Of bugs & men | Home Page of Prof. Niyaz Ahmed

Professor of Biotechnology & Bioinformatics

Founding Editor-in-Chief, Gut Pathogens (Springer-Nature) – Impact Factor 4.2

Prof. Niyaz Ahmed is an One Health epidemiologist and professor of Biotechnology and Bioinformatics at the University of Hyderabad, India. Prof. Ahmed has contributed pioneering research in the area of Molecular Epidemiology in India, for which he was given the ‘Shanti Swarup Bhatnagar Prize’, India’s foremost Science Prize, in the area of Medical Sciences in 2016. He also served as the Senior Director at the International Centre for Diarrheal Disease Research, Bangladesh (icddr, b) in an international leadership position from Nov 2016 to March 2020 (UN eq scale D1 step 8). A Fellow of the American Academy of Microbiology, the Royal Society of Chemistry (UK), the Royal Society of Biology (UK) and the National Academy of Sciences India, Prof. Ahmed serves as the founder Editor-in-Chief of Gut Pathogens journal since 2008.  In 2017, Dr Ahmed was awarded the Microsoft Azure for Research Award in Public Health to work towards genomics of identification of new genes, new proteins and novel pathways underlying the multiple drug resistance phenotypes in bacteria.  Dr Ahmed has earlier received the ‘University of Hyderabad Chancellor’s Award’ from the then Chancellor of the University, Dr C. Rangarajan (the former Governor of the state of Andhra Pradesh and the former Governor of the Reserve Bank of India). He is also the recipient of the ‘National Bioscience Award’ of the Government of India. In March 2022, Prof. Ahmed was profiled in the ’75 under 50 – scientists shaping India’ compendium released by the Indian Government. 

Dr Ahmed also holds appointment as Adjunct Professor of the Academy of Scientific and Innovative Research. He is the Corresponding Fellow of the European Helicobacter and Microbiota Study Group.  In 2011, Prof. Ahmed was invited to the position of Academic Icon Professor in Courtesy at the University of Malaya in Kuala Lumpur, Malaysia in a visiting capacity, which he occupied until 2015.

Research contributions in One Health arena: Dr Ahmed’s contribution to veterinary medicine and animal sciences entails molecular infection epidemiology and genome sequence based evolutionary dynamics of zoonotic (leptospirosis, salmonellosis, colibacillosis, bovine TB, Johne’s disease) and food borne infections (Yersinia enterocolitica, Helicobacter pullorum) as well as the surveillance of antimicrobial resistance in public health and farm animal settings. Dr Ahmed contributed pioneering efforts in characterizing tuberculosis in sea lions through molecular and genomic markers in 2003 and provided working evidence for a new species of tubercle bacilli in seals (Ahmed N. et al. Infection Genetics and Evolution, 2003 Feb;2(3):193-199). These and other studies of Dr Ahmed form the base, and precede the realms of disease control and prevention through vaccines in order to achieve thriftiness in farm animals and survival and conservation of the captive and exotic species, needed to meet the goals entailing trans-boundary infection control, animal health, production and development in sustainable agriculture, wildlife and animal husbandry.  Dr Ahmed’s research team has lately been active in the area of largescale genomics of antimicrobial resistant pathogens wherein they decipher novel resistance genes and functional pathways relevant in shaping fitness advantages in bacteria. Artificial intelligence based surveillance of such pathogens in community habitats, clinics, water bodies, foods, human dense settings (such as refugee camps, urban slums) and open enviroenments constitute some of the ongoing projects in his lab.

Academic contribution and capacity building at UoH: At the University of Hyderabad, Dr Ahmed was among the founding faculty members of the newly created Department of Biotechnology & Bioinformatics. Dr Ahmed supervised 20 PhD scholars thus far and several post-doctoral scientists worked under his guidance. Through his pioneering and translational work in public health microbiology in India and South Asia, Ahmed contributed founding efforts to the development of Molecular Infection Epidemiology  and  made seminal contributions to host-pathogen epidemiology of bacterial pathogens. In this direction, he successfully leveraged his collaborative linkages for research student exchange/joint-supervision at the University through international bilateral science cooperation instruments such as the  Indo-German Internationales Graduiertenkolleg – GRK1673 of which Dr Ahmed had been the co-ordinator/spokesperson from the Indian side.

International leadership at icddr,b:  Dr Ahmed joined icddr,b as its Senior Director at the invitation of its management and the Board of Trustees. At iddr,b, Dr Ahmed contributed to several developments and reforms, both as Senior Director and as Research Integrity Officer. He was a member of the senior leadership team of icddr,b and a member of its Central Committee when icddr,b won the  Conrad N. Hilton Humanitarian Award in 2017.  He brought several new grants and programs, initiated genomics research and created world-class laboratory facilities at icddr,b. Dr Ahmed contributed to augment the revenues of icddr,b through spearheading high quality diagnostic services whereby the revenues from such services increased several fold during his tenure. As a part of his leadership and vision, Dr Ahmed developed state of art containment labs, biorepositories, bioinformatics platforms and a modern animal house, and made all these facilities fully self sustaining as of March 2020.  At icddr,b, Dr Ahmed also overseen benchmarking of  500 plus diagnostic tests and parameters according to ISO15189 and ISO15190 accreditation regimes. In addition to his contribution to administration and the development of diagnostic services at icddr,b, Dr Ahmed carried out pioneering research on the genomic basis of seasonality of Cholera in Bangladesh and worked extensively on the problem of antimicrobial resistance in municipal and refugee settings.

