Early Life Antibiotic Exposure and Intestinal Colonization by Enterobacteriaceae upon Admission to a Neonatal Referral Unit: A Case–Control Study

Background/Objectives: Intestinal colonization by Enterobacteriaceae, including extended-spectrum β-lactamase-producing (ESBL-E) and carbapenemase-producing (E-CPE) strains, is an early marker of multidrug-resistant infections in neonates, particularly those transferred from lower-complexity hospitals. This study aimed to identify factors associated with intestinal Enterobacteriaceae colonization upon admission to a level IV neonatal referral unit in Colombia, with a focus on prior antibiotic exposure. Methods: We conducted a retrospective case–control study, including all neonates transferred from peripheral hospitals and screened with rectal swabs at admission. Cases were neonates colonized with Enterobacteriaceae, and controls were non-colonized neonates admitted during the same period. Multivariable logistic regression models were used to evaluate three exposure dimensions: prior antibiotic use (yes/no), number of agents, and the WHO AWaRe classification. A secondary analysis was performed to assess the factors associated with ESBL-E and E-CPE colonization. Results: Among the 435 referred neonates, 87 (20.0%) were colonized, predominantly Klebsiella pneumoniae (53.6%) and Escherichia coli (19.5%). Prior antibiotic use (aOR 3.01; 95% CI 1.47–6.37), exposure to two agents (aOR 4.13; 95% CI 1.94–8.89) and use of AWaRe Access antibiotics (aOR 22.2; 95% CI 5.83–101) were strongly associated with colonization. Longer hospitalization and central catheter use were also associated with greater colonization odds, whereas total parenteral nutrition showed a protective association. In the sub-analysis, Access, Watch, and Reserve antibiotics were independently associated with ESBL-E and E-CPE colonization. Conclusions: Among transferred neonates, prior antibiotic exposure, particularly AWaRe-classified agents, showed the strongest association with intestinal colonization by Enterobacteriaceae, including ESBL-E/CPE phenotypes. Strengthening antimicrobial stewardship in referral facilities and implementing risk-based screening at admission may help reduce colonization and limit the spread of resistance.