Hospital acquired infections (HAI) may affect every patient who is in contact with the healthcare setting however severely ill patients, whose immune system is compromised due to disease, treatment and extreme age, and whose natural defense barriers are bypassed by invasive devices and procedures, are mostly affected. Recent decade experience suggests that 75% of these infections are preventable. HAI are a leading cause of mortality and morbidity. In Israel it is estimated that hospital acquired infection contribute result in 4-6,000 fatalities annually. These infections are caused by opportunistic pathogens arising from the patient`s own flora or from the hospital environment. Most of the bacterial causative pathogens are resistant to commonly used antibiotic agents, many are multidrug resistant and over the last decade extremely drug resistant organisms have become prevalent in many countries. The modes of emergence and spread of various pathogens differ. Moreover, similar pathogens and resistant mechanism may have different epidemiology at different settings and may change overtime. Molecular studies combined with conventional epidemiology are required to understand the epidemiology. It is crucial to understand the epidemiology in order to design effective control measures. Moving from the short term epidemiology to wider and prolonged duration requires increasingly sophisticated molecular typing techniques. Whole genome sequencing is emerging as the gold standard methodology, however, cost and the expertise and time required for analysis are limiting factors. MALDI TOF technology is emerging as a standard diagnostic tool in clinical microbiology laboratories and may offer typing capabilities which may assist the local epidemiologists.
