Table 1 Tools available in pathogenic Gram-negative and Gram-positive bacteria for genome modification

Recombineering

Homologous recombination of linear DNA utilizing λ-Red enzymes Gam, Exo and Bet

Salmonella enterica [26] ^a

Escherichia coli [23] ^a

Pseudomonas aeruginosa [29] ^a Streptomyces coelicolor [28] ^b

Shigella dysenteriae [50] ^a

pORTMAGE

Portable Multiplex Automated Genome Engineering (MAGE)

Utilizing recombineering

Salmonella enterica [35]^a

Targetrons

Retrohoming of Mobile Group II Introns by reverse splicing and insertion in genome

Clostridium perfringens [38] ^b

Vibrio Cholera [78] ^a

Yersinia pseudotuberculosis [79] ^a

Staphylococcus aureus [80]^b

Phage Engineering

CRISPR/Cas9

Delivery of CRISPR genes and RNA guides for sequence specific antimicrobials

Carbapenem-resistant Enterobacteriaceae

Enterohemorrhagic Escherichia coli [55] ^a

Antisense RNA

Post-transcriptional gene silencing

Staphylococcus aureus [81] ^b

Streptomyces coelicolor [82] ^b