Molecular epidemiology and antimicrobial resistance of extended-spectrum beta-lactamase-producing Enterobacter cloacae complex in obstetric and neonatal units in Tanga, Tanzania

Abstract

Enterobacter cloacae complex (ECC) poses a significant threat to neonatal healthcare, particularly in resource-limited settings. This study aimed at characterizing the molecular epidemiology and antimicrobial resistance of ESBL-producing ECC isolates collected from two hospitals in Tanga. A cross section survey was conducted between May 2022 and March 2023, swabs were collected from neonates, mothers, hands of healthcare workers and the environment. Isolates were identified using the Chromogenic agar, API 20 E and Vitek 2, antimicrobial susceptibility testing (AST) was performed according to the EUCAST guidelines. Whole-genome analysis was performed to characterize sequence types (STs), resistance genes, virulence genes and the associated plasmids. Phylogenetic relatedness of the isolates recovered from different sources was assessed to detect transmission pathways. A total of 132 ECC isolates were recovered, with environmental samples (65.90%, n/N = 87/132) yielding more isolates than human sources (34.10%, n/N = 45/132). ECC colonization was observed in 5.9% of neonates, of whom 62% acquired colonization during hospitalization, indicating nosocomial transmission. MDR was prevalent (73.4%), with high resistance rates to third-generation cephalosporins, and notable carbapenem resistance (10.5%). Genomic analysis identified a high diversity of beta-lactamase genes, dominated by blaCTX-M-15 (88%) and blaACT genes (94%), alongside carbapenemase genes blaNDM-1 and blaNDM-5 (12.1%). Notably, colistin resistance gene mcr-10.1 was exclusively associated with ST66 isolates,highlighting the emergence of locally significant ECC lineages with resistance against last-resort antibiotic like colistin, not commonly used in Tanzania. ST346 was the most dominant sequence type (24.2%), circulating across human and environmental samples, demonstrating repeated transmission and persistent colonization in hospital wards. The co-occurrence of MDR and virulence factors in temporal clusters underscores the enhanced potential for invasive infections. This study emphasizes the critical need for rigorous environmental hygiene measures and enhanced infection prevention and control (IPC) strategies to limit the dissemination of multidrug resistant ECC in neonatal healthcare settings.