US 12,383,599 B2
System and method for combating infections due to antibiotic induced pathogens
Sharmila Shekhar Mande, Pune (IN); Swadha Anand, Pune (IN); and Preethi Alagarai Sampath, Pune (IN)
Assigned to Tata Consultancy Services Limited, Mumbai (IN)
Appl. No. 17/596,180
Filed by Tata Consultancy Services Limited, Mumbai (IN)
PCT Filed Jun. 5, 2020, PCT No. PCT/IB2020/055305
§ 371(c)(1), (2) Date Dec. 3, 2021,
PCT Pub. No. WO2020/245781, PCT Pub. Date Dec. 10, 2020.
Claims priority of application No. 201921022521 (IN), filed on Jun. 6, 2019.
Prior Publication US 2022/0233637 A1, Jul. 28, 2022
Int. Cl. C12N 15/70 (2006.01); A61K 31/7088 (2006.01); A61K 38/16 (2006.01); A61K 38/46 (2006.01); C12N 15/10 (2006.01); C12Q 1/689 (2018.01)
CPC A61K 38/164 (2013.01) [A61K 31/7088 (2013.01); A61K 38/465 (2013.01); C12N 15/1072 (2013.01); C12Q 1/689 (2013.01); C12Q 2600/158 (2013.01)] 18 Claims
 
1. A method for combating infections due to antibiotic induced pathogens, the method comprising:
obtaining a sample from an infected area;
isolating and extracting DNA from the obtained sample using one of a laboratory method;
sequencing the isolated DNA using a sequencer;
detecting presence of the antibiotic induced pathogens using a plurality of detection methods, wherein the antibiotic induced pathogens comprise one or more of Clostridium difficile, vancomycin-resistant Enterococcus faecalis and vancomycin-resistant Enterococcus faecium from the isolated DNA of the sample;
preparing and administering an engineered polynucleotide construct on the infected area to combat the infections due to the antibiotic induced pathogens, wherein the engineered polynucleotide construct is comprising:
one or more of a set of nucleotide repeat sequences identified and selected with multiple copies at dispersed locations on the candidate pathogen genomes of one or more of the Clostridium difficile, vancomycin-resistant Enterococcus faecalis and vancomycin-resistant Enterococcus faecium genomes, wherein the set of nucleotide repeat sequences comprises one or more of the sequence of Sequence ID 001, the sequence of Sequence ID 002, the sequence of Sequence ID 003, the sequence of the reverse complement of Sequence ID 001, the sequence of the reverse complement of Sequence ID 002 or the sequence of the reverse complement of Sequence ID 003,
a first enzyme capable of nicking and cleaving the identified set of nucleotide sequences, and
a second enzyme capable of removal of a set of neighborhood genes flanking the set of nucleotide repeat sequences;
checking the efficacy of the administered engineered polynucleotide construct to combat the antibiotic induced pathogens after a predefined time period; and
re-administering the engineered polynucleotide construct if the antibiotic induced pathogens are still present in the infected area post administering.