Cv Niyazahmed India
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Curriculum Vitae of Dr Niyaz Ahmed
1) Name: Niyaz Ahmed 2) Nationality and Date of Birth: Indian, December 25, 1971 3) Contact Details and Affiliation: Staff Scientist and Group Leader, Pathogen Evolution Group Centre for DNA Fingerprinting and Diagnostics (CDFD),
Hyderabad, India Tel. 91 40 27151344 Fax. 91 40 27155610 Cell. 91 98 66282630, http://www.cdfd.org.in/stfniya.html 4) Brief Introduction Dr Niyaz Ahmed holds a graduate degree in Veterinary Medicine and a post graduate degree in Molecular Biology. He is currently the leader of the Pathogen Evolution Program at the CDFD (a premier institute of enquiry and learning in modern biology, funded by the Federal Government of India), Hyderabad. His research involves molecular genetic mechanisms underlying evolution of fitness and virulence in pathogenic bacteria such as Helicobacters, Mycobacteria and Spirochetes. He has been working on several important research projects funded by national and international agencies such as the DBT, ICMR, WHO, ISID, INSERM, WOTRO etc. Dr Ahmed has authored 60 research papers in high impact journals. He is the co-founder and secretary of the International Society for Genomic and Evolutionary Microbiology, an international learned body, currently headquartered at Sassari, Italy. He is an elected member of the National Academy of Sciences of India. 5) Principal Research Interests (brief) Molecular epidemiology and evolution of bacterial pathogens, evolution of virulence and fitness in pathogenic bacteria, biology of the human gastric pathogen H. pylori and its role in gastric cancers.
6) Summary of Principal Research Achievements Helicobacter pylori, Mycobacterium tuberculosis and leptospira and are some of the bacterial pathogens that trigger diseases with a complex interplay between infection dynamics, pathogen biology and host immune responses. The whole genome sequence determination has greatly facilitated our understanding of these pathogens. The human gastric pathogen H. pylori is presumed to be co-evolved with its human host and is again a very highly diverse and robust pathogen. Our 'geographic genomics' study tests the theory that H. pylori existed in humans as a benign bacterium for thousands of years until it acquired some virulence factors from the microorganisms abundant in the human societies of the neolithic period, after the domestication of agriculture and livestock. We found traces of East Asian ancestry in the gene pool of Native Peruvian strains (Amerindian?). This finding supports ancient human migration across the Beringstrait (20,000 years BP). We also attempted to support the idea that the major single virulence factor of the bacterium, the cag Pathogenicity Island (cagPAI) was acquired during different times, at different places in the world and from a 'local' microbial source. We followed this with theoretical approaches to find significant overlap among the H. pylori population expansion time and domestication of agriculture in the world. This study provides some new insights into the ancient origins and diversity of H. pylori and the significance of such diversity in the development of gastroduodenal pathology. Why has this bacterium survived for this long time in humans? Does this association makes the colonization beneficial or of low biological cost? These are the questions that need to be answered in the near future. Tuberculosis is the disease with a highest morbidity and mortality worldwide. The disease haunts millions of people in India with a huge death rate. The genetic diversity and evolutionary history of the underlying M. tuberculosis strains are largely unknown in the context of this country that has earned dubious distinctions for tuberculosis prevalence. Our ongoing, large-scale analysis of hundreds of strains of tubercle bacilli highlighted a clear predominance of ancestral M. tuberculosis genotypes in the Indian subcontinent, compared to other regions of the world, and support the opinion that India is a historically ancient endemic focus of tuberculosis. It is hypothesized that such 'ancient' bacilli are relatively 'docile' than some of the highly 'killer' ones such as the highly disseminating Beijing types which harbor inherent propensity to acquire multiple drug resistance (MDR) and are spreading in India through major metropolitan cities. Beijing strains are likely to evade and replace ancestral reservoirs of M. tuberculosis in the country. If that happens, India will probably face large, institutional outbreaks involving hospital wards, prisons, schools etc. This is perhaps a major issue that needs to be addressed in the post-genomic scenario, with the same magnitude of zeal that researchers have shown towards drug discovery and diagnostic or vaccine development. Leptospirosis is another major pestilence, a worldwide zoonosis caused by the spirochetes of the genus Leptospira. The leptospires have been extremely diverse pathogens having more than three hundred different strains or serovars with specific geographic distribution. But this enormous inventory of serovars, based mainly on an ever-changing surface antigen repertoire, throws an artificial and unreliable scenario of strain diversity. It is therefore difficult to track strains whose molecular identity keeps changing according to the host and the environmental niches they inhabit and cross through. To address this problem, we have developed highly sophisticated genotyping systems based on integrated genome analysis approaches to correctly identify and track leptospiral strains. These approaches are expected to greatly facilitate epidemiology of leptospirosis apart from deciphering the origins and evolution of leptospires in a global sense. 7) Technology for licensing/freelancing
A) Genomics platform for molecular fingerprinting of H. pylori strains and an integrated database of disease associated and benign strains from different human populations -genoBASE pylori ® (http://www.cdfd.org.in/amplibase/HP)
B) Genomics platform for highthroughput molecular genotyping of M. tuberculosis and a global knowledgebase of circulating genotypes in endemic and non-endemic zones of the world -AmpliBASE MT ® (http://www.cdfd.org.in/amplibase/) 8) Relevant job positions held, including current position Staff Scientist III and Group Leader, Pathogen Evolution Group, CDFD: August 2003 till date Staff Scientist II, CDFD: September 1998 to August 2003 Staff Scientist II, CDFD on contractual appointment: March 1998 to September 1998 Research Fellowship, Molecular Biology Laboratory, National Dairy Research Institute, Karnal, India: July 1995 to June 1998. 10) Important professional and intellectual recognition held
•
General Secretary, International Society for Genomic and Evolutionary Microbiology (ISOGEM), University of Sassari, Italy (April 2005 till date).
