Thesis and Guide details:
Details of CSIR Fellowship/ Associateship held, if any or from other sources/ agencies.
Significant foreign assignments:
(a) Significant contributions to science and/ or technology development by the nominee
based on the work done in India during most part of last 5 years:
Dr Niyaz Ahmed’s contributions are internationally known in the context of Functional
Molecular Infection Epidemiology of bacterial pathogens. His research group has over the
last several years systematically unraveled molecular epidemiology based on genome
dynamics of pathogens namely H. pylori, M. tuberculosis and enteropathogens entailing
spectrum of human diseases occurring in geographically distinct patient populations (Ahmed
et al., 2008. Nature Rev Microbiol. 6:387-94; Kumar et al, 2015. Nucleic Acids Res.
43:324-35; Baddam et al., 2014. Scientific Reports 4:7457).
Dr Ahmed generated and harnessed clinical, genomic and demographic data in the form of
a unified epidemiological approach to define the H. pylori pan genome in an evolutionary
context and to understand the boundaries and vertices of the plasticity region cluster of H.
pylori that has been traditionally assumed to shape and shelter several novel genes
imparting virulence based fitness advantage to the pathogen. Apart from plasticity, the
conserved genomic information was systematically used to analyze genome evolution
patterns of more than four hundred distinct Helicobacter isolates to dissect natural history in
the context of peopling and human anthropology in different countries (Kumar et al., 2015.
Nucleic Acids Res. 43:324-35, Ahmed N et al., 2008. Nature Rev Microbiol. 6:387-94;
Devi SM et al, 2006. BMC Genomics 7:191; Devi SM et al, 2007. BMC Genomics 8:184).
Some of the major observations from these pioneering studies of Dr Ahmed comprised of
the Indian H. pylori’s ancestral relationships with the western isolates and that H. pylori in
some multiethnic settings such as Malaysia evolve and adapt in a host specific manner. This
has bearing on our understanding of the host – pathogen coevolution and co-migration.
Similarly, Dr Ahmed’s group has developed and maintained a rigorous model of
chronological evolution of bacterial genomes in the form of serial isolates of H. pylori
obtained from different niches of the stomach of a single patient, obtained across a decade
(Prouzet-Mauleon et al., 2005. J Clin Microbiol 43:4237-4241 and Alvi et al., 2007. J Clin
Microbiol. 45:4039-4043). Whole genome sequences of these isolates have now been
completed by Dr Ahmed (GenBank Genomes IDs: CP002184, CP002571, CP002572) and
these genomes have been viewed by the community as an invaluable tool in understanding
chronological evolution of H. pylori and have a great bearing on the understanding of
pathogen survival and adaptation through genomic recasting (Devi et al., 2010 J Bacteriol;
Avasthi et al., 2011 J Bacteriol). Further, a series of putative virulence factors were gleaned
by Dr Ahmed from the plasticity region cluster and elsewhere from the maximum common
gene pool of H. pylori and were functionally characterized including those from the core
(Hussain et al., 2008 PLoS ONE 3:e1481) and the flexible genome compartments (Rizwan
et al., 2008 J Bacteriol. 190:1146-1151; Alvi et al., 2011 PLoS ONE, 6(7): e22530).
Important among these are the virulence factors encoded by the genomic plasticity region
genes which constitute a putative type IV secretion system, acquired horizontally. Two of
these virulence factors (JH940 and HP986) potentially interacted with the human immune
system. The HP986 appears to be involved in Helicobacter persistence. Most persistent
microbes seemingly evolve strategies to foil host responses and gain niche. However, it
seems that there is fine tuning between microbial immune evasion and maintenance of the
(b) Impact of the contributions in the field concerned:
Over the years, Dr Ahmed’s contributions in the area of molecular epidemiology have famed
him as internationally acclaimed scientist who contributed extremely valuable state of art in
the area of genomics, epidemiology and disease biology of major human and veterinary
pathogens, namely, Mycobacterium tuberculosis, Helicobacter pylori, Leptospira interrogans
and pathogenic Escherichia coli. Ahmed’s work unraveled novel pathogenic mechanisms
and survival strategies of the above pathogens while rendering immense contribution to
microbial research in India, a country embattled and challenged with infection burden. In
particular, Dr Ahmed’s work based on adaptive evolution of single H. pylori strains in
individual stomachs over extended periods of colonization has given impetus to the
emerging field of ‘chronological evolution’ (Prouzet-Mauleon et al., 2005, J Clin Microbiol;
Alvi et al., 2007, J Clin Microbiol, Kumar et al., 2012, J Bacteriol). Recently, Dr Ahmed’s
group has ushered into the next generation sequencing of pathogenic bacteria and has
completed whole genome sequences of the three H. pylori isolates hierarchically obtained
from a single patient (Devi et al., 2010 J Bacteriol; Avasthi et al., 2011 J Bacteriol, Kumar et
al., 2012, J Bacteriol); this is especially relevant to the adaptation mechanisms of chronic
pathogens such as H. pylori. The H. pylori research community including clinicians and
researchers are very enthusiastic about this novel contribution and that these genomes will
form basis for a new discipline of ‘replicative genomics’ of pathogens in single patients in
future studies (Ahmed N, 2010 Gut Pathogens). Technologically, this work has potential
implications for genetic stability testing of bacterial vaccine vehicles during colonization.
Dr Ahmed’s work resulted in important strategic funding instruments and collaborative
networks as follows:
1. Indo-German IRTG 1673: An International Network of Excellence funded by the German
Research Foundation wherein Dr Ahmed is the Speaker from the Indian side (2010-2014).
2. University of Malaya High Impact Research Grant – Molecular Genetics (Dr Ahmed is the
Principal collaborator also with Prof. Barry Marshall, Nobel Laureate) (2010-2015).
3. Department of Biotechnology, GOI: Helicobacter pylori genome program under the Infection
Biology Task Force.
Another work of Dr Ahmed and colleagues demonstrating population structure of M.
tuberculosis in India (Ahmed et al., 2004 J Clin Microbiol) and that the ancestral strains of M.
tuberculosis are predominant in this part of the country (Gutierrez+Ahmed et al., 2006
Emerg Infect Dis) led to the popular working hypothesis that these ancestral strains could be
more responsive to antitubercular therapy because of their possible adaptive evolution.
Studies have been designed to validate this, especially, the treatment success rates under
DOTS program in India are highly suggestive of this possibility (WHO Report on TB, 2010).
In appreciation of this fact, the Department of Biotechnology, Government of India has
established a Centre of Excellence on tuberculosis (CoE TB) in Hyderabad wherein Dr
Ahmed’s studies form an important component.
Places where work of last 5 years has been referred/ cited in Books, Reviews:
Names of the industries in which the technology (ies) has (have) been used :
The achievements already been recognised by Awards by any learned body:
The Awardee a fellow of the Indian National Science Academy/Indian Academy of Sciences/National
Academy of Sciences/Others:
The Awardee delivered invited lecture(s) in India/abroad and/or chaired any scientific
Internatiional Conference Symposium:
List of Awardee's 10 most significant publications.
List of Awardee's 5 most significant publications during the last 5 years
List of Awardee's 5 most significant publications from out of work done in India
during the last five years:
Complete list of publications in standard refereed journals:
Complete list of publications with foreign collaborators (indicating your status
List of papers published in Conferences /Symposia/ Seminars, etc:
List of the most outstanding Technical Reports/ Review Articles:
Statement regarding collaboration with scientists abroad:
Total number of patents granted in last five years.
Details of Books published: