Niyaz Ahmed DVM PhD
Staff Scientist and Group Leader
Pathogen Evolution Laboratory
CDFD
Academic and Community Activity

General Secretary,  ISOGEM
Section Editor, PLoS ONE
Assoc. Editor, Infectious Agents & Cancer
Assoc. Editor, Ann Clin Microb Antimicrobials
Assoc. Editor, Acta Veterinaria Scandinavica
Faculty Member, Faculty of 1000 Medicine/Biol
Corres. Fellow, Eur Helicobacter Study Group
Popular highlights of our activity

History debugged: Down to Earth Magazine
Birth place of Tuberculosis: New Scientist (London)
Birth place of TB: The Times of India (Delhi)
The bug's revenge: The Telegraph (Kolkata)
Genome of M. indicus: Wall Street Journal
Research interests in this lab constitute analyzing trends in genomic diversity of bacterial pathogens with reference
to evolution of survival mechanisms, metabolic machinery and virulence apparatuses etc. and their impact on
dissemination dynamics, invasion, persistence, signaling events, molecular pathogenesis, strain evolution and
prevention measures.  Pathogen genome is analyzed through decipherment of genomic and proteomic diversity as
a function of flexibility in gene content (plasticity zones, large deletions), gene order (transposition), and gene
regulation (allelic variation, synonymous substitutions, strand displacements), possibly aimed at evolution of fittest
genotypes, corresponding to changing host niches and the environment.

Ahmed is an elected member of the National Academy
of Sciences, India and is currently studying global
diversity and evolution of two important pathogens,
viz, M. tuberculosis and Helicobacter pylori. Another
important pathogen of recent interest is Leptospira
interrogans where the research theme is - how a
saprophytic organism evolves into a deadly human
pathogen?  Dr Ahmed is a founder of the ISOGEM,
a scientific society headquartered at Sassari in Italy
and serves as its General Secretary. Dr Ahmed is a
co-principal investigator in the Mycobacterium w  
(Mycobacterium indicus pranii) genome program,
India's first whole genome sequencing project.   

He has published more than 65  research papers in scientific journals of high repute. He is an Academic Editor of
PLOS ONE, a top tier Open Access journal of high repute. Ahmed also serves as Associate Editor of Annals
of Clinical Microbiology and Antimicrobials,  Associate Editor of Infectious Agents and Cancer and Associate
Editor of Acta Veterinaria Scandinavica. Ahmed is a Faculty of the Faculty of 1000 Medicine, the next generation
literature evaluation and awareness service for medicine. He was recently elected as the Fellow
of the European Helicobacter Study Group (EHSG)


Lay summary of ongoing projects and principal 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 tested 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 supported
ancient human migration across the Bering-strait
(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.

Another research project within our group looks at the pathogenic roles of different H. pylori proteins encoded by
the core genome (housekeeping) and flexible genome (plasticity region cluster) content of the bacillus.

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 hund-
-reds 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 dissemina-
-ting Beijing genotypes  with an 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. 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.  
                                                                                                                                        Last updated: April 7, 2008.
This website is sponsored and owned by ISOGEM.
All content for fair use unless otherwise stated
Ahmed Lab @ CDFD
Current Group Members

Dr Niyaz Ahmed, PI    Email: niyaz[at]cdfd.org.in
Dr Ayesha Alvi - DST Young Scientist  
Dr Mohammed Rizwan - Post-doctoral Fellow
Ms Heleena Moni - Project Assistant
Dr M Krishnaveni - Post-doctoral Fellow
Mr B Krishnamurthy - Lab Technician/Tradsman
Mr Wasim Ahmad -  Lab Assistant
With H. E.  Dr Kalam, the then President of India  June 05
With Nobelist Prof. Barry Marshall - Sept 2005
With Nobelist Prof. Peter Deherty, 2007
Recent publications

1.Ahmed N, Dobrindt U, Hacker J and Hasnain SE
(2008) . Genomic fluidity and pathogenic bacteria:
applications in diagnostics, epidemiology and
intervention. Nature Rev Microbiol. 6: 387-394

2. Hussain MA, Naveed SA, Sechi LA....Ahmed N
(2008). Isocitrate Dehydrogenase of Helicobacter
pylori Potentially Induces Humoral Immune Response
in Subjects with Peptic Ulcer Disease and Gastritis.
PLoS ONE. 3:e1481. [View xml]

3. Rizwan M, Alvi A and Ahmed N (2008). Novel
protein antigen (JHP940) from the genomic plasticity
region of Helicobacter pylori induces tumor necrosis
factor alpha and interleukin-8 secretion by human
macrophages. J Bacteriol. 190:1146-51.

4. Sechi LA, Rosu V, .. Ahmed N, Zanetti S (2008).
Humoral immune responses of type 1 diabetes
patients to Mycobacterium avium subsp.
paratuberculosis lend support to the infectious trigger
hypothesis. Clin Vaccine Immunol. 15:320-6.

5. Akhter Y, .., Ahmed N, Hasnain SE.(2008).
Genome scale portrait of cAMP-receptor protein
(CRP) regulons in mycobacteria points to their role in
pathogenesis. Gene. 407:148-58.

6. Ahmed N, Saini V...Hasnain SE (2007). Molecular
analysis of a leprosy immunotherapeutic bacillus
provides insights into mycobacterium evolution.PLoS
ONE. 2:e968. [View xml] [press report]

7. Devi SM, Ahmed I, Francalacci P, Hussain MA,
Alvi A, Sechi LA, Megraud F and Ahmed N (2007).
Ancestral European Origins of Helicobacter pylori in
India. BMC Genomics 8:184 [PDF, for media
spotlight -->> click here]

8.  Banerjee S, Nandyala AK, Raviprasad P, Ahmed
N and Hasnain SE (2007). Iron dependent Iron
binding activity of M. tuberculosis aconitase. J
Bacteriol. 189:4046-4052.

9.  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 7:191. [PDF]

10. Gutierrez MC, Ahmed N (joint first authors),
Willery E, ... 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.  
[PDF, for media spotlight -->> click here]

11. 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.

12. 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. 43:4237-4241.

13. Carroll I M, Ahmed N, ... 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.

14. Hasnain SE and Ahmed N (2004) Leptospirosis.
Lancet Infect Dis 4:543-544.

15.  Ahmed N, Alam M, .. Sechi LA, Gilman RH,
Hasnain SE (2004). Molecular genotyping of a large,
multicentric collection of tubercle bacilli indicates
geographical partitioning of strain variation and has
implications for global epidemiology of
Mycobacterium tuberculosis. J Clin Microbiol.
42:3240-3247



For complete list of publications click   --- here

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