•
Elected to the membership of the National Academy of Sciences of India (lifetime).
•
Served as an Executive Committee member of the Indian Leptospirosis Society (for 2003-2005).
•
Associate Editor, Annals of Clinical Microbiology and Antimicrobials (ACMA), a BioMed Central journal (January 2005 till date).
•
Member of the Editorial Board, Infectious Agents and Cancer (IAC), a BioMed Central journal (September 2006 till date).
11) Important publications in peer reviewed journals 1. 2.
3. 4.
5.
6. 7.
Devi SM, Ahmed I, Khan AA, Rahman SA, Alvi A, Sechi LA and Ahmed N (2006). Genomes of Helicobacter pylori from native Peruvians suggest admixture of ancestral and modern lineages and reveal a western type cag-pathogenicity island. BMC Genomics 7(1):191. Gutierrez MC, Ahmed N (joint first authors), Willery E, Narayanan S, Hasnain SE, Chauhan DS, Katoch VM, Vincent V, Locht C and Supply P (2006) Predominance of ancestral lineages of Mycobacterium tuberculosis in India suggests an ancient focus of tuberculosis in South Asia. Emerging Infectious Dis 12: 367-374. Rao KR, Ahmed N, Sriramula S, Sechi LA and Hasnain SE (2006) Rapid identification of M. tuberculosis Beijing genotypes on the basis of the Mycobacterial Interspersed Repeat Unit locus 26 signature. J Clin Microbiol 44(1):274-277. Sechi LA, Ahmed N, Felis GE, Dupre I, Cannas S, Fadda G, Bua A, Zanetti S. (2006) Immunogenicity and cytoadherence of recombinant heparin binding haemagglutinin (HBHA) of Mycobacterium avium subsp. paratuberculosis: Functional promiscuity or a role in virulence? Vaccine 24:236-243. Sechi LA, Mara L, Cappai P, Frothingam R, Ortu S, Leoni A, Ahmed N and Zanetti S (2006). Immunization with DNA vaccines encoding different mycobacterial antigens elicits a Th1 type immune response in lambs and protects against Mycobacterium avium subspecies paratuberculosis infection. Vaccine 24:229-235. Kenchappa P, Rao KR, Ahmed N, Joshi S, Ghousunnissa S, Vijayalakshmi V, and Murthy K. J. R. (2006). Fluorescent Amplified Fragment Length Polymorphism based molecular epidemiology of hospital infections in a tertiary care setting in Hyderabad, India. Infection Genetics Evol. 6:220-227. Ali SM, Khan AA, Ahmed I, Musaddiq M, Ahmed KS, Polasa H, Rao LV, Habibullah CM, Sechi LA, Ahmed N (2005) Antimicrobial activities of Eugenol and Cinnamaldehyde against the human gastric pathogen Helicobacter pylori. Ann Clin Microbiol Antimicrob 4:20.
8. 9. 10. 11.
12. 13. 14. 15. 16.
17. 18.
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20. 21.
22. 23. 24. 25.