Dr Ahmed has an inclusive and holistic vision for capacity building, in the developing countries of South Asia, in frontier areas of modern biology entailing infectious disease control. This vision reflects in his operational philosophy, ethics and governance at all times.

Dr Ahmed was inspired by the People’s President, Dr APJ Abdul Kalam

Important publications of Dr Ahmed and teams:

(Access here all publications of Dr Ahmed through pubMED)

Saini P, Bandsode V, Singh A, Mendem SK, Semmler T, Alam M, Ahmed N. Genomic
insights into virulence, antimicrobial resistance, and adaptation acumen of Escherichia coli isolated from an urban environment. mBio 2024 Feb
20:e0354523. 

Singh A, Lankapalli AK, Mendem SK, Semmler T, Ahmed N. Unraveling the evolutionary dynamics of toxin-antitoxin systems in diverse genetic lineages of Escherichia coli including the high-risk clonal complexes. mBio 2024 Jan
16;15(1):e0302323

Shaik S, Singh A, Suresh A, Ahmed N. Genome Informatics and Machine Learning-Based Identification of Antimicrobial Resistance-Encoding Features and Virulence Attributes in Escherichia coli Genomes Representing Globally Prevalent Lineages, Including High-Risk Clonal Complexes. mBio 2022 Feb 15;13(1):e0379621 (Editor’s Pick)

Shaik S, Suresh A, Ahmed N. Genome Dynamics and Evolution of Multiple-Drug-Resistant Bacteria: Implications for Global Infection Control Priorities. J Infect Dis. 2021 Dec 20;224(12 Suppl 2):S876-S882. 

Qaria MA, Qumar S, Sepe LP, Ahmed N. Cholesterol glucosylation-based survival strategy in Helicobacter pylori. Helicobacter 2021 Apr;26(2):e12777. 

Suresh A, Shaik S, Baddam R, Ranjan A, Qumar S, Jadhav S, Semmler T, Ghazi IA, Wieler LH, Ahmed N. Evolutionary Dynamics Based on Comparative Genomics of Pathogenic Escherichia coli Lineages Harboring Polyketide Synthase (pks) Island. mBio 2021 Mar 2;12(1):e03634-20.  (Editor’s Pick)

Mahmud ZH, Kabir MH, Ali S, Moniruzzaman M, Imran KM, Nafiz TN, Islam MS, Hussain A, Hakim SAI, Worth M, Ahmed D, Johnston D, Ahmed N. Extended-Spectrum Beta-Lactamase-Producing Escherichia coli in Drinking Water Samples From a Forcibly Displaced, Densely Populated Community Setting in Bangladesh. Front. Public Health 2020 Jun 18;8:228.  

Baddam R, Sarker N, Ahmed D, Mazumder R, Abdullah A, Morshed R, Hussain A, Begum S, Shahrin L, Khan AI, Islam MS, Ahmed T, Alam M, Clemens JD, Ahmed N. Genome Dynamics of Vibrio cholerae Isolates Linked to Seasonal Outbreaks of Cholera in Dhaka, Bangladesh. mBio 2020 Feb 11;11(1). pii: e03339-19. 

Mahmud ZH, Islam MS, Imran KM, Hakim SAI, Worth M, Ahmed A, Hossan S, Haider M, Islam MR, Hossain F, Johnston D, Ahmed N. Occurrence of Escherichia coli and faecal coliforms in drinking water at source and household point-of-use in Rohingya camps, Bangladesh. Gut Pathog. 2019 Nov 1;11:52. 

Qaria MA, Kumar N, Hussain A, Qumar S, Doddam SN, Sepe LP, Ahmed N. Roles of Cholesteryl-α-Glucoside Transferase and Cholesteryl Glucosides in Maintenance of Helicobacter pylori Morphology, Cell Wall Integrity, and Resistance to Antibiotics. mBio 2018 Nov 27;9(6). 

Islam MA, Roy S, Nabi A, Solaiman S, Rahman M, Huq M, Siddiquee NA, Ahmed N. Microbiological quality assessment of milk at different stages of the dairy value chain in a developing country setting. Int J Food Microbiol. 2018 Aug 2;278:11-19. 

