collaboration for case-control study 
Organisation University of Ibadan
Department Department of Biochemistry
Country Nigeria 
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 
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
 
Description Antibiotic Awareness Week: Open panel for the public 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact During World Antibiotic Awareness Week in November last year, we held panel discussion in Ibadan, Nigeria featuring lecturers and students of pharmaceutical microbiology with physicians and pharmacists, which Iruka Okeke organized, curated and moderated. In addition to Iruka, there were two other Professors that study antimicrobial resistance, a researcher studying resistance in livestock, a practicing infectious disease physician and a pharmacist. The event was attended by about 150 people.
Year(s) Of Engagement Activity 2017
URL http://apps.who.int/world-antibiotic-awareness-week/activities/en#/grid-content
 
Description Curbing Infectious Diseases Ideas Lab at the World Economic Forum 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact The event was an 'Ideas Lab" at the 2018 World Economic Forum sponsored by the Wellcome Trust. Its objective was to inform world leaders and other Davos attendeefs about cutting edge science being performed in Africa with three Africa-based scientists, George Warimbe, Iruka Okeke and Tolullah Oni as speakers. The session was moderated by Francis Collins of the NIH and each speaker also held a separate 'Ask About' session at the WEF for attendees who wanted more information.
Year(s) Of Engagement Activity 2018
URL https://www.youtube.com/watch?v=NwasmJRW2kY
 
Description Emerging Public Health Leaders in Nigeria 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact The activity was organized to provide young graduates with information about careers in public health and public health-related fields. Six practioners, including myself were asked to describe what they do and the career path that got them there and then there was a panel discussion and questions from the audience. I discussed and responded to questions on biomedical research with connections to public health
Year(s) Of Engagement Activity 2018
 
Description Grand Challenge Meeding presentations 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Four presentations were made at the 2019 Grand Challenges meeting
A TED talk to a large plenary audience: Going for routine: Doing our best work every day. African Innovation Rapid-fire talk.
A talk to in smaller break out session on genomic surveilance: Genomic surveillance of antimicrobial resistance in Nigeria. Grand Challenges Annual Meeting, Addis Ababa, 27-30 October 2019.
A poster: Enteroaggregative Escherichia coli (EAEC) Antibiofilm Agents in Pathogen Box
I was part of a panel in the final plenary: Women and Girls at the Center of Development.
Year(s) Of Engagement Activity 2019
 
Description Handle Antibiotics With Care Interactive Panel for Antibiotic Awareness Week 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact The Department of Pharmaceutical Microbiology of Faculty of Pharmacy led by Prof Iruka N. Okeke on Tuesday, 13 November, 2018 held a panel discussion on Handle Antibiotics with Care to commemorate the World Antibiotics Awareness Week (WAAW). The discussion involved panellists from different fields. There were over hundred attendees at the event including Univesity of Ibadan staff and students and other members of the public.
List of panellists
1) Prof EO Adeleke - Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan
2) Prof Bolanle Adeniyi - Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan
3) Prof Aderemi Kehinde - Medical Doctor and Clinical Microbiologist, UCH, Ibadan
4) Mr Wale Adeniyi - PhD student from the Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan
The event started at 12:15pm with a short welcome and introduction given by the moderator, Prof Iruka Okeke. In her welcome address she stated that antimicrobial resistance is inevitable but could be controlled. Thereafter she proceeded to the first question to the panellist which was how has organisms changed over time to become resistant to antibiotics or antimicrobials.

The audience contributed various questions and comments. Among these were a request for an explanation of what misuse/abuse of antibiotics actually means. Prof B. Adeniyi responded by citing inappropriate prescription is an example of misuse is skipping doses and irregular use of drugs is abuse. Another question asked was whether the Widal test is appropriate to diagnose typhoid fever. Prof Iruka Okeke responded that Widal test done is to check for antibodies that have been stimulated by Salmonella typhi and individuals can test positive if they have previously had typhoid. She also mentioned that the Widal test is diffcult to read and prone to error but there were alternate tests for typhoid fever such as blood culture.

Another attendee commented that regulations should be enforced to reduce accessibility to drugs, water supply should be made available for use especially in toilets, quality of water should be monitored to ensure potable water. Also only animals that are ill should be treated by a vet.
Also, question was raised on whether over the counter drugs are really bad. Prof Iruka Okeke responded that over the counter drugs are illegal in some cases, with antibiotics being a specific example but that drugs like pain killers and antimalarials are allowed to be sold over the counter in medicine stores, the latter after a malaria diagnosis test has been done. rof Kehinde Aderemi contributed that over the counter drugs is not so good when there is no prescription. Another response was that people might not survive without over the counter drugs but antibiotics should not be allowed to be sold over the counter.
In conclusion of the event Prof. Iruka Okeke said the causes of infections that warrant treatment of antibiotics should be attacked first so that fewer antibiotics will be needed. And antibiotics should only be taken if they have been prescribed by a qualified health professional who has taken the appropriate steps to diagnose and infection. She also enjoined everyone to join the AMR campaign and spread it everywhere since there are no alternative for antibiotics yet. The meeting ended at about 2pm.
Year(s) Of Engagement Activity 2018
 
Description Panel Discussion: The Future of Antibiotics Depends on All of Us 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact We organized and moderated a panel discussion on antibiotic stewardship and resistance. The panelists included a physician, a pharmacist, a vet and a genomic epidemiologist. Attending invitees included about 150 students from area secondary schools, health professionals, patients, and the general public.
Year(s) Of Engagement Activity 2019
 
Description Public Lecture: 2019. Olumbe Bassir Memorial Lecture 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Holding on and letting go: Dissecting attachment by an exceptional bacterial colonizer. Biennual Olumbe Bassir Memorial Lecture Otunba Subomi Balogun Conference Centre, University of Ibadan on the 18th of June 2019. Published Bodija, Ibadan : Bookbuilders, Editions Africa, 2019. 30 pages ISBN 9789789211968, NLM ID:101763549
Year(s) Of Engagement Activity 2019
 
Description Radio Interview on Diamond FM for Antimicrobial Resistance Awareness Week 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Media (as a channel to the public)
Results and Impact A live radio interview on antibiotics and antibiotic resistance, which was aired during World Antibiotic Awareness Week
Year(s) Of Engagement Activity 2019
 
Description Short Expert Talk at The Economist event: Antibiotic Resistance 2019: Preventing an Apocalypse 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Event organizer's description of my presentation: Spotlight: Science 101
If developing antibiotics were simple, there would be more than one or two prospects in the pipeline, even for the most resistant Gram-negative bacterial infections. Why is the science so hard, and what prospective antibiotics look most promising?
Year(s) Of Engagement Activity 2019
URL https://events.economist.com/events-conferences/emea/amr2019
 
Description Stakeholder meeting for Salmonella surveillance 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact We conducted a stakeholder meeting open to the public to report the results of two year's surveillance for blood-borne Salmonella in Ibadan metropolis. We described our enrollment and blood culture of over 3000 febrile patients in the metropolitan Ibadan area and our principal findings, which were that bacteriamia, and in particular Salmonella Typhi are predominant causes of febrile illness in Ibadan. the data we have collected is sufficient to provide evidence to justify improved diagnostics and introduction of Typhoid Conjugate Vaccines. We believe our findings are pivotal to understanding the burden of invasive Salmonella disease, constitute evidence to support best practices for typhoid diagnosis and treated, and have the potential to be used to support a GAVI application for access to the new typhoid conjugate vaccine.
Year(s) Of Engagement Activity 2019