Rao KR, Kauser F, Sriramula S, Zanetti S, Sechi LA, Ahmed N and Hasnain SE (2005). Analysis of genomic downsizing based on region of difference (RD) polymorphism profiling of Mycobacterium tuberculosis patient isolates reveals geographic partitioning. J Clin Microbiol 43:5978-5982. Sechi LA, Gazouli M, Ikonomopoulos J, Lukas JC, Scanu AM, Ahmed N, Fadda G and Zanetti S. (2005) Mycobacterium avium subsp. paratuberculosis, genetic susceptibility to Crohn's disease and the Sardinians: The way ahead. J Clin Microbiol 43:5275-5277. Ali S M, Khan AA, Tiwari SK, Ahmed N, Rao LV and Habibullah CM. Association between cagpathogenicity island in Helicobacter pylori isolates from peptic ulcer, gastric carcinoma and nonulcer dyspepsia subjects with histological changes. World J Gastroenterol. 11:6815-6822. Prouzet-Mauleon V, Hussain MA, Lamouliatte H, Kauser F, Megraud F and Ahmed N. (2005) Pathogen evolution in vivo: genome dynamics of two isolates obtained nine years apart from a duodenal ulcer patient infected with a single Helicobacter pylori strain. J Clin Microbiol. 43:42374241. Kauser F, Hussain MA, Ahmed I....Sechi LA and Ahmed N. (2005) Comparing genomes of Helicobacter pylori isolates recovered from ulcer disease patients in England. BMC Microbiol. 5:32. Ahmed N (2005) 23 years of the discovery of Helicobacter pylori: Is the debate over? Annals Clin Microbiol Antimicrobials 4:17. Kauser F, Hussain M A, Ahmed I, Ahmad N, Habeeb A, Khan A A and Ahmed N (2005) Comparing genomes of Helicobacter pylori strains from the high altitude desert of Ladakh, India J Clin Microbiol 43:1538-1545. Ahmed N and Sechi LA (2005) Helicobacter pylori and gastroduodenal pathology: New threats of the old friend. Annals Clin Microbiol Antimicrobials 4:1. Tiwari SK, Khan AA, Khan SA, Ali SM, Habeeb A, Kauser F, Hussain MA, Ahmed N and Habibullah CM. (2005). PCR based analysis of the cag-PAI of Helicobacter pylori from saliva: An approach for rapid molecular genotyping in correlation with disease status. J Gasteroenterol Hepatol 20:1560-1566. Hasnain SE and Ahmed N (2004). Leptospirosis. LANCET Infectious Dis 4: 543. Kauser F, Khan AA, Hussain MA, Carroll IM, Ahmad N, Tiwari S, Shouche Y, Das B, Alam M, Ali SM, Habibullah CM, Sierra R, Megraud F, Sechi LA and Ahmed N (2004). The cag pathogenicity island (cag-PAI) of Helicobacter pylori is disrupted in majority of patient isolates from different human populations. J Clin Microbiol 42: 5302-5308. Abid Hussain M, Kauser F, Khan A A, Tiwari S, Habibullah CM and Ahmed N (2004). Molecular genotyping of Helicobacter pylori isolates from different human populations using genomic fingerprinting of ERIC regions: Implications in strain identification and geographic evolution. J Clin Microbiol. 42: 2372-2378. Vijayachari P, Ahmed N, Sugunan AP, Ghousunnissa S, Rajender Rao K, Hasnain SE and Sehgal SC (2004). Fluorescent amplified fragment length polymorphism (FAFLP) based molecular epidemiology of Leptospirosis in India. J Clin Microbiol 42: 3575-3580. Ahmed N, Alam M, Rajender Rao K, Kauser F, Ashok Kumar N, Qazi N N, Sangal V, Sharma VD, Das R, Katoch VM, Murthy KJR, Suneetha S, Sharma S K, Sechi LA, Gilman RH and Hasnain SE (2004). Molecular genotyping of a large, multi-centric collection of tubercle bacilli indicates geographical partitioning of strain variation: Implications in global epidemiology of M. tuberculosis. J Clin Microbiol 42:3240-3247. Carroll I M, Khan AA and Ahmed N (2004). Revisiting the pestilence of Helicobacter pylori: insights into geographical genomics and pathogen evolution. Infection Genet Evol 4: 81-90. Carroll I M, Ahmed N, Beesley S M, Khan A A, Ghousunnissa S, O Morain C A, Habibullah CM and Smyth C J (2004) Microevolution between paired antral and paired ant ral and corpus Helicobacter pylori isolates recovered from individual patients. J Med Microbiol 53: 669-677. Majeed A A, Ahmed N, Rao K R, Ghousunnissa S, Kausar F, Bose B, Nagarajaram H A, Katoch V M, Cousins D V, Sechi L A, Gilman R H and Hasnain S E. (2004) AmpliBASE MT: A Mycobacterium tuberculosis diversity knowledgebase. Bioinformatics 20: 989-992. Siddiqi N, Das R, Pathak N, Banerjee S, Ahmed N, Katoch V M, and Hasnain SE (2004) Mycobacterium tuberculosis isolate with a distinct genomic identity overexpresses a TAP like efflux pump. Infection 32:109-111.
26. 27.
