Halil İbrahim ATABAY, Prof. Dr.

 

 

   Phone: +90 (232)-750 6282

   Fax     : +90 (232)-750 61 96

  email  : halilatabay[at]iyte.edu.tr

            

 DVM, Veterinary Faculty, İstanbul University, İstanbul, Turkey (1992)

 PhD,  Division of Food Animal Science, Bristol University, England (1998)

    

 PhD thesis

 ‘The Ecology of Campylobacters and Related Organisms in Food Animals’ (supervisor Dr Janet E.L. Corry)

Postdoctoral study and scientific visits

 2001-2002         Senior Research Scientist-Danish Veterinary Institute, Dept. Poutry, Fish and Fur Animals, Aarhus, Denmark

August, 2006      Visiting scientist-Department of Microbiology, Faculty of Medicine, Lund University, Sweden

 
     RESEARCH INTERESTS

  • Conventional and molecular isolation/detection and identification of foodborne pathogens with particular references to Campylobacter, Arcobacter and Helicobacter species in various types of samples

  • Use of PCR assays for the detection and identification of bacterial species

  • Genotyping of foodborne pathogenic bacteria using nuclic acid-based subtyping techniques

  • Determination of the antibiotic susceptibility of pathogenic bacteria
  PROFESSIONAL EXPERIENCE

Professor, İzmir Institute of Technology                                                2009-

Food Engineering Department, Urla, İzmir, Turkey

 

Associate Professor, İzmir Institute of Technology                                2007 -2009

Food Engineering Department, Urla, İzmir, Turkey

 

Associate Professor, Kafkas University                                                  2003 - 2007

Veterinary Faculty, Kars, Turkey

 

Assistant Professor, Kafkas University                                                  1999 - 2003

Veterinary Faculty, Kars, Turkey

 

Research Assistant, Kafkas University                                                   1993 - 1999

Veterinary Faculty, Kars, Turkey

 

   HONORS

  • 1993 awarded a scholarship by a competitive nation-wide examination by the Higher Educational Council of Turkey in order to do a PhD in England.

  • 1996 FEMS Fellow, fellowship from the Federation of European Microbiological Societies was awarded to work for five weeks at the Danish State Veterinary Laboratory, Copenhagen, Denmark, gaining experience in both genotyping and phenotyping methods for differentiation of bacterial species and strains (a full report regarding this visit was published in Society of Applied Bacteriology Newsletter, March 1997).

       PROJECTS INVOLVED    

  1. Comparison of the productivity of cefoperazone amphotericin teicoplanin (CAT) agar and modified charcoal cefoperazone deoxycholate (mCCD) agar for various strains of Campylobacter, Arcobacter and Helicobacter pullorum.

  2. Assessment of a newly developed Oxoid Arcobacter Enrcihment medium and comparison with two media developed for enrichment of Campylobacter and Arcobacter spp. using standard strains of both species.

  3. Evaluation of Oxoid Arcobacter Enrichment Medium using naturally contaminated meat samples. 

          These projects were successfully completed and full reports were submitted to the Company at the end of the each project.

  1. The prevalence of Arcobacter spp. on chicken meat sold in Turkish markets and the sub-typing of the isolates using RAPD-PCR.  Project No. TUBITAK/TOGTAG/TARP-2376.

  2. The importance of poultry campylobacteria in human diseases (granted by Danish Research Council, grant no. 53-01-0004).  The prevalence and diversity of Arcobacter species in broiler chickens, turkeys and ducks were investigated using conventional isolation and molecular detection methods (a multiplex–PCR assay) at the Danish Veterianry Institute,  Department of Poultry, Fish and Fur Animals, Arhus, Denmark.  The project also involved identification of isolated strains using a comphrehensive phenotypic scheme and a PCR technique.  Subtyping of the isolates were also performed using RAPD-PCR, PFGE and AFLP.  

         Involved for two months with a EU granted project entitled Decontamination of foods using high temperature under sub-atmospheric pressure’ as a Research   Assistant run by University of Bristol, Division of Food Animal Science.   

