# Genomic epidemiology of extended-spectrum beta-lactamase-producing Escherichia coli and Klebsiella pneumoniae in Mwanza, Tanzania

## TL;DR

This study identifies high-risk antibiotic-resistant bacteria in a hospital in Tanzania, highlighting the spread of dangerous clones and the need for better infection control.

## Contribution

First documentation of ESBL-producing Klebsiella pneumoniae ST2390 in neonatology units and genomic analysis of ESBL clones in Mwanza, Tanzania.

## Key findings

- ESBL-producing Escherichia coli ST131 is the predominant high-risk clone in Mwanza hospitals.
- ESBL-producing Klebsiella pneumoniae ST2390 is newly identified and associated with neonatal bloodstream infections.
- Genomic analysis reveals clonal clusters of ESBL bacteria in medical and neonatology wards.

## Abstract

•Predominance of globally recognised high-risk clone extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli ST131.•First documentation and predominance of ESBL-producing Klebsiella pneumoniae ST2390 associated with bloodstream infections in the neonatology units.•The cgMLST-based Neighbour-Joining (NJ) phylogenetic analysis revealed clonal clusters involving high-risk clone ESBL-EC ST131 in medical and neonatology wards, and newly detected ESBL-KP ST2390 in the neonatology ward/unit.

Predominance of globally recognised high-risk clone extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli ST131.

First documentation and predominance of ESBL-producing Klebsiella pneumoniae ST2390 associated with bloodstream infections in the neonatology units.

The cgMLST-based Neighbour-Joining (NJ) phylogenetic analysis revealed clonal clusters involving high-risk clone ESBL-EC ST131 in medical and neonatology wards, and newly detected ESBL-KP ST2390 in the neonatology ward/unit.

Extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-EC) and Klebsiella pneumoniae (ESBL-KP) represent major clinical threats globally. Genomic epidemiological data remain scarce in low- and middle-income countries, limiting a comprehensive understanding of antimicrobial-resistant pathogen diversity and clonal distribution. The present study investigated the genomic epidemiology of ESBL-EC and ESBL-KP isolates in Mwanza, Tanzania.

This cross-sectional hospital-based study employed whole-genome sequencing to characterise ESBL-EC (n = 39) and ESBL-KP (n = 49) isolated from patients with bloodstream, urinary tract, and wound infections at a zonal referral hospital between June 2019–June 2020 and March–August 2023.

Thirteen sequence types (STs) were identified among ESBL-EC, predominantly ST131 (30.7%) and ST648 (28.2%). ESBL-KP comprised 15 STs, with ST2390 (24.5%) and ST17 (18.4%) being the most common. The blaCTX−M-15 gene was detected in 87.2% of ESBL-EC and 95.9% of ESBL-KP. IncFII was the dominant plasmid replicon in ESBL-EC (63.9%) and ESBL-KP (83.7%), while repB was detected exclusively in ESBL-KP (28.6%), particularly among ST2390. ESBL-EC showed significantly higher resistance to ciprofloxacin (P < 0.01), whereas ESBL-KP demonstrated higher resistance to gentamicin and piperacillin-tazobactam (both P < 0.01). The cgMLST-based Neighbour-Joining phylogenetic analysis revealed substantial genetic diversity and identified clonal clusters involving the high-risk clone ESBL-EC ST131. Clusters of ESBL-EC ST131 and ST648 were observed across medical and neonatology wards, while ESBL-KP ST2390 clusters were mainly confined to neonatology wards.

This study highlights clonal clusters, the first report of ESBL-KP ST2390, and the predominance of the virulent high-risk clone ESBL-EC ST131 in Mwanza, Tanzania. Underscoring the critical need for reinforced infection control strategies and genomic surveillance.