We evaluated an infection control (IC) program influenced by personnel and material resource shortages on the incidence of bloodstream infections (BSI) due to carbapenem-resistant Klebsiella pneumoniae (CRKP), Acinetobacter baumannii (CRAB), and Pseudomonas aeruginosa (CRPA) in an endemic region. Between January 2010 and December 2015, all BSI episodes caused by CRKP, CRAB, and CRPA were recorded. An IC bundle was implemented in January 2012. We evaluated the effect of the interventions on BSI rates between the pre-intervention (2010-2011) and intervention (2012-2013) periods, using an interrupted time-series model. From 2014, when interventions were still applied, BSI incidence was gradually increased. For this reason, we evaluated with a linear mixed effects model several factors possibly contributing to this increase for the years 2012-2015, which was considered as the intervention/follow-up period. During the study period, 351 patients with BSI were recorded, with a total of 538 episodes; the majority (83.6%) occurred in the intensive care unit (ICU). The BSI incidence rate per year during 2010-2015 for ICU patients was 21.03/19.63/17.32/14.45/22.85/25.02 per 1000 patient-days, respectively, with the reduction in BSI levels after the start of intervention marginal (p = 0.054). During the follow-up period (2014-2015), the most influential factors for the increased BSI incidence were the reduced participation in educational courses and compliance with hand hygiene. The implementation of IC interventions reduced the BSI incidence rates, particularly for ICU patients. However, factors possibly related to the restrictions of human and material resources apparently contributed to the observed expansion of BSI in our endemic setting.