 

        EXPERIENCE AND ACHIEVEMENTS

  • have a broad background within the field of conventional isolation, identification and subtyping Campylobacter, Arcobacter and Helicobacter spp. Also have experience in working with various molecular techniques (such as agarose gel electrophoresis, SDS-PAGE, PFGE, PCR, AFLP, restriction endonuclease analysis).

  • involved in numerous projects and lectures (both undergraduate and postgraduate) related to the area of microbiology.

  • spent two weeks at the Chemistry Laboratory of the University of Reading UK learning the  Pyrolysis Mass Spectrometry technique and applying this technique to the differentiation of various strains of Campylobacter and related taxa, and

  • spent one week at the Preston Public Health Laboratory (Campylobacter Reference Unit UK), working on the isolation, identification and sub-typing of Campylobacter spp. from human faeces with Dr. David Wareing under the supervision of Prof. F.J. Bolton.

 

         REVIEWER

  • Veterinary Microbiology

  • Journal of Applied Microbiology

  • Applied and Environmental Microbiology

  • FEMS Microbiology Letters

  • FEMS Immunology and Medical Microbiology

  • Letters in Applied Microbiology

  • International Journal of Food  Microbiology

  • Turkish Journal of Veterinary and Animal Sciences
  PUBLICATIONS

  Total Number of Citations : 400 (Source: Web of Science)

   RESEARCH ARTICLES PUBLISHED  

A1. Atabay, H.I., J.E.L. Corry and S.L.W. On, ‘Isolation and characterization of a novel catalase-negative, urease-positive Campylobacter from cattle faeces,'  Letters in Applied Microbiology, 24, 59-64 (1997).

A2. Atabay, H.I. and J.E.L. Corry, ‘The prevalence of campylobacters and arcobacters in broiler chickens,’  Journal of Applied Microbiology  83, 619-626 (1997).

A3. Corry, J.E.L. and H.I. Atabay, ‘Comparison of the productivity of cefoperazone amphotericin teicoplanin (CAT) agar and modified charcoal cefoperazone deoxycholate (mCCD) agar for various strains of Campylobacter, Arcobacter and Helicobacter pullorum,’  International Journal of Food Microbiology , 38, 201-209 (1997).

A4. Atabay, H.I. and J.E.L. Corry, ‘The isolation and prevalence of campylobacters from dairy cattle using a variety of methods,’ Journal of Applied Microbiology, 84, 733-740 (1998).

A5. On, S.L.W., H.I. Atabay, J.E.L. Corry, C.S. Harrington, and P. Vandamme, ‘Emended description of Campylobacter sputorum and revision of its infrasubspecific (biovar) divisions, including C. sputorum biovar paraureolyticus, a urease-producing variant from cattle and humans,’  International Journal of Systematic Bacteriology, 48, 195-206 (1998).

A6. Atabay, H.I. and J.E.L. Corry, ‘Evaluation of a new arcobacter enrichment medium and comparison with two media developed for enrichment of Campylobacter spp.,’ International Journal of Food Microbiology , 41, 53-58 (1998).

A7. Atabay, H.I., J.E.L. Corry and S.L.W. On, ‘Diversity and prevalence of  Arcobacter spp. in broiler chickens,’ Journal of Applied Microbiology, 84, 1007-1016 (1998).

A8. Atabay, H.I., J.E.L. Corry and S.L.W. On, ‘Identification of unusual Campylobacter-like isolates from poultry products as Helicobacter pullorum,’ Journal of Applied Microbiology, 84, 1017-1024 (1998).

A9. Ridsdale, J.A., H.I. Atabay and J.E.L. Corry, ‘Prevalence of campylobacters and arcobacters in ducks at the abattoir,’ Journal of Applied Microbiology, 85, 567-573 (1998).

A10. On, S.L.W., H.I. Atabay and J.E.L. Corry, ‘Clonality of Campylobacter sputorum bv. paraureolyticus determined by macrorestriction profiling and biotyping, and evidence for long-term persistent infection in cattle,’  Epidemiology and Infection, 122, 175-182 (1999).

