REPORT FOR THE PFIZER FOUNDATION

  • Name: Samie Amidou
  • Dates of training fellowship at UVa: August 2005 to December 2006
  • Home Institution: University of Venda, Thohoyandou, South Africa
  • Title/position there before coming to UVa: PhD fellow, part-time Lecturer

Summary of training at UVa

During my fellowship at the University of Virginia, I worked at the Center for Global Health, under the mentorship of Dr. Richard Guerrant. I have learned methods useful for the evaluation of intestinal infections in a community. These include molecular biology methods as well as biochemical methods. The introduction to statistical methods has been of tremendous importance in the analysis of data obtained from the laboratory and field studies. By participating in different projects being conducted in the laboratory, attending conferences, seminars and workshops I have gained the skills and experience necessary for the initiation of my career as a scientist and the establishment of strong collaborations with the University of Virginia and other institutions around the world. In brief, this program has given me the special opportunity to learn and share with scientists from the University of Virginia but also scientists from all over the world.   

Research activities and outcomes during training

The aim of my study was to understand the distribution of different parasitic and bacterial organisms involved in diarrheal diseases in the Venda population. Stool samples and serum samples were collected from hospitals and primary schools in the Venda region and shipped to the University of Virginia prior to my arrival. Different methods including conventional PCR, real time quantitative PCR, PCR-RFLP, Trichrome staining and Immunofluorescence (merifluor) were used to detect and characterize different organisms, mainly Cryptosporidium spp, Entamoeba histolytica, Microsporidia, Campylobacter spp, Arcobacter spp, Helicobacter pylori (H. pylori), Enteroaggregative E. coli (EAEC) and Clostridium difficile (C. diff) from the stool samples. I related the presence of these organisms to the physical presentation of the stools as well as the lactoferrin content and the occult blood content of the stools. The lactoferrin content of the stool informs the presence or not of intestinal inflammation in the patient who provided the stool specimen. Agglutination and ELISA tests were used to detect and quantify the lactoferrin level in the stools and the Hemoccult was used to determine the presence of occult blood in the stools. The results obtained have indicated that most of the organisms sought were a common cause of diarrhea and inflammation in the Venda region. Of interest was the ubiquitous presence of Cryptosporidium in the whole population without distinction between patients visiting the hospitals and school children. Cryptosporidium hominis was the most common species observed (About 80% of all Cryptosporidium infections) while C. parvum was found in about 20% of the samples tested. Helicobacter pylori was also present in the whole population and was even more common among the school children. However, E. histolytica and Campylobacter spp were mostly found in the hospitals and mostly in diarrheal samples. Campylobacter concisus was described for the first time in this population and was found in about 3% of the population. Arcobacter spp were also described but A. butzleri was the only species associated with diarrhea and intestinal inflammation. Enterocytozoon bieneusi was the only microsporidial species found in the population and was the most common pathogen in HIV-positive patients but was not associated with inflammation. This study has laid the foundation for further investigations of the impact of diarrheal diseases on the Venda population.

Conferences attended

  • 55th Annual meeting of the American Society of Tropical Medicine and Hygiene, November 12 - 16, 2006, Atlanta, Georgia, USA
  • Infectious Diseases and Biodefense Research Day, October 23, 2006, University of Virginia, Charlottesville, Va, USA
  • XIth International Conference on Parasitology, 5 to 11 August 2006, Glasgow, Scotland
  • DMID International Research in Infectious Diseases (IRID) Annual Meeting, May 28 to June 1st 2006, Washington DC, USA
  • General Meeting, American Society for Microbiology, May 21st to 25th 2006, Orlando, Fla, USA
  • 1st Annual Medical School Symposium on Global Health, Friday October 14th 2005, Charlottesville, Va, USA
  • 25th Annual Department of Internal Medicine Research Day 2006 Monday May 1st, Charlottesville Va, USA
  • American Society of Tropical Medicine and Hygiene (ASTMH) 54th Annual meeting, December 11 - 15 , 2005, Hilton Washington Hotel and Towers, Washington, DC, USA
  • Microbes in a Changing World: International Union of Microbiology Societies (IUMS) Congress, July 23 - 28, San Francisco, CA, USA

Special training (Courses and Seminars)

