DBDiaSNP: An Open-Source Knowledgebase of Genetic Polymorphisms and Resistance Genes Related to Diarrheal Pathogens

Abstract

Diarrhea is a highly common infection among children, responsible for significant morbidity and mortality rate worldwide. After pneumonia, diarrhea remains the second leading cause of neonatal deaths. Numerous viral, bacterial, and parasitic enteric pathogens are associated with diarrhea. With increasing antibiotic resistance among enteric pathogens, there is an urgent need for global surveillance of the mutations and resistance genes primarily responsible for resistance to antibiotic treatment. Single Nucleotide Polymorphisms are important in this regard as they have a vast potential to be utilized as molecular diagnostics for gene-disease or pharmacogenomics association studies linking genotype to phenotype. DBDiaSNP is a comprehensive repository of mutations and resistance genes among various diarrheal pathogens and hosts to advance breakthroughs that will find applications from development of sequence-based diagnostic tools to drug discovery. It contains information about 946 mutations and 326 resistance genes compiled from literature and various web resources. As of March 2015, it houses various pathogen genes and the mutations responsible for antibiotic resistance. The pathogens include, for example, DEC (Diarrheagenic E.coli), Salmonella spp., Campylobacter spp., Shigella spp., Clostridium difficile, Aeromonas spp., Helicobacter pylori, Entamoeba histolytica, Vibrio cholera, and viruses. It also includes mutations from hosts (e.g., humans, pigs, others) that render them either susceptible or resistant to a certain type of diarrhea. DBDiaSNP is therefore intended as an integrated open access database for researchers and clinicians working on diarrheal diseases. Additionally, we note that the DBDiaSNP is one of the first antibiotic resistance databases for the diarrheal pathogens covering mutations and resistance genes that have clinical relevance from a broad range of pathogens and hosts. For future translational research involving integrative biology and global health, the database offers veritable potentials, particularly for developing countries and worldwide monitoring and personalized effective treatment of pathogens associated with diarrhea. The database is accessible on the public domain at http://www.juit.ac.in/attachments/dbdiasnp/.

Antibiotics-Induced Obesity: A Mitochondrial Perspective

“…When the existence of antibiotic-resistant strains of microorganisms was first reported about 70 years ago [49], it may have been overlooked due to the presence of other drugs that could potentially treat these infections. But the widespread, unregulated use of antibiotics has led to the emergence of several drug-resistant microorganisms causing diseases such as typhoid [50], cholera [51], diarrheal illness [52], enterococcal infections [53], gonorrhea [54,55], urinary tract infections [56], malaria [57], HIV [58], tuberculosis [59], and other respiratory infections [60] including influenza [61].…”

Antibiotic Resistance and Potential Pathogenicity of an Isolate <i>Salmonella enterica enterica</i> Based on Genomic Comparison with of 103 and 2199 Strains Obtained from Contaminated Chicken Meat in Mexico

“…Specific toxins related to Salmonella symptomatology have been hard to pinpoint, as the host susceptibility factor appears to be central for salmonello-sis symptoms development. Comparison of the hereby reported genomes with the DBDiaSNP database failed to provide sequences directly related to diarrhea symptoms [40]. In the reported genome, we encountered SPI-4 pathogenicity island, reported elsewhere to be related to the severity of the diarrhea [41].…”