The most effective means of reducing microbes in root canal:
Following measures should be taken to be completely rid of these irritants:

Thorough cleaning and shaping of the root canal system: Thorough cleaning and shaping followed by three-dimensional obturation of the root canals have shown to produce complete healing of periradicular tissue. Complete debridement of canal should be done with adjunctive use of irrigants like sodium hypochlorite, which efficiently removes bacteria as well as their substrate from irregularities of canal system, where instruments cannot reach such as fins, indentations, cul de-sacs, etc.
Oxygenating a canal simply by opening it is detrimental to anaerobes. Use of oxygenating agents as glyoxide can be of great help, but care should be taken to avoid the inoculation of these oxygenating agents into periapical tissues. 
A tooth with serous or purulent or hemorrhagic exudate should be allowed to drain with rubber dam in place for a time under supervision. An abscess which is a potent irritant, has an elevated osmotic pressure. This attracts more tissue fluid and thus more edema and pain. Drainage by canal or by soft tissues decrease discomfort caused by inflammatory mediators. 
Antibiotics should also be considered as adjunctive in severe infections. The choice of antibiotic agent should be done on the knowledge of microorganisms associated with endodontic infections. 
Intracanal medicaments play an important role in combating the microorganisms.
Frequent medication of root canal
Complete debridement through instrumentation
Systemic antibiotics
All of the above