Methods for detecting and treating polymicrobial infections, wherein a mixed population of microbes (e.g., bacteria) are present in a patient sample and the microbes are not first isolated from the sample. For example, the present invention describes specific polymicrobial infections and methods of treating said infections, wherein a particular antibiotic or a group of antibiotics are selected based on the composition of the polymicrobial infections.

The present invention relates to methods for diagnosing chronic kidney disease in a feline, including early-stage chronic kidney disease, by using microbiome including specific genera and species. In one embodiment, the method can comprise measuring an absolute abundance of fecal bacteria including Faecalibacterium, Turicibacter, Streptococcus, Bifidobacterium, Bacteroides, E. coli, and C. hiranonis; calculating a dysbiosis index based on the fecal bacteria; and determining that the feline has chronic kidney disease if the dysbiosis index is greater than or equal to 0.5.

The present invention relates to methods for diagnosing chronic kidney disease in a feline, including early-stage chronic kidney disease, by using microbiome including specific genera and species. In one embodiment, the method can comprise measuring an absolute abundance of fecal bacteria including Faecalibacterium, Turicibacter, Streptococcus, Bifidobacterium, Bacteroides, E. coli, and C. hiranonis; calculating a dysbiosis index based on the fecal bacteria; and determining that the feline has chronic kidney disease if the dysbiosis index is greater than or equal to 0.5.

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 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.

Disclosed is a method for identifying methicillin-resistant Staphylococcus aureus through detection a mass signal at m/z of 6580-6600 in the MALDI-TOF mass spectrum. Also disclosed is a novel peptide biomarker, which consists of SEQ NO ID:5 and the use thereof for detection and/or identification of methicillin-resistant Staphylococcus aureus.

Disclosed is a method for identifying methicillin-resistant Staphylococcus aureus through detection a mass signal at m/z of 6580-6600 in the MALDI-TOF mass spectrum. Also disclosed is a novel peptide biomarker, which consists of SEQ NO ID:5 and the use thereof for detection and/or identification of methicillin-resistant Staphylococcus aureus.

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.