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Ahmed N, Caviedes L, Alam M, Rao K R, Sangal V, Sheen P, Gilaman RH and Hasnain SE (2003). Distinctiveness of Mycobacterium tuberculosis genotypes from Human Immunodeficiency Virus Type 1-Seropositive and -Seronegative patients in Lima, Peru. J Clinical Microbiol 41: 1712-1716. Ahmed N, Alam M, Majeed A A, Rahman S A, Cataldi A, Cousins D and Hasnain, S. E. (2003). Genome sequence based, comparative analysis of the fluorescent amplified fragment length polymorphisms (FAFLP) of tubercle bacilli from seals provides molecular evidence for a new species within the Mycobacterium tuberculosis complex. Infection Genet Evol 2:193-199. Carroll I M, Ahmed N, Beesley S M, Khan A A, O'Morain C A and Smyth C J (2003) Fine Structure Molecular Typing of Irish Helicobacter pylori Isolates and their Genetic Relatedness to Strains from Four Different Continents. J Clin Microbiol 41:5755-5759. Cousins D V, Bernardelli A, Bastida R, Cataldi A, Quse V, Dow S, Redrobe S, Duignan P, Murray A, Dupont C, Ahmed N et al. (2003). Tuberculosis in seals is caused by a novel member of the Mycobcterium tuberculosis complex: Mycobacterium tuberculosis subsp. pinnipedae subsp. nov. Int J Systematic Evolutionary Microbiol 53: 1305-1314. Ahmed N, Bal A, Khan A A, Alam M, Kagal A, Arjunwadkar V, Rajput A, Majeed A A, Rahman S A, Banerjee S, Joshi S, Bharadwaj R (2002) Whole genome fingerprinting and genotyping of multiple drug resistant (MDR) isolates of Pseudomonas aeruginosa from endophthalmitis patients in India. Infection Genet Evol 1: 237-242. Siddiqi N, Shamim M, Hussain S, Choudhary R K, Ahmed N, Prachee, Banerjee S, Savithri G R, Alam M, Pathak N, Amin A, Hanief M, Katoch V M, Sharma S K, and Hasnain S E (2002). Molecular Characterization of Multidrug-Resistant Isolates of Mycobacterium tuberculosis from Patients in North India. Antimicrob Agents Chemother. 46: 443-450. Panicker S G, Reddy ABM, Mandal A K, Ahmed N, Nagarajaram H A, Hasnain SE and Balasubramanian D (2002). Identification of novel mutations causing familial primary congenital glaucoma in Indian pedigrees. Investigative Ophthalmol Visual Sci 43 (5):1358-1366. Ahmed N, Khan J R and Ganai N A (1999). DNA amplification assay for rapid detection of bovine tubercle bacilli in semen. Animal Reprod Sci 57: 15-21. Ahmed N. (1999). Evaluation of PCR technique in rapid diagnosis of tuberculosis in dairy cattle. Livestock International. 3: 9-13. Ahmed N, Mohanty A K, Batish V K, Mukhopadhyay U. and Grover S (1998). PCR-based Rapid detection of Mycobacterium tuberculosis in blood from immunocompetent patients with pulmonary tuberculosis. J Clinical Microbiol 36 : 3094-3095.
12) PhD students supervised. Either simply number completed or, if space, name of students and titles of their theses Supervised 1: U Rajkumar, PhD Vet Medicine (submitted 2006). NG Ranga Agricultural University, Hyderabad Co-supervised 1: Ian M Carroll, Trinity College Dublin, Ireland (Submitted 2004). 13) Relevant administration experience (committees etc.) 1. Served as a member of the Purchase Committee (Foreign Purchases) of the Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad in 1999-2000 and 2006-2007. 2. Served as a member of the selection committee for PhD students at Centre for DNA Fingerprinting and Diagnostics (CDFD) from 1999-2005. 3. Served as a member of the selection committee for post-doctoral fellows, project assistants and supporting staff at Centre for DNA Fingerprinting and Diagnostics (CDFD) for several occasions during 1999-2006. 4. Serving as General Secretary and Board Member, International Society for Genomic and Evolutionary Microbiology (ISOGEM), University of Sassari, Italy. 5. Associate Editor, Annals of Clinical Microbiology and Antimicrobials (ACMA), a Biomed Central journal. 6. Served as an Executive Committee member of the Indian Leptospirosis Society for 2003-2005.
14) Organization of scientific seminars, meetings and workshops 1. Organizing committee member: International Conference on Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases (MEEGID 5), Nov. 2000, Hyderabad, India 2. Organizing secretary: Third Indo-Australian Conference on Biotechnology, March 6-8, 2006, Hyderabad, India 3. Organizing committee member: International Conference and 6th Scientific Meeting of the Indian Leptospirosis Society, June 20-22, 2006, Hyderabad, India 15) Project management, including project name, contract number, time period, budget 1) The Helicobacter pylori genome program: Genome sequencing, functional analysis and comparative genomics of the strains obtained from Indian patients Level of participation: Principal Investigator; Funding agency: Dept. of Biotechnology, Govt. of India Total funding available for the program: Rupees 8.1 Million; Duration of the program: 3 years (20012004). 2) Molecular genetics and functional genomics of M. tuberculosis patient isolates in India. Level of participation: Co-Principal Investigator; Funding agency: UNDP-World Bank-WHO special program for research and training in tropical diseases (TDR); Total funding: US$ 70,000; Duration of the program: 2 years (2001-2002). 3) The Mycobacterium w genome sequencing program. Level of participation: Co-Principal Investigator; Funding agency: Dept. of Biotechnology, Govt. of India Total funding: Rupees 3.5 Million; Duration of the program: 3 years (2004-2007). 16) Description of the Institute and competence relevant for the present and future research activity The Centre for DNA Fingerprinting and Diagnostics (CDFD) is an autonomous organization funded by the Department of Biotechnology (DBT), Ministry of Science and Technology, Government of India. CDFD receives funding also from other agencies on specific collaborative projects. In addition, DNA Fingerprinting and Diagnostics services provided by the centre support some of the activities. The Centre is recognized by the Manipal Academy of Higher Education for pursuing Ph.D. programme in Life Sciences. The centre is equipped with world class state-of-the-art instrumentation and computing infrastructure to facilitate working in frontier areas of research in Life Sciences. There are presently fifteen groups working on diverse research areas related to genetics, molecular and cell biology, cancer biology, pathogen biology, HIV biology, Immunology etc. and the centre continues to attract leaders in related disciplines. CDFD is supported with a strong Bioinformatics facility and is the India node of the European Molecular Biology Network (EMBnet). CDFD is also a Sun Microsystem’s Centre of Excellence in Medical Bioinformatics. CDFD is located in the fastest growing metropolitan city of Hyderabad, more popularly known as Cyberabad for its initiative and pioneering role in developing the state during the past few years in the area of information technology. CDFD is currently housed in two buildings one constituting the laboratory situated in Nacharam and another constituting the administration in Gandipet. CDFD is likely to move to the new building at Gandipet around 2007. The construction of the new building is already complete. CDFD provides a congenial work atmosphere.
