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1. WO2022140302 - SEQUENCING MICROBIAL CELL-FREE NUCLEIC ACIDS TO DETECT INFLAMMATION, SECONDARY INFECTION, AND DISEASE SEVERITY

Publication Number WO/2022/140302
Publication Date 30.06.2022
International Application No. PCT/US2021/064445
International Filing Date 20.12.2021
IPC
C12Q 1/6869 2018.1
CCHEMISTRY; METALLURGY
12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
1Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
68involving nucleic acids
6869Methods for sequencing
C12Q 1/6855 2018.1
CCHEMISTRY; METALLURGY
12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
1Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
68involving nucleic acids
6844Nucleic acid amplification reactions
6853using modified primers or templates
6855Ligating adaptors
C40B 40/06 2006.1
CCHEMISTRY; METALLURGY
40COMBINATORIAL TECHNOLOGY
BCOMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES, IN SILICO LIBRARIES
40Libraries per se, e.g. arrays, mixtures
04Libraries containing only organic compounds
06Libraries containing nucleotides or polynucleotides, or derivatives thereof
G16B 30/10 2019.1
GPHYSICS
16INFORMATION AND COMMUNICATION TECHNOLOGY SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
30ICT specially adapted for sequence analysis involving nucleotides or amino acids
10Sequence alignment; Homology search
Applicants
  • KARIUS, INC. [US]/[US]
  • UNIVERSITY OF PITTSBURGH - OF THE COMMONWEALTH SYSTEM OF HIGHER EDUCATION [US]/[US]
Inventors
  • AHMED, Asim
  • DUTTAGUPTA, Radha
  • KITSIOS, Georgios D.
Agents
  • HUDSPITH, Karl
Priority Data
63/128,55221.12.2020US
63/139,24519.01.2021US
63/199,49703.01.2021US
Publication Language English (en)
Filing Language English (EN)
Designated States
Title
(EN) SEQUENCING MICROBIAL CELL-FREE NUCLEIC ACIDS TO DETECT INFLAMMATION, SECONDARY INFECTION, AND DISEASE SEVERITY
(FR) SÉQUENÇAGE D'ACIDES NUCLÉIQUES ACELLULAIRES MICROBIENS POUR DÉTECTER UNE INFLAMMATION ET UNE INFECTION SECONDAIRE ET POUR DÉTERMINER LA GRAVITÉ D'UNE MALADIE
Abstract
(EN) Described herein is a method of detecting secondary infection in a patient, particularly a patient with a primary infection that is a pneumonia, a COVID-19 infection, or a COVID-19 pneumonia. In some cases, the secondary infection is a secondary bacterial infection, e.g., secondary bacterial pneumonia. In some cases, the methods provided herein detect a hyper-inflammatory response or severity of disease, e.g., indicating a severe COVID-19 infection, or provide a risk of death from a disease (e.g., COVID-19). This disclosure also provides method of detecting a localized respiratory infection in a subject by quantifying microbial cell-free nucleic acids (e.g., mdfDNA) from plasma from the subject. In some cases, the subject is not bacteremic when plasma is collected from the subject. This disclosure also provides systems, such as nucleic acid-sequencing systems with increased reliability for detecting secondary infections, particularly in patients with culture-negative pneumonia.
(FR) La divulgation concerne une méthode de détection d'une infection secondaire chez un patient, en particulier un patient souffrant d'une infection primaire qui est une pneumonie, une infection à COVID-19 ou une pneumonie due à la COVID-19. Dans certains cas, l'infection secondaire est une infection bactérienne secondaire, par exemple une pneumonie bactérienne secondaire. Dans certains cas, les méthodes de la présente divulgation permettent de détecter une réponse hyper-inflammatoire ou de déterminer la gravité d'une maladie, par exemple en révélant une infection grave à COVID-19, ou permettent de déterminer un risque de décès dû à une maladie (par exemple la COVID-19). La présente divulgation concerne également un procédé de détection d'une infection respiratoire localisée chez un sujet par quantification d'acides nucléiques acellulaires microbiens (par exemple de l'ADNmdf) à partir de plasma provenant du sujet. Dans certains cas, le sujet n'est pas septicémique lorsque du plasma est recueilli auprès de ce dernier. La présente divulgation concerne en outre des systèmes, tels que des systèmes de séquençage d'acides nucléiques présentant une fiabilité accrue pour la détection d'infections secondaires, en particulier chez des patients présentant une pneumonie à culture négative.
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