![]() We present a tool that provides an in silico antibiogram for eight drugs. Models demonstrate high performance and robustness to class imbalanced datasets.Ĭonclusion: Whole genome sequencing enables the prediction of antimicrobial resistance in Gram-negative bacteria. The input is the WGS data in terms of the coverage of known antibiotic resistance genes by shotgun sequencing reads. Methods and Findings: We have used NCBI BioSample database to train and cross-validate eight XGBoost-based machine learning models to predict drug resistance to cefepime, cefotaxime, ceftriaxone, ciprofloxacin, gentamicin, levofloxacin, meropenem, and tobramycin tested in Acinetobacter baumannii, Escherichia coli, Enterobacter cloacae, Klebsiella aerogenes, and Klebsiella pneumoniae. The prediction of antimicrobial resistance in Gram-negative bacteria, often the cause of serious systemic infections, is more challenging as genotype-to-phenotype (drug resistance) relationship is more complex than for most Gram-positive organisms. High-throughput sequencing technology, such as whole genome sequencing (WGS), may have the capacity to rapidly guide the clinical decision-making process. 5Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United Statesīackground: Early detection of antimicrobial resistance in pathogens and prescription of more effective antibiotics is a fast-emerging need in clinical practice.4Department of Pediatrics, University of Cincinnati, Cincinnati, OH, United States.3Division of Infectious Diseases, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States.2Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States.1Department of Biomedical Informatics, University of Cincinnati, Cincinnati, OH, United States.read more, and tularemia Tularemia Tularemia is infection that is caused by the gram-negative bacteria Francisella tularensis, which is acquired when people have direct contact with infected wild animals, usually rabbits. The bacteria are spread mainly by the rat flea. read more, plague Plague and Other Yersinia Infections Plague is a severe infection caused by the gram-negative bacteria Yersinia pestis and often involving the lymph nodes and/or lungs. Botulism toxins, usually consumed in food, can weaken or paralyze. read more, botulism Botulism Botulism is a rare, life-threatening poisoning caused by toxins produced by the anaerobic bacteria Clostridium botulinum. Anthrax may affect the skin, the lungs, or, rarely, the digestive. These bacteria include those that cause anthrax Anthrax Anthrax is a potentially fatal infection with Bacillus anthracis, a gram-positive, rod-shaped bacteria (see figure ). Such use is contrary to international law and has rarely taken place during formal warfare in modern history, despite the. Many resident flora are actually helpful to people-for example, by helping them digest food or by preventing the growth of other, more dangerous bacteria.Ĭertain bacteria have the potential to be used as biological weapons Biological Weapons Biological warfare is the use of microbiological agents as weapons. There are at least as many bacteria in our resident flora as there are cells in the body. Such bacteria are called resident flora Resident Flora Healthy people live in harmony with most of the microorganisms that establish themselves on or in (colonize) nonsterile parts of the body, such as the skin, nose, mouth, throat, large intestine. Many bacteria live on and in the bodies of people and animals-on the skin and in the airways, mouth, and digestive, reproductive, and urinary tracts-without causing any harm. Some bacteria have been reported even to live in radioactive waste. They live in soil, seawater, and deep within the earth’s crust. ![]() There are thousands of different kinds of bacteria, and they live in every conceivable environment all over the world. They are among the earliest known life forms on earth. Bacteria are microscopic, single-celled organisms. ![]()
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