Ranjan A, Shaik S, Nandanwar N, Hussain A, Tiwari SK, Semmler T, Jadhav S, Wieler LH, Alam M, Colwell RR, Ahmed N. Comparative Genomics of Escherichia coli  Isolated from Skin and Soft Tissue and Other Extraintestinal Infections. mBio 2017 Aug 15;8(4). 

Doddam SN, Peddireddy V, Ahmed N. Mycobacterium tuberculosis DosR Regulon Gene Rv2004c Encodes a Novel Antigen with Pro-inflammatory Functions and Potential Diagnostic Application for Detection of Latent Tuberculosis. Front Immunol. 2017 Jun 24;8:7. 

Peddireddy V, Doddam SN, Ahmed N. Mycobacterial Dormancy Systems and Host Responses in Tuberculosis. Front Immunol. 2017 Feb 15;8:84. 

Qumar S, Majid M, Kumar N, Tiwari SK, Semmler T, Devi S, Baddam R, Hussain A, Shaik S, Ahmed N. Genome dynamics and molecular infection epidemiology of multi-drug resistant Helicobacter pullorum isolates obtained from broiler and country chickens in India. Appl Environ Microbiol. 2016 Dec 15;83. 

Devi S, Ansari SA, Tenguria S, Kumar N, Ahmed N. Multipronged regulatory functions of a novel endonuclease (TieA) from Helicobacter pylori. Nucleic Acids Res. 2015 Nov 2;44(19):9393-9412.

Ranjan A, Shaik S, Mondal A, Nandanwar N, Hussain A, Semmler T, Kumar N, Tiwari S, Jadhav S, Wieler LH, Ahmed N. Molecular epidemiology and genome dynamics of New Delhi metallo-beta-lactamase (NDM) producing extraintestinal pathogenic E. coli (ExPEC) strains from India. Antimicrob Agents Chemother. 2015 Oct 21;60(11):6795-6805. 

Ranjan A, Shaik S, Hussain A, Nandanwar N, Semmler T, Jadhav S, Wieler LH, Ahmed N. Genomic and functional portrait of a highly virulent, CTX-M-15-producing H30-Rx subclone of Escherichia coli sequence type (ST) 131. Antimicrob Agents Chemother. 2015, 59:6087-95. 

Kumar N, Mariappan V, Baddam R, Lankapalli AK, Shaik S, Goh KL, Loke MF, Perkins T, Benghezal M, Hasnain SE, Vadivelu J, Marshall BJ, Ahmed N. Comparative genomic analysis of Helicobacter pylori from Malaysia identifies three distinct lineages suggestive of differential evolution. Nucleic Acids Res. 2015 Jan;43(1):324-35.

Baddam R, Kumar N, Shaik S, Lankapalli AK, Ahmed N. Genome dynamics and evolution of Salmonella Typhi strains from the typhoid-endemic zones. Scientific Rep 2014 Dec 12;4:7457. 

Hussain A, Ranjan A, Nandanwar N, Babbar A, Jadhav S, Ahmed N. Genotypic and phenotypic profiles of Escherichia coli isolates belonging to clinical sequence type 131 (ST131), clinical non-ST131, and fecal non-ST131 lineages from India. Antimicrob Agents Chemother. 2014, 58:7240-9. 

Hussain A, Ewers C, Nandanwar N, Guenther S, Jadhav S, Wieler LH, Ahmed N. Multiresistant uropathogenic Escherichia coli from a region in India where urinary tract infections are endemic: genotypic and phenotypic characteristics of sequence type 131 isolates of the CTX-M-15 extended-spectrum-β-lactamase-producing lineage. Antimicrob Agents Chemother. 2012, 56:6358-65. 

Ahmed N, Dobrindt U, Hacker J, Hasnain SE. Genomic fluidity and pathogenic bacteria: applications in diagnostics, epidemiology and intervention. Nat Rev Microbiol. 2008 6:387-94. 

Sechi LA, Paccagnini D, Salza S, Pacifico A, Ahmed N, Zanetti S. Mycobacterium avium subspecies paratuberculosis bacteremia in type 1 diabetes mellitus: an infectious trigger? Clin Infect Dis. 2008 Jan 1;46(1):148-9. 

Alvi A, Devi SM, Ahmed I, Hussain MA, Rizwan M, Lamouliatte H, Megraud F, Ahmed N. Microevolution of Helicobacter pylori type IV secretion systems in an ulcer disease patient over a ten-year period. J Clin Microbiol. 2007 Dec;45(12):4039-43. 

Prouzet-Mauleon V, Hussain MA, Lamouliatte H, Kauser F, Megraud F, Ahmed N. Pathogen evolution in vivo: genome dynamics of two isolates obtained 9 years apart from a duodenal ulcer patient infected with a single Helicobacter pylori strain. J Clin Microbiol. 2005 Aug;43(8):4237-41. 

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, Ahmed N. The cag pathogenicity island of Helicobacter pylori is disrupted in the majority of patient isolates from different human populations. J Clin Microbiol. 2004 Nov;42(11):5302-8.