1) Name: Niyaz Ahmed 2) Nationality and Date of Birth: Indian, December 25, 1971 3) Contact Details and Affiliation: Staff Scientist and Group Leader, Pathogen Evolution Group Centre for DNA Fingerprinting and Diagnostics (CDFD),
Hyderabad, India Tel. 91 40 27151344 Fax. 91 40 27155610 Cell. 91 98 66282630
6) Summary of Principal Research Achievements Helicobacter pylori, Mycobacterium tuberculosis and leptospira and are some of the bacterial pathogens that trigger diseases with a complex interplay between infection dynamics, pathogen biology and host immune responses. The whole genome sequence determination has greatly facilitated our understanding of these pathogens. The human gastric pathogen H. pylori is presumed to be co-evolved with its human host and is again a very highly diverse and robust pathogen. Our 'geographic genomics' study tests the theory that H. pylori existed in humans as a benign bacterium for thousands of years until it acquired some virulence factors from the microorganisms abundant in the human societies of the neolithic period, after the domestication of agriculture and livestock. We found traces of East Asian ancestry in the gene pool of Native Peruvian strains (Amerindian?). This finding supports ancient human migration across the Beringstrait (20,000 years BP). We also attempted to support the idea that the major single virulence factor of the bacterium, the cag Pathogenicity Island (cagPAI) was acquired during different times, at different places in the world and from a 'local' microbial source. We followed this with theoretical approaches to find significant overlap among the H. pylori population expansion time and domestication of agriculture in the world. This study provides some new insights into the ancient origins and diversity of H. pylori and the significance of such diversity in the development of gastroduodenal pathology. Why has this bacterium survived for this long time in humans? Does this association makes the colonization beneficial or of low biological cost? These are the questions that need to be answered in the near future. Tuberculosis is the disease with a highest morbidity and mortality worldwide. The disease haunts millions of people in India with a huge death rate. The genetic diversity and evolutionary history of the underlying M. tuberculosis strains are largely unknown in the context of this country that has earned dubious distinctions for tuberculosis prevalence. Our ongoing, large-scale analysis of hundreds of strains of tubercle bacilli highlighted a clear predominance of ancestral M. tuberculosis genotypes in the Indian subcontinent, compared to other regions of the world, and support the opinion that India is a historically ancient endemic focus of tuberculosis. It is hypothesized that such 'ancient' bacilli are relatively 'docile' than some of the highly 'killer' ones such as the highly disseminating Beijing types which harbor inherent propensity to acquire multiple drug resistance (MDR) and are spreading in India through major metropolitan cities. Beijing strains are likely to evade and replace ancestral reservoirs of M. tuberculosis in the country. If that happens, India will probably face large, institutional outbreaks involving hospital wards, prisons, schools etc. This is perhaps a major issue that needs to be addressed in the post-genomic scenario, with the same magnitude of zeal that researchers have shown towards drug discovery and diagnostic or vaccine development. Leptospirosis is another major pestilence, a worldwide zoonosis caused by the spirochetes of the genus Leptospira. The leptospires have been extremely diverse pathogens having more than three hundred different strains or serovars with specific geographic distribution. But this enormous inventory of serovars, based mainly on an ever-changing surface antigen repertoire, throws an artificial and unreliable scenario of strain diversity. It is therefore difficult to track strains whose molecular identity keeps changing according to the host and the environmental niches they inhabit and cross through. To address this problem, we have developed highly sophisticated genotyping systems based on integrated genome analysis approaches to correctly identify and track leptospiral strains. These approaches are expected to greatly facilitate epidemiology of leptospirosis apart from deciphering the origins and evolution of leptospires in a global sense. 7) Technology for licensing/freelancing
A) Genomics platform for molecular fingerprinting of H. pylori strains and an integrated database of disease associated and benign strains from different human populations -genoBASE pylori ® (http://www.cdfd.org.in/amplibase/HP)
B) Genomics platform for highthroughput molecular genotyping of M. tuberculosis and a global knowledgebase of circulating genotypes in endemic and non-endemic zones of the world -AmpliBASE MT ® (http://www.cdfd.org.in/amplibase/) 8) Relevant job positions held, including current position Staff Scientist III and Group Leader, Pathogen Evolution Group, CDFD: August 2003 till date Staff Scientist II, CDFD: September 1998 to August 2003 Staff Scientist II, CDFD on contractual appointment: March 1998 to September 1998 Research Fellowship, Molecular Biology Laboratory, National Dairy Research Institute, Karnal, India: July 1995 to June 1998. 10) Important professional and intellectual recognition held
•
General Secretary, International Society for Genomic and Evolutionary Microbiology (ISOGEM), University of Sassari, Italy (April 2005 till date).
