Abstract: Compositions and methods for detecting bacterial pathogens containing microbial resistance genes in a sample, as well as methods for selecting a treatment for human infections involving such organisms. The methods involve carrying out a series of reactions in parallel where each reaction involves detecting a bacterial species or resistance gene in a sample using a CRISPR-Cas13a reaction. In some embodiments, the methods involve culturing a blood sample to increase the concentration of bacteria in the sample and/or direct detection of bacterial pathogens and/or microbial resistance genes in a blood sample.