DRUG DEVELOPMENT RESEARCH 72 : 162–177 (2011) Research Overview In Silico Subtractive Genomics for Target Identification in Human Bacterial Pathogens Debmalya Barh, 1,4Ã Sandeep Tiwari, 2 Neha Jain, 2 Amjad Ali, 3 Anderson Rodrigues Santos, 3 Amarendra Narayan Misra, 4 Vasco Azevedo, 3 and Anil Kumar 2 1 Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur WB-721172, India 2 School of Biotechnology, Devi Ahilya University, Khandwa Rd., Indore 452001, India 3 Laborato ´rio de Gene ´tica Celular e Molecular, Departamento de Biologia Geral, Instituto de Cie ˆncias Biolo ´ gicas, Universidade Federal de Minas Gerais, CP 486, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil 4 Department of Biosciences and Biotechnology, School of Biotechnology, Fakir Mohan University, Jnan Bigyan Vihar, Balasore, 756020 Orissa, India Strategy, Management and Health Policy Enabling Technology, Genomics, Proteomics Preclinical Research Preclinical Development Toxicology, Formulation Drug Delivery, Pharmacokinetics Clinical Development Phases I-III Regulatory, Quality, Manufacturing Postmarketing Phase IV ABSTRACT Target identification is the first step in the drug and vaccine discovery process; in silico subtractive genomics is widely used in this process. Using this approach, in recent years, a large number of targets have been identified for bacterial pathogens that are either drug resistant or for which no suitable vaccine is available; most such reports concern a specific pathogen. The in silico method reduces the time as well as the cost of target screening. Although a powerful technique that can be applied to a wide range of pathogens, there are many pitfalls in the analysis and interpretation of the data. We review this approach, including targets that have been identified with this technique and various other aspects, including advantages and disadvantages. We also discuss our own experiences using this technology. Drug Dev Res 72:162–177, 2011. r 2010 Wiley-Liss, Inc. Key words: drug target; essential genes; subtractive genomics; bacterial pathogen INTRODUCTION Although high-throughput techniques and syn- thetic chemistry are an integral part of today’s drug discovery process, accelerating the process manifold, the introduction of a new drug on the market still takes 10–15 years and therefore requires a huge investment [Plotkin, 2005]. Technological advancements, along with improved and innovative strategies, could reduce the cost and the time required to develop a new drug. Most infectious diseases are caused by bacterial pathogens. An increase of 58% in the mortality rate due to such infectious diseases has been reported from 1980 to 1992 in the United States [Pinner et al., 1996]. According to the 2004 World Health Organization Report [www.who.int/whr/2004/annex/topic/en/annex_ 2_en.pdf], 16.4 million people died worldwide in that year from bacterial infectious diseases. Although several antibiotics are currently available for each bacterial pathogen, the emerging drug-resistant strains of such pathogens make them difficult to control, DDR Published online in Wiley Online Library (wileyonlinelibrary. com). DOI: 10.1002/ddr.20413 Ã Correspondence to: Debmalya Barh, Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur WB-721172, India. E-mail: dr.barh@gmail.com  c 2010 Wiley-Liss, Inc.