  • Statistical Analysis for Genetic Epidemiology (SAGE) Short course. 14th - 15th December 2006, Newcomb Hall, University of Virginia, Organized by Dr. Robert Elston of the Case Western Reserve University, Cleveland, Ohio, USA
  • Introduction to Microarray Data Analysis, December 7th - December 8th, 2006. Presented by the Pathogen Functional Genomic Resource Centre (PFGRC) at the Institute of Genomic Research (TIGR), Rockville, Maryland, USA
  • Knockouts (and Knock-ins) in Parasites: Promises and Challenges, by the American Society of Tropical Medicine and Hygiene. November 11, 2006, Atlanta Marriott Marquis, Atlanta, Georgia, USA
  • Bioinformatics: Prokaryotic Annotation and Analysis Training, 10th - 12th October 2006, The Institute For Genomic Research, Rockville, MD, USA
  • Microbes and Mucosal Immunity, June 28th to July 1st 2006, Jordan Hall Conference Center, University of Virginia, Charlottesville, Va, USA
  • Introduction to Clinical Research Faculty Development Program, May - June 2006, University of Virginia, Charlottesville, Va, USA
  • Introduction to Flow Cytometry, November 14 - 16, 2005, University of Virginia, Charlottesville, Va, USA
  • Chemical Safety and Waste Training, September 2005, University of Virginia, Charlottesville, Va, USA
  • Bloodborne Pathogen and Biosafety Training, August 2005 and September 2006, University of Virginia, Charlottesville, Va, USA
  • Laboratory Animal Care and Use Training, October 28, 2005, University of Virginia, Charlottesville, Va, USA
  • Laboratory Animal Handling, August 2005, University of Virginia, Charlottesville, Va, USA
  • Shipping of Infectious Substances, November 10, 2005, University of Virginia, Charlottesville, Va, USA

PUBLICATIONS

Published in Peer reviewed journals

1.         Samie A., Obi CL, Barrett LJ, Powell SM, Guerrant RL. Prevalence of Campylobacter species, Helicobacter pylori and Arcobacter species in stool samples from the Venda region, Limpopo, South Africa: Studies using molecular diagnostic methods, Journal of Infection (2006), doi:10.1016/j.jinf.2006.10.047

2.         Samie A, Obi LC, Bessong PO,  Stroup S, Houpt E, Guerrant RL (2006) Prevalence And Species Distribution Of E. Histolytica And E. Dispar In The Venda Region, Limpopo, South Africa. American Journal of Tropical Medicine and Hygiene, Sep 1, 2006, Volume 75, Number 3.

3.         Samie A, Bessong PO, Obi CL, Sevilleja JEAD, Stroup S, Houpt E, Guerrant RL (2006) Cryptosporidium species: Preliminary descriptions of the prevalence and genotype distribution among school children and hospital patients in the Venda region, Limpopo Province, South Africa. Experimental Parasitology. 114: 314 - 322.

4.         Steiner TS, Samie A, Guerrant RL, (2006) Infectious Diarrhea: New Pathogens and New Challenges in Developed and Developing Areas. Clinical Infectious Diseases, 43(4):408-10.

Submitted for Publication

1.         Samie A, Obi CL, Tzipori S, Weiss LM, Guerrant RL. (2006). Microsporidiosis in South Africa: PCR detection in stool samples of HIV positive and HIV negative individuals and school children in the Vhembe district, Limpopo Province. Transactions of the Royal Society of Tropical Medicine and Hygiene (September 2006)

2.         Parr JB, Sevilleja JE, Samie A, Alcantara C, Stroup SE, Fayer R, Houpt ER, Guerrant RL. (2006) Detection and Quantification of Cryptosporidium parvum in HCT-8 Cells and Human Fecal Specimens using Real-time PCR. AJTMH (October 2006).

In Preparation

1.         Samie A, Obi CL, Barrett L, Dillingham R, Sevilleja JE, Guerrant RL. (2006) Molecular Detection of Three Plasmid - Borne Genes of Enteroaggregative Escherichia coli in stool samples of patients and school children in the Vhembe district, Limpopo, South Africa, to be submitted to AJTMH

2.         Samie A, Obi CL, Stroup S, Houpt E, Njayou M, Sabeta CT, Mduluza T, Guerrant RL. Genetic diversity of Entamoeba histolytica from Africa based on the serine- rich gene polymorphism. To be submitted to Exp Parasitol

3.         Samie A, Obi CL, Guerrant RL. Community acquired Clostridium difficile in the Venda region, South Africa.

Conference presentations

  • Samie A, Obi CL, Tzipori S, Weiss LM, Guerrant RL. (2006). Microsporidiosis in South Africa: PCR detection in stool samples of HIV positive and HIV negative individuals and school children in the Vhembe district, Limpopo Province. Transactions of the Royal Society of Tropical Medicine and Hygiene. 55th annual meeting of the ASTMH, November 12 - 16, 2006, Atlanta, Georgia
  • Samie A, Obi CL, Dillingham R, Guerrant RL. Distribution of Enteroaggregative Escherichia coli virulence-related genes by multiplex PCR in stool samples of HIV-positive and HIV-negative individuals and primary school children in Venda, South Africa. Infectious Diseases and Biodefense Research Day, October 23, 2006, University of Virginia, Charlottesville, Va, USA
  • Samie A, Obi CL, Stroup S, Houpt E, Guerrant RL. Prevalence and Genetic Diversity of Entamoeba histolytica from Africa Based on the Serine-Rich Gene Polymorphism. 11th International Congress of Parasitology, 6th to 11th August 2006, SECC, Glasgow, Scotland.
  • Samie A, Bessong PO, Obi CL, Stroup S, Houpt E, Guerrant RL. Genetic Diversity of Entamoeba Histolytica from Africa Based on the Serine- Rich Gene Polymorphism DMID International Research in Infectious Diseases (IRID) Annual Meeting, May 30 - June 2, 2006. Washington, DC, USA.
  • Samie A, Bessong PO, Obi CL, Sevilleja JEAD, Stroup S, Houpt E, Guerrant RL (2006) Prevalence and genotype distribution of Cryptosporidium species among school children and hospital patients in the Venda region, Limpopo Province, South Africa. ASM general Meeting, May 2006, Orlando, Fla, USA.
  • Samie A, Obi CL, Barrett L, Dillingham R, Sevilleja JE, Guerrant RL . Prevalence of enteroaggregative Escherichia coli (EAGEC) based on the "aggR" gene sequences in stool samples of HIV-positive and HIV-negative individuals in the Venda region, Limpopo, South Africa. 25th Annual Department of Internal Medicine Research Day 2006 Monday May 1st, Charlottesville, Va, USA
  • Samie A, Obi CL, Ramalivhana J (2005) Antibiotic Susceptibility Profiles and Inhibitory Activities of Selected Medicinal Plant Extracts Against Environmental and Clinical Campylobacter Isolated in the Venda Region of South Africa IUMS Congress, 23 - 28 July 2005, San Francisco, CA, USA