•
Elected to the membership of the National Academy of Sciences of India (lifetime).
•
Served as an Executive Committee member of the Indian Leptospirosis Society (for 2003-2005).
•
Associate Editor, Annals of Clinical Microbiology and Antimicrobials (ACMA), a BioMed Central journal (January 2005 till date).
•
Member of the Editorial Board, Infectious Agents and Cancer (IAC), a BioMed Central journal (September 2006 till date).
11) Important publications in peer reviewed journals 1. 2.
3. 4.
5.
6. 7.
Devi SM, Ahmed I, Khan AA, Rahman SA, Alvi A, Sechi LA and Ahmed N (2006). Genomes of Helicobacter pylori from native Peruvians suggest admixture of ancestral and modern lineages and reveal a western type cag-pathogenicity island. BMC Genomics 7(1):191. Gutierrez MC, Ahmed N (joint first authors), Willery E, Narayanan S, Hasnain SE, Chauhan DS, Katoch VM, Vincent V, Locht C and Supply P (2006) Predominance of ancestral lineages of Mycobacterium tuberculosis in India suggests an ancient focus of tuberculosis in South Asia. Emerging Infectious Dis 12: 367-374. Rao KR, Ahmed N, Sriramula S, Sechi LA and Hasnain SE (2006) Rapid identification of M. tuberculosis Beijing genotypes on the basis of the Mycobacterial Interspersed Repeat Unit locus 26 signature. J Clin Microbiol 44(1):274-277. Sechi LA, Ahmed N, Felis GE, Dupre I, Cannas S, Fadda G, Bua A, Zanetti S. (2006) Immunogenicity and cytoadherence of recombinant heparin binding haemagglutinin (HBHA) of Mycobacterium avium subsp. paratuberculosis: Functional promiscuity or a role in virulence? Vaccine 24:236-243. Sechi LA, Mara L, Cappai P, Frothingam R, Ortu S, Leoni A, Ahmed N and Zanetti S (2006). Immunization with DNA vaccines encoding different mycobacterial antigens elicits a Th1 type immune response in lambs and protects against Mycobacterium avium subspecies paratuberculosis infection. Vaccine 24:229-235. Kenchappa P, Rao KR, Ahmed N, Joshi S, Ghousunnissa S, Vijayalakshmi V, and Murthy K. J. R. (2006). Fluorescent Amplified Fragment Length Polymorphism based molecular epidemiology of hospital infections in a tertiary care setting in Hyderabad, India. Infection Genetics Evol. 6:220-227. Ali SM, Khan AA, Ahmed I, Musaddiq M, Ahmed KS, Polasa H, Rao LV, Habibullah CM, Sechi LA, Ahmed N (2005) Antimicrobial activities of Eugenol and Cinnamaldehyde against the human gastric pathogen Helicobacter pylori. Ann Clin Microbiol Antimicrob 4:20.
8. 9. 10. 11.
12. 13. 14. 15. 16.
17. 18.
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20. 21.
22. 23. 24. 25.
Rao KR, Kauser F, Sriramula S, Zanetti S, Sechi LA, Ahmed N and Hasnain SE (2005). Analysis of genomic downsizing based on region of difference (RD) polymorphism profiling of Mycobacterium tuberculosis patient isolates reveals geographic partitioning. J Clin Microbiol 43:5978-5982. Sechi LA, Gazouli M, Ikonomopoulos J, Lukas JC, Scanu AM, Ahmed N, Fadda G and Zanetti S. (2005) Mycobacterium avium subsp. paratuberculosis, genetic susceptibility to Crohn's disease and the Sardinians: The way ahead. J Clin Microbiol 43:5275-5277. Ali S M, Khan AA, Tiwari SK, Ahmed N, Rao LV and Habibullah CM. Association between cagpathogenicity island in Helicobacter pylori isolates from peptic ulcer, gastric carcinoma and nonulcer dyspepsia subjects with histological changes. World J Gastroenterol. 11:6815-6822. Prouzet-Mauleon V, Hussain MA, Lamouliatte H, Kauser F, Megraud F and Ahmed N. (2005) Pathogen evolution in vivo: genome dynamics of two isolates obtained nine years apart from a duodenal ulcer patient infected with a single Helicobacter pylori strain. J Clin Microbiol. 43:42374241. Kauser F, Hussain MA, Ahmed I....Sechi LA and Ahmed N. (2005) Comparing genomes of Helicobacter pylori isolates recovered from ulcer disease patients in England. BMC Microbiol. 5:32. Ahmed N (2005) 23 years of the discovery of Helicobacter pylori: Is the debate over? Annals Clin Microbiol Antimicrobials 4:17. Kauser F, Hussain M A, Ahmed I, Ahmad N, Habeeb A, Khan A A and Ahmed N (2005) Comparing genomes of Helicobacter pylori strains from the high altitude desert of Ladakh, India J Clin Microbiol 43:1538-1545. Ahmed N and Sechi LA (2005) Helicobacter pylori and gastroduodenal pathology: New threats of the old friend. Annals Clin Microbiol Antimicrobials 4:1. Tiwari SK, Khan AA, Khan SA, Ali SM, Habeeb A, Kauser F, Hussain MA, Ahmed N and Habibullah CM. (2005). PCR based analysis of the cag-PAI of Helicobacter pylori from saliva: An approach for rapid molecular genotyping in correlation with disease status. J Gasteroenterol Hepatol 20:1560-1566. Hasnain SE and Ahmed N (2004). Leptospirosis. LANCET Infectious Dis 4: 543. Kauser F, Khan AA, Hussain MA, Carroll IM, Ahmad N, Tiwari S, Shouche Y, Das B, Alam M, Ali SM, Habibullah CM, Sierra R, Megraud F, Sechi LA and Ahmed N (2004). The cag pathogenicity island (cag-PAI) of Helicobacter pylori is disrupted in majority of patient isolates from different human populations. J Clin Microbiol 42: 5302-5308. Abid Hussain M, Kauser F, Khan A A, Tiwari S, Habibullah CM and Ahmed N (2004). Molecular genotyping of Helicobacter pylori isolates from different human populations using genomic fingerprinting of ERIC regions: Implications in strain identification and geographic evolution. J Clin Microbiol. 