Assays and methods for detecting resistance to beta-lactam antibiotics including detection of multiple β-lactamase family specific gene targets by polymerase chain reaction or microarray. One or more kits including primers and/or probes for identification of β-lactamase genes selected from the group consisting of one or more of the following: MOX-like, FOX-like, ACC-like, ACT/MIR-like, CMY-2-like, DHA-like, CTX-M-14-like, CTX-M-15-like, VIM-like, NDM-like, IMP-like, KPC-like, and OXA-48-like, OXA-51-like, OXA-143-like, OXA-58-like, OXA-23-like, OXA-24/40-like, TEM-like, and SHV-like. A kit may also include one or more primers and/or probes for the identification a non-beta lactamase gene family which confers antibiotic resistance, such as the MCR-1 gene.

This document provides methods and materials involved in assessing mammals (e.g., humans) for arthritis. For example, methods and materials for assessing a mammal's gut microbial diversity to identify the mammal as having arthritis (e.g., rheumatoid arthritis) are provided. This document also provides methods and materials involved in treating arthritis.

The present invention provides methods and compositions involving microbiome signatures and their association with oral complications of cancer therapy.

Provided is a method of diagnosing lymphoma by analyzing an increase or decrease in contents of specific bacterial extracellular vesicles by performing bacterial metagenomic analysis using normal individual and subject-derived samples, wherein a lymphoma risk group may be diagnosed and predicted early to delay the time of onset or prevent the onset of lymphoma with proper cure, and after onset, early diagnosis may be performed, thereby reducing the incidence of lymphoma and increasing a therapeutic effect.

Provided is a method of diagnosing lymphoma by analyzing an increase or decrease in contents of specific bacterial extracellular vesicles by performing bacterial metagenomic analysis using normal individual and subject-derived samples, wherein a lymphoma risk group may be diagnosed and predicted early to delay the time of onset or prevent the onset of lymphoma with proper cure, and after onset, early diagnosis may be performed, thereby reducing the incidence of lymphoma and increasing a therapeutic effect.

The present disclosure provides methods and materials for determining if antibiotic resistant H. pylori is present in a sample. The methods may comprise obtaining a threshold level of H. pylori DNA from the sample, amplifying a region of the H. pylori DNA to generate multiple copies of the region of the H. pylori DNA, sequencing the multiple copies of the region of the H. pylori DNA, comparing sequences of multiple copies of the region of the H. pylori DNA to a reference sequence, identifying the presence of a mutation in multiple copies of the region of the H. pylori DNA, and determining a number of the multiple copies of the region of the H. pylori DNA with the mutation, wherein antibiotic resistant H. pylori is present in the sample when the number of the multiple copies of the region of the H. pylori DNA with the mutation is above a predetermined amount.

The present disclosure provides methods and materials for determining if antibiotic resistant H. pylori is present in a sample. The methods may comprise obtaining a threshold level of H. pylori DNA from the sample, amplifying a region of the H. pylori DNA to generate multiple copies of the region of the H. pylori DNA, sequencing the multiple copies of the region of the H. pylori DNA, comparing sequences of multiple copies of the region of the H. pylori DNA to a reference sequence, identifying the presence of a mutation in multiple copies of the region of the H. pylori DNA, and determining a number of the multiple copies of the region of the H. pylori DNA with the mutation, wherein antibiotic resistant H. pylori is present in the sample when the number of the multiple copies of the region of the H. pylori DNA with the mutation is above a predetermined amount.

Disclosed herein are methods and compositions for detecting Bordetella pertussis and Bordetella parapertussis by detecting the presence of the IS481 and IS1001 genomic insertion sequences, respectively.

Disclosed herein are methods and compositions for detecting Bordetella pertussis and Bordetella parapertussis by detecting the presence of the IS481 and IS1001 genomic insertion sequences, respectively.

The invention provides systems and methods for rapid automated identification of microbes and antimicrobial susceptibility testing (AST) directly from a patient specimen, without specimen preparation. Specimens are loaded into an analytical cartridge for processing. Analytical cartridges are preloaded with species-specific labels that are used to identify and enumerate microbes in the specimen. Instruments, such as analyzers can be used to interact with analytical cartridges to carry out methods of the invention all within the cartridge.