A11. Aydin, F., H.I. Atabay and M. Akan, ‘The isolation and characterization of Campylobacter jejuni subsp. jejuni from domestic geese (Anser anser),’ Journal of Applied Microbiology, 90, 637-642 (2001).

A12. Atabay, H.I. and F. Aydin, ‘Susceptibility of Arcobacter butzleri isolates to 23 antimicrobial agents,’ Letters in Applied Microbiology, 33, 430-433 (2001).

A13. Atabay, H.I., D.D. Bang, F. Aydin, H.M. Erdogan and M. Madsen, ‘Discrimination of Arcobacter butzleri isolates from Turkish poultry by polymerase chain reaction-mediated DNA fingerprinring. Letters in Applied Microbiology, 35, 141-145 (2002).

A14. Atabay, H.I., Aydin, F., Houf, K., Sahin, M. And Vandamme, P. ‘The prevalence of Arcobacter spp. on chicken carcasses sold in retail markets in Turkey, and identification of the isolates using SDS-PAGE (Short Comm.). International Journal of Food Microbiology , 81: 21-28 (2002).

A15. On, S.L.W., Harrington, C.S. and Atabay, H.I. (2003) ‘Differentiation of Arcobacter species by numerical analysis of AFLP profiles and description of a novel Arcobacter from pig abortions and turkey faeces. Journal of Applied Microbiology 95(5):1096-105.

A16. On, S.L: W., Atabay, H.I., Amisu, K.O., Coker, A.O. and Harrington, C.S. (2004). ‘Genotyping and genetic diversity of Arcobacter butzleri by amplified fragment length polymorphism (AFLP) analysis.  Letters in Applied Microbiology 39(4):347-352.

A17. Ongor, H., Çetinkaya, B., Acik, M.N., Atabay, H.I. (2004). ‘Investigation of Arcobacters in Meat and Faecal Samples of Clinically Healthy Cattle in Turkey. Letters in Applied Microbiology 38:339-344.

A18. Sahin, M Atabay, H.I., , Bicakci, Z. And Unver A. (2006) ‘Cases of Tularaemia in Turkey. European Journal of Infectious Diseases. Kobe Journal od Medicine (in press).

A19. Yaman, H., Elmali, M., Ulukanli, Z., Atabay, H.I. AND  Tekinsen K.K. (2005). ‘Presence of Campylobacter (C.jejuni) in recreational, lake and stream water and fresh fish in Turkey Archıv Fur Lebensmıttelhygıene 56, 83-86.

A20. Ünver, A., Erdoğan H.M., Atabay, H.I., Sahin, M. And Celebi, O. (2006) ‘Isolation, identificaion, and molecular characterization of Brucella melitensis from aborted sheep fetuses in Kars, Turkey. Revue Méd. Vét. 157, 42-46.

A21. Akkaya, L., Kenar, B., Atabay, H.I. and Alisarli, M. (2006) ‘The prevalence of verocytotoxigenic E. coli O157:H7 in minced and ground beef sold in Afyon Province, Turkey. Archiv Für Lebensittelhygiene 57, 10-12.

A22. Akkaya, L., Atabay, H.I., Kenar, B. and Alisarli, M. (2006) ‘Prevalence of verocytotoxigenic E. coli O157:H7 on chicken carcasses sold in Turkey. Bull. Vet. Inst. Pulawy 50, 513-516

A23. Atabay, H.I., Waino, M. and Madsen, M. (2006) ‘Detection and diversity of various  Arcobacter species in Danish poultry. International Journal of Food Microbiology 109: 139-145.

A24. Aydin, F., Gumussoy, K.S., Atabay, H.I. Ica, T. and Sen, S. (2007) ‘Molecular analysis of Arcobacter species isolated from various places in Turkey using RAPD-PCR. Journal of Applied Microbiology, 103: 27-35.

