A method for distinguishing among a first group of microorganisms belonging to a first taxon of Gram negative bacteria, the first group of bacteria exhibiting a mechanism of resistance to a treatment; a second group of microorganisms belonging to a second taxon of Gram negative bacteria, the second taxon of bacteria being different than said first taxon, and exhibiting a mechanism of resistance to a treatment identical to the mechanism of the first group; and a third group of Gram negative bacteria that is not resistant to the treatment.

Methods and systems for Resonant Raman spectroscopy are provided. Methods according to certain embodiments include irradiating a sample with a monochromatic light source at a first irradiation intensity and a second irradiation intensity, determining the intensity of one or more of the Resonant Raman scattering and fluorescence scattering at the first irradiation intensity and second irradiation intensity, calculating a rate of change of one or more of the intensity of Resonant Raman scattering and fluorescence in response to the change in irradiation intensity from the first irradiation intensity to the second irradiation intensity and comparing one or more of the rate of change in the intensity of Resonant Raman scattering and the rate of change in the intensity of fluorescence scattering with the rate of change in the irradiation intensity by the monochromatic light source to determine the Resonant Raman response of the sample. Methods also include determining the presence or absence of a microorganism in a sample and correcting for variations associated with measurement instrumentation (e.g., monochromatic light source) and variations associated with the sample (e.g., fluorescence from non-target compounds). Also provided are methods for determining the antimicrobial susceptibility of a microorganism to an antimicrobial agent as well as methods for characterizing a phenotype of an unknown microorganism in a sample. Systems for practicing the subject methods are also provided.

Methods and systems for Resonant Raman spectroscopy are provided. Methods according to certain embodiments include irradiating a sample with a monochromatic light source at a first irradiation intensity and a second irradiation intensity, determining the intensity of one or more of the Resonant Raman scattering and fluorescence scattering at the first irradiation intensity and second irradiation intensity, calculating a rate of change of one or more of the intensity of Resonant Raman scattering and fluorescence in response to the change in irradiation intensity from the first irradiation intensity to the second irradiation intensity and comparing one or more of the rate of change in the intensity of Resonant Raman scattering and the rate of change in the intensity of fluorescence scattering with the rate of change in the irradiation intensity by the monochromatic light source to determine the Resonant Raman response of the sample. Methods also include determining the presence or absence of a microorganism in a sample and correcting for variations associated with measurement instrumentation (e.g., monochromatic light source) and variations associated with the sample (e.g., fluorescence from non-target compounds). Also provided are methods for determining the antimicrobial susceptibility of a microorganism to an antimicrobial agent as well as methods for characterizing a phenotype of an unknown microorganism in a sample. Systems for practicing the subject methods are also provided.

The invention provides a method for identifying methicillin resistant Staphylococcus aureus (MRSA) in a bacterial sample comprising the steps: classifying bacteria in the sample as Staphylococcus aureus (SA) and determining the presence or absence of the phenol soluble modulin peptide or a variant thereof wherein the presence of the PSM-mec peptide or variant thereof indicates methicillin resistant Staphylococcus aureus. The variant is preferably the formylated version of the PSM-mec peptide having a mass to charge ratio of 2415 in a singly protonated state.

The invention provides a method for identifying methicillin resistant Staphylococcus aureus (MRSA) in a bacterial sample comprising the steps: classifying bacteria in the sample as Staphylococcus aureus (SA) and determining the presence or absence of the phenol soluble modulin peptide or a variant thereof wherein the presence of the PSM-mec peptide or variant thereof indicates methicillin resistant Staphylococcus aureus. The variant is preferably the formylated version of the PSM-mec peptide having a mass to charge ratio of 2415 in a singly protonated state.

A biological system for generating and preserving a repository of personalized, humanized transplantable cells, tissues, and organs for transplantation, wherein the biological system is biologically active and metabolically active, the biological system having genetically reprogrammed cells, tissues, and organs in a non-human animal for transplantation into a human recipient, wherein the non-human animal does not present one or more surface glycan epitopes and specific sequences from the wild-type swine's SLA is replaced with a synthetic nucleotides based on a human captured reference sequence from a human recipient's HLA.

A biological system for generating and preserving a repository of personalized, humanized transplantable cells, tissues, and organs for transplantation, wherein the biological system is biologically active and metabolically active, the biological system having genetically reprogrammed cells, tissues, and organs in a non-human animal for transplantation into a human recipient, wherein the non-human animal does not present one or more surface glycan epitopes and specific sequences from the wild-type swine's SLA is replaced with a synthetic nucleotides based on a human captured reference sequence from a human recipient's HLA.

Methods for monitoring the environmental hygiene of an area includes inoculating one or more test items or sampling devices with at least one target and providing the inoculated test items or sampling devices for testing using at least one standard detection protocol. The test is reviewed to determine whether the protocol solicits a reaction to each target. If a target solicits the intended result, then the standard detection protocol for that target is determined to be proficient. Methods for monitoring the effectiveness environmental hygiene for an area to ascertain the proficiency to the testing or sampling of at least one test surface includes providing at least one target and testing or sampling the test surface. A test item or sampling device is tested with at least one standard detection protocol and the test is reviewed to determine whether the at least one target is detected as intended by the protocol.

Methods for monitoring the environmental hygiene of an area includes inoculating one or more test items or sampling devices with at least one target and providing the inoculated test items or sampling devices for testing using at least one standard detection protocol. The test is reviewed to determine whether the protocol solicits a reaction to each target. If a target solicits the intended result, then the standard detection protocol for that target is determined to be proficient. Methods for monitoring the effectiveness environmental hygiene for an area to ascertain the proficiency to the testing or sampling of at least one test surface includes providing at least one target and testing or sampling the test surface. A test item or sampling device is tested with at least one standard detection protocol and the test is reviewed to determine whether the at least one target is detected as intended by the protocol.

A method of taking a skin sample can include placing an adhesive onto a portion of skin and lifting the adhesive from the skin. A skin sample may then be tested while still on the adhesive, for example, by inoculating the sample with a bacterium, fungus, virus, or a combination.