Prevalence of β-Lactamases-Encoding Genes Among ESBL-Producing Enterobacterales Colonizing Neonates in a Neonatal Intensive Care Unit from Brazil

Background/Objectives: Extended-spectrum β-lactamase (ESBL)-producing Enterobacterales represent a major concern in neonatal intensive care units (NICUs), where colonization may precede infection and contribute to the spread of antimicrobial resistance. This study aimed to investigate the distribution of β-lactamase-encoding genes among Enterobacterales colonizing neonates in a Brazilian NICU. Methods: Rectal swab samples (n = 427) were collected over a one-year period. Forty-six isolates recovered on ESBL-selective chromogenic medium were subsequently phenotypically confirmed as ESBL producers by the disk approximation method. Bacterial identification was performed by MALDI-TOF MS, and the presence of blaCTX-M, blaSHV, and blaTEM genes was determined by PCR. Multidrug resistance (MDR) and Multiple Antibiotic Resistance (MAR) Index were determined according to international criteria. Results: Overall, 41.3% of isolates were classified as MDR, and the mean MAR Index was 0.234 ± 0.130. The blaCTX-M gene was the most frequently detected (33%), followed by blaSHV (13%) and blaTEM (11%). Simultaneous occurrence of multiple β-lactamase genes was observed in a small number of isolates (17.4%), mainly associated with Escherichia coli and Klebsiella pneumoniae. MDR was significantly associated with the detection of at least one of the investigated β-lactamase genes (83.3% vs. 14.3%; Fisher’s exact test, p < 0.001; OR = 30.0). Conclusions: Our findings show that β-lactamase genes, particularly the ESBL gene blaCTX-M, are present among colonizing Enterobacterales in neonates and highlight the importance of monitoring these genetic determinants in NICU settings.