A25. Atabay, H.I., Unver, A., Sahin, M., Otlu, S., Elmali, M. And Yaman, H. (2007) ‘Isolation of various Arcobacter species from Domestic Geese (Anser anser). Veterinary Microbiology (in press).                                                                                                                            

A.26. Corry, J.E.L. and H.I. Atabay, (2001). ‘Poultry as a source of Campylobacter and related oranisms,’  Journal of Applied Microbiology,90, 96S-114S.

A27. Aydın, F., H.İ. Atabay, O. Genç, H. Atahan ve M. Bölük, ‘Kars yöresinde Şarbonun epizootiyolojisi ve epidemiyolojisi.  1995-2000 yıllarına ait olguların değerlendirilmesi ve değişik orijinli Bacillus anthracis suşlarının özellikleri,’ Kafkas Üniversitesi, Veteriner Fakültesi Dergisi, 6 (1-2), 55-59 (2000).

A28. Atabay, H.İ. ve F. Aydın, ‘Mastâ antimikrobik rezistotiplendirme metodunun broylerlerden izole edilen Arcobacter butzleri suşlarına uygulanması’  Veteriner Bilimleri Dergisi, 17 (1), 149-152 (2001).

A29. Beytut, E., H.I. Atabay and Akca, A, ‘Tuberculosis and sarcosporidiosis in the periorbital location in a hen, Kafkas Üniversitesi, Veteriner Fakültesi Dergisi, 7 (2), 213-217 (2001).

A30. Aydın, F., H.İ. Atabay and E. Beytut, ‘Lamb deaths associated with Camylobacter coli,’ Veteriner Hekimleri Mikrobiyoloji Dergisi, 1 (1), 31-33 (2001).

A31. Atabay, H.I., F. Aydin, C. Helps and M. Sahin, ‘Identification of Arcobacter isolates using 16S rDNA restriction endonuclease analysis of PCR products (ARDRA),’ Veteriner Hekimleri Mikrobiyoloji Dergisi, 1 (1), 56-61 (2001).

A32. Unver, A., M. Çitil, H.İ. Atabay, S. Otlu ve  M. Şahin. Yenidoğan Buzağı İshallerinden Salmonella ve Citrobacter Türlerinin İzolasyon ve İdentifikasyonu. Kafkas Üniversitesi, Veteriner Fakültesi Dergisi, 11(1): 51-53 (2005).

A33. Unver, A., H. M. Erdogan, H.İ. Atabay, M. Şahin, V. Güneş, M. Çitil, ve H. İ. Gökçe  . Sığır atıklarından izole edilen Brucella türlerinin RAPD-PCR ile genotiplendirilmesi. Kafkas Üniversitesi, Veteriner Fakültesi Dergisi, (2005).

A34. Unver, A., H.İ. Atabay, , M. Şahin, Ö. Çelebi ve K. Gençtav. Arcobacter türlerinin atık kuzulardan izolasyonu ve multipleks PZR ile identifikasyonu. Kafkas Üniversitesi, Veteriner Fakültesi Dergisi, (2005).

A35 Aydın, F. ve H.I. Atabay, ‘Arcobacter türleri: Sınıflandırma, genel özellikler, izolasyon ve identifikasyon metotları,’ Veteriner Hekimleri Mikrobiyoloji Dergisi.  

INTERNATIONAL CONFERENCES

B1.Atabay, H.I., J.E.L. Corry and D.E. Post, ‘Comparison of the productivity of a variety of selective media for Campylobacter and Arcobacter species and Helicobacter pullorum,’  Abstracts of the 8th Int. Workshop on Campylobacters, Helicobacters and Related Organisms, A1/2, Winchester, England, 1995 (sözlü bildiri).

B2. Atabay, H.I., J.E.L. Corry and S.L.W. On, ‘Detection of various Arcobacter spp. in broiler chickens,’ Abstracts of the 137th Ordinary Meeting of Society for General Microbiology, Heriot-Watt University (24-27 March), P3, Edinburgh, UK., 1997 (poster).