Future plans

Upon my return to the University of Venda, my home institution, I will finish my thesis and hope to graduate in May 2007.

My research interest will be centered on the development of measures and intervention strategies for the prevention of diarrheal diseases in Africa in general and in Venda in particular. This involves the understanding of microbiological and socio-cultural factors involved in the transmission of diarrheal diseases in the region. The genetic factors that might be involved in the resistance or susceptibility of individuals to diarrheal pathogens as well as the long-term impact of diarrheal diseases in the community will be of special interest. The research I have conducted has set the basis for a continued strong collaboration with researchers in South Africa. This will be of great value in the implementation of diarrheal diseases research at the University of Venda.

In the recent future, I would like to understand the origin of Cryptosporidium infections in the Venda region. For that, environmental waters including river water, sewage and treated sewage from waste water treatment plants, pipe water, stored water in homes and animal feces will be screened from Cryptosporidium. If found, the Cryptosporidium isolates will be genotyped and the genotypes will be compared to those obtained from human subjects including those with diarrhea and those without diarrhea. This study will help uncover the source of transmission of Cryptosporidium in the population and the design of prevention strategies to curb the potential effect of these infections, mainly in children.

This project will set the basis and help initiate the study of the long-term impact of diarrheal diseases in the Venda population. It will aslo illuminate the impact of genetic polymorphisms of individuals on the susceptibility or resistance to diarrheal diseases, which constitute my long term goal.

Mentoring

At the Center for Global Health, apart from the exceptional mentoring of Dr Guerrant, I have learned from almost all the other fellows from Brazil, the Philippines, Haiti, Ethiopia, Japan and the USA. I have participated in other projects and discussions being conducted in the laboratory. Especially I have contributed to the study on the detection of Clostridium difficile in samples from the University of Virginia Health System in collaboration with Dr. Laurie Archbald-Panone, Dr. Cirle Alcantara and Jason Franaziak. I have also participated in the detection of intestinal pathogens from stool samples from HIV/AIDS patients from Haiti in collaboration with Dr. Rebecca Dillingham, Kate Dupnik, Etna Eyma and Dr. Em Sevilleja. I also learned about the impact of Cryptosporidial infection in nourished and malnourished mice as well as the impact of the supplementation with Alanine Glutamine on infection and malnutrition in mice with the help of colleagues from Brazil. I also participated in the development and confirmation of real time quantitative PCR for the detection of Cryptosporidium in cell cultures, clinical and environmental samples together with Dr EM Sevilleja and Jonathan Parr. I have also collaborated with Drs Eric Houpt, Suzanne Stroup and Carol Gilchrist on my study on Entamoeba histolytica.

I also participated in the committee for the selection of Center for Global Health Scholars from the University of Virginia to other institutions around the world and helped some UVa students in the development of ideas that could be implemented during their summer break studies abroad, mainly those with intention to travel to South Africa. I am currently working with two medical students at the University of Virginia to help them develop project proposals that could be implemented during their summer research program in South Africa and I have in the past worked with three other students on their projects. We will continue to communicate to strengthen the ties and help University of Virginia students to visit, learn and do research in South Africa and in Venda particularly. I hope to develop in the future grant proposals in collaboration with the Center for Global Health to be implemented in South Africa. The research will be conducted in sites in South Africa and the Center for Global Health at the University of Virginia. 

I hope to maintain this collaboration that will be of tremendous help for the building of important projects for the alleviation of diseases in human communities and the improvement of the health of individuals around the world and mainly in developing countries such as those where I come from.

My sincere thanks to the Center for Global Health and the Ellison and Pfizer Foundations. Special thanks to Pfizer Initiative in International Health Director W. Michael Scheld. In addition, thanks to Dr. Guerrant and the folks at the Center for Global Health.