![]() Since the discovery and widespread use of antibiotics (AB) in the early 20th century, resistance to those same AB has generally developed rapidly often even within the first years of introduction ( Marston et al., 2016). The stand-alone version of the predictor is available at. The demo version of the tool with pre-processed samples is available at. Predictions are accompanied with a reliability index that may further facilitate the decision making process. 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.A change in antibiotics or surgical intervention may be required.Pieter-Jan Van Camp 1,2 David B. Lack of response should prompt repeat blood and urine cultures and, possibly, imaging studies. Treatment failure may be caused by resistant organisms, underlying anatomic/functional abnormalities, or immunosuppressed states. Urine culture should be repeated one to two weeks after completion of antibiotic therapy. The standard duration of therapy is seven to 14 days. In hospitalized patients, intravenous treatment is recommended with a fluoroquinolone, aminoglycoside with or without ampicillin, or a third-generation cephalosporin. Indications for inpatient treatment include complicated infections, sepsis, persistent vomiting, failed outpatient treatment, or extremes of age. Other effective alternatives include extended-spectrum penicillins, amoxicillin-clavulanate potassium, cephalosporins, and trimethoprim-sulfamethoxazole. Outpatient oral antibiotic therapy with a fluoroquinolone is successful in most patients with mild uncomplicated pyelonephritis. The use of blood cultures should be reserved for patients with an uncertain diagnosis, those who are immunocompromised, and those who are suspected of having hematogenous infections. Urine cultures are positive in 90 percent of patients with acute pyelonephritis, and cultures should be obtained before antibiotic therapy is initiated. The combination of the leukocyte esterase test and the nitrite test (with either test proving positive) has a sensitivity of 75 to 84 percent and a specificity of 82 to 98 percent for urinary tract infection. The most common etiologic cause is infection with Escherichia coli. ![]() There are approximately 250,000 cases of acute pyelonephritis each year, resulting in more than 100,000 hospitalizations.
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