Method and system for identification of candidate target sites for combating pathogens

A method for identification of candidate target sites for combating pathogenic infection due to pathogens, the method comprising:

• obtaining a sample from an infected area;
• extracting DNA from the obtained sample using DNA extraction methods;
• sequencing the isolated DNA using a sequencer;
• detecting a pathogen from the sequenced DNA;
• identifying a set of nucleotide repeat sequences in the extracted DNA which are occurring more than a predefined number of times in a pathogen genome,
• wherein the set of nucleotide repeat sequences corresponding to one or more than one strain of the pathogen,
• wherein the set of nucleotide repeat sequences are found in multiple copies at distant locations on the genomes of all pathogenic strains of a candidate genus or species and these nucleotide repeat sequences do not show more than the two-nucleotide sequence similarity based match to genome sequences corresponding to genera or species other than the genome sequences of the pathogens belonging to the candidate genus or species or with genomes of commensal strains within the candidate genus or species,
• wherein the set of nucleotide repeat sequences are selected if the set of nucleotide repeat sequences are present only in the candidate genus of the pathogen,
• wherein distant locations refer to a distance greater than a predetermined number of nucleotide base pairs;
• identifying a set of neighborhood genes present upstream and downstream of the set of nucleotide repeat sequences;
• categorizing the set of neighborhood genes according to their functional roles in the pathogen based on their involvement in pathways;
• testing the presence of a secondary structure in the identified set of nucleotide sequences;
• preparing and administering an engineered polynucleotide construct on the infected area to treat the pathogenic infection by cleaving the set of nucleotide repeat sequences and removing flanking genes,
• wherein the engineered polynucleotide construct is administered to the target bacterial cell using a bacterial, a plasmid or a viral vector,
• wherein the engineered polynucleotide construct is in the form of an oral medicine, topical creams, nasal administration, aerosol sprays, an injectable cocktail,
• wherein the engineered polynucleotide construct comprises:
• one or more of the identified set of nucleotide repeat sequences occurring in multiple copies at dispersed locations on candidate pathogen genomes of one or more of Streptococcus pneumonia, Staphylococcus epidermidis, Mycobacterium tuberculosis, Pseudomonas aeruginosa, Klebsiella pneumoniae, Staphylococcus aureus, Xanthomonas axonopodis, Clostridium genomes, wherein the set of nucleotide repeat sequences comprises one or more of a Sequence ID 001, and reverse complement of the Sequence ID 001,
• a first enzyme capable of nicking and cleaving the identified set of nucleotide repeat sequences, and
• a second enzyme capable of removal of a set of neighborhood genes flanking the set of nucleotide repeat sequences;
• assessing the efficacy of the administered construct;
• and
• re-administering the engineered polynucleotide construct repetitively in case the pathogen presence is detected at the infected area post administering, till the pathogen is completely eliminated,
• wherein the engineered polynucleotide construct targets the identified set of nucleotide repeat sequences on the pathogen genome along with important functional genes flanking the identified set of nucleotide repeat sequences to debilitate multiple important functions of the pathogen simultaneously and disrupt the overall functioning of the pathogen to carry out changes including gene silencing, gene recombination, gene substitution with a new function,
• wherein the important functional genes refer to the genes in pathogens which encode for proteins which are critical for survival, pathogenicity, interaction with the host, adherence to the host or for the virulence of bacteria, and
• wherein the minimum predefined number of genes to be considered in genomic neighborhood is 10.