B3.Atabay, H.I., J.A. Ridsdale, J.E.L. Corry and S.L.W. On, ‘Campylobacter, Arcobacter and Helicobacter spp. in broiler chickens and ducks,’ Abstracts of the 9th Int. Workshop on Campylobacter, Helicobacter and Related Organisms, I-1, Cape Town, South Africa,1997 (poster).

B4. Atabay, H.I. and J.E.L. Corry, ‘Assessment of performance of Oxoid Arcbacter Enrichment Medium and comparison with other enrichment media,’ Abstracts of the 9th International Workshop on Campylobacter, Helicobacter and Related Organisms, A1 Cape Town, South Africa, 1997 (poster).

B5. On, S.L.W., H.I. Atabay, J.E.L. Corry, C.S. Harrington and P. Vandamme, ‘Urease-positive Campylobacter sputorum: zoonotic implications. Abstracts of the 9th International Workshop on Campylobacter, Helicobactes and Related Organisms, J9, Cape Town, South Africa, 1997.

B6. On, S.L.W., H.I. Atabay and C.S. Harrington, ‘Evaluation of a probability matrix for identifying campylobacteria,’ Campylobacter, Helicobacter and related organisms, Proc. 9th International Workshop on Campylobacter, Helicobacter and Related Organisms, ed. Lastovica, A.J., D.G. Newell and E.E. Lasrovica, 232-235, Cape Town University, South Africa, 1997 (poster).

B7. Atabay, H.I., S.L.W. On and J.E.L. Corry, ‘Use of novel techniques for the isolation of unusual campylobacters,’ Abstracts of the Pathogenic Microorganisms in Poultry and Eggs/Monitoring Producers, Rapid Detection Methods and Techniques, European Commision COST Action 97, Working Group 4 Workshop, Institute for Animal Health, Compton, Newbury, UK, 1996 (sözlü bildiri ve poster).

B8. Ridsdale, J.A., H.I. Atabay and J.E.L. Corry, ‘Campylobacter and Arcobacter spp. isolated from the carcasses and caeca of commercially reared ducks,’ Abstracts of the Congress on Anaerobic Bacteria and Anaerobic Infections (Anaerobe Society of the Americas), 32PP, 24-26 April, Buenos Aires, Argentina, 1999 (poster).

B9. Atabay, H.I., J.E.L. Corry, C. Helps, W.K. Kwenin and J.A. Ridsdale, ‘Isolation of Arcobacter spp. from naturally contaminated samples using Oxoid Arcobacter Enrichment Medium and identification using SDS-PAGE and 16SrDNA restriction analysis’  Abstracts of the 10th Int. Workshop on Campylobacter, Helicobacter and Related Organisms, RE1, 12-16 September, Baltimore, USA 1999.

B10. Corry, J.E.L. and H.I. Atabay, ‘Poultry as a source of Campylobacter and related oranisms.  ‘Campylobacter, Helicobacter and Arcobacter’,’  Society for Applied Microbiology, Summer 2000 Conference, S15, University of Strathclyde, Glasgow, UK, 2000 (Invited speaker).

B11. Atabay, H.I. and J.E.L.  Corry, ‘Resistotyping of Helicobacter pullorum strains isolated from broiler chickens,’ Abstracts of the 11th Int. Workshop on Campylobacter, Helicobacter and Related Organisms, Freiburg, Germany, Int. J. Medical Microbiol., 291, (supl. 31), P-28, 2001 (poster).

B12. Atabay, H.I., F. Aydın, P. Vandamme and K.  Houf, ‘The prevalence of arcobacters on chicken carcasses sold in retail markets in Turkey and identification of the isolates using SDS-PAGE of whole-cell proteins and a multiplex-PCR assay,’ Abstracts of the 11th Int. Workshop on Campylobacter, Helicobacter and Related Organisms, Freiburg, Germany, Int. J. Medical Microbiol., 291, (supl. 31), P-02, 2001 (poster).

