Emergence of carbapenem-producing enterobacteriaceae (CPE) and other multidrug-resistant gram-negative bacteria in neonates at a tertiary-level NICU in Tanzania: a point prevalence study

Journal article, 2025

Aim: Multidrug-resistant (MDR) Gram-negative bacilli pose a significant threat in neonatal care. This study aimed to evaluate the point prevalence and molecular characteristics of intestinal MDR colonization in neonates at Muhimbili National Hospital, Tanzania. Method: We conducted a point prevalence study with faecal samples from 51 neonates born ≥26 weeks gestational age (41% girls, mean 31.6 ± 3.8 weeks) admitted to the neonatal intensive care unit (NICU) at Muhimbili National Hospital on 17 May 2022. The median age at sampling was 8 days (interquartile range 11 days). Samples were cultured on chromogenic agar, and positive colonies underwent antimicrobial susceptibility testing. Whole-genome sequencing and plasmid analysis using Optical DNA Mapping (ODM) were performed on carbapenem-resistant isolates. Results: Among the 51 neonates, 31 (60.7%) were colonized by ESBL-producing Klebsiella pneumoniae (EP-KP) and/or Escherichia coli (EP-EC). Of these, 15 isolates were carbapenem-producing Enterobacteriaceae (CPE) harboring blaNDM-5, blaCTX-M-15, and eight also carried blaOXA-181. The most prevalent carbapenemase-producing Klebsiella pneumoniae (CP-KP) sequence type (ST) was ST437, part of the high-risk clonal complex CC11, while the most common carbapenemase-producing E. coli (CP-EC) was ST167. Both CP-KP and CP-EC were MDR isolates encoding blaCTX-M-15 and blaNDM-5. Optical DNA Mapping showed that the blaNDM-5 encoding plasmids in at least six carbapenem-producing isolates (four KP ST437 and two EC ST167) were similar, suggesting plasmid transfer. Conclusion: A high prevalence of colonization with high-risk clones was observed in neonates, highlighting the urgent need for strengthened MDR-surveillance, infection control, and antibiotic stewardship in the NICU at MNH.