Background

Infections due to multi-drug resistant Enterobacteriaceae (MDR-E) are a global challenge, especially on low resource setting (LRS) neonatal units with high mortality in preterm neonates. Maternal MDR-E carriage is a risk-factor for neonatal carriage in HIC but the contribution towards acquisition in LRS is unknown. We aimed to characterise neonatal MDR-E carriage and explore associations with maternal carriage via detailed clinical, microbiological and genomic analyses.

Methods

This cross-sectional study at the Gambian teaching hospital involved weekly collection of skin/peri-anal swabs from neonates <2000g and <24h, with maternal recto-vaginal swabs. We conducted conventional microbiology for Enterobacteriaceae and isolates were whole genome sequenced (Illumina platform) to identify sequence types. Antibiotic resistance gene carriage was determined using abriccate with MDR diagnosed if genes coded for resistance to >=3 antimicrobial classes. Maximum likelihood phylogenetic trees were generated from core aligned SNPs using RAxML

Results

137 swabs from 34 neonates and 23 mothers, (21 dyads) yielded 135 Enterobacteriaceae. 82% of isolates had genotypic MDR, mostly K pneumoniae (98%, 43/44) and E coli (84%, 42/50). 22%(17/34) of neonates carried ≥1 MDR-E at admission rising to 85% (11/13) by 7d. K pneumoniae and E coli strains were heterogeneous with no evidence of clonal outbreaks. Paired E coli (6 dyads) and K pneumoniae (5 dyads) were unrelated on SNP-distance analysis. Two or more antibiotic resistance genes were identified in all K pneumoniae (median 13.5 genes) and E coli (median 7.5 genes) with wide diversity of ESBL, AMP-C, fluoroquinolone and septrin resistant genes.

Fig1. Phylogeny trees for K.pneumoniae (top) and Escherichia coli (bottom) isolates

Conclusions

Our results suggest rapid acquisition of MDR-E during hospitalization without genomic evidence of maternal transmission. Environmental surveillance is required for insights to guide infection prevention strategies.

Clinical Trial Registration

Not applicable as no clinical trial is involved