B13. Atabay, H.I., M. Wainø and M.  Madsen, ‘Comparison of PCR and conventional isolation methods for detection of arcobacters in Danish poultry.  Identification of isolates using multiplex-PCR and phenotypic tests,’  Abstracts of the 11th Int. Workshop on Campylobacter, Helicobacter and Related Organisms, Freiburg, Germany, Int. J. Medical Microbiol., 291, (supl. 31), P-05, 2001 (poster).

B14. Corry, J.E.L., V.M. Allen, F. Aydin, H.I. Atabay, S.A., Bull, G. Domingue and T.  Humphrey, ‘Colonisation of broiler chickens with thermophilic campylobacters in three different integrated poultry companies during rearing and slaughter,’ Abstracts of the 11th Int. Workshop on Campylobacter, Helicobacter and Related Organisms, Freiburg, Germany, Int. J. Medical Microbiol., 291, (supl. 31), E-27, 2001 (poster).

B15. Atabay, H.I. and F.  Aydin, ‘Susceptibility of Arcobacter butzleri isolates to various microbial agents,’ Abstracts of the 11th Int. Workshop on Campylobacter, Helicobacter and Related Organisms, Freiburg, Germany, Int. J. Medical Microbiol., 291, (supl. 31), P-07, 2001 (poster).

B16. On, S.L.W., K. Amisu, R.D. Isopekhi, A.O. Coker, E. Oolsson-Engvall, F. Aydin, H.I. Atabay and C.S. Harrington, ‘Genetic diversity of Arcobacter butzleri investigated by AFLP profiling: identification of Nigeria, Turkish and Swedish clonal types,’ Abstracts of the 11th Int. Workshop on Campylobacter, Helicobacter and Related Organisms, Germany, Int. J. Medical Microbiol., 291, (supl. 31), P-03, 2001 (poster).  

     

BOOK CHAPTER

C1. Corry, J.E.L., Atabay, H.I., Forsythe, S.J. and Mansfield, L.P. (2003) Culture media for the isolation of camplyobacters, helicobacters and arcobacters (Chapter 18).  Kitap: Handbook of Culture Media for Food Microbiology ed. Corry J.E.L., Curtis, G.D.W. and Baird, R.M. sayfa: 271-316. Elsevier: Hollanda

NATIONAL CONFERENCES  

D1. Atabay, H. İ. ve F. Aydın, ‘Mast resistotyping metodunun broilerlerden izole edilen Arcobacter butzleri suşlarına uygulanması,’  IV. Ulusal Veteriner Mikrobiyoloji Kongresi (Uluslararası Katılımlı), Özet no. 38, Ankara, 2000 (sözlü bildiri).

D2. Şahin, M., A. Ünver, S. Otlu ve H.İ. Atabay. Atlarda Neorickettsia risticii ve Brucella abortus’un seroprevalansının araştırılması. VI. Ulusal Veteriner Mikrobiyoloji Kongresi (Uluslararası Katılımlı), 14-16 Eylül 2004, Elazığ (sözlü bildiri).

D3. Şahin, M., H.İ. Atabay, S. Otlu ve A. Ünver ve Ö. Çelebi. Kars ve çevresininde bulunan insan, sığır ve koyunlarda brusellozisin prevelansının serolojik ve kültürel metotlarla araştırılması. VI. Ulusal Veteriner Mikrobiyoloji Kongresi (Uluslararası Katılımlı), 14-16 Eylül 2004, Elazığ (Poster).

D4. Ünver, A., H.M. Erdoğan, H.İ. Atabay, M. Şahin, V. Güneş, M. Çitil ve Halil İ. Gökçe. Sığır atıklarından izole edilen Brucella türlerinin RAPD-PCR ile genotiplendirilmesi. Veteriner İç Hastalıkları Kongresi, 4-7 Temmuz 2005, Kars.

D5. Atabay, H.İ., ‘FEMS Fellowship Report,’ Society for Applied Bacteriology (İngiltere) Newsletter, 19-20 March, 1997.