42: 2372-2378. Vijayachari P, Ahmed N, Sugunan AP, Ghousunnissa S, Rajender Rao K, Hasnain SE and Sehgal SC (2004). Fluorescent amplified fragment length polymorphism (FAFLP) based molecular epidemiology of Leptospirosis in India. J Clin Microbiol 42: 3575-3580. Ahmed N, Alam M, Rajender Rao K, Kauser F, Ashok Kumar N, Qazi N N, Sangal V, Sharma VD, Das R, Katoch VM, Murthy KJR, Suneetha S, Sharma S K, Sechi LA, Gilman RH and Hasnain SE (2004). Molecular genotyping of a large, multi-centric collection of tubercle bacilli indicates geographical partitioning of strain variation: Implications in global epidemiology of M. tuberculosis. J Clin Microbiol 42:3240-3247. Carroll I M, Khan AA and Ahmed N (2004). Revisiting the pestilence of Helicobacter pylori: insights into geographical genomics and pathogen evolution. Infection Genet Evol 4: 81-90. Carroll I M, Ahmed N, Beesley S M, Khan A A, Ghousunnissa S, O Morain C A, Habibullah CM and Smyth C J (2004) Microevolution between paired antral and paired ant ral and corpus Helicobacter pylori isolates recovered from individual patients. J Med Microbiol 53: 669-677. Majeed A A, Ahmed N, Rao K R, Ghousunnissa S, Kausar F, Bose B, Nagarajaram H A, Katoch V M, Cousins D V, Sechi L A, Gilman R H and Hasnain S E. (2004) AmpliBASE MT: A Mycobacterium tuberculosis diversity knowledgebase. Bioinformatics 20: 989-992. Siddiqi N, Das R, Pathak N, Banerjee S, Ahmed N, Katoch V M, and Hasnain SE (2004) Mycobacterium tuberculosis isolate with a distinct genomic identity overexpresses a TAP like efflux pump. Infection 32:109-111.
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Ahmed N, Caviedes L, Alam M, Rao K R, Sangal V, Sheen P, Gilaman RH and Hasnain SE (2003). Distinctiveness of Mycobacterium tuberculosis genotypes from Human Immunodeficiency Virus Type 1-Seropositive and -Seronegative patients in Lima, Peru. J Clinical Microbiol 41: 1712-1716. Ahmed N, Alam M, Majeed A A, Rahman S A, Cataldi A, Cousins D and Hasnain, S. E. (2003). Genome sequence based, comparative analysis of the fluorescent amplified fragment length polymorphisms (FAFLP) of tubercle bacilli from seals provides molecular evidence for a new species within the Mycobacterium tuberculosis complex. Infection Genet Evol 2:193-199. Carroll I M, Ahmed N, Beesley S M, Khan A A, O'Morain C A and Smyth C J (2003) Fine Structure Molecular Typing of Irish Helicobacter pylori Isolates and their Genetic Relatedness to Strains from Four Different Continents. J Clin Microbiol 41:5755-5759. Cousins D V, Bernardelli A, Bastida R, Cataldi A, Quse V, Dow S, Redrobe S, Duignan P, Murray A, Dupont C, Ahmed N et al. (2003). Tuberculosis in seals is caused by a novel member of the Mycobcterium tuberculosis complex: Mycobacterium tuberculosis subsp. pinnipedae subsp. nov. Int J Systematic Evolutionary Microbiol 53: 1305-1314. Ahmed N, Bal A, Khan A A, Alam M, Kagal A, Arjunwadkar V, Rajput A, Majeed A A, Rahman S A, Banerjee S, Joshi S, Bharadwaj R (2002) Whole genome fingerprinting and genotyping of multiple drug resistant (MDR) isolates of Pseudomonas aeruginosa from endophthalmitis patients in India. Infection Genet Evol 1: 237-242. Siddiqi N, Shamim M, Hussain S, Choudhary R K, Ahmed N, Prachee, Banerjee S, Savithri G R, Alam M, Pathak N, Amin A, Hanief M, Katoch V M, Sharma S K, and Hasnain S E (2002). Molecular Characterization of Multidrug-Resistant Isolates of Mycobacterium tuberculosis from Patients in North India. Antimicrob Agents Chemother. 46: 443-450. Panicker S G, Reddy ABM, Mandal A K, Ahmed N, Nagarajaram H A, Hasnain SE and Balasubramanian D (2002). Identification of novel mutations causing familial primary congenital glaucoma in Indian pedigrees. Investigative Ophthalmol Visual Sci 43 (5):1358-1366. Ahmed N, Khan J R and Ganai N A (1999). DNA amplification assay for rapid detection of bovine tubercle bacilli in semen. Animal Reprod Sci 57: 15-21. Ahmed N. (1999). Evaluation of PCR technique in rapid diagnosis of tuberculosis in dairy cattle. Livestock International. 3: 9-13. Ahmed N, Mohanty A K, Batish V K, Mukhopadhyay U. and Grover S (1998). PCR-based Rapid detection of Mycobacterium tuberculosis in blood from immunocompetent patients with pulmonary tuberculosis. J Clinical Microbiol 36 : 3094-3095.
12) PhD students supervised. Either simply number completed or, if space, name of students and titles of their theses Supervised 1: U Rajkumar, PhD Vet Medicine (submitted 2006). NG Ranga Agricultural University, Hyderabad Co-supervised 1: Ian M Carroll, Trinity College Dublin, Ireland (Submitted 2004). 13) Relevant administration experience (committees etc.) 1. Served as a member of the Purchase Committee (Foreign Purchases) of the Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad in 1999-2000 and 2006-2007. 2. Served as a member of the selection committee for PhD students at Centre for DNA Fingerprinting and Diagnostics (CDFD) from 1999-2005. 3. Served as a member of the selection committee for post-doctoral fellows, project assistants and supporting staff at Centre for DNA Fingerprinting and Diagnostics (CDFD) for several occasions during 1999-2006. 4. Serving as General Secretary and Board Member, International Society for Genomic and Evolutionary Microbiology (ISOGEM), University of Sassari, Italy. 5. Associate Editor, Annals of Clinical Microbiology and Antimicrobials (ACMA), a Biomed Central journal. 6. Served as an Executive Committee member of the Indian Leptospirosis Society for 2003-2005.
14) Organization of scientific seminars, meetings and workshops 1. Organizing committee member: International Conference on Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases (MEEGID 5), Nov. 2000, Hyderabad, India 2. Organizing secretary: Third Indo-Australian Conference on Biotechnology, March 6-8, 2006, Hyderabad, India 3. Organizing committee member: International Conference and 6th Scientific Meeting of the Indian Leptospirosis Society, June 20-22, 2006, Hyderabad, India 15) Project management, including project name, contract number, time period, budget 1) The Helicobacter pylori genome program: Genome sequencing, functional analysis and comparative genomics of the strains obtained from Indian patients Level of participation: Principal Investigator; Funding agency: Dept. of Biotechnology, Govt. of India Total funding available for the program: Rupees 8.1 Million; Duration of the program: 3 years (20012004). 2) Molecular genetics and functional genomics of M. tuberculosis patient isolates in India. Level of participation: Co-Principal Investigator; Funding agency: UNDP-World Bank-WHO special program for research and training in tropical diseases (TDR); Total funding: US$ 70,000; Duration of the program: 2 years (2001-2002). 3) The Mycobacterium w genome sequencing program. Level of participation: Co-Principal Investigator; Funding agency: Dept. of Biotechnology, Govt. of India Total funding: Rupees 3.5 Million; Duration of the program: 3 years (2004-2007). 16) Description of the Institute and competence relevant for the present and future research activity The Centre for DNA Fingerprinting and Diagnostics (CDFD) is an autonomous organization funded by the Department of Biotechnology (DBT), Ministry of Science and Technology, Government of India. CDFD receives funding also from other agencies on specific collaborative projects. In addition, DNA Fingerprinting and Diagnostics services provided by the centre support some of the activities. The Centre is recognized by the Manipal Academy of Higher Education for pursuing Ph.D. programme in Life Sciences. The centre is equipped with world class state-of-the-art instrumentation and computing infrastructure to facilitate working in frontier areas of research in Life Sciences. There are presently fifteen groups working on diverse research areas related to genetics, molecular and cell biology, cancer biology, pathogen biology, HIV biology, Immunology etc. and the centre continues to attract leaders in related disciplines. CDFD is supported with a strong Bioinformatics facility and is the India node of the European Molecular Biology Network (EMBnet). CDFD is also a Sun Microsystem’s Centre of Excellence in Medical Bioinformatics. CDFD is located in the fastest growing metropolitan city of Hyderabad, more popularly known as Cyberabad for its initiative and pioneering role in developing the state during the past few years in the area of information technology. CDFD is currently housed in two buildings one constituting the laboratory situated in Nacharam and another constituting the administration in Gandipet. CDFD is likely to move to the new building at Gandipet around 2007. The construction of the new building is already complete. CDFD provides a